diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml index 87333d2b..271d89c5 100644 --- a/.github/workflows/main.yaml +++ b/.github/workflows/main.yaml @@ -19,7 +19,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"] + python-version: ["3.10", "3.11", "3.12", "3.13"] fail-fast: false steps: diff --git a/cache/envo/terms.csv b/cache/envo/terms.csv index 25f5be26..036eeb34 100644 --- a/cache/envo/terms.csv +++ b/cache/envo/terms.csv @@ -46,4 +46,14 @@ ENVO:00000080,mountain range,2025-11-03T17:34:10.519896 ENVO:01001899,reef,2025-11-03T17:34:10.520210 ENVO:00000264,seamount,2025-11-03T17:34:10.520572 ENVO:00000267,submarine canyon,2025-11-03T17:34:10.520770 -ENVO:00000247,volcano,2025-11-03T17:34:10.520956 \ No newline at end of file +ENVO:00000247,volcano,2025-11-03T17:34:10.520956ENVO:00002030,aquatic biome,2025-11-25T07:59:01.134445 +ENVO:00002229,arenosol,2025-11-25T07:59:01.134917 +ENVO:00000134,permafrost,2025-11-25T07:59:01.135208 +ENVO:00002269,thermocline,2025-11-25T07:59:01.135467 +ENVO:00000133,glacier,2025-11-25T07:59:01.135704 +ENVO:00002234,acrisol,2025-11-25T07:59:01.135959 +ENVO:00005774,peat soil,2025-11-25T07:59:01.136199 +ENVO:00005767,manured soil,2025-11-25T07:59:01.136442 +ENVO:00002273,fluvisol,2025-11-25T07:59:01.136678 +ENVO:00000873,freshwater biome,2025-11-25T07:59:01.137110 +ENVO:00002030,aquatic biome,2025-11-25T08:16:30.607490 diff --git a/cache/ncbitaxon/terms.csv b/cache/ncbitaxon/terms.csv index f45ad9aa..7155cc56 100644 --- a/cache/ncbitaxon/terms.csv +++ b/cache/ncbitaxon/terms.csv @@ -217,3 +217,131 @@ NCBITaxon:920,Acidithiobacillus ferrooxidans,2025-10-19T07:20:50.733817 NCBITaxon:2705,,2025-10-19T07:20:50.734601 NCBITaxon:5061,Aspergillus niger,2025-10-19T07:20:50.735200 NCBITaxon:180,Leptospirillum ferrooxidans,2025-10-19T07:42:42.936346 +NCBITaxon:575584,Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841,2025-11-25T07:58:49.063394 +NCBITaxon:28377,Anolis carolinensis,2025-11-25T07:58:49.064465 +NCBITaxon:7165,Anopheles gambiae,2025-11-25T07:58:49.065376 +NCBITaxon:224324,Aquifex aeolicus VF5,2025-11-25T07:58:49.066183 +NCBITaxon:330879,Aspergillus fumigatus Af293,2025-11-25T07:58:49.067073 +NCBITaxon:1392,Bacillus anthracis,2025-11-25T07:58:49.067983 +NCBITaxon:226900,Bacillus cereus ATCC 14579,2025-11-25T07:58:49.068706 +NCBITaxon:226186,Bacteroides thetaiotaomicron VPI-5482,2025-11-25T07:58:49.069375 +NCBITaxon:684364,Batrachochytrium dendrobatidis JAM81,2025-11-25T07:58:49.070006 +NCBITaxon:3711,Brassica rapa,2025-11-25T07:58:49.070706 +NCBITaxon:15368,Brachypodium distachyon,2025-11-25T07:58:49.071449 +NCBITaxon:224911,Bradyrhizobium diazoefficiens USDA 110,2025-11-25T07:58:49.072116 +NCBITaxon:7739,Branchiostoma floridae,2025-11-25T07:58:49.072843 +NCBITaxon:6238,Caenorhabditis briggsae,2025-11-25T07:58:49.073496 +NCBITaxon:192222,Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819,2025-11-25T07:58:49.074143 +NCBITaxon:237561,Candida albicans SC5314,2025-11-25T07:58:49.074796 +NCBITaxon:1136231,Candida orthopsilosis Co 90-125,2025-11-25T07:58:49.075428 +NCBITaxon:573826,Candida dubliniensis CD36,2025-11-25T07:58:49.076012 +NCBITaxon:284593,Nakaseomyces glabratus CBS 138,2025-11-25T07:58:49.076722 +NCBITaxon:578454,Candida parapsilosis CDC317,2025-11-25T07:58:49.077472 +NCBITaxon:294747,Candida tropicalis MYA-3404,2025-11-25T07:58:49.078175 +NCBITaxon:324602,Chloroflexus aurantiacus J-10-fl,2025-11-25T07:58:49.078858 +NCBITaxon:272561,Chlamydia trachomatis D/UW-3/CX,2025-11-25T07:58:49.079602 +NCBITaxon:7719,Ciona intestinalis,2025-11-25T07:58:49.080086 +NCBITaxon:290338,Citrobacter koseri ATCC BAA-895,2025-11-25T07:58:49.080657 +NCBITaxon:306902,Clavispora lusitaniae ATCC 42720,2025-11-25T07:58:49.081298 +NCBITaxon:441771,Clostridium botulinum A str. Hall,2025-11-25T07:58:49.081986 +NCBITaxon:227377,Coxiella burnetii RSA 493,2025-11-25T07:58:49.082551 +NCBITaxon:214684,Cryptococcus deneoformans JEC21,2025-11-25T07:58:49.083203 +NCBITaxon:6669,Daphnia pulex,2025-11-25T07:58:49.083997 +NCBITaxon:284592,Debaryomyces hansenii CBS767,2025-11-25T07:58:49.084428 +NCBITaxon:243230,Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539,2025-11-25T07:58:49.085143 +NCBITaxon:5786,Dictyostelium purpureum,2025-11-25T07:58:49.085676 +NCBITaxon:515635,Dictyoglomus turgidum DSM 6724,2025-11-25T07:58:49.086429 +NCBITaxon:83334,Escherichia coli O157:H7,2025-11-25T07:58:49.087039 +NCBITaxon:227321,Aspergillus nidulans FGSC A4,2025-11-25T07:58:49.087501 +NCBITaxon:565655,Enterococcus casseliflavus EC20,2025-11-25T07:58:49.088032 +NCBITaxon:226185,Enterococcus faecalis V583,2025-11-25T07:58:49.088340 +NCBITaxon:1353,Enterococcus gallinarum,2025-11-25T07:58:49.088879 +NCBITaxon:294381,Entamoeba histolytica HM-1:IMSS,2025-11-25T07:58:49.089530 +NCBITaxon:284811,Eremothecium gossypii ATCC 10895,2025-11-25T07:58:49.090373 +NCBITaxon:12118,Foot-and-mouth disease virus O,2025-11-25T07:58:49.091008 +NCBITaxon:190304,Fusobacterium nucleatum subsp. nucleatum ATCC 25586,2025-11-25T07:58:49.091581 +NCBITaxon:243231,Geobacter sulfurreducens PCA,2025-11-25T07:58:49.091903 +NCBITaxon:184922,Giardia lamblia ATCC 50803,2025-11-25T07:58:49.092617 +NCBITaxon:251221,Gloeobacter violaceus PCC 7421,2025-11-25T07:58:49.093423 +NCBITaxon:3635,Gossypium hirsutum,2025-11-25T07:58:49.094083 +NCBITaxon:71421,Haemophilus influenzae Rd KW20,2025-11-25T07:58:49.094743 +NCBITaxon:272558,Halalkalibacterium halodurans C-125,2025-11-25T07:58:49.095143 +NCBITaxon:64091,Halobacterium salinarum NRC-1,2025-11-25T07:58:49.095738 +NCBITaxon:928302,Hepatitis B virus C/ayr human/Japan/Okamoto,2025-11-25T07:58:49.096397 +NCBITaxon:10360,Human herpesvirus 5 strain AD169,2025-11-25T07:58:49.097196 +NCBITaxon:295027,Human herpesvirus 5 strain Merlin,2025-11-25T07:58:49.097940 +NCBITaxon:63746,Hepatitis C virus (isolate H77),2025-11-25T07:58:49.098677 +NCBITaxon:4232,Helianthus annuus,2025-11-25T07:58:49.099381 +NCBITaxon:6412,Helobdella robusta,2025-11-25T07:58:49.100109 +NCBITaxon:10299,Human alphaherpesvirus 1 strain 17,2025-11-25T07:58:49.100771 +NCBITaxon:112509,Hordeum vulgare subsp. vulgare,2025-11-25T07:58:49.101549 +NCBITaxon:333760,Human papillomavirus 16,2025-11-25T07:58:49.102228 +NCBITaxon:327105,HIV-1 O_ANT70,2025-11-25T07:58:49.102836 +NCBITaxon:6945,Ixodes scapularis,2025-11-25T07:58:49.103438 +NCBITaxon:51240,Juglans regia,2025-11-25T07:58:49.103912 +NCBITaxon:105231,Klebsormidium nitens,2025-11-25T07:58:49.104542 +NCBITaxon:1125630,Klebsiella pneumoniae subsp. pneumoniae HS11286,2025-11-25T07:58:49.105222 +NCBITaxon:574,Klebsiella pneumoniae subsp. ozaenae,2025-11-25T07:58:49.105835 +NCBITaxon:374847,Candidatus Korarchaeum cryptofilum OPF8,2025-11-25T07:58:49.106446 +NCBITaxon:4236,Lactuca sativa,2025-11-25T07:58:49.107041 +NCBITaxon:189518,Leptospira interrogans serovar Lai str. 56601,2025-11-25T07:58:49.107789 +NCBITaxon:7918,Lepisosteus oculatus,2025-11-25T07:58:49.108404 +NCBITaxon:169963,Listeria monocytogenes EGD-e,2025-11-25T07:58:49.109095 +NCBITaxon:379508,Lodderomyces elongisporus NRRL YB-4239,2025-11-25T07:58:49.109736 +NCBITaxon:3983,Manihot esculenta,2025-11-25T07:58:49.110502 +NCBITaxon:3197,Marchantia polymorpha,2025-11-25T07:58:49.111039 +NCBITaxon:645098,Measles virus strain Ichinose-B95a,2025-11-25T07:58:49.111673 +NCBITaxon:188937,Methanosarcina acetivorans C2A,2025-11-25T07:58:49.112292 +NCBITaxon:243232,Methanocaldococcus jannaschii DSM 2661,2025-11-25T07:58:49.112647 +NCBITaxon:81824,Monosiga brevicollis,2025-11-25T07:58:49.113261 +NCBITaxon:13616,Monodelphis domestica,2025-11-25T07:58:49.114005 +NCBITaxon:243273,Mycoplasmoides genitalium G37,2025-11-25T07:58:49.114881 +NCBITaxon:5270,Mycosarcoma maydis,2025-11-25T07:58:49.115646 +NCBITaxon:272634,Mycoplasmoides pneumoniae M129,2025-11-25T07:58:49.116197 +NCBITaxon:419947,Mycobacterium tuberculosis H37Ra,2025-11-25T07:58:49.116818 +NCBITaxon:4432,Nelumbo nucifera,2025-11-25T07:58:49.117816 +NCBITaxon:45351,Nematostella vectensis,2025-11-25T07:58:49.118616 +NCBITaxon:367110,Neurospora crassa OR74A,2025-11-25T07:58:49.119311 +NCBITaxon:436308,Nitrosopumilus maritimus SCM1,2025-11-25T07:58:49.119945 +NCBITaxon:9258,Ornithorhynchus anatinus,2025-11-25T07:58:49.120565 +NCBITaxon:321614,Parastagonospora nodorum SN15,2025-11-25T07:58:49.121253 +NCBITaxon:3218,Physcomitrium patens,2025-11-25T07:58:49.121792 +NCBITaxon:164328,Phytophthora ramorum,2025-11-25T07:58:49.122596 +NCBITaxon:294746,Meyerozyma guilliermondii ATCC 6260,2025-11-25T07:58:49.123078 +NCBITaxon:3694,Populus trichocarpa,2025-11-25T07:58:49.123867 +NCBITaxon:54126,Pristionchus pacificus,2025-11-25T07:58:49.124618 +NCBITaxon:3760,Prunus persica,2025-11-25T07:58:49.125221 +NCBITaxon:418459,Puccinia graminis f. sp. tritici CRL 75-36-700-3,2025-11-25T07:58:49.125841 +NCBITaxon:178306,Pyrobaculum aerophilum str. IM2,2025-11-25T07:58:49.126579 +NCBITaxon:243090,Rhodopirellula baltica SH 1,2025-11-25T07:58:49.127229 +NCBITaxon:273057,Saccharolobus solfataricus P2,2025-11-25T07:58:49.127891 +NCBITaxon:99287,Salmonella enterica subsp. enterica serovar Typhimurium str. LT2,2025-11-25T07:58:49.128644 +NCBITaxon:402676,Schizosaccharomyces japonicus yFS275,2025-11-25T07:58:49.129321 +NCBITaxon:665079,Sclerotinia sclerotiorum 1980 UF-70,2025-11-25T07:58:49.130029 +NCBITaxon:211586,Shewanella oneidensis MR-1,2025-11-25T07:58:49.130811 +NCBITaxon:623,Shigella flexneri,2025-11-25T07:58:49.131448 +NCBITaxon:4558,Sorghum bicolor,2025-11-25T07:58:49.132057 +NCBITaxon:3562,Spinacia oleracea,2025-11-25T07:58:49.132717 +NCBITaxon:1901,Streptomyces clavuligerus,2025-11-25T07:58:49.133461 +NCBITaxon:100226,Streptomyces coelicolor A3(2),2025-11-25T07:58:49.134176 +NCBITaxon:301447,Streptococcus pyogenes serotype M1,2025-11-25T07:58:49.135049 +NCBITaxon:373153,Streptococcus pneumoniae D39,2025-11-25T07:58:49.135791 +NCBITaxon:7668,Strongylocentrotus purpuratus,2025-11-25T07:58:49.136320 +NCBITaxon:1111708,Synechocystis sp. PCC 6803 substr. Kazusa,2025-11-25T07:58:49.136967 +NCBITaxon:35128,Thalassiosira pseudonana,2025-11-25T07:58:49.137483 +NCBITaxon:3641,Theobroma cacao,2025-11-25T07:58:49.137980 +NCBITaxon:69014,Thermococcus kodakarensis KOD1,2025-11-25T07:58:49.138585 +NCBITaxon:243274,Thermotoga maritima MSB8,2025-11-25T07:58:49.138986 +NCBITaxon:289376,Thermodesulfovibrio yellowstonii DSM 11347,2025-11-25T07:58:49.139613 +NCBITaxon:10228,Trichoplax adhaerens,2025-11-25T07:58:49.140130 +NCBITaxon:7070,Tribolium castaneum,2025-11-25T07:58:49.140719 +NCBITaxon:412133,Trichomonas vaginalis G3,2025-11-25T07:58:49.141336 +NCBITaxon:10254,Vaccinia virus WR,2025-11-25T07:58:49.141954 +NCBITaxon:587200,Variola virus human/India/Ind3/1967,2025-11-25T07:58:49.142570 +NCBITaxon:243277,Vibrio cholerae O1 biovar El Tor str. N16961,2025-11-25T07:58:49.142992 +NCBITaxon:29760,Vitis vinifera,2025-11-25T07:58:49.143594 +NCBITaxon:10338,Human herpesvirus 3 strain Dumas,2025-11-25T07:58:49.144182 +NCBITaxon:190485,Xanthomonas campestris pv. campestris str. ATCC 33913,2025-11-25T07:58:49.144783 +NCBITaxon:284591,Yarrowia lipolytica CLIB122,2025-11-25T07:58:49.145309 +NCBITaxon:632,Yersinia pestis,2025-11-25T07:58:49.145944 +NCBITaxon:64320,Zika virus,2025-11-25T07:58:49.146541 diff --git a/docs/governance.md b/docs/governance.md new file mode 100644 index 00000000..7da5749e --- /dev/null +++ b/docs/governance.md @@ -0,0 +1,148 @@ +# Governance and Stewardship + +This document describes the governance model for value sets in this repository. + +## Current Status + +Most value sets in this repository are currently in **DRAFT** status. This means: + +- They are functional and can be used in downstream applications +- They have not yet undergone formal review +- Their structure and content may change +- Community feedback is welcome and encouraged + +## Source of Truth Model + +Value sets in this repository fall into two categories: + +### 1. Mirrored Value Sets (External Stewardship) + +Some value sets are **mirrors** of authoritative definitions maintained by external organizations. +For these, the external organization is the Source of Truth (SoT), and this repository provides +a LinkML-compatible representation. + +Examples include: + +| Value Set | Steward | Source | +|-----------|---------|--------| +| GO Evidence Codes | [Gene Ontology Consortium](https://geneontology.org) | ECO mappings | +| Phenopackets Enums | [GA4GH Phenopackets](https://phenopackets.org) | Phenopacket Schema | +| INSDC Vocabularies | [Genomic Standards Consortium](https://gensc.org) | INSDC controlled vocabularies | + +For mirrored value sets: + +- Changes to the authoritative source should be reflected here +- Issues with the underlying definitions should be reported to the steward organization +- This repository tracks the `source` and `stewards` annotations for provenance + +### 2. Community Value Sets (Internal Stewardship) + +Some value sets are **originated and maintained** within this repository. For these, +this repository is the Source of Truth. + +For community value sets: + +- Stewardship is managed through working groups +- Changes follow the contribution and review process described below +- The goal is to mature these to STANDARD status through community review + +## Maturity Levels + +Value sets progress through maturity levels (defined in `StandardsMaturityLevel`): + +| Status | Description | +|--------|-------------| +| `DRAFT` | Initial development, may change significantly | +| `WORKING_DRAFT` | Active work by a working group | +| `COMMITTEE_DRAFT` | Under formal review | +| `CANDIDATE_RECOMMENDATION` | Ready for implementation testing | +| `PROPOSED_STANDARD` | Stable, ready for adoption | +| `STANDARD` | Approved and published | +| `MATURE_STANDARD` | Well-established with wide adoption | +| `SUPERSEDED` | Replaced by a newer version | +| `WITHDRAWN` | No longer recommended | + +## Stewardship Metadata + +Each value set should include stewardship metadata: + +```yaml +enums: + MyValueSet: + title: My Value Set + description: Description of the value set + status: DRAFT + contributors: + - orcid:0000-0000-0000-0000 + instantiates: + - valuesets_meta:ValueSetEnumDefinitionWithStewardship + annotations: + stewards: https://example.org/steward + publishers: https://example.org/publisher +``` + +### Stewardship Roles + +Following [FHIR MetadataResource](https://build.fhir.org/metadataresource.html) patterns: + +- **Stewards**: Organizations responsible for ongoing curation and maintenance +- **Publishers**: Organizations responsible for release and distribution +- **Endorsers**: Organizations that officially recommend the value set for adoption + +## Contributing + +### Proposing New Value Sets + +1. Open an issue describing the value set and its use case +2. If accepted, submit a PR with the value set in DRAFT status +3. Include appropriate metadata (title, description, contributors) +4. Map permissible values to ontology terms where applicable + +### Becoming a Steward + +Stewards are responsible for: + +- Reviewing proposed changes to value sets in their domain +- Ensuring value sets remain accurate and up-to-date +- Responding to community feedback and issues +- Coordinating with external stewards for mirrored value sets + +To become a steward or join a working group: + +**[Sign up here](https://example.org/valuesets-stewardship-signup)** (placeholder) + +### Review Process + +For value sets to advance from DRAFT to higher maturity levels: + +1. **Working Group Review**: Domain experts review the value set +2. **Community Feedback**: Open period for community input +3. **Steward Approval**: Designated steward(s) approve the advancement +4. **Status Update**: PR to update the status field + +## Governance Bodies + +### Steering Committee + +(To be established) + +Responsibilities: +- Overall project governance +- Resolving disputes +- Approving new working groups + +### Working Groups + +Domain-specific working groups are responsible for value sets in their area: + +| Domain | Working Group | Status | +|--------|---------------|--------| +| Bioinformatics | TBD | Planned | +| Clinical/Healthcare | TBD | Planned | +| Earth Sciences | TBD | Planned | + +## Contact + +- **Issues**: [GitHub Issues](https://github.com/linkml/valuesets/issues) +- **Discussions**: [GitHub Discussions](https://github.com/linkml/valuesets/discussions) +- **Stewardship Signup**: [Sign up form](https://example.org/valuesets-stewardship-signup) diff --git a/docs/schema/valuesets.yaml b/docs/schema/valuesets.yaml index 24c46f5c..a73fc417 100644 --- a/docs/schema/valuesets.yaml +++ b/docs/schema/valuesets.yaml @@ -115,6 +115,12 @@ prefixes: valuesets: prefix_prefix: valuesets prefix_reference: https://w3id.org/valuesets/ + orcid: + prefix_prefix: orcid + prefix_reference: https://orcid.org/ + valuesets_meta: + prefix_prefix: valuesets_meta + prefix_reference: https://w3id.org/valuesets/meta/ default_prefix: valuesets default_range: string types: @@ -390,18 +396,38 @@ enums: RelativeTimeEnum: name: RelativeTimeEnum definition_uri: https://w3id.org/valuesets/RelativeTimeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition + description: Temporal relationships between events or time points + title: Relative Time from_schema: https://w3id.org/valuesets/core + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: BEFORE: text: BEFORE + description: Occurs before the reference time point AFTER: text: AFTER + description: Occurs after the reference time point AT_SAME_TIME_AS: text: AT_SAME_TIME_AS + description: Occurs at the same time as the reference time point PresenceEnum: name: PresenceEnum definition_uri: https://w3id.org/valuesets/PresenceEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition + description: Classification of whether an entity is present, absent, or at detection + limits + title: Presence Status from_schema: https://w3id.org/valuesets/core + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: PRESENT: text: PRESENT @@ -418,8 +444,15 @@ enums: ContributorType: name: ContributorType definition_uri: https://w3id.org/valuesets/ContributorType + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: The type of contributor being represented. + title: Contributor Type from_schema: https://w3id.org/common-value-sets/contributor + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: PERSON: text: PERSON @@ -434,9 +467,16 @@ enums: DataAbsentEnum: name: DataAbsentEnum definition_uri: https://w3id.org/valuesets/DataAbsentEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Used to specify why the normally expected content of the data element is missing. + title: Data Absent from_schema: http://terminology.hl7.org/CodeSystem/data-absent-reason# + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: unknown: text: unknown @@ -506,14 +546,14 @@ enums: negative-infinity: text: negative-infinity description: The numeric value is excessively low and unrepresentable due - to a floating point processing error. + to a floating point processing error. meaning: fhir_data_absent_reason:negative-infinity is_a: error title: Negative Infinity (NINF) positive-infinity: text: positive-infinity description: The numeric value is excessively high and unrepresentable due - to a floating point processing error. + to a floating point processing error. meaning: fhir_data_absent_reason:positive-infinity is_a: error title: Positive Infinity (PINF) @@ -532,7 +572,14 @@ enums: PredictionOutcomeType: name: PredictionOutcomeType definition_uri: https://w3id.org/valuesets/PredictionOutcomeType + instantiates: + - valuesets_meta:ValueSetEnumDefinition + title: Prediction Outcome Type from_schema: https://w3id.org/valuesets/statistics + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: TP: text: TP @@ -549,8 +596,15 @@ enums: VitalStatusEnum: name: VitalStatusEnum definition_uri: https://w3id.org/valuesets/VitalStatusEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: The vital status of a person or organism + title: Vital Status from_schema: https://w3id.org/valuesets/health + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: ALIVE: text: ALIVE @@ -574,8 +628,15 @@ enums: VaccinationStatusEnum: name: VaccinationStatusEnum definition_uri: https://w3id.org/valuesets/VaccinationStatusEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: The vaccination status of an individual + title: Vaccination Status from_schema: https://w3id.org/valuesets/health/vaccination + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: VACCINATED: text: VACCINATED @@ -613,8 +674,15 @@ enums: VaccinationPeriodicityEnum: name: VaccinationPeriodicityEnum definition_uri: https://w3id.org/valuesets/VaccinationPeriodicityEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: The periodicity or frequency of vaccination + title: Vaccination Periodicity from_schema: https://w3id.org/valuesets/health/vaccination + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: SINGLE_DOSE: text: SINGLE_DOSE @@ -645,8 +713,15 @@ enums: VaccineCategoryEnum: name: VaccineCategoryEnum definition_uri: https://w3id.org/valuesets/VaccineCategoryEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: The broad category or type of vaccine + title: Vaccine Category from_schema: https://w3id.org/valuesets/health/vaccination + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: LIVE_ATTENUATED_VACCINE: text: LIVE_ATTENUATED_VACCINE @@ -689,7 +764,14 @@ enums: HealthcareEncounterClassification: name: HealthcareEncounterClassification definition_uri: https://w3id.org/valuesets/HealthcareEncounterClassification + instantiates: + - valuesets_meta:ValueSetEnumDefinition + title: Healthcare Encounter Classification from_schema: https://w3id.org/valuesets/healthcare + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: Inpatient Visit: text: Inpatient Visit @@ -743,9 +825,16 @@ enums: EducationLevel: name: EducationLevel definition_uri: https://w3id.org/valuesets/EducationLevel + instantiates: + - valuesets_meta:ValueSetEnumDefinitionWithSource description: Years of education that a person has completed + title: Education Level from_schema: https://w3id.org/valuesets/demographics source: https://terminology.hl7.org/CodeSystem-v3-EducationLevel.html + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: ELEM: text: ELEM @@ -786,9 +875,16 @@ enums: MaritalStatus: name: MaritalStatus definition_uri: https://w3id.org/valuesets/MaritalStatus + instantiates: + - valuesets_meta:ValueSetEnumDefinitionWithSource description: The domestic partnership status of a person + title: Marital Status from_schema: https://w3id.org/valuesets/demographics source: https://www.hl7.org/fhir/valueset-marital-status.html + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: ANNULLED: text: ANNULLED @@ -841,9 +937,16 @@ enums: EmploymentStatus: name: EmploymentStatus definition_uri: https://w3id.org/valuesets/EmploymentStatus + instantiates: + - valuesets_meta:ValueSetEnumDefinitionWithSource description: Employment status of a person + title: Employment Status from_schema: https://w3id.org/valuesets/demographics source: https://terminology.hl7.org/CodeSystem-v2-0066.html + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: FULL_TIME_EMPLOYED: text: FULL_TIME_EMPLOYED @@ -896,9 +999,16 @@ enums: HousingStatus: name: HousingStatus definition_uri: https://w3id.org/valuesets/HousingStatus + instantiates: + - valuesets_meta:ValueSetEnumDefinitionWithSource description: Housing status of patients per UDS Plus HRSA standards + title: Housing Status from_schema: https://w3id.org/valuesets/demographics source: https://www.fhir.org/guides/hrsa/uds-plus/CodeSystem-udsplus-housing-status-codes.html + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: HOMELESS_SHELTER: text: HOMELESS_SHELTER @@ -931,10 +1041,17 @@ enums: GenderIdentity: name: GenderIdentity definition_uri: https://w3id.org/valuesets/GenderIdentity + instantiates: + - valuesets_meta:ValueSetEnumDefinitionWithSource description: Gender identity codes indicating an individual's personal sense of gender + title: Gender Identity from_schema: https://w3id.org/valuesets/demographics source: https://terminology.hl7.org/ValueSet-gender-identity.html + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: FEMALE: text: FEMALE @@ -959,9 +1076,16 @@ enums: OmbRaceCategory: name: OmbRaceCategory definition_uri: https://w3id.org/valuesets/OmbRaceCategory + instantiates: + - valuesets_meta:ValueSetEnumDefinitionWithSource description: Office of Management and Budget (OMB) race category codes + title: Omb Race Category from_schema: https://w3id.org/valuesets/demographics source: https://www.hl7.org/fhir/us/core/ValueSet-omb-race-category.html + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: AMERICAN_INDIAN_OR_ALASKA_NATIVE: text: AMERICAN_INDIAN_OR_ALASKA_NATIVE @@ -998,9 +1122,16 @@ enums: OmbEthnicityCategory: name: OmbEthnicityCategory definition_uri: https://w3id.org/valuesets/OmbEthnicityCategory + instantiates: + - valuesets_meta:ValueSetEnumDefinitionWithSource description: Office of Management and Budget (OMB) ethnicity category codes + title: Omb Ethnicity Category from_schema: https://w3id.org/valuesets/demographics source: https://www.hl7.org/fhir/us/core/ValueSet-omb-ethnicity-category.html + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: HISPANIC_OR_LATINO: text: HISPANIC_OR_LATINO @@ -1021,7 +1152,14 @@ enums: CaseOrControlEnum: name: CaseOrControlEnum definition_uri: https://w3id.org/valuesets/CaseOrControlEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition + title: Case Or Control from_schema: https://w3id.org/valuesets/investigation + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: CASE: text: CASE @@ -1034,7 +1172,14 @@ enums: StudyDesignEnum: name: StudyDesignEnum definition_uri: https://w3id.org/valuesets/StudyDesignEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition + title: Study Design from_schema: https://w3id.org/valuesets/investigation + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT reachable_from: source_nodes: - OBI:0500000 @@ -1044,7 +1189,14 @@ enums: InvestigativeProtocolEnum: name: InvestigativeProtocolEnum definition_uri: https://w3id.org/valuesets/InvestigativeProtocolEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition + title: Investigative Protocol from_schema: https://w3id.org/valuesets/investigation + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT reachable_from: source_nodes: - OBI:0000272 @@ -1054,7 +1206,14 @@ enums: SampleProcessingEnum: name: SampleProcessingEnum definition_uri: https://w3id.org/valuesets/SampleProcessingEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition + title: Sample Processing from_schema: https://w3id.org/valuesets/investigation + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT reachable_from: source_nodes: - OBI:0000094 @@ -1064,9 +1223,23 @@ enums: GOEvidenceCode: name: GOEvidenceCode definition_uri: https://w3id.org/valuesets/GOEvidenceCode + instantiates: + - valuesets_meta:ValueSetEnumDefinitionWithStewardship + annotations: + stewards: + tag: stewards + value: https://geneontology.org + publishers: + tag: publishers + value: https://geneontology.org description: Gene Ontology evidence codes mapped to Evidence and Conclusion Ontology (ECO) terms + title: GO Evidence Code from_schema: https://w3id.org/linkml/valuesets/bio/go_evidence + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: STANDARD permissible_values: EXP: text: EXP @@ -1228,9 +1401,23 @@ enums: GOElectronicMethods: name: GOElectronicMethods definition_uri: https://w3id.org/valuesets/GOElectronicMethods + instantiates: + - valuesets_meta:ValueSetEnumDefinitionWithStewardship + annotations: + stewards: + tag: stewards + value: https://geneontology.org + publishers: + tag: publishers + value: https://geneontology.org description: Electronic annotation methods used in Gene Ontology, identified by GO_REF codes + title: GO Electronic Methods from_schema: https://w3id.org/linkml/valuesets/bio/go_evidence + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: STANDARD permissible_values: INTERPRO2GO: text: INTERPRO2GO @@ -1315,7 +1502,14 @@ enums: OrganismTaxonEnum: name: OrganismTaxonEnum definition_uri: https://w3id.org/valuesets/OrganismTaxonEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition + title: Organism Taxon from_schema: https://w3id.org/linkml/valuesets/bio/taxonomy + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT reachable_from: source_nodes: - NCBITaxon:1 @@ -1325,9 +1519,16 @@ enums: CommonOrganismTaxaEnum: name: CommonOrganismTaxaEnum definition_uri: https://w3id.org/valuesets/CommonOrganismTaxaEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Common model organisms used in biological research, mapped to NCBI Taxonomy IDs + title: Common Organism Taxa from_schema: https://w3id.org/linkml/valuesets/bio/taxonomy + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: BACTERIA: text: BACTERIA @@ -1752,8 +1953,15 @@ enums: TaxonomicRank: name: TaxonomicRank definition_uri: https://w3id.org/valuesets/TaxonomicRank + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Standard taxonomic ranks used in biological classification + title: Taxonomic Rank from_schema: https://w3id.org/linkml/valuesets/bio/taxonomy + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: DOMAIN: text: DOMAIN @@ -1812,8 +2020,15 @@ enums: BiologicalKingdom: name: BiologicalKingdom definition_uri: https://w3id.org/valuesets/BiologicalKingdom + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Major kingdoms/domains of life + title: Biological Kingdom from_schema: https://w3id.org/linkml/valuesets/bio/taxonomy + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: BACTERIA: text: BACTERIA @@ -1851,8 +2066,15 @@ enums: CellCyclePhase: name: CellCyclePhase definition_uri: https://w3id.org/valuesets/CellCyclePhase + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Major phases of the eukaryotic cell cycle + title: Cell Cycle Phase from_schema: https://w3id.org/linkml/valuesets/bio/cell_cycle + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: G0: text: G0 @@ -1922,8 +2144,15 @@ enums: MitoticPhase: name: MitoticPhase definition_uri: https://w3id.org/valuesets/MitoticPhase + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Stages of mitosis (M phase) + title: Mitotic Phase from_schema: https://w3id.org/linkml/valuesets/bio/cell_cycle + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: PROPHASE: text: PROPHASE @@ -1995,8 +2224,15 @@ enums: CellCycleCheckpoint: name: CellCycleCheckpoint definition_uri: https://w3id.org/valuesets/CellCycleCheckpoint + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Cell cycle checkpoints that regulate progression + title: Cell Cycle Checkpoint from_schema: https://w3id.org/linkml/valuesets/bio/cell_cycle + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: G1_S_CHECKPOINT: text: G1_S_CHECKPOINT @@ -2052,8 +2288,15 @@ enums: MeioticPhase: name: MeioticPhase definition_uri: https://w3id.org/valuesets/MeioticPhase + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Phases specific to meiotic cell division + title: Meiotic Phase from_schema: https://w3id.org/linkml/valuesets/bio/cell_cycle + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: MEIOSIS_I: text: MEIOSIS_I @@ -2130,8 +2373,15 @@ enums: CellCycleRegulator: name: CellCycleRegulator definition_uri: https://w3id.org/valuesets/CellCycleRegulator + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of cell cycle regulatory molecules + title: Cell Cycle Regulator from_schema: https://w3id.org/linkml/valuesets/bio/cell_cycle + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: CYCLIN: text: CYCLIN @@ -2200,8 +2450,15 @@ enums: CellProliferationState: name: CellProliferationState definition_uri: https://w3id.org/valuesets/CellProliferationState + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Cell proliferation and growth states + title: Cell Proliferation State from_schema: https://w3id.org/linkml/valuesets/bio/cell_cycle + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: PROLIFERATING: text: PROLIFERATING @@ -2262,8 +2519,15 @@ enums: DNADamageResponse: name: DNADamageResponse definition_uri: https://w3id.org/valuesets/DNADamageResponse + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: DNA damage response pathways during cell cycle + title: DNA Damage Response from_schema: https://w3id.org/linkml/valuesets/bio/cell_cycle + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: CELL_CYCLE_ARREST: text: CELL_CYCLE_ARREST @@ -2296,12 +2560,19 @@ enums: GenomeFeatureType: name: GenomeFeatureType definition_uri: https://w3id.org/valuesets/GenomeFeatureType + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: 'Genome feature types from SOFA (Sequence Ontology Feature Annotation). This is the subset of Sequence Ontology terms used in GFF3 files. Organized hierarchically following the Sequence Ontology structure.' + title: Genome Feature Type from_schema: https://w3id.org/linkml/valuesets/bio/genome_features + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: REGION: text: REGION @@ -2711,10 +2982,17 @@ enums: MetazoanAnatomicalStructure: name: MetazoanAnatomicalStructure definition_uri: https://w3id.org/valuesets/MetazoanAnatomicalStructure + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: 'Any anatomical structure found in metazoan organisms, including organs, tissues, and body parts' + title: Metazoan Anatomical Structure from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT reachable_from: source_ontology: obo:uberon source_nodes: @@ -2725,8 +3003,15 @@ enums: HumanAnatomicalStructure: name: HumanAnatomicalStructure definition_uri: https://w3id.org/valuesets/HumanAnatomicalStructure + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Anatomical structures specific to humans (Homo sapiens) + title: Human Anatomical Structure from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT reachable_from: source_ontology: obo:uberon source_nodes: @@ -2737,8 +3022,15 @@ enums: PlantAnatomicalStructure: name: PlantAnatomicalStructure definition_uri: https://w3id.org/valuesets/PlantAnatomicalStructure + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Any anatomical structure found in plant organisms + title: Plant Anatomical Structure from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT reachable_from: source_ontology: obo:po source_nodes: @@ -2749,10 +3041,17 @@ enums: CellType: name: CellType definition_uri: https://w3id.org/valuesets/CellType + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: 'Any cell type from the Cell Ontology (CL), including native and experimentally modified cells' + title: Cell Type from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT reachable_from: source_ontology: obo:cl source_nodes: @@ -2763,8 +3062,15 @@ enums: NeuronType: name: NeuronType definition_uri: https://w3id.org/valuesets/NeuronType + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Neuron cell types from the Cell Ontology + title: Neuron Type from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT reachable_from: source_ontology: obo:cl source_nodes: @@ -2775,8 +3081,15 @@ enums: ImmuneCell: name: ImmuneCell definition_uri: https://w3id.org/valuesets/ImmuneCell + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Immune system cell types (leukocytes and their subtypes) + title: Immune Cell from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT reachable_from: source_ontology: obo:cl source_nodes: @@ -2787,8 +3100,15 @@ enums: StemCell: name: StemCell definition_uri: https://w3id.org/valuesets/StemCell + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Stem cell types and progenitor cells + title: Stem Cell from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT reachable_from: source_ontology: obo:cl source_nodes: @@ -2800,8 +3120,15 @@ enums: Disease: name: Disease definition_uri: https://w3id.org/valuesets/Disease + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Human diseases from the Mondo Disease Ontology + title: Disease from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT reachable_from: source_ontology: obo:mondo source_nodes: @@ -2812,8 +3139,15 @@ enums: InfectiousDisease: name: InfectiousDisease definition_uri: https://w3id.org/valuesets/InfectiousDisease + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Infectious diseases caused by pathogenic organisms + title: Infectious Disease from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT reachable_from: source_ontology: obo:mondo source_nodes: @@ -2824,8 +3158,15 @@ enums: Cancer: name: Cancer definition_uri: https://w3id.org/valuesets/Cancer + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Neoplastic and cancerous diseases + title: Cancer from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT reachable_from: source_ontology: obo:mondo source_nodes: @@ -2837,8 +3178,15 @@ enums: GeneticDisease: name: GeneticDisease definition_uri: https://w3id.org/valuesets/GeneticDisease + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Hereditary and genetic diseases + title: Genetic Disease from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT reachable_from: source_ontology: obo:mondo source_nodes: @@ -2850,8 +3198,15 @@ enums: ChemicalEntity: name: ChemicalEntity definition_uri: https://w3id.org/valuesets/ChemicalEntity + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Any chemical entity from ChEBI ontology + title: Chemical Entity from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT reachable_from: source_ontology: obo:chebi source_nodes: @@ -2862,8 +3217,15 @@ enums: Drug: name: Drug definition_uri: https://w3id.org/valuesets/Drug + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Pharmaceutical drugs and medications + title: Drug from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT reachable_from: source_ontology: obo:chebi source_nodes: @@ -2875,8 +3237,15 @@ enums: Metabolite: name: Metabolite definition_uri: https://w3id.org/valuesets/Metabolite + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Metabolites and metabolic intermediates + title: Metabolite from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT reachable_from: source_ontology: obo:chebi source_nodes: @@ -2887,8 +3256,15 @@ enums: Protein: name: Protein definition_uri: https://w3id.org/valuesets/Protein + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Proteins and protein complexes + title: Protein from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT reachable_from: source_ontology: obo:pr source_nodes: @@ -2899,8 +3275,15 @@ enums: Phenotype: name: Phenotype definition_uri: https://w3id.org/valuesets/Phenotype + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Phenotypic abnormalities from Human Phenotype Ontology + title: Phenotype from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT reachable_from: source_ontology: obo:hp source_nodes: @@ -2911,8 +3294,15 @@ enums: ClinicalFinding: name: ClinicalFinding definition_uri: https://w3id.org/valuesets/ClinicalFinding + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Clinical findings and observations + title: Clinical Finding from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT reachable_from: source_ontology: obo:hp source_nodes: @@ -2923,8 +3313,15 @@ enums: BiologicalProcess: name: BiologicalProcess definition_uri: https://w3id.org/valuesets/BiologicalProcess + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Biological processes from Gene Ontology + title: Biological Process from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT reachable_from: source_ontology: obo:go source_nodes: @@ -2935,8 +3332,15 @@ enums: MetabolicProcess: name: MetabolicProcess definition_uri: https://w3id.org/valuesets/MetabolicProcess + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Metabolic processes and pathways + title: Metabolic Process from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT reachable_from: source_ontology: obo:go source_nodes: @@ -2947,8 +3351,15 @@ enums: MolecularFunction: name: MolecularFunction definition_uri: https://w3id.org/valuesets/MolecularFunction + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Molecular functions from Gene Ontology + title: Molecular Function from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT reachable_from: source_ontology: obo:go source_nodes: @@ -2959,8 +3370,15 @@ enums: CellularComponent: name: CellularComponent definition_uri: https://w3id.org/valuesets/CellularComponent + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Cellular components and locations from Gene Ontology + title: Cellular Component from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT reachable_from: source_ontology: obo:go source_nodes: @@ -2971,8 +3389,15 @@ enums: SequenceFeature: name: SequenceFeature definition_uri: https://w3id.org/valuesets/SequenceFeature + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Sequence features from the Sequence Ontology + title: Sequence Feature from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT reachable_from: source_ontology: obo:so source_nodes: @@ -2983,8 +3408,15 @@ enums: GeneFeature: name: GeneFeature definition_uri: https://w3id.org/valuesets/GeneFeature + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Gene-related sequence features + title: Gene Feature from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT reachable_from: source_ontology: obo:so source_nodes: @@ -2995,8 +3427,15 @@ enums: Environment: name: Environment definition_uri: https://w3id.org/valuesets/Environment + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Environmental systems and biomes + title: Environment from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT reachable_from: source_ontology: obo:envo source_nodes: @@ -3008,8 +3447,15 @@ enums: EnvironmentalMaterial: name: EnvironmentalMaterial definition_uri: https://w3id.org/valuesets/EnvironmentalMaterial + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Environmental materials and substances + title: Environmental Material from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT reachable_from: source_ontology: obo:envo source_nodes: @@ -3020,8 +3466,15 @@ enums: Quality: name: Quality definition_uri: https://w3id.org/valuesets/Quality + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Phenotypic qualities and attributes from PATO + title: Quality from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT reachable_from: source_ontology: obo:pato source_nodes: @@ -3032,8 +3485,15 @@ enums: PhysicalQuality: name: PhysicalQuality definition_uri: https://w3id.org/valuesets/PhysicalQuality + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Physical qualities like size, shape, color + title: Physical Quality from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT reachable_from: source_ontology: obo:pato source_nodes: @@ -3044,8 +3504,15 @@ enums: SampleType: name: SampleType definition_uri: https://w3id.org/valuesets/SampleType + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of biological samples used in structural biology + title: Sample Type from_schema: https://w3id.org/valuesets/bio/structural_biology + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: PROTEIN: text: PROTEIN @@ -3074,8 +3541,15 @@ enums: StructuralBiologyTechnique: name: StructuralBiologyTechnique definition_uri: https://w3id.org/valuesets/StructuralBiologyTechnique + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Structural biology experimental techniques + title: Structural Biology Technique from_schema: https://w3id.org/valuesets/bio/structural_biology + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: CRYO_EM: text: CRYO_EM @@ -3164,8 +3638,15 @@ enums: CryoEMPreparationType: name: CryoEMPreparationType definition_uri: https://w3id.org/valuesets/CryoEMPreparationType + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of cryo-EM sample preparation + title: Cryo EM Preparation Type from_schema: https://w3id.org/valuesets/bio/structural_biology + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: VITREOUS_ICE: text: VITREOUS_ICE @@ -3182,8 +3663,15 @@ enums: CryoEMGridType: name: CryoEMGridType definition_uri: https://w3id.org/valuesets/CryoEMGridType + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of electron microscopy grids + title: Cryo EM Grid Type from_schema: https://w3id.org/valuesets/bio/structural_biology + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: C_FLAT: text: C_FLAT @@ -3236,8 +3724,15 @@ enums: VitrificationMethod: name: VitrificationMethod definition_uri: https://w3id.org/valuesets/VitrificationMethod + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Methods for sample vitrification + title: Vitrification Method from_schema: https://w3id.org/valuesets/bio/structural_biology + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: PLUNGE_FREEZING: text: PLUNGE_FREEZING @@ -3276,8 +3771,15 @@ enums: CrystallizationMethod: name: CrystallizationMethod definition_uri: https://w3id.org/valuesets/CrystallizationMethod + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Methods for protein crystallization + title: Crystallization Method from_schema: https://w3id.org/valuesets/bio/structural_biology + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: VAPOR_DIFFUSION_HANGING: text: VAPOR_DIFFUSION_HANGING @@ -3333,8 +3835,15 @@ enums: XRaySource: name: XRaySource definition_uri: https://w3id.org/valuesets/XRaySource + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of X-ray sources + title: X Ray Source from_schema: https://w3id.org/valuesets/bio/structural_biology + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: SYNCHROTRON: text: SYNCHROTRON @@ -3379,8 +3888,15 @@ enums: Detector: name: Detector definition_uri: https://w3id.org/valuesets/Detector + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of detectors for structural biology + title: Detector from_schema: https://w3id.org/valuesets/bio/structural_biology + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: DIRECT_ELECTRON: text: DIRECT_ELECTRON @@ -3426,8 +3942,15 @@ enums: WorkflowType: name: WorkflowType definition_uri: https://w3id.org/valuesets/WorkflowType + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of computational processing workflows + title: Workflow Type from_schema: https://w3id.org/valuesets/bio/structural_biology + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: MOTION_CORRECTION: text: MOTION_CORRECTION @@ -3519,8 +4042,15 @@ enums: FileFormat: name: FileFormat definition_uri: https://w3id.org/valuesets/FileFormat + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: File formats used in structural biology + title: File Format from_schema: https://w3id.org/valuesets/bio/structural_biology + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: MRC: text: MRC @@ -3625,8 +4155,15 @@ enums: DataType: name: DataType definition_uri: https://w3id.org/valuesets/DataType + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of structural biology data + title: Data Type from_schema: https://w3id.org/valuesets/bio/structural_biology + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: MICROGRAPH: text: MICROGRAPH @@ -3694,8 +4231,15 @@ enums: ProcessingStatus: name: ProcessingStatus definition_uri: https://w3id.org/valuesets/ProcessingStatus + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Status of data processing workflows + title: Processing Status from_schema: https://w3id.org/valuesets/bio/structural_biology + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: RAW: text: RAW @@ -3724,8 +4268,15 @@ enums: CoordinationGeometry: name: CoordinationGeometry definition_uri: https://w3id.org/valuesets/CoordinationGeometry + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Coordination geometry of metal centers in protein structures + title: Coordination Geometry from_schema: https://w3id.org/valuesets/bio/structural_biology + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: LINEAR: text: LINEAR @@ -3866,8 +4417,15 @@ enums: MetalLigandType: name: MetalLigandType definition_uri: https://w3id.org/valuesets/MetalLigandType + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of metal-containing chemical components + title: Metal Ligand Type from_schema: https://w3id.org/valuesets/bio/structural_biology + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: METAL_CATION: text: METAL_CATION @@ -3886,8 +4444,15 @@ enums: ProteinModificationType: name: ProteinModificationType definition_uri: https://w3id.org/valuesets/ProteinModificationType + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of protein modifications + title: Protein Modification Type from_schema: https://w3id.org/valuesets/bio/structural_biology + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: METAL_COORDINATION: text: METAL_COORDINATION @@ -3929,9 +4494,16 @@ enums: BiosafetyLevelEnum: name: BiosafetyLevelEnum definition_uri: https://w3id.org/valuesets/BiosafetyLevelEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Biosafety levels (BSL) defining containment requirements for biological agents + title: Biosafety Level from_schema: https://w3id.org/linkml/valuesets/bio/biosafety + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: BSL1: text: BSL1 @@ -3968,9 +4540,23 @@ enums: InsdcMissingValueEnum: name: InsdcMissingValueEnum definition_uri: https://w3id.org/valuesets/InsdcMissingValueEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinitionWithStewardship + annotations: + stewards: + tag: stewards + value: https://gensc.org + publishers: + tag: publishers + value: https://www.insdc.org description: INSDC (International Nucleotide Sequence Database Collaboration) controlled vocabulary for missing values in sequence records + title: Insdc Missing Value from_schema: https://w3id.org/linkml/valuesets/bio/insdc_missing_values + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: STANDARD permissible_values: NOT_APPLICABLE: text: NOT_APPLICABLE @@ -4082,6 +4668,15 @@ enums: InsdcGeographicLocationEnum: name: InsdcGeographicLocationEnum definition_uri: https://w3id.org/valuesets/InsdcGeographicLocationEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinitionWithStewardship + annotations: + stewards: + tag: stewards + value: https://gensc.org + publishers: + tag: publishers + value: https://www.insdc.org description: 'INSDC controlled vocabulary for geographic locations of collected samples. @@ -4090,7 +4685,12 @@ enums: Countries use ISO 3166-1 alpha-2 codes from Library of Congress as canonical identifiers.' + title: Insdc Geographic Location from_schema: https://w3id.org/linkml/valuesets/bio/insdc_geographic_locations + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: STANDARD permissible_values: AFGHANISTAN: text: AFGHANISTAN @@ -5308,8 +5908,15 @@ enums: name: ViralGenomeTypeEnum definition_uri: https://w3id.org/valuesets/ViralGenomeTypeEnum conforms_to: https://en.wikipedia.org/wiki/Baltimore_classification + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of viral genomes based on Baltimore classification + title: Viral Genome Type from_schema: https://w3id.org/linkml/valuesets/bio/viral_genome_types + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: DNA: text: DNA @@ -5409,8 +6016,15 @@ enums: PlantSexEnum: name: PlantSexEnum definition_uri: https://w3id.org/valuesets/PlantSexEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Plant reproductive and sexual system types + title: Plant Sex from_schema: https://w3id.org/linkml/valuesets/bio/plant_sex + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: ANDRODIOECIOUS: text: ANDRODIOECIOUS @@ -5534,8 +6148,15 @@ enums: RelToOxygenEnum: name: RelToOxygenEnum definition_uri: https://w3id.org/valuesets/RelToOxygenEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Organism's relationship to oxygen for growth and survival + title: Rel To Oxygen from_schema: https://w3id.org/linkml/valuesets/bio/relationship_to_oxygen + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: AEROBE: text: AEROBE @@ -5578,8 +6199,15 @@ enums: TrophicLevelEnum: name: TrophicLevelEnum definition_uri: https://w3id.org/valuesets/TrophicLevelEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Trophic levels are the feeding position in a food chain + title: Trophic Level from_schema: https://w3id.org/linkml/valuesets/bio/trophic_levels + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: AUTOTROPH: text: AUTOTROPH @@ -5720,7 +6348,14 @@ enums: HumanDevelopmentalStage: name: HumanDevelopmentalStage definition_uri: https://w3id.org/valuesets/HumanDevelopmentalStage + instantiates: + - valuesets_meta:ValueSetEnumDefinition + title: Human Developmental Stage from_schema: https://w3id.org/valuesets/bio/developmental_stages + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: ZYGOTE_STAGE: text: ZYGOTE_STAGE @@ -5838,7 +6473,14 @@ enums: MouseDevelopmentalStage: name: MouseDevelopmentalStage definition_uri: https://w3id.org/valuesets/MouseDevelopmentalStage + instantiates: + - valuesets_meta:ValueSetEnumDefinition + title: Mouse Developmental Stage from_schema: https://w3id.org/valuesets/bio/developmental_stages + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: ZYGOTE_STAGE: text: ZYGOTE_STAGE @@ -5949,8 +6591,15 @@ enums: DayOfWeek: name: DayOfWeek definition_uri: https://w3id.org/valuesets/DayOfWeek + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Days of the week following ISO 8601 standard (Monday = 1) + title: Day Of Week from_schema: https://w3id.org/linkml/valuesets/time/temporal + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: MONDAY: text: MONDAY @@ -6053,8 +6702,15 @@ enums: Month: name: Month definition_uri: https://w3id.org/valuesets/Month + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Months of the year + title: Month from_schema: https://w3id.org/linkml/valuesets/time/temporal + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: JANUARY: text: JANUARY @@ -6263,8 +6919,15 @@ enums: Quarter: name: Quarter definition_uri: https://w3id.org/valuesets/Quarter + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Calendar quarters + title: Quarter from_schema: https://w3id.org/linkml/valuesets/time/temporal + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: Q1: text: Q1 @@ -6297,8 +6960,15 @@ enums: Season: name: Season definition_uri: https://w3id.org/valuesets/Season + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Seasons of the year (Northern Hemisphere) + title: Season from_schema: https://w3id.org/linkml/valuesets/time/temporal + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: SPRING: text: SPRING @@ -6350,8 +7020,15 @@ enums: TimePeriod: name: TimePeriod definition_uri: https://w3id.org/valuesets/TimePeriod + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Common time periods and intervals + title: Time Period from_schema: https://w3id.org/linkml/valuesets/time/temporal + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: HOURLY: text: HOURLY @@ -6419,8 +7096,15 @@ enums: TimeOfDay: name: TimeOfDay definition_uri: https://w3id.org/valuesets/TimeOfDay + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Common times of day + title: Time Of Day from_schema: https://w3id.org/linkml/valuesets/time/temporal + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: DAWN: text: DAWN @@ -6474,8 +7158,15 @@ enums: BusinessTimeFrame: name: BusinessTimeFrame definition_uri: https://w3id.org/valuesets/BusinessTimeFrame + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Common business and financial time frames + title: Business Time Frame from_schema: https://w3id.org/linkml/valuesets/time/temporal + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: REAL_TIME: text: REAL_TIME @@ -6563,8 +7254,15 @@ enums: GeologicalEra: name: GeologicalEra definition_uri: https://w3id.org/valuesets/GeologicalEra + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Major geological eras + title: Geological Era from_schema: https://w3id.org/linkml/valuesets/time/temporal + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: PRECAMBRIAN: text: PRECAMBRIAN @@ -6581,8 +7279,15 @@ enums: HistoricalPeriod: name: HistoricalPeriod definition_uri: https://w3id.org/valuesets/HistoricalPeriod + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Major historical periods + title: Historical Period from_schema: https://w3id.org/linkml/valuesets/time/temporal + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: PREHISTORIC: text: PREHISTORIC @@ -6617,9 +7322,15 @@ enums: PublicationType: name: PublicationType definition_uri: https://w3id.org/valuesets/PublicationType + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of academic and research publications title: Publication Type from_schema: https://w3id.org/linkml/valuesets/academic/research + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: JOURNAL_ARTICLE: text: JOURNAL_ARTICLE @@ -6810,8 +7521,15 @@ enums: PeerReviewStatus: name: PeerReviewStatus definition_uri: https://w3id.org/valuesets/PeerReviewStatus + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Status of peer review process + title: Peer Review Status from_schema: https://w3id.org/linkml/valuesets/academic/research + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: NOT_PEER_REVIEWED: text: NOT_PEER_REVIEWED @@ -6855,8 +7573,15 @@ enums: AcademicDegree: name: AcademicDegree definition_uri: https://w3id.org/valuesets/AcademicDegree + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Academic degrees and qualifications + title: Academic Degree from_schema: https://w3id.org/linkml/valuesets/academic/research + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: BA: text: BA @@ -7104,8 +7829,15 @@ enums: LicenseType: name: LicenseType definition_uri: https://w3id.org/valuesets/LicenseType + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Common software and content licenses + title: License Type from_schema: https://w3id.org/linkml/valuesets/academic/research + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: MIT: text: MIT @@ -7188,8 +7920,15 @@ enums: ResearchField: name: ResearchField definition_uri: https://w3id.org/valuesets/ResearchField + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Major research fields and disciplines + title: Research Field from_schema: https://w3id.org/linkml/valuesets/academic/research + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: PHYSICS: text: PHYSICS @@ -7311,8 +8050,15 @@ enums: FundingType: name: FundingType definition_uri: https://w3id.org/valuesets/FundingType + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of research funding + title: Funding Type from_schema: https://w3id.org/linkml/valuesets/academic/research + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: GRANT: text: GRANT @@ -7349,8 +8095,15 @@ enums: ManuscriptSection: name: ManuscriptSection definition_uri: https://w3id.org/valuesets/ManuscriptSection + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Sections of a scientific manuscript or publication + title: Manuscript Section from_schema: https://w3id.org/linkml/valuesets/academic/research + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: TITLE: text: TITLE @@ -7706,8 +8459,15 @@ enums: ResearchRole: name: ResearchRole definition_uri: https://w3id.org/valuesets/ResearchRole + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Roles in research and authorship + title: Research Role from_schema: https://w3id.org/linkml/valuesets/academic/research + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: CONCEPTUALIZATION: text: CONCEPTUALIZATION @@ -7800,8 +8560,15 @@ enums: OpenAccessType: name: OpenAccessType definition_uri: https://w3id.org/valuesets/OpenAccessType + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of open access publishing + title: Open Access Type from_schema: https://w3id.org/linkml/valuesets/academic/research + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: GOLD: text: GOLD @@ -7827,8 +8594,15 @@ enums: CitationStyle: name: CitationStyle definition_uri: https://w3id.org/valuesets/CitationStyle + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Common citation and reference styles + title: Citation Style from_schema: https://w3id.org/linkml/valuesets/academic/research + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: APA: text: APA @@ -7866,6 +8640,8 @@ enums: USDOENationalLaboratoryEnum: name: USDOENationalLaboratoryEnum definition_uri: https://w3id.org/valuesets/USDOENationalLaboratoryEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: 'United States Department of Energy National Laboratories. @@ -7882,10 +8658,15 @@ enums: with the Office of Science stewarding 10 of the 17 laboratories. ' + title: USDOE National Laboratory comments: - All organization names mapped to ROR (Research Organization Registry) identifiers - See https://www.energy.gov/national-laboratories for official information from_schema: https://w3id.org/linkml/valuesets/academic/organizations + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: AMES_LABORATORY: text: AMES_LABORATORY @@ -8232,6 +9013,8 @@ enums: USFederalFundingAgencyEnum: name: USFederalFundingAgencyEnum definition_uri: https://w3id.org/valuesets/USFederalFundingAgencyEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: 'Major United States Federal Research Funding Agencies. @@ -8241,10 +9024,15 @@ enums: supporting universities, national laboratories, and other research institutions. ' + title: US Federal Funding Agency comments: - All agency names mapped to ROR (Research Organization Registry) identifiers - Includes primary research funding agencies from_schema: https://w3id.org/linkml/valuesets/academic/organizations + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: NIH: text: NIH @@ -8401,6 +9189,8 @@ enums: NIHInstituteCenterEnum: name: NIHInstituteCenterEnum definition_uri: https://w3id.org/valuesets/NIHInstituteCenterEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: 'National Institutes of Health (NIH) Institutes and Centers. @@ -8410,10 +9200,15 @@ enums: diseases or body systems. These are the major NIH ICs that fund extramural research. ' + title: NIH Institute Center comments: - All mapped to ROR (Research Organization Registry) identifiers - Focuses on major funding institutes from_schema: https://w3id.org/linkml/valuesets/academic/organizations + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: NCI: text: NCI @@ -8605,6 +9400,8 @@ enums: StandardsOrganizationEnum: name: StandardsOrganizationEnum definition_uri: https://w3id.org/valuesets/StandardsOrganizationEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: 'Major International Standards Development Organizations. @@ -8615,10 +9412,15 @@ enums: engineering. ' + title: Standards Organization comments: - All mapped to ROR (Research Organization Registry) identifiers where available - Includes standards bodies commonly referenced in research from_schema: https://w3id.org/linkml/valuesets/academic/organizations + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: ISO: text: ISO @@ -8687,6 +9489,8 @@ enums: UNSpecializedAgencyEnum: name: UNSpecializedAgencyEnum definition_uri: https://w3id.org/valuesets/UNSpecializedAgencyEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: 'United Nations Specialized Agencies. @@ -8697,10 +9501,15 @@ enums: in their respective fields. ' + title: UN Specialized Agency comments: - All mapped to ROR (Research Organization Registry) identifiers - Includes major UN agencies relevant to research and development from_schema: https://w3id.org/linkml/valuesets/academic/organizations + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: WHO: text: WHO @@ -8783,8 +9592,15 @@ enums: EnergySource: name: EnergySource definition_uri: https://w3id.org/valuesets/EnergySource + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of energy sources and generation methods + title: Energy Source from_schema: https://w3id.org/linkml/valuesets/energy/energy + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: SOLAR: text: SOLAR @@ -9025,8 +9841,15 @@ enums: EnergyUnit: name: EnergyUnit definition_uri: https://w3id.org/valuesets/EnergyUnit + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Units for measuring energy + title: Energy Unit from_schema: https://w3id.org/linkml/valuesets/energy/energy + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: JOULE: text: JOULE @@ -9254,8 +10077,15 @@ enums: PowerUnit: name: PowerUnit definition_uri: https://w3id.org/valuesets/PowerUnit + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Units for measuring power (energy per time) + title: Power Unit from_schema: https://w3id.org/linkml/valuesets/energy/energy + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: WATT: text: WATT @@ -9357,8 +10187,15 @@ enums: EnergyEfficiencyRating: name: EnergyEfficiencyRating definition_uri: https://w3id.org/valuesets/EnergyEfficiencyRating + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Energy efficiency ratings and standards + title: Energy Efficiency Rating from_schema: https://w3id.org/linkml/valuesets/energy/energy + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: A_PLUS_PLUS_PLUS: text: A_PLUS_PLUS_PLUS @@ -9477,8 +10314,15 @@ enums: BuildingEnergyStandard: name: BuildingEnergyStandard definition_uri: https://w3id.org/valuesets/BuildingEnergyStandard + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Building energy efficiency standards and certifications + title: Building Energy Standard from_schema: https://w3id.org/linkml/valuesets/energy/energy + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: PASSIVE_HOUSE: text: PASSIVE_HOUSE @@ -9522,8 +10366,15 @@ enums: GridType: name: GridType definition_uri: https://w3id.org/valuesets/GridType + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of electrical grid systems + title: Grid Type from_schema: https://w3id.org/linkml/valuesets/energy/energy + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: MAIN_GRID: text: MAIN_GRID @@ -9546,8 +10397,15 @@ enums: EnergyStorageType: name: EnergyStorageType definition_uri: https://w3id.org/valuesets/EnergyStorageType + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of energy storage systems + title: Energy Storage Type from_schema: https://w3id.org/linkml/valuesets/energy/energy + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: LITHIUM_ION_BATTERY: text: LITHIUM_ION_BATTERY @@ -9664,8 +10522,15 @@ enums: EmissionScope: name: EmissionScope definition_uri: https://w3id.org/valuesets/EmissionScope + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Greenhouse gas emission scopes (GHG Protocol) + title: Emission Scope from_schema: https://w3id.org/linkml/valuesets/energy/energy + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: SCOPE_1: text: SCOPE_1 @@ -9705,8 +10570,15 @@ enums: CarbonIntensity: name: CarbonIntensity definition_uri: https://w3id.org/valuesets/CarbonIntensity + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Carbon intensity levels for energy sources + title: Carbon Intensity from_schema: https://w3id.org/linkml/valuesets/energy/energy + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: ZERO_CARBON: text: ZERO_CARBON @@ -9753,8 +10625,15 @@ enums: ElectricityMarket: name: ElectricityMarket definition_uri: https://w3id.org/valuesets/ElectricityMarket + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of electricity markets and pricing + title: Electricity Market from_schema: https://w3id.org/linkml/valuesets/energy/energy + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: SPOT_MARKET: text: SPOT_MARKET @@ -9789,8 +10668,15 @@ enums: FossilFuelTypeEnum: name: FossilFuelTypeEnum definition_uri: https://w3id.org/valuesets/FossilFuelTypeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of fossil fuels used for energy generation + title: Fossil Fuel Type from_schema: https://w3id.org/linkml/valuesets/energy/fossil_fuels + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: COAL: text: COAL @@ -9810,8 +10696,15 @@ enums: ReactorTypeEnum: name: ReactorTypeEnum definition_uri: https://w3id.org/valuesets/ReactorTypeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Nuclear reactor types based on design and operational characteristics + title: Reactor Type from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/reactor_types + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: PWR: text: PWR @@ -10114,8 +11007,15 @@ enums: ReactorGenerationEnum: name: ReactorGenerationEnum definition_uri: https://w3id.org/valuesets/ReactorGenerationEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Nuclear reactor generational classifications + title: Reactor Generation from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/reactor_types + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: GENERATION_I: text: GENERATION_I @@ -10202,8 +11102,15 @@ enums: ReactorCoolantEnum: name: ReactorCoolantEnum definition_uri: https://w3id.org/valuesets/ReactorCoolantEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Primary coolant types used in nuclear reactors + title: Reactor Coolant from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/reactor_types + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: LIGHT_WATER: text: LIGHT_WATER @@ -10329,8 +11236,15 @@ enums: ReactorModeratorEnum: name: ReactorModeratorEnum definition_uri: https://w3id.org/valuesets/ReactorModeratorEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Neutron moderator types used in nuclear reactors + title: Reactor Moderator from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/reactor_types + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: LIGHT_WATER: text: LIGHT_WATER @@ -10405,8 +11319,15 @@ enums: ReactorNeutronSpectrumEnum: name: ReactorNeutronSpectrumEnum definition_uri: https://w3id.org/valuesets/ReactorNeutronSpectrumEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Neutron energy spectrum classifications + title: Reactor Neutron Spectrum from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/reactor_types + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: THERMAL: text: THERMAL @@ -10450,8 +11371,15 @@ enums: ReactorSizeCategoryEnum: name: ReactorSizeCategoryEnum definition_uri: https://w3id.org/valuesets/ReactorSizeCategoryEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Nuclear reactor size classifications + title: Reactor Size Category from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/reactor_types + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: LARGE: text: LARGE @@ -10517,8 +11445,15 @@ enums: NuclearFuelTypeEnum: name: NuclearFuelTypeEnum definition_uri: https://w3id.org/valuesets/NuclearFuelTypeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of nuclear fuel materials and compositions + title: Nuclear Fuel Type from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_fuels + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: NATURAL_URANIUM: text: NATURAL_URANIUM @@ -10767,8 +11702,15 @@ enums: UraniumEnrichmentLevelEnum: name: UraniumEnrichmentLevelEnum definition_uri: https://w3id.org/valuesets/UraniumEnrichmentLevelEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Standard uranium-235 enrichment level classifications + title: Uranium Enrichment Level from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_fuels + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: NATURAL: text: NATURAL @@ -10857,8 +11799,15 @@ enums: FuelFormEnum: name: FuelFormEnum definition_uri: https://w3id.org/valuesets/FuelFormEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Physical forms of nuclear fuel + title: Fuel Form from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_fuels + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: OXIDE_PELLETS: text: OXIDE_PELLETS @@ -10960,8 +11909,15 @@ enums: FuelAssemblyTypeEnum: name: FuelAssemblyTypeEnum definition_uri: https://w3id.org/valuesets/FuelAssemblyTypeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of fuel assembly configurations + title: Fuel Assembly Type from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_fuels + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: PWR_ASSEMBLY: text: PWR_ASSEMBLY @@ -11055,8 +12011,15 @@ enums: FuelCycleStageEnum: name: FuelCycleStageEnum definition_uri: https://w3id.org/valuesets/FuelCycleStageEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Stages in the nuclear fuel cycle + title: Fuel Cycle Stage from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_fuels + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: MINING: text: MINING @@ -11167,8 +12130,15 @@ enums: FissileIsotopeEnum: name: FissileIsotopeEnum definition_uri: https://w3id.org/valuesets/FissileIsotopeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Fissile isotopes used in nuclear fuel + title: Fissile Isotope from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_fuels + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: URANIUM_233: text: URANIUM_233 @@ -11249,9 +12219,16 @@ enums: IAEAWasteClassificationEnum: name: IAEAWasteClassificationEnum definition_uri: https://w3id.org/valuesets/IAEAWasteClassificationEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: IAEA General Safety Requirements radioactive waste classification scheme + title: IAEA Waste Classification from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_waste + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: EXEMPT_WASTE: text: EXEMPT_WASTE @@ -11380,8 +12357,15 @@ enums: NRCWasteClassEnum: name: NRCWasteClassEnum definition_uri: https://w3id.org/valuesets/NRCWasteClassEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: US NRC 10 CFR 61 low-level radioactive waste classification + title: NRC Waste Class from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_waste + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: CLASS_A: text: CLASS_A @@ -11472,8 +12456,15 @@ enums: WasteHeatGenerationEnum: name: WasteHeatGenerationEnum definition_uri: https://w3id.org/valuesets/WasteHeatGenerationEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Heat generation categories for radioactive waste + title: Waste Heat Generation from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_waste + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: NEGLIGIBLE_HEAT: text: NEGLIGIBLE_HEAT @@ -11523,8 +12514,15 @@ enums: WasteHalfLifeCategoryEnum: name: WasteHalfLifeCategoryEnum definition_uri: https://w3id.org/valuesets/WasteHalfLifeCategoryEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Half-life categories for radioactive waste classification + title: Waste Half Life Category from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_waste + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: VERY_SHORT_LIVED: text: VERY_SHORT_LIVED @@ -11574,8 +12572,15 @@ enums: WasteDisposalMethodEnum: name: WasteDisposalMethodEnum definition_uri: https://w3id.org/valuesets/WasteDisposalMethodEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Methods for radioactive waste disposal + title: Waste Disposal Method from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_waste + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: CLEARANCE: text: CLEARANCE @@ -11670,8 +12675,15 @@ enums: WasteSourceEnum: name: WasteSourceEnum definition_uri: https://w3id.org/valuesets/WasteSourceEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Sources of radioactive waste generation + title: Waste Source from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_waste + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: NUCLEAR_POWER_PLANTS: text: NUCLEAR_POWER_PLANTS @@ -11788,8 +12800,15 @@ enums: TransuranicWasteCategoryEnum: name: TransuranicWasteCategoryEnum definition_uri: https://w3id.org/valuesets/TransuranicWasteCategoryEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Transuranic waste classifications (US system) + title: Transuranic Waste Category from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_waste + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: CONTACT_HANDLED_TRU: text: CONTACT_HANDLED_TRU @@ -11849,8 +12868,15 @@ enums: INESLevelEnum: name: INESLevelEnum definition_uri: https://w3id.org/valuesets/INESLevelEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: International Nuclear and Radiological Event Scale (INES) levels + title: INES Level from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_safety + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: LEVEL_0: text: LEVEL_0 @@ -12003,8 +13029,15 @@ enums: EmergencyClassificationEnum: name: EmergencyClassificationEnum definition_uri: https://w3id.org/valuesets/EmergencyClassificationEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Nuclear emergency action levels and classifications + title: Emergency Classification from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_safety + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: NOTIFICATION_UNUSUAL_EVENT: text: NOTIFICATION_UNUSUAL_EVENT @@ -12094,8 +13127,15 @@ enums: NuclearSecurityCategoryEnum: name: NuclearSecurityCategoryEnum definition_uri: https://w3id.org/valuesets/NuclearSecurityCategoryEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: IAEA nuclear material security categories (INFCIRC/225) + title: Nuclear Security Category from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_safety + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: CATEGORY_I: text: CATEGORY_I @@ -12179,8 +13219,15 @@ enums: SafetySystemClassEnum: name: SafetySystemClassEnum definition_uri: https://w3id.org/valuesets/SafetySystemClassEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Nuclear safety system classifications (based on IEEE and ASME standards) + title: Safety System Class from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_safety + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: CLASS_1E: text: CLASS_1E @@ -12254,8 +13301,15 @@ enums: ReactorSafetyFunctionEnum: name: ReactorSafetyFunctionEnum definition_uri: https://w3id.org/valuesets/ReactorSafetyFunctionEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Fundamental nuclear reactor safety functions + title: Reactor Safety Function from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_safety + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: REACTIVITY_CONTROL: text: REACTIVITY_CONTROL @@ -12342,8 +13396,15 @@ enums: DefenseInDepthLevelEnum: name: DefenseInDepthLevelEnum definition_uri: https://w3id.org/valuesets/DefenseInDepthLevelEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Defense in depth barrier levels for nuclear safety + title: Defense In Depth Level from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_safety + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: LEVEL_1: text: LEVEL_1 @@ -12419,8 +13480,15 @@ enums: RadiationProtectionZoneEnum: name: RadiationProtectionZoneEnum definition_uri: https://w3id.org/valuesets/RadiationProtectionZoneEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Radiation protection zone classifications for nuclear facilities + title: Radiation Protection Zone from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_safety + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: EXCLUSION_AREA: text: EXCLUSION_AREA @@ -12515,8 +13583,15 @@ enums: NuclearFacilityTypeEnum: name: NuclearFacilityTypeEnum definition_uri: https://w3id.org/valuesets/NuclearFacilityTypeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of nuclear facilities and infrastructure + title: Nuclear Facility Type from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_facilities + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: COMMERCIAL_POWER_PLANT: text: COMMERCIAL_POWER_PLANT @@ -12791,8 +13866,15 @@ enums: PowerPlantStatusEnum: name: PowerPlantStatusEnum definition_uri: https://w3id.org/valuesets/PowerPlantStatusEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Operational status of nuclear power plants + title: Power Plant Status from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_facilities + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: UNDER_CONSTRUCTION: text: UNDER_CONSTRUCTION @@ -12909,8 +13991,15 @@ enums: ResearchReactorTypeEnum: name: ResearchReactorTypeEnum definition_uri: https://w3id.org/valuesets/ResearchReactorTypeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of research reactors + title: Research Reactor Type from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_facilities + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: POOL_TYPE: text: POOL_TYPE @@ -13013,8 +14102,15 @@ enums: FuelCycleFacilityTypeEnum: name: FuelCycleFacilityTypeEnum definition_uri: https://w3id.org/valuesets/FuelCycleFacilityTypeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of nuclear fuel cycle facilities + title: Fuel Cycle Facility Type from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_facilities + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: IN_SITU_LEACH_MINE: text: IN_SITU_LEACH_MINE @@ -13145,8 +14241,15 @@ enums: WasteFacilityTypeEnum: name: WasteFacilityTypeEnum definition_uri: https://w3id.org/valuesets/WasteFacilityTypeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of nuclear waste management facilities + title: Waste Facility Type from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_facilities + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: SPENT_FUEL_POOL: text: SPENT_FUEL_POOL @@ -13277,8 +14380,15 @@ enums: NuclearShipTypeEnum: name: NuclearShipTypeEnum definition_uri: https://w3id.org/valuesets/NuclearShipTypeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of nuclear-powered vessels + title: Nuclear Ship Type from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_facilities + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: AIRCRAFT_CARRIER: text: AIRCRAFT_CARRIER @@ -13385,8 +14495,15 @@ enums: ReactorOperatingStateEnum: name: ReactorOperatingStateEnum definition_uri: https://w3id.org/valuesets/ReactorOperatingStateEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Operational states of nuclear reactors + title: Reactor Operating State from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_operations + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: STARTUP: text: STARTUP @@ -13595,8 +14712,15 @@ enums: MaintenanceTypeEnum: name: MaintenanceTypeEnum definition_uri: https://w3id.org/valuesets/MaintenanceTypeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of nuclear facility maintenance activities + title: Maintenance Type from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_operations + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: PREVENTIVE_MAINTENANCE: text: PREVENTIVE_MAINTENANCE @@ -13737,8 +14861,15 @@ enums: LicensingStageEnum: name: LicensingStageEnum definition_uri: https://w3id.org/valuesets/LicensingStageEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Nuclear facility licensing stages + title: Licensing Stage from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_operations + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: SITE_PERMIT: text: SITE_PERMIT @@ -13879,8 +15010,15 @@ enums: FuelCycleOperationEnum: name: FuelCycleOperationEnum definition_uri: https://w3id.org/valuesets/FuelCycleOperationEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Nuclear fuel cycle operational activities + title: Fuel Cycle Operation from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_operations + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: URANIUM_EXPLORATION: text: URANIUM_EXPLORATION @@ -14070,8 +15208,15 @@ enums: ReactorControlModeEnum: name: ReactorControlModeEnum definition_uri: https://w3id.org/valuesets/ReactorControlModeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Reactor control and safety system operational modes + title: Reactor Control Mode from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_operations + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: MANUAL_CONTROL: text: MANUAL_CONTROL @@ -14178,8 +15323,15 @@ enums: OperationalProcedureEnum: name: OperationalProcedureEnum definition_uri: https://w3id.org/valuesets/OperationalProcedureEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Standard nuclear facility operational procedures + title: Operational Procedure from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_operations + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: STARTUP_PROCEDURE: text: STARTUP_PROCEDURE @@ -14320,8 +15472,15 @@ enums: MiningType: name: MiningType definition_uri: https://w3id.org/valuesets/MiningType + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of mining operations + title: Mining Type from_schema: https://w3id.org/linkml/valuesets/industry/mining + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: OPEN_PIT: text: OPEN_PIT @@ -14494,8 +15653,15 @@ enums: MineralCategory: name: MineralCategory definition_uri: https://w3id.org/valuesets/MineralCategory + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Categories of minerals and materials + title: Mineral Category from_schema: https://w3id.org/linkml/valuesets/industry/mining + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: PRECIOUS_METALS: text: PRECIOUS_METALS @@ -14573,12 +15739,19 @@ enums: CriticalMineral: name: CriticalMineral definition_uri: https://w3id.org/valuesets/CriticalMineral + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: 'Critical minerals essential for economic and national security, particularly for clean energy, defense, and technology applications. Based on US Geological Survey and EU critical raw materials lists.' + title: Critical Mineral from_schema: https://w3id.org/linkml/valuesets/industry/mining + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: LITHIUM: text: LITHIUM @@ -15260,8 +16433,15 @@ enums: CommonMineral: name: CommonMineral definition_uri: https://w3id.org/valuesets/CommonMineral + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Common minerals extracted through mining + title: Common Mineral from_schema: https://w3id.org/linkml/valuesets/industry/mining + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: GOLD: text: GOLD @@ -15492,8 +16672,15 @@ enums: MiningEquipment: name: MiningEquipment definition_uri: https://w3id.org/valuesets/MiningEquipment + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of mining equipment + title: Mining Equipment from_schema: https://w3id.org/linkml/valuesets/industry/mining + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: DRILL_RIG: text: DRILL_RIG @@ -15620,8 +16807,15 @@ enums: OreGrade: name: OreGrade definition_uri: https://w3id.org/valuesets/OreGrade + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Classification of ore grades + title: Ore Grade from_schema: https://w3id.org/linkml/valuesets/industry/mining + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: HIGH_GRADE: text: HIGH_GRADE @@ -15674,8 +16868,15 @@ enums: MiningPhase: name: MiningPhase definition_uri: https://w3id.org/valuesets/MiningPhase + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Phases of mining operations + title: Mining Phase from_schema: https://w3id.org/linkml/valuesets/industry/mining + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: EXPLORATION: text: EXPLORATION @@ -15729,8 +16930,15 @@ enums: MiningHazard: name: MiningHazard definition_uri: https://w3id.org/valuesets/MiningHazard + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Mining-related hazards and risks + title: Mining Hazard from_schema: https://w3id.org/linkml/valuesets/industry/mining + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: CAVE_IN: text: CAVE_IN @@ -15817,8 +17025,15 @@ enums: EnvironmentalImpact: name: EnvironmentalImpact definition_uri: https://w3id.org/valuesets/EnvironmentalImpact + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Environmental impacts of mining + title: Environmental Impact from_schema: https://w3id.org/linkml/valuesets/industry/mining + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: HABITAT_DESTRUCTION: text: HABITAT_DESTRUCTION @@ -15882,8 +17097,15 @@ enums: ExtractiveIndustryFacilityTypeEnum: name: ExtractiveIndustryFacilityTypeEnum definition_uri: https://w3id.org/valuesets/ExtractiveIndustryFacilityTypeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of extractive industry facilities + title: Extractive Industry Facility Type from_schema: https://w3id.org/linkml/valuesets/industry/extractive_industry + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: MINING_FACILITY: text: MINING_FACILITY @@ -15900,8 +17122,15 @@ enums: ExtractiveIndustryProductTypeEnum: name: ExtractiveIndustryProductTypeEnum definition_uri: https://w3id.org/valuesets/ExtractiveIndustryProductTypeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of products extracted from extractive industry facilities + title: Extractive Industry Product Type from_schema: https://w3id.org/linkml/valuesets/industry/extractive_industry + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: MINERAL: text: MINERAL @@ -15939,8 +17168,15 @@ enums: MiningMethodEnum: name: MiningMethodEnum definition_uri: https://w3id.org/valuesets/MiningMethodEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Methods used for extracting minerals from the earth + title: Mining Method from_schema: https://w3id.org/linkml/valuesets/industry/extractive_industry + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: UNDERGROUND: text: UNDERGROUND @@ -15961,8 +17197,15 @@ enums: WellTypeEnum: name: WellTypeEnum definition_uri: https://w3id.org/valuesets/WellTypeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of wells used for extracting fluid resources + title: Well Type from_schema: https://w3id.org/linkml/valuesets/industry/extractive_industry + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: OIL: text: OIL @@ -15983,8 +17226,15 @@ enums: OutcomeTypeEnum: name: OutcomeTypeEnum definition_uri: https://w3id.org/valuesets/OutcomeTypeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of prediction outcomes for classification tasks + title: Outcome Type from_schema: https://w3id.org/linkml/valuesets/statistics/prediction_outcomes + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: TP: text: TP @@ -16005,8 +17255,15 @@ enums: PersonStatusEnum: name: PersonStatusEnum definition_uri: https://w3id.org/valuesets/PersonStatusEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Vital status of a person (living or deceased) + title: Person Status from_schema: https://w3id.org/linkml/valuesets/social/person_status + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: ALIVE: text: ALIVE @@ -16026,8 +17283,15 @@ enums: MimeType: name: MimeType definition_uri: https://w3id.org/valuesets/MimeType + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Common MIME types for various file formats + title: Mime Type from_schema: https://w3id.org/linkml/valuesets/computing/mime_types + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: APPLICATION_JSON: text: APPLICATION_JSON @@ -16292,8 +17556,15 @@ enums: MimeTypeCategory: name: MimeTypeCategory definition_uri: https://w3id.org/valuesets/MimeTypeCategory + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Categories of MIME types + title: Mime Type Category from_schema: https://w3id.org/linkml/valuesets/computing/mime_types + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: APPLICATION: text: APPLICATION @@ -16325,8 +17596,15 @@ enums: TextCharset: name: TextCharset definition_uri: https://w3id.org/valuesets/TextCharset + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Character encodings for text content + title: Text Charset from_schema: https://w3id.org/linkml/valuesets/computing/mime_types + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: UTF_8: text: UTF_8 @@ -16364,8 +17642,15 @@ enums: CompressionType: name: CompressionType definition_uri: https://w3id.org/valuesets/CompressionType + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Compression types used with Content-Encoding + title: Compression Type from_schema: https://w3id.org/linkml/valuesets/computing/mime_types + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: GZIP: text: GZIP @@ -16385,8 +17670,15 @@ enums: StateOfMatterEnum: name: StateOfMatterEnum definition_uri: https://w3id.org/valuesets/StateOfMatterEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: The physical state or phase of matter + title: State Of Matter from_schema: https://w3id.org/valuesets/physics/states-of-matter + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: SOLID: text: SOLID @@ -16429,8 +17721,15 @@ enums: AirPollutantEnum: name: AirPollutantEnum definition_uri: https://w3id.org/valuesets/AirPollutantEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Common air pollutants and air quality indicators + title: Air Pollutant from_schema: https://w3id.org/valuesets/environmental-health/exposures + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: PM2_5: text: PM2_5 @@ -16489,8 +17788,15 @@ enums: PesticideTypeEnum: name: PesticideTypeEnum definition_uri: https://w3id.org/valuesets/PesticideTypeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Categories of pesticides by target organism or chemical class + title: Pesticide Type from_schema: https://w3id.org/valuesets/environmental-health/exposures + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: HERBICIDE: text: HERBICIDE @@ -16540,8 +17846,15 @@ enums: HeavyMetalEnum: name: HeavyMetalEnum definition_uri: https://w3id.org/valuesets/HeavyMetalEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Heavy metals of environmental health concern + title: Heavy Metal from_schema: https://w3id.org/valuesets/environmental-health/exposures + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: LEAD: text: LEAD @@ -16592,8 +17905,15 @@ enums: ExposureRouteEnum: name: ExposureRouteEnum definition_uri: https://w3id.org/valuesets/ExposureRouteEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Routes by which exposure to environmental agents occurs + title: Exposure Route from_schema: https://w3id.org/valuesets/environmental-health/exposures + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: INHALATION: text: INHALATION @@ -16693,8 +18013,15 @@ enums: ExposureSourceEnum: name: ExposureSourceEnum definition_uri: https://w3id.org/valuesets/ExposureSourceEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Common sources of environmental exposures + title: Exposure Source from_schema: https://w3id.org/valuesets/environmental-health/exposures + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: AMBIENT_AIR: text: AMBIENT_AIR @@ -16773,8 +18100,15 @@ enums: WaterContaminantEnum: name: WaterContaminantEnum definition_uri: https://w3id.org/valuesets/WaterContaminantEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Common water contaminants + title: Water Contaminant from_schema: https://w3id.org/valuesets/environmental-health/exposures + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: LEAD: text: LEAD @@ -16835,8 +18169,15 @@ enums: EndocrineDisruptorEnum: name: EndocrineDisruptorEnum definition_uri: https://w3id.org/valuesets/EndocrineDisruptorEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Common endocrine disrupting chemicals + title: Endocrine Disruptor from_schema: https://w3id.org/valuesets/environmental-health/exposures + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: BPA: text: BPA @@ -16884,8 +18225,15 @@ enums: ExposureDurationEnum: name: ExposureDurationEnum definition_uri: https://w3id.org/valuesets/ExposureDurationEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Duration categories for environmental exposures + title: Exposure Duration from_schema: https://w3id.org/valuesets/environmental-health/exposures + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: ACUTE: text: ACUTE @@ -16914,8 +18262,15 @@ enums: SmokingStatusEnum: name: SmokingStatusEnum definition_uri: https://w3id.org/valuesets/SmokingStatusEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Tobacco and nicotine consumption status + title: Smoking Status from_schema: https://w3id.org/valuesets/environmental-health/exposures + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: CURRENT_SMOKER: text: CURRENT_SMOKER @@ -16937,8 +18292,15 @@ enums: ExposureStressorTypeEnum: name: ExposureStressorTypeEnum definition_uri: https://w3id.org/valuesets/ExposureStressorTypeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of exposure stressors by their origin or nature + title: Exposure Stressor Type from_schema: https://w3id.org/valuesets/environmental-health/exposures + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: BIOLOGICAL_AGENT: text: BIOLOGICAL_AGENT @@ -16971,8 +18333,15 @@ enums: ExposureTransportPathEnum: name: ExposureTransportPathEnum definition_uri: https://w3id.org/valuesets/ExposureTransportPathEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Transport medium through which exposure stressor reaches the recipient + title: Exposure Transport Path from_schema: https://w3id.org/valuesets/environmental-health/exposures + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: AIR_TRANSPORT_PATH: text: AIR_TRANSPORT_PATH @@ -16990,8 +18359,15 @@ enums: ExposureFrequencyEnum: name: ExposureFrequencyEnum definition_uri: https://w3id.org/valuesets/ExposureFrequencyEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Temporal pattern of exposure occurrence + title: Exposure Frequency from_schema: https://w3id.org/valuesets/environmental-health/exposures + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: INTERMITTENT: text: INTERMITTENT @@ -17004,8 +18380,15 @@ enums: StudyPopulationEnum: name: StudyPopulationEnum definition_uri: https://w3id.org/valuesets/StudyPopulationEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Specific population groups commonly studied in exposure research + title: Study Population from_schema: https://w3id.org/valuesets/environmental-health/exposures + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: CHILDREN: text: CHILDREN @@ -17048,8 +18431,15 @@ enums: CountryCodeISO2Enum: name: CountryCodeISO2Enum definition_uri: https://w3id.org/valuesets/CountryCodeISO2Enum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: ISO 3166-1 alpha-2 country codes (2-letter codes) + title: Country Code ISO2 from_schema: https://w3id.org/valuesets/geography/geographic-codes + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: US: text: US @@ -17354,8 +18744,15 @@ enums: CountryCodeISO3Enum: name: CountryCodeISO3Enum definition_uri: https://w3id.org/valuesets/CountryCodeISO3Enum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: ISO 3166-1 alpha-3 country codes (3-letter codes) + title: Country Code ISO3 from_schema: https://w3id.org/valuesets/geography/geographic-codes + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: USA: text: USA @@ -17540,8 +18937,15 @@ enums: USStateCodeEnum: name: USStateCodeEnum definition_uri: https://w3id.org/valuesets/USStateCodeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: United States state and territory codes + title: US State Code from_schema: https://w3id.org/valuesets/geography/geographic-codes + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: AL: text: AL @@ -17714,8 +19118,15 @@ enums: CanadianProvinceCodeEnum: name: CanadianProvinceCodeEnum definition_uri: https://w3id.org/valuesets/CanadianProvinceCodeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Canadian province and territory codes + title: Canadian Province Code from_schema: https://w3id.org/valuesets/geography/geographic-codes + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: AB: text: AB @@ -17759,8 +19170,15 @@ enums: CompassDirection: name: CompassDirection definition_uri: https://w3id.org/valuesets/CompassDirection + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Cardinal and intercardinal compass directions + title: Compass Direction from_schema: https://w3id.org/valuesets/geography/geographic-codes + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: NORTH: text: NORTH @@ -17925,8 +19343,15 @@ enums: RelativeDirection: name: RelativeDirection definition_uri: https://w3id.org/valuesets/RelativeDirection + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Relative directional terms + title: Relative Direction from_schema: https://w3id.org/valuesets/geography/geographic-codes + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: FORWARD: text: FORWARD @@ -18004,8 +19429,15 @@ enums: WindDirection: name: WindDirection definition_uri: https://w3id.org/valuesets/WindDirection + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Wind direction nomenclature (named for where wind comes FROM) + title: Wind Direction from_schema: https://w3id.org/valuesets/geography/geographic-codes + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: NORTHERLY: text: NORTHERLY @@ -18097,8 +19529,15 @@ enums: ContinentEnum: name: ContinentEnum definition_uri: https://w3id.org/valuesets/ContinentEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Continental regions + title: Continent from_schema: https://w3id.org/valuesets/geography/geographic-codes + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: AFRICA: text: AFRICA @@ -18124,8 +19563,15 @@ enums: UNRegionEnum: name: UNRegionEnum definition_uri: https://w3id.org/valuesets/UNRegionEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: United Nations regional classifications + title: UN Region from_schema: https://w3id.org/valuesets/geography/geographic-codes + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: EASTERN_AFRICA: text: EASTERN_AFRICA @@ -18196,8 +19642,15 @@ enums: LanguageCodeISO639_1Enum: name: LanguageCodeISO639_1Enum definition_uri: https://w3id.org/valuesets/LanguageCodeISO6391Enum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: ISO 639-1 two-letter language codes + title: Language Code ISO639_1 from_schema: https://w3id.org/valuesets/geography/geographic-codes + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: EN: text: EN @@ -18292,8 +19745,15 @@ enums: TimeZoneEnum: name: TimeZoneEnum definition_uri: https://w3id.org/valuesets/TimeZoneEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Common time zones + title: Time Zone from_schema: https://w3id.org/valuesets/geography/geographic-codes + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: UTC: text: UTC @@ -18364,8 +19824,15 @@ enums: CurrencyCodeISO4217Enum: name: CurrencyCodeISO4217Enum definition_uri: https://w3id.org/valuesets/CurrencyCodeISO4217Enum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: ISO 4217 currency codes + title: Currency Code ISO4217 from_schema: https://w3id.org/valuesets/geography/geographic-codes + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: USD: text: USD @@ -18466,8 +19933,15 @@ enums: SentimentClassificationEnum: name: SentimentClassificationEnum definition_uri: https://w3id.org/valuesets/SentimentClassificationEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Standard labels for sentiment analysis classification tasks + title: Sentiment Classification from_schema: https://w3id.org/linkml/valuesets/data_science/sentiment_analysis + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: POSITIVE: text: POSITIVE @@ -18498,8 +19972,15 @@ enums: FineSentimentClassificationEnum: name: FineSentimentClassificationEnum definition_uri: https://w3id.org/valuesets/FineSentimentClassificationEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Fine-grained sentiment analysis labels with intensity levels + title: Fine Sentiment Classification from_schema: https://w3id.org/linkml/valuesets/data_science/sentiment_analysis + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: VERY_POSITIVE: text: VERY_POSITIVE @@ -18546,8 +20027,15 @@ enums: BinaryClassificationEnum: name: BinaryClassificationEnum definition_uri: https://w3id.org/valuesets/BinaryClassificationEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Generic binary classification labels + title: Binary Classification from_schema: https://w3id.org/linkml/valuesets/data_science/binary_classification + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: POSITIVE: text: POSITIVE @@ -18572,8 +20060,15 @@ enums: SpamClassificationEnum: name: SpamClassificationEnum definition_uri: https://w3id.org/valuesets/SpamClassificationEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Standard labels for spam/ham email classification + title: Spam Classification from_schema: https://w3id.org/linkml/valuesets/data_science/binary_classification + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: SPAM: text: SPAM @@ -18599,8 +20094,15 @@ enums: AnomalyDetectionEnum: name: AnomalyDetectionEnum definition_uri: https://w3id.org/valuesets/AnomalyDetectionEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Labels for anomaly detection tasks + title: Anomaly Detection from_schema: https://w3id.org/linkml/valuesets/data_science/binary_classification + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: NORMAL: text: NORMAL @@ -18624,8 +20126,15 @@ enums: ChurnClassificationEnum: name: ChurnClassificationEnum definition_uri: https://w3id.org/valuesets/ChurnClassificationEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Customer churn prediction labels + title: Churn Classification from_schema: https://w3id.org/linkml/valuesets/data_science/binary_classification + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: RETAINED: text: RETAINED @@ -18653,8 +20162,15 @@ enums: FraudDetectionEnum: name: FraudDetectionEnum definition_uri: https://w3id.org/valuesets/FraudDetectionEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Fraud detection classification labels + title: Fraud Detection from_schema: https://w3id.org/linkml/valuesets/data_science/binary_classification + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: LEGITIMATE: text: LEGITIMATE @@ -18677,8 +20193,15 @@ enums: QualityControlEnum: name: QualityControlEnum definition_uri: https://w3id.org/valuesets/QualityControlEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Quality control classification labels + title: Quality Control from_schema: https://w3id.org/linkml/valuesets/data_science/quality_control + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: PASS: text: PASS @@ -18703,8 +20226,15 @@ enums: DefectClassificationEnum: name: DefectClassificationEnum definition_uri: https://w3id.org/valuesets/DefectClassificationEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Manufacturing defect classification + title: Defect Classification from_schema: https://w3id.org/linkml/valuesets/data_science/quality_control + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: NO_DEFECT: text: NO_DEFECT @@ -18743,8 +20273,15 @@ enums: name: BasicEmotionEnum definition_uri: https://w3id.org/valuesets/BasicEmotionEnum conforms_to: https://en.wikipedia.org/wiki/Basic_emotions + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Ekman's six basic emotions commonly used in emotion recognition + title: Basic Emotion from_schema: https://w3id.org/linkml/valuesets/data_science/emotion_classification + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: ANGER: text: ANGER @@ -18799,8 +20336,15 @@ enums: name: ExtendedEmotionEnum definition_uri: https://w3id.org/valuesets/ExtendedEmotionEnum conforms_to: https://en.wikipedia.org/wiki/Emotion_classification + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Extended emotion set including complex emotions + title: Extended Emotion from_schema: https://w3id.org/linkml/valuesets/data_science/emotion_classification + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: ANGER: text: ANGER @@ -18858,8 +20402,15 @@ enums: PriorityLevelEnum: name: PriorityLevelEnum definition_uri: https://w3id.org/valuesets/PriorityLevelEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Standard priority levels for task/issue classification + title: Priority Level from_schema: https://w3id.org/linkml/valuesets/data_science/priority_severity + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: CRITICAL: text: CRITICAL @@ -18905,8 +20456,15 @@ enums: SeverityLevelEnum: name: SeverityLevelEnum definition_uri: https://w3id.org/valuesets/SeverityLevelEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Severity levels for incident/bug classification + title: Severity Level from_schema: https://w3id.org/linkml/valuesets/data_science/priority_severity + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: CRITICAL: text: CRITICAL @@ -18943,8 +20501,15 @@ enums: ConfidenceLevelEnum: name: ConfidenceLevelEnum definition_uri: https://w3id.org/valuesets/ConfidenceLevelEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Confidence levels for predictions and classifications + title: Confidence Level from_schema: https://w3id.org/linkml/valuesets/data_science/priority_severity + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: VERY_HIGH: text: VERY_HIGH @@ -18984,8 +20549,15 @@ enums: NewsTopicCategoryEnum: name: NewsTopicCategoryEnum definition_uri: https://w3id.org/valuesets/NewsTopicCategoryEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Common news article topic categories + title: News Topic Category from_schema: https://w3id.org/linkml/valuesets/data_science/text_classification + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: POLITICS: text: POLITICS @@ -19041,8 +20613,15 @@ enums: ToxicityClassificationEnum: name: ToxicityClassificationEnum definition_uri: https://w3id.org/valuesets/ToxicityClassificationEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Text toxicity classification labels + title: Toxicity Classification from_schema: https://w3id.org/linkml/valuesets/data_science/text_classification + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: NON_TOXIC: text: NON_TOXIC @@ -19089,8 +20668,15 @@ enums: IntentClassificationEnum: name: IntentClassificationEnum definition_uri: https://w3id.org/valuesets/IntentClassificationEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Common chatbot/NLU intent categories + title: Intent Classification from_schema: https://w3id.org/linkml/valuesets/data_science/text_classification + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: GREETING: text: GREETING @@ -19135,8 +20721,15 @@ enums: SimpleSpatialDirection: name: SimpleSpatialDirection definition_uri: https://w3id.org/valuesets/SimpleSpatialDirection + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Basic spatial directional terms for general use + title: Simple Spatial Direction from_schema: https://w3id.org/linkml/valuesets/spatial/spatial_qualifiers + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: LEFT: text: LEFT @@ -19210,11 +20803,18 @@ enums: AnatomicalSide: name: AnatomicalSide definition_uri: https://w3id.org/valuesets/AnatomicalSide + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: 'Anatomical sides as defined in the Biological Spatial Ontology (BSPO). An anatomical region bounded by a plane perpendicular to an axis through the middle.' + title: Anatomical Side from_schema: https://w3id.org/linkml/valuesets/spatial/spatial_qualifiers + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: LEFT: text: LEFT @@ -19401,8 +21001,15 @@ enums: AnatomicalRegion: name: AnatomicalRegion definition_uri: https://w3id.org/valuesets/AnatomicalRegion + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Anatomical regions based on spatial position + title: Anatomical Region from_schema: https://w3id.org/linkml/valuesets/spatial/spatial_qualifiers + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: ANTERIOR_REGION: text: ANTERIOR_REGION @@ -19479,8 +21086,15 @@ enums: AnatomicalAxis: name: AnatomicalAxis definition_uri: https://w3id.org/valuesets/AnatomicalAxis + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Anatomical axes defining spatial organization + title: Anatomical Axis from_schema: https://w3id.org/linkml/valuesets/spatial/spatial_qualifiers + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: ANTERIOR_POSTERIOR: text: ANTERIOR_POSTERIOR @@ -19535,8 +21149,15 @@ enums: AnatomicalPlane: name: AnatomicalPlane definition_uri: https://w3id.org/valuesets/AnatomicalPlane + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Standard anatomical planes for sectioning + title: Anatomical Plane from_schema: https://w3id.org/linkml/valuesets/spatial/spatial_qualifiers + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: SAGITTAL: text: SAGITTAL @@ -19607,8 +21228,15 @@ enums: SpatialRelationship: name: SpatialRelationship definition_uri: https://w3id.org/valuesets/SpatialRelationship + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Spatial relationships between anatomical structures + title: Spatial Relationship from_schema: https://w3id.org/linkml/valuesets/spatial/spatial_qualifiers + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: ADJACENT_TO: text: ADJACENT_TO @@ -19699,8 +21327,15 @@ enums: CellPolarity: name: CellPolarity definition_uri: https://w3id.org/valuesets/CellPolarity + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Spatial polarity in cells and tissues + title: Cell Polarity from_schema: https://w3id.org/linkml/valuesets/spatial/spatial_qualifiers + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: APICAL: text: APICAL @@ -19761,8 +21396,15 @@ enums: name: CrystalSystemEnum definition_uri: https://w3id.org/valuesets/CrystalSystemEnum conforms_to: https://en.wikipedia.org/wiki/Crystal_system + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: The seven crystal systems in crystallography + title: Crystal System from_schema: https://w3id.org/linkml/valuesets/materials_science/crystal_structures + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: TRICLINIC: text: TRICLINIC @@ -19818,8 +21460,15 @@ enums: name: BravaisLatticeEnum definition_uri: https://w3id.org/valuesets/BravaisLatticeEnum conforms_to: https://en.wikipedia.org/wiki/Bravais_lattice + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: The 14 Bravais lattices describing all possible crystal lattices + title: Bravais Lattice from_schema: https://w3id.org/linkml/valuesets/materials_science/crystal_structures + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: PRIMITIVE_TRICLINIC: text: PRIMITIVE_TRICLINIC @@ -19913,8 +21562,15 @@ enums: ElectricalConductivityEnum: name: ElectricalConductivityEnum definition_uri: https://w3id.org/valuesets/ElectricalConductivityEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Classification of materials by electrical conductivity + title: Electrical Conductivity from_schema: https://w3id.org/linkml/valuesets/materials_science/material_properties + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: CONDUCTOR: text: CONDUCTOR @@ -19945,8 +21601,15 @@ enums: MagneticPropertyEnum: name: MagneticPropertyEnum definition_uri: https://w3id.org/valuesets/MagneticPropertyEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Classification of materials by magnetic properties + title: Magnetic Property from_schema: https://w3id.org/linkml/valuesets/materials_science/material_properties + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: DIAMAGNETIC: text: DIAMAGNETIC @@ -19971,8 +21634,15 @@ enums: OpticalPropertyEnum: name: OpticalPropertyEnum definition_uri: https://w3id.org/valuesets/OpticalPropertyEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Optical properties of materials + title: Optical Property from_schema: https://w3id.org/linkml/valuesets/materials_science/material_properties + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: TRANSPARENT: text: TRANSPARENT @@ -20007,8 +21677,15 @@ enums: ThermalConductivityEnum: name: ThermalConductivityEnum definition_uri: https://w3id.org/valuesets/ThermalConductivityEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Classification by thermal conductivity + title: Thermal Conductivity from_schema: https://w3id.org/linkml/valuesets/materials_science/material_properties + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: HIGH_THERMAL_CONDUCTOR: text: HIGH_THERMAL_CONDUCTOR @@ -20029,8 +21706,15 @@ enums: MechanicalBehaviorEnum: name: MechanicalBehaviorEnum definition_uri: https://w3id.org/valuesets/MechanicalBehaviorEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Mechanical behavior of materials under stress + title: Mechanical Behavior from_schema: https://w3id.org/linkml/valuesets/materials_science/material_properties + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: ELASTIC: text: ELASTIC @@ -20066,8 +21750,15 @@ enums: MicroscopyMethodEnum: name: MicroscopyMethodEnum definition_uri: https://w3id.org/valuesets/MicroscopyMethodEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Microscopy techniques for material characterization + title: Microscopy Method from_schema: https://w3id.org/linkml/valuesets/materials_science/characterization_methods + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: SEM: text: SEM @@ -20128,8 +21819,15 @@ enums: SpectroscopyMethodEnum: name: SpectroscopyMethodEnum definition_uri: https://w3id.org/valuesets/SpectroscopyMethodEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Spectroscopy techniques for material analysis + title: Spectroscopy Method from_schema: https://w3id.org/linkml/valuesets/materials_science/characterization_methods + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: XRD: text: XRD @@ -20198,8 +21896,15 @@ enums: ThermalAnalysisMethodEnum: name: ThermalAnalysisMethodEnum definition_uri: https://w3id.org/valuesets/ThermalAnalysisMethodEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Thermal analysis techniques + title: Thermal Analysis Method from_schema: https://w3id.org/linkml/valuesets/materials_science/characterization_methods + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: DSC: text: DSC @@ -20239,8 +21944,15 @@ enums: MechanicalTestingMethodEnum: name: MechanicalTestingMethodEnum definition_uri: https://w3id.org/valuesets/MechanicalTestingMethodEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Mechanical testing methods + title: Mechanical Testing Method from_schema: https://w3id.org/linkml/valuesets/materials_science/characterization_methods + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: TENSILE: text: TENSILE @@ -20277,8 +21989,15 @@ enums: MaterialClassEnum: name: MaterialClassEnum definition_uri: https://w3id.org/valuesets/MaterialClassEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Major classes of materials + title: Material Class from_schema: https://w3id.org/linkml/valuesets/materials_science/material_types + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: METAL: text: METAL @@ -20325,8 +22044,15 @@ enums: PolymerTypeEnum: name: PolymerTypeEnum definition_uri: https://w3id.org/valuesets/PolymerTypeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of polymer materials + title: Polymer Type from_schema: https://w3id.org/linkml/valuesets/materials_science/material_types + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: THERMOPLASTIC: text: THERMOPLASTIC @@ -20363,8 +22089,15 @@ enums: MetalTypeEnum: name: MetalTypeEnum definition_uri: https://w3id.org/valuesets/MetalTypeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of metallic materials + title: Metal Type from_schema: https://w3id.org/linkml/valuesets/materials_science/material_types + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: FERROUS: text: FERROUS @@ -20399,8 +22132,15 @@ enums: CompositeTypeEnum: name: CompositeTypeEnum definition_uri: https://w3id.org/valuesets/CompositeTypeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of composite materials + title: Composite Type from_schema: https://w3id.org/linkml/valuesets/materials_science/material_types + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: FIBER_REINFORCED: text: FIBER_REINFORCED @@ -20439,8 +22179,15 @@ enums: SynthesisMethodEnum: name: SynthesisMethodEnum definition_uri: https://w3id.org/valuesets/SynthesisMethodEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Common material synthesis and processing methods + title: Synthesis Method from_schema: https://w3id.org/linkml/valuesets/materials_science/synthesis_methods + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: SOL_GEL: text: SOL_GEL @@ -20534,8 +22281,15 @@ enums: CrystalGrowthMethodEnum: name: CrystalGrowthMethodEnum definition_uri: https://w3id.org/valuesets/CrystalGrowthMethodEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Methods for growing single crystals + title: Crystal Growth Method from_schema: https://w3id.org/linkml/valuesets/materials_science/synthesis_methods + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: CZOCHRALSKI: text: CZOCHRALSKI @@ -20594,8 +22348,15 @@ enums: AdditiveManufacturingEnum: name: AdditiveManufacturingEnum definition_uri: https://w3id.org/valuesets/AdditiveManufacturingEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: 3D printing and additive manufacturing methods + title: Additive Manufacturing from_schema: https://w3id.org/linkml/valuesets/materials_science/synthesis_methods + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: FDM: text: FDM @@ -20647,8 +22408,15 @@ enums: TraditionalPigmentEnum: name: TraditionalPigmentEnum definition_uri: https://w3id.org/valuesets/TraditionalPigmentEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Traditional artist pigments and their colors + title: Traditional Pigment from_schema: https://w3id.org/valuesets/materials_science/pigments_dyes + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: TITANIUM_WHITE: text: TITANIUM_WHITE @@ -21047,8 +22815,15 @@ enums: IndustrialDyeEnum: name: IndustrialDyeEnum definition_uri: https://w3id.org/valuesets/IndustrialDyeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Industrial and textile dyes + title: Industrial Dye from_schema: https://w3id.org/valuesets/materials_science/pigments_dyes + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: INDIGO: text: INDIGO @@ -21206,8 +22981,15 @@ enums: FoodColoringEnum: name: FoodColoringEnum definition_uri: https://w3id.org/valuesets/FoodColoringEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Food coloring and natural food dyes + title: Food Coloring from_schema: https://w3id.org/valuesets/materials_science/pigments_dyes + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: FD_C_RED_40: text: FD_C_RED_40 @@ -21405,8 +23187,15 @@ enums: AutomobilePaintColorEnum: name: AutomobilePaintColorEnum definition_uri: https://w3id.org/valuesets/AutomobilePaintColorEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Common automobile paint colors + title: Automobile Paint Color from_schema: https://w3id.org/valuesets/materials_science/pigments_dyes + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: ARCTIC_WHITE: text: ARCTIC_WHITE @@ -21516,8 +23305,15 @@ enums: BasicColorEnum: name: BasicColorEnum definition_uri: https://w3id.org/valuesets/BasicColorEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Basic color names commonly used in everyday language + title: Basic Color from_schema: https://w3id.org/valuesets/visual/colors + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: RED: text: RED @@ -21650,8 +23446,15 @@ enums: WebColorEnum: name: WebColorEnum definition_uri: https://w3id.org/valuesets/WebColorEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Standard HTML/CSS named colors (147 colors) + title: Web Color from_schema: https://w3id.org/valuesets/visual/colors + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: INDIAN_RED: text: INDIAN_RED @@ -22600,8 +24403,15 @@ enums: X11ColorEnum: name: X11ColorEnum definition_uri: https://w3id.org/valuesets/X11ColorEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: X11/Unix system colors (extended set) + title: X11 Color from_schema: https://w3id.org/valuesets/visual/colors + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: X11_AQUA: text: X11_AQUA @@ -22678,8 +24488,15 @@ enums: ColorSpaceEnum: name: ColorSpaceEnum definition_uri: https://w3id.org/valuesets/ColorSpaceEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Color space and model types + title: Color Space from_schema: https://w3id.org/valuesets/visual/colors + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: RGB: text: RGB @@ -22711,8 +24528,15 @@ enums: EyeColorEnum: name: EyeColorEnum definition_uri: https://w3id.org/valuesets/EyeColorEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Human eye color phenotypes + title: Eye Color from_schema: https://w3id.org/valuesets/bio/biological_colors + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: BROWN: text: BROWN @@ -22807,8 +24631,15 @@ enums: HairColorEnum: name: HairColorEnum definition_uri: https://w3id.org/valuesets/HairColorEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Human hair color phenotypes + title: Hair Color from_schema: https://w3id.org/valuesets/bio/biological_colors + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: BLACK: text: BLACK @@ -22932,8 +24763,15 @@ enums: FlowerColorEnum: name: FlowerColorEnum definition_uri: https://w3id.org/valuesets/FlowerColorEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Common flower colors + title: Flower Color from_schema: https://w3id.org/valuesets/bio/biological_colors + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: RED: text: RED @@ -23092,8 +24930,15 @@ enums: AnimalCoatColorEnum: name: AnimalCoatColorEnum definition_uri: https://w3id.org/valuesets/AnimalCoatColorEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Animal coat/fur colors + title: Animal Coat Color from_schema: https://w3id.org/valuesets/bio/biological_colors + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: BLACK: text: BLACK @@ -23256,8 +25101,15 @@ enums: SkinToneEnum: name: SkinToneEnum definition_uri: https://w3id.org/valuesets/SkinToneEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Human skin tone classifications (Fitzpatrick scale based) + title: Skin Tone from_schema: https://w3id.org/valuesets/bio/biological_colors + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: TYPE_I: text: TYPE_I @@ -23340,8 +25192,15 @@ enums: PlantLeafColorEnum: name: PlantLeafColorEnum definition_uri: https://w3id.org/valuesets/PlantLeafColorEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Plant leaf colors (including seasonal changes) + title: Plant Leaf Color from_schema: https://w3id.org/valuesets/bio/biological_colors + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: GREEN: text: GREEN @@ -23457,8 +25316,15 @@ enums: DNABaseEnum: name: DNABaseEnum definition_uri: https://w3id.org/valuesets/DNABaseEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Standard DNA nucleotide bases (canonical) + title: DNA Base from_schema: https://w3id.org/valuesets/bio/sequence_alphabets + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: A: text: A @@ -23527,8 +25393,15 @@ enums: DNABaseExtendedEnum: name: DNABaseExtendedEnum definition_uri: https://w3id.org/valuesets/DNABaseExtendedEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Extended DNA alphabet with IUPAC ambiguity codes + title: DNA Base Extended from_schema: https://w3id.org/valuesets/bio/sequence_alphabets + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: A: text: A @@ -23699,8 +25572,15 @@ enums: RNABaseEnum: name: RNABaseEnum definition_uri: https://w3id.org/valuesets/RNABaseEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Standard RNA nucleotide bases (canonical) + title: RNA Base from_schema: https://w3id.org/valuesets/bio/sequence_alphabets + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: A: text: A @@ -23769,8 +25649,15 @@ enums: RNABaseExtendedEnum: name: RNABaseExtendedEnum definition_uri: https://w3id.org/valuesets/RNABaseExtendedEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Extended RNA alphabet with IUPAC ambiguity codes + title: RNA Base Extended from_schema: https://w3id.org/valuesets/bio/sequence_alphabets + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: A: text: A @@ -23935,8 +25822,15 @@ enums: AminoAcidEnum: name: AminoAcidEnum definition_uri: https://w3id.org/valuesets/AminoAcidEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Standard amino acid single letter codes + title: Amino Acid from_schema: https://w3id.org/valuesets/bio/sequence_alphabets + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: A: text: A @@ -24378,8 +26272,15 @@ enums: AminoAcidExtendedEnum: name: AminoAcidExtendedEnum definition_uri: https://w3id.org/valuesets/AminoAcidExtendedEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Extended amino acid alphabet with ambiguity codes and special characters + title: Amino Acid Extended from_schema: https://w3id.org/valuesets/bio/sequence_alphabets + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: A: text: A @@ -24697,8 +26598,15 @@ enums: CodonEnum: name: CodonEnum definition_uri: https://w3id.org/valuesets/CodonEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Standard genetic code codons (DNA) + title: Codon from_schema: https://w3id.org/valuesets/bio/sequence_alphabets + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: TTT: text: TTT @@ -25355,8 +27263,15 @@ enums: NucleotideModificationEnum: name: NucleotideModificationEnum definition_uri: https://w3id.org/valuesets/NucleotideModificationEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Common nucleotide modifications + title: Nucleotide Modification from_schema: https://w3id.org/valuesets/bio/sequence_alphabets + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: FIVE_METHYL_C: text: FIVE_METHYL_C @@ -25476,8 +27391,15 @@ enums: SequenceQualityEnum: name: SequenceQualityEnum definition_uri: https://w3id.org/valuesets/SequenceQualityEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Sequence quality indicators (Phred scores) + title: Sequence Quality from_schema: https://w3id.org/valuesets/bio/sequence_alphabets + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: Q0: text: Q0 @@ -25573,12 +27495,18 @@ enums: IUPACNucleotideCode: name: IUPACNucleotideCode definition_uri: https://w3id.org/valuesets/IUPACNucleotideCode + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: 'Complete IUPAC nucleotide codes including ambiguous bases for DNA/RNA sequences. Used in FASTA and other sequence formats to represent uncertain nucleotides.' title: IUPAC Nucleotide Ambiguity Codes from_schema: https://w3id.org/linkml/valuesets/bio/sequence_chemistry + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: A: text: A @@ -25642,10 +27570,16 @@ enums: StandardAminoAcid: name: StandardAminoAcid definition_uri: https://w3id.org/valuesets/StandardAminoAcid + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: The 20 standard proteinogenic amino acids with IUPAC single-letter codes title: Standard Amino Acids from_schema: https://w3id.org/linkml/valuesets/bio/sequence_chemistry + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: A: text: A @@ -25730,11 +27664,17 @@ enums: IUPACAminoAcidCode: name: IUPACAminoAcidCode definition_uri: https://w3id.org/valuesets/IUPACAminoAcidCode + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: 'Complete IUPAC amino acid codes including standard amino acids, rare amino acids, and ambiguity codes' title: IUPAC Amino Acid Codes from_schema: https://w3id.org/linkml/valuesets/bio/sequence_chemistry + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: A: text: A @@ -25851,9 +27791,15 @@ enums: SequenceAlphabet: name: SequenceAlphabet definition_uri: https://w3id.org/valuesets/SequenceAlphabet + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of sequence alphabets used in bioinformatics title: Sequence Alphabet Types from_schema: https://w3id.org/linkml/valuesets/bio/sequence_chemistry + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: DNA: text: DNA @@ -25885,12 +27831,18 @@ enums: SequenceQualityEncoding: name: SequenceQualityEncoding definition_uri: https://w3id.org/valuesets/SequenceQualityEncoding + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: 'Quality score encoding standards used in FASTQ files and sequencing data. Different platforms and software versions use different ASCII offsets.' title: Sequence Quality Score Encodings from_schema: https://w3id.org/linkml/valuesets/bio/sequence_chemistry + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: SANGER: text: SANGER @@ -25960,11 +27912,17 @@ enums: GeneticCodeTable: name: GeneticCodeTable definition_uri: https://w3id.org/valuesets/GeneticCodeTable + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: 'NCBI genetic code translation tables for different organisms. Table 1 is the universal genetic code used by most organisms.' title: NCBI Genetic Code Translation Tables from_schema: https://w3id.org/linkml/valuesets/bio/sequence_chemistry + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: TABLE_1: text: TABLE_1 @@ -26209,9 +28167,15 @@ enums: SequenceStrand: name: SequenceStrand definition_uri: https://w3id.org/valuesets/SequenceStrand + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Strand orientation for nucleic acid sequences title: DNA/RNA Strand Orientation from_schema: https://w3id.org/linkml/valuesets/bio/sequence_chemistry + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: PLUS: text: PLUS @@ -26230,9 +28194,15 @@ enums: SequenceTopology: name: SequenceTopology definition_uri: https://w3id.org/valuesets/SequenceTopology + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Topological structure of nucleic acid molecules title: Sequence Topology from_schema: https://w3id.org/linkml/valuesets/bio/sequence_chemistry + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: LINEAR: text: LINEAR @@ -26251,9 +28221,15 @@ enums: SequenceModality: name: SequenceModality definition_uri: https://w3id.org/valuesets/SequenceModality + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of sequence data based on experimental method title: Sequence Data Modality from_schema: https://w3id.org/linkml/valuesets/bio/sequence_chemistry + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: SINGLE_CELL: text: SINGLE_CELL @@ -26282,10 +28258,16 @@ enums: SequencingPlatform: name: SequencingPlatform definition_uri: https://w3id.org/valuesets/SequencingPlatform + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Major DNA/RNA sequencing platforms and instruments used in genomics research title: Sequencing Platforms and Instruments from_schema: https://w3id.org/linkml/valuesets/bio/sequencing_platforms + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: ILLUMINA_HISEQ_2000: text: ILLUMINA_HISEQ_2000 @@ -26702,9 +28684,15 @@ enums: SequencingChemistry: name: SequencingChemistry definition_uri: https://w3id.org/valuesets/SequencingChemistry + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Fundamental chemical methods used for DNA/RNA sequencing title: Sequencing Chemistry Methods from_schema: https://w3id.org/linkml/valuesets/bio/sequencing_platforms + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: SEQUENCING_BY_SYNTHESIS: text: SEQUENCING_BY_SYNTHESIS @@ -26751,9 +28739,15 @@ enums: LibraryPreparation: name: LibraryPreparation definition_uri: https://w3id.org/valuesets/LibraryPreparation + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Methods for preparing sequencing libraries from nucleic acid samples title: Library Preparation Methods from_schema: https://w3id.org/linkml/valuesets/bio/sequencing_platforms + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: GENOMIC_DNA: text: GENOMIC_DNA @@ -26815,9 +28809,15 @@ enums: SequencingApplication: name: SequencingApplication definition_uri: https://w3id.org/valuesets/SequencingApplication + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Primary applications or assays using DNA/RNA sequencing title: Sequencing Applications from_schema: https://w3id.org/linkml/valuesets/bio/sequencing_platforms + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: WHOLE_GENOME_SEQUENCING: text: WHOLE_GENOME_SEQUENCING @@ -26892,9 +28892,15 @@ enums: ReadType: name: ReadType definition_uri: https://w3id.org/valuesets/ReadType + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Configuration of sequencing reads generated by different platforms title: Sequencing Read Types from_schema: https://w3id.org/linkml/valuesets/bio/sequencing_platforms + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: SINGLE_END: text: SINGLE_END @@ -26919,9 +28925,15 @@ enums: SequenceFileFormat: name: SequenceFileFormat definition_uri: https://w3id.org/valuesets/SequenceFileFormat + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Standard file formats used for storing sequence data title: Sequence File Formats from_schema: https://w3id.org/linkml/valuesets/bio/sequencing_platforms + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: FASTA: text: FASTA @@ -27096,9 +29108,15 @@ enums: DataProcessingLevel: name: DataProcessingLevel definition_uri: https://w3id.org/valuesets/DataProcessingLevel + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Levels of processing applied to raw sequencing data title: Sequence Data Processing Levels from_schema: https://w3id.org/linkml/valuesets/bio/sequencing_platforms + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: RAW: text: RAW @@ -27133,11 +29151,18 @@ enums: CdsPhaseType: name: CdsPhaseType definition_uri: https://w3id.org/valuesets/CdsPhaseType + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: For features of type CDS (coding sequence), the phase indicates where the feature begins with reference to the reading frame. The phase is one of the integers 0, 1, or 2, indicating the number of bases that should be removed from the beginning of this feature to reach the first base of the next codon. + title: Cds Phase Type from_schema: https://w3id.org/common-value-sets/genomics + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: PHASE_0: text: PHASE_0 @@ -27154,11 +29179,18 @@ enums: ContigCollectionType: name: ContigCollectionType definition_uri: https://w3id.org/valuesets/ContigCollectionType + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: The type of the contig set; the type of the 'omics data set. Terms are taken from the Genomics Standards Consortium where possible. See the GSC checklists at https://genomicsstandardsconsortium.github.io/mixs/ for the controlled vocabularies used. + title: Contig Collection Type from_schema: https://w3id.org/common-value-sets/genomics + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: ISOLATE: text: ISOLATE @@ -27204,9 +29236,16 @@ enums: StrandType: name: StrandType definition_uri: https://w3id.org/valuesets/StrandType + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: The strand that a feature appears on relative to a landmark. Also encompasses unknown or irrelevant strandedness. + title: Strand Type from_schema: https://w3id.org/common-value-sets/genomics + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: NEGATIVE: text: NEGATIVE @@ -27230,8 +29269,15 @@ enums: SequenceType: name: SequenceType definition_uri: https://w3id.org/valuesets/SequenceType + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: The type of sequence being represented. + title: Sequence Type from_schema: https://w3id.org/common-value-sets/genomics + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: NUCLEIC_ACID: text: NUCLEIC_ACID @@ -27242,9 +29288,16 @@ enums: ProteinEvidenceForExistence: name: ProteinEvidenceForExistence definition_uri: https://w3id.org/valuesets/ProteinEvidenceForExistence + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: The evidence for the existence of a biological entity. See https://www.uniprot.org/help/protein_existence and https://www.ncbi.nlm.nih.gov/genbank/evidence/. + title: Protein Evidence For Existence from_schema: https://w3id.org/common-value-sets/protein_evidence + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: EXPERIMENTAL_EVIDENCE_AT_PROTEIN_LEVEL: text: EXPERIMENTAL_EVIDENCE_AT_PROTEIN_LEVEL @@ -27271,8 +29324,15 @@ enums: RefSeqStatusType: name: RefSeqStatusType definition_uri: https://w3id.org/valuesets/RefSeqStatusType + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: RefSeq status codes, taken from https://www.ncbi.nlm.nih.gov/genbank/evidence/. + title: Ref Seq Status Type from_schema: https://w3id.org/common-value-sets/protein_evidence + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: MODEL: text: MODEL @@ -27311,9 +29371,16 @@ enums: CurrencyChemical: name: CurrencyChemical definition_uri: https://w3id.org/valuesets/CurrencyChemical + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Common metabolic currency molecules and cofactors that serve as energy carriers, electron donors/acceptors, and group transfer agents in cellular metabolism. + title: Currency Chemical from_schema: https://w3id.org/common-value-sets/currency_chemicals + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: ATP: text: ATP @@ -27387,9 +29454,16 @@ enums: PlantDevelopmentalStage: name: PlantDevelopmentalStage definition_uri: https://w3id.org/valuesets/PlantDevelopmentalStage + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Major developmental stages in the plant life cycle, from seed germination through senescence. Based on the Plant Ontology (PO) standardized stages. + title: Plant Developmental Stage from_schema: https://w3id.org/common-value-sets/plant_developmental_stages + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: SEED_GERMINATION_STAGE: text: SEED_GERMINATION_STAGE @@ -27467,9 +29541,16 @@ enums: UniProtSpeciesCode: name: UniProtSpeciesCode definition_uri: https://w3id.org/valuesets/UniProtSpeciesCode + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: UniProt species mnemonic codes for reference proteomes with associated metadata + title: Uni Prot Species Code from_schema: https://w3id.org/common-value-sets/uniprot_species + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: SP_9ABAC: text: SP_9ABAC @@ -31369,9 +33450,15 @@ enums: LipidCategory: name: LipidCategory definition_uri: https://w3id.org/valuesets/LipidCategory + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Major categories of lipids based on SwissLipids classification title: Lipid Category from_schema: https://w3id.org/valuesets/bio/lipid_categories + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: LIPID: text: LIPID @@ -31434,9 +33521,15 @@ enums: PeakAnnotationSeriesLabel: name: PeakAnnotationSeriesLabel definition_uri: https://w3id.org/valuesets/PeakAnnotationSeriesLabel + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of peak annotations in mass spectrometry data title: Peak Annotation Series Label from_schema: https://w3id.org/common-value-sets/bio/proteomics_standards + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: PEPTIDE: text: PEPTIDE @@ -31476,9 +33569,15 @@ enums: PeptideIonSeries: name: PeptideIonSeries definition_uri: https://w3id.org/valuesets/PeptideIonSeries + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of peptide fragment ion series in mass spectrometry title: Peptide Ion Series from_schema: https://w3id.org/common-value-sets/bio/proteomics_standards + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: B: text: B @@ -31536,9 +33635,15 @@ enums: MassErrorUnit: name: MassErrorUnit definition_uri: https://w3id.org/valuesets/MassErrorUnit + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Units for expressing mass error in mass spectrometry title: Mass Error Unit from_schema: https://w3id.org/common-value-sets/bio/proteomics_standards + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: PPM: text: PPM @@ -31558,6 +33663,8 @@ enums: name: InteractionDetectionMethod definition_uri: https://w3id.org/valuesets/InteractionDetectionMethod conforms_to: HUPO-PSI + instantiates: + - valuesets_meta:ValueSetEnumDefinitionWithConformance annotations: standard: tag: standard @@ -31569,6 +33676,10 @@ enums: title: Interaction Detection Method from_schema: https://w3id.org/common-value-sets/bio/psi_mi source: http://purl.obolibrary.org/obo/mi.owl + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: TWO_HYBRID: text: TWO_HYBRID @@ -31646,10 +33757,16 @@ enums: name: InteractionType definition_uri: https://w3id.org/valuesets/InteractionType conforms_to: HUPO-PSI + instantiates: + - valuesets_meta:ValueSetEnumDefinitionWithConformance description: Types of molecular interactions title: Interaction Type from_schema: https://w3id.org/common-value-sets/bio/psi_mi source: http://purl.obolibrary.org/obo/mi.owl + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: PHYSICAL_ASSOCIATION: text: PHYSICAL_ASSOCIATION @@ -31709,10 +33826,16 @@ enums: name: ExperimentalRole definition_uri: https://w3id.org/valuesets/ExperimentalRole conforms_to: HUPO-PSI + instantiates: + - valuesets_meta:ValueSetEnumDefinitionWithConformance description: Role played by a participant in the experiment title: Experimental Role from_schema: https://w3id.org/common-value-sets/bio/psi_mi source: http://purl.obolibrary.org/obo/mi.owl + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: BAIT: text: BAIT @@ -31766,10 +33889,16 @@ enums: name: BiologicalRole definition_uri: https://w3id.org/valuesets/BiologicalRole conforms_to: HUPO-PSI + instantiates: + - valuesets_meta:ValueSetEnumDefinitionWithConformance description: Physiological role of an interactor title: Biological Role from_schema: https://w3id.org/common-value-sets/bio/psi_mi source: http://purl.obolibrary.org/obo/mi.owl + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: ENZYME: text: ENZYME @@ -31817,9 +33946,15 @@ enums: ParticipantIdentificationMethod: name: ParticipantIdentificationMethod definition_uri: https://w3id.org/valuesets/ParticipantIdentificationMethod + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Methods to identify interaction participants title: Participant Identification Method from_schema: https://w3id.org/common-value-sets/bio/psi_mi + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: MASS_SPECTROMETRY: text: MASS_SPECTROMETRY @@ -31859,9 +33994,15 @@ enums: FeatureType: name: FeatureType definition_uri: https://w3id.org/valuesets/FeatureType + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Molecular features affecting interactions title: Feature Type from_schema: https://w3id.org/common-value-sets/bio/psi_mi + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: BINDING_SITE: text: BINDING_SITE @@ -31918,9 +34059,15 @@ enums: InteractorType: name: InteractorType definition_uri: https://w3id.org/valuesets/InteractorType + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of molecular species in interactions title: Interactor Type from_schema: https://w3id.org/common-value-sets/bio/psi_mi + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: PROTEIN: text: PROTEIN @@ -31980,9 +34127,15 @@ enums: ConfidenceScore: name: ConfidenceScore definition_uri: https://w3id.org/valuesets/ConfidenceScore + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of confidence scoring methods title: Confidence Score Types from_schema: https://w3id.org/common-value-sets/bio/psi_mi + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: INTACT_MISCORE: text: INTACT_MISCORE @@ -32003,9 +34156,15 @@ enums: ExperimentalPreparation: name: ExperimentalPreparation definition_uri: https://w3id.org/valuesets/ExperimentalPreparation + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Sample preparation methods title: Experimental Preparation from_schema: https://w3id.org/common-value-sets/bio/psi_mi + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: RECOMBINANT_EXPRESSION: text: RECOMBINANT_EXPRESSION @@ -32037,12 +34196,19 @@ enums: BioticInteractionType: name: BioticInteractionType definition_uri: https://w3id.org/valuesets/BioticInteractionType + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: 'Types of biotic interactions between organisms, based on RO:0002437 (biotically interacts with). These represent ecological relationships where at least one partner is an organism. ' + title: Biotic Interaction Type from_schema: https://w3id.org/valuesets/ecological-interactions + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: BIOTICALLY_INTERACTS_WITH: text: BIOTICALLY_INTERACTS_WITH @@ -32386,11 +34552,18 @@ enums: MineralogyFeedstockClass: name: MineralogyFeedstockClass definition_uri: https://w3id.org/valuesets/MineralogyFeedstockClass + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: 'Types of mineral feedstock sources for extraction and processing operations, including primary and secondary sources. ' + title: Mineralogy Feedstock Class from_schema: https://w3id.org/valuesets/mining-processing + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: HARDROCK_PRIMARY: text: HARDROCK_PRIMARY @@ -32419,11 +34592,18 @@ enums: BeneficiationPathway: name: BeneficiationPathway definition_uri: https://w3id.org/valuesets/BeneficiationPathway + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: 'Methods for mineral separation and concentration aligned with advanced ore processing initiatives (AOI-2). ' + title: Beneficiation Pathway from_schema: https://w3id.org/valuesets/mining-processing + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: ORE_SORTING: text: ORE_SORTING @@ -32455,11 +34635,18 @@ enums: InSituChemistryRegime: name: InSituChemistryRegime definition_uri: https://w3id.org/valuesets/InSituChemistryRegime + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: 'Chemical leaching systems for in-situ extraction with associated parameters including pH, Eh, temperature, and ionic strength. ' + title: In Situ Chemistry Regime from_schema: https://w3id.org/valuesets/mining-processing + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: ACIDIC_SULFATE: text: ACIDIC_SULFATE @@ -32485,11 +34672,18 @@ enums: ExtractableTargetElement: name: ExtractableTargetElement definition_uri: https://w3id.org/valuesets/ExtractableTargetElement + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: 'Target elements for extraction, particularly rare earth elements (REE) and critical minerals. ' + title: Extractable Target Element from_schema: https://w3id.org/valuesets/mining-processing + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: REE_LA: text: REE_LA @@ -32570,11 +34764,18 @@ enums: SensorWhileDrillingFeature: name: SensorWhileDrillingFeature definition_uri: https://w3id.org/valuesets/SensorWhileDrillingFeature + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: 'Measurement while drilling (MWD) and logging while drilling (LWD) features for orebody ML and geosteering applications. ' + title: Sensor While Drilling Feature from_schema: https://w3id.org/valuesets/mining-processing + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: WOB: text: WOB @@ -32603,11 +34804,18 @@ enums: ProcessPerformanceMetric: name: ProcessPerformanceMetric definition_uri: https://w3id.org/valuesets/ProcessPerformanceMetric + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: 'Key performance indicators for mining and processing operations tied to SMART milestones and sustainability goals. ' + title: Process Performance Metric from_schema: https://w3id.org/valuesets/mining-processing + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: RECOVERY_PCT: text: RECOVERY_PCT @@ -32633,11 +34841,18 @@ enums: BioleachOrganism: name: BioleachOrganism definition_uri: https://w3id.org/valuesets/BioleachOrganism + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: 'Microorganisms used in bioleaching and biomining operations, including engineered strains. ' + title: Bioleach Organism from_schema: https://w3id.org/valuesets/mining-processing + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: ACIDITHIOBACILLUS_FERROOXIDANS: text: ACIDITHIOBACILLUS_FERROOXIDANS @@ -32657,11 +34872,18 @@ enums: BioleachMode: name: BioleachMode definition_uri: https://w3id.org/valuesets/BioleachMode + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: 'Mechanisms of bioleaching including indirect and direct bacterial action. ' + title: Bioleach Mode from_schema: https://w3id.org/valuesets/mining-processing + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: INDIRECT_BIOLEACH_ORGANIC_ACIDS: text: INDIRECT_BIOLEACH_ORGANIC_ACIDS @@ -32675,11 +34897,18 @@ enums: AutonomyLevel: name: AutonomyLevel definition_uri: https://w3id.org/valuesets/AutonomyLevel + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: 'Levels of autonomy for mining systems including drilling, hauling, and sorting robots (relevant for Topic 1 initiatives). ' + title: Autonomy Level from_schema: https://w3id.org/valuesets/mining-processing + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: ASSISTIVE: text: ASSISTIVE @@ -32696,11 +34925,18 @@ enums: RegulatoryConstraint: name: RegulatoryConstraint definition_uri: https://w3id.org/valuesets/RegulatoryConstraint + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: 'Regulatory and community constraints affecting mining operations, particularly for in-situ extraction and community engagement. ' + title: Regulatory Constraint from_schema: https://w3id.org/valuesets/mining-processing + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: AQUIFER_PROTECTION: text: AQUIFER_PROTECTION @@ -32718,8 +34954,15 @@ enums: SubatomicParticleEnum: name: SubatomicParticleEnum definition_uri: https://w3id.org/valuesets/SubatomicParticleEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Fundamental and composite subatomic particles + title: Subatomic Particle from_schema: https://w3id.org/valuesets/chemistry/chemical_entities + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: ELECTRON: text: ELECTRON @@ -33138,8 +35381,15 @@ enums: BondTypeEnum: name: BondTypeEnum definition_uri: https://w3id.org/valuesets/BondTypeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of chemical bonds + title: Bond Type from_schema: https://w3id.org/valuesets/chemistry/chemical_entities + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: SINGLE: text: SINGLE @@ -33258,8 +35508,15 @@ enums: PeriodicTableBlockEnum: name: PeriodicTableBlockEnum definition_uri: https://w3id.org/valuesets/PeriodicTableBlockEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Blocks of the periodic table + title: Periodic Table Block from_schema: https://w3id.org/valuesets/chemistry/chemical_entities + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: S_BLOCK: text: S_BLOCK @@ -33312,8 +35569,15 @@ enums: ElementFamilyEnum: name: ElementFamilyEnum definition_uri: https://w3id.org/valuesets/ElementFamilyEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Chemical element families/groups + title: Element Family from_schema: https://w3id.org/valuesets/chemistry/chemical_entities + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: ALKALI_METALS: text: ALKALI_METALS @@ -33430,8 +35694,15 @@ enums: ElementMetallicClassificationEnum: name: ElementMetallicClassificationEnum definition_uri: https://w3id.org/valuesets/ElementMetallicClassificationEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Metallic character classification + title: Element Metallic Classification from_schema: https://w3id.org/valuesets/chemistry/chemical_entities + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: METALLIC: text: METALLIC @@ -33460,8 +35731,15 @@ enums: HardOrSoftEnum: name: HardOrSoftEnum definition_uri: https://w3id.org/valuesets/HardOrSoftEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: HSAB (Hard Soft Acid Base) classification + title: Hard Or Soft from_schema: https://w3id.org/valuesets/chemistry/chemical_entities + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: HARD: text: HARD @@ -33496,8 +35774,15 @@ enums: BronstedAcidBaseRoleEnum: name: BronstedAcidBaseRoleEnum definition_uri: https://w3id.org/valuesets/BronstedAcidBaseRoleEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: "Br\xF8nsted-Lowry acid-base roles" + title: Bronsted Acid Base Role from_schema: https://w3id.org/valuesets/chemistry/chemical_entities + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: ACID: text: ACID @@ -33530,8 +35815,15 @@ enums: LewisAcidBaseRoleEnum: name: LewisAcidBaseRoleEnum definition_uri: https://w3id.org/valuesets/LewisAcidBaseRoleEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Lewis acid-base roles + title: Lewis Acid Base Role from_schema: https://w3id.org/valuesets/chemistry/chemical_entities + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: LEWIS_ACID: text: LEWIS_ACID @@ -33556,8 +35848,15 @@ enums: OxidationStateEnum: name: OxidationStateEnum definition_uri: https://w3id.org/valuesets/OxidationStateEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Common oxidation states + title: Oxidation State from_schema: https://w3id.org/valuesets/chemistry/chemical_entities + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: MINUS_4: text: MINUS_4 @@ -33692,8 +35991,15 @@ enums: ChiralityEnum: name: ChiralityEnum definition_uri: https://w3id.org/valuesets/ChiralityEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Chirality/stereochemistry descriptors + title: Chirality from_schema: https://w3id.org/valuesets/chemistry/chemical_entities + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: R: text: R @@ -33760,8 +36066,15 @@ enums: NanostructureMorphologyEnum: name: NanostructureMorphologyEnum definition_uri: https://w3id.org/valuesets/NanostructureMorphologyEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of nanostructure morphologies + title: Nanostructure Morphology from_schema: https://w3id.org/valuesets/chemistry/chemical_entities + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: NANOTUBE: text: NANOTUBE @@ -33840,8 +36153,15 @@ enums: ReactionTypeEnum: name: ReactionTypeEnum definition_uri: https://w3id.org/valuesets/ReactionTypeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of chemical reactions + title: Reaction Type from_schema: https://w3id.org/valuesets/chemistry/reactions + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: SYNTHESIS: text: SYNTHESIS @@ -34001,8 +36321,15 @@ enums: ReactionMechanismEnum: name: ReactionMechanismEnum definition_uri: https://w3id.org/valuesets/ReactionMechanismEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Reaction mechanism types + title: Reaction Mechanism from_schema: https://w3id.org/valuesets/chemistry/reactions + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: SN1: text: SN1 @@ -34083,8 +36410,15 @@ enums: CatalystTypeEnum: name: CatalystTypeEnum definition_uri: https://w3id.org/valuesets/CatalystTypeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of catalysts + title: Catalyst Type from_schema: https://w3id.org/valuesets/chemistry/reactions + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: HOMOGENEOUS: text: HOMOGENEOUS @@ -34176,8 +36510,15 @@ enums: ReactionConditionEnum: name: ReactionConditionEnum definition_uri: https://w3id.org/valuesets/ReactionConditionEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Reaction conditions + title: Reaction Condition from_schema: https://w3id.org/valuesets/chemistry/reactions + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: ROOM_TEMPERATURE: text: ROOM_TEMPERATURE @@ -34269,8 +36610,15 @@ enums: ReactionRateOrderEnum: name: ReactionRateOrderEnum definition_uri: https://w3id.org/valuesets/ReactionRateOrderEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Reaction rate orders + title: Reaction Rate Order from_schema: https://w3id.org/valuesets/chemistry/reactions + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: ZERO_ORDER: text: ZERO_ORDER @@ -34326,8 +36674,15 @@ enums: EnzymeClassEnum: name: EnzymeClassEnum definition_uri: https://w3id.org/valuesets/EnzymeClassEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: EC enzyme classification + title: Enzyme Class from_schema: https://w3id.org/valuesets/chemistry/reactions + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: OXIDOREDUCTASE: text: OXIDOREDUCTASE @@ -34416,8 +36771,15 @@ enums: SolventClassEnum: name: SolventClassEnum definition_uri: https://w3id.org/valuesets/SolventClassEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Classes of solvents + title: Solvent Class from_schema: https://w3id.org/valuesets/chemistry/reactions + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: PROTIC: text: PROTIC @@ -34496,8 +36858,15 @@ enums: ThermodynamicParameterEnum: name: ThermodynamicParameterEnum definition_uri: https://w3id.org/valuesets/ThermodynamicParameterEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Thermodynamic parameters + title: Thermodynamic Parameter from_schema: https://w3id.org/valuesets/chemistry/reactions + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: ENTHALPY: text: ENTHALPY @@ -34562,9 +36931,15 @@ enums: ReactionDirectionality: name: ReactionDirectionality definition_uri: https://w3id.org/valuesets/ReactionDirectionality + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: The directionality of a chemical reaction or process title: Reaction Directionality from_schema: https://w3id.org/common-value-sets/chemistry/reaction_directionality + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: LEFT_TO_RIGHT: text: LEFT_TO_RIGHT @@ -34613,8 +36988,15 @@ enums: SafetyColorEnum: name: SafetyColorEnum definition_uri: https://w3id.org/valuesets/SafetyColorEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: ANSI/ISO standard safety colors + title: Safety Color from_schema: https://w3id.org/valuesets/industry/safety_colors + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: SAFETY_RED: text: SAFETY_RED @@ -34744,8 +37126,15 @@ enums: TrafficLightColorEnum: name: TrafficLightColorEnum definition_uri: https://w3id.org/valuesets/TrafficLightColorEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Traffic signal colors (international) + title: Traffic Light Color from_schema: https://w3id.org/valuesets/industry/safety_colors + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: RED: text: RED @@ -34813,8 +37202,15 @@ enums: HazmatColorEnum: name: HazmatColorEnum definition_uri: https://w3id.org/valuesets/HazmatColorEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Hazardous materials placarding colors (DOT/UN) + title: Hazmat Color from_schema: https://w3id.org/valuesets/industry/safety_colors + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: ORANGE: text: ORANGE @@ -34911,8 +37307,15 @@ enums: FireSafetyColorEnum: name: FireSafetyColorEnum definition_uri: https://w3id.org/valuesets/FireSafetyColorEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Fire safety equipment and signage colors + title: Fire Safety Color from_schema: https://w3id.org/valuesets/industry/safety_colors + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: FIRE_RED: text: FIRE_RED @@ -34965,8 +37368,15 @@ enums: MaritimeSignalColorEnum: name: MaritimeSignalColorEnum definition_uri: https://w3id.org/valuesets/MaritimeSignalColorEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Maritime signal and navigation colors + title: Maritime Signal Color from_schema: https://w3id.org/valuesets/industry/safety_colors + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: PORT_RED: text: PORT_RED @@ -35036,8 +37446,15 @@ enums: AviationLightColorEnum: name: AviationLightColorEnum definition_uri: https://w3id.org/valuesets/AviationLightColorEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Aviation lighting colors + title: Aviation Light Color from_schema: https://w3id.org/valuesets/industry/safety_colors + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: RED_BEACON: text: RED_BEACON @@ -35120,8 +37537,15 @@ enums: ElectricalWireColorEnum: name: ElectricalWireColorEnum definition_uri: https://w3id.org/valuesets/ElectricalWireColorEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Electrical wire color codes (US/International) + title: Electrical Wire Color from_schema: https://w3id.org/valuesets/industry/safety_colors + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: BLACK_HOT: text: BLACK_HOT @@ -35227,8 +37651,15 @@ enums: BloodTypeEnum: name: BloodTypeEnum definition_uri: https://w3id.org/valuesets/BloodTypeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: ABO and Rh blood group classifications + title: Blood Type from_schema: https://w3id.org/valuesets/medical/clinical + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: A_POSITIVE: text: A_POSITIVE @@ -35375,8 +37806,15 @@ enums: AnatomicalSystemEnum: name: AnatomicalSystemEnum definition_uri: https://w3id.org/valuesets/AnatomicalSystemEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Major anatomical systems of the body + title: Anatomical System from_schema: https://w3id.org/valuesets/medical/clinical + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: CARDIOVASCULAR: text: CARDIOVASCULAR @@ -35491,8 +37929,14 @@ enums: MedicalSpecialtyEnum: name: MedicalSpecialtyEnum definition_uri: https://w3id.org/valuesets/MedicalSpecialtyEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition title: Medical specialties and subspecialties from_schema: https://w3id.org/valuesets/medical/clinical + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: ANESTHESIOLOGY: text: ANESTHESIOLOGY @@ -35572,8 +38016,14 @@ enums: DrugRouteEnum: name: DrugRouteEnum definition_uri: https://w3id.org/valuesets/DrugRouteEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition title: Routes of drug administration from_schema: https://w3id.org/valuesets/medical/clinical + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: ORAL: text: ORAL @@ -35730,8 +38180,14 @@ enums: VitalSignEnum: name: VitalSignEnum definition_uri: https://w3id.org/valuesets/VitalSignEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition title: Standard vital signs from_schema: https://w3id.org/valuesets/medical/clinical + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: HEART_RATE: text: HEART_RATE @@ -35813,8 +38269,14 @@ enums: DiagnosticTestTypeEnum: name: DiagnosticTestTypeEnum definition_uri: https://w3id.org/valuesets/DiagnosticTestTypeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition title: Types of diagnostic tests from_schema: https://w3id.org/valuesets/medical/clinical + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: BLOOD_TEST: text: BLOOD_TEST @@ -35937,8 +38399,14 @@ enums: SymptomSeverityEnum: name: SymptomSeverityEnum definition_uri: https://w3id.org/valuesets/SymptomSeverityEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition title: Severity levels for symptoms from_schema: https://w3id.org/valuesets/medical/clinical + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: ABSENT: text: ABSENT @@ -35997,8 +38465,14 @@ enums: AllergyTypeEnum: name: AllergyTypeEnum definition_uri: https://w3id.org/valuesets/AllergyTypeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition title: Types of allergic reactions from_schema: https://w3id.org/valuesets/medical/clinical + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: DRUG: text: DRUG @@ -36048,8 +38522,14 @@ enums: VaccineTypeEnum: name: VaccineTypeEnum definition_uri: https://w3id.org/valuesets/VaccineTypeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition title: Types of vaccines from_schema: https://w3id.org/valuesets/medical/clinical + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: LIVE_ATTENUATED: text: LIVE_ATTENUATED @@ -36096,8 +38576,14 @@ enums: BMIClassificationEnum: name: BMIClassificationEnum definition_uri: https://w3id.org/valuesets/BMIClassificationEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition title: Body Mass Index classifications from_schema: https://w3id.org/valuesets/medical/clinical + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: UNDERWEIGHT: text: UNDERWEIGHT @@ -36147,8 +38633,15 @@ enums: MRIModalityEnum: name: MRIModalityEnum definition_uri: https://w3id.org/valuesets/MRIModalityEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: MRI imaging modalities and techniques + title: MRI Modality from_schema: https://w3id.org/valuesets/medical/neuroimaging + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: STRUCTURAL_T1: text: STRUCTURAL_T1 @@ -36366,8 +38859,15 @@ enums: MRISequenceTypeEnum: name: MRISequenceTypeEnum definition_uri: https://w3id.org/valuesets/MRISequenceTypeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: MRI pulse sequence types + title: MRI Sequence Type from_schema: https://w3id.org/valuesets/medical/neuroimaging + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: GRADIENT_ECHO: text: GRADIENT_ECHO @@ -36469,8 +38969,15 @@ enums: MRIContrastTypeEnum: name: MRIContrastTypeEnum definition_uri: https://w3id.org/valuesets/MRIContrastTypeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: MRI image contrast mechanisms + title: MRI Contrast Type from_schema: https://w3id.org/valuesets/medical/neuroimaging + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: T1_WEIGHTED: text: T1_WEIGHTED @@ -36557,8 +39064,15 @@ enums: FMRIParadigmTypeEnum: name: FMRIParadigmTypeEnum definition_uri: https://w3id.org/valuesets/FMRIParadigmTypeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: fMRI experimental paradigm types + title: FMRI Paradigm Type from_schema: https://w3id.org/valuesets/medical/neuroimaging + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: BLOCK_DESIGN: text: BLOCK_DESIGN @@ -36646,9 +39160,16 @@ enums: FamilyRelationship: name: FamilyRelationship definition_uri: https://w3id.org/valuesets/FamilyRelationship + instantiates: + - valuesets_meta:ValueSetEnumDefinitionWithSource description: Family relationships used in pedigree and family history documentation + title: Family Relationship from_schema: https://w3id.org/valuesets/medical/family_history source: https://terminology.hl7.org/2.1.0/ValueSet-v3-FamilyMember.html + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: PARENT: text: PARENT @@ -37005,8 +39526,15 @@ enums: FamilyHistoryStatus: name: FamilyHistoryStatus definition_uri: https://w3id.org/valuesets/FamilyHistoryStatus + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Status of family history information availability + title: Family History Status from_schema: https://w3id.org/valuesets/medical/family_history + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: COMPLETED: text: COMPLETED @@ -37031,8 +39559,15 @@ enums: GeneticRelationship: name: GeneticRelationship definition_uri: https://w3id.org/valuesets/GeneticRelationship + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Genetic relationship types for pedigree analysis + title: Genetic Relationship from_schema: https://w3id.org/valuesets/medical/family_history + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: BIOLOGICAL: text: BIOLOGICAL @@ -37061,11 +39596,18 @@ enums: RaceOMB1997Enum: name: RaceOMB1997Enum definition_uri: https://w3id.org/valuesets/RaceOMB1997Enum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: 'Race categories following OMB 1997 standards used by NIH and federal agencies. Respondents may select multiple races.' + title: Race OMB1997 from_schema: https://w3id.org/linkml/valuesets/clinical/nih_demographics + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: AMERICAN_INDIAN_OR_ALASKA_NATIVE: text: AMERICAN_INDIAN_OR_ALASKA_NATIVE @@ -37158,9 +39700,16 @@ enums: EthnicityOMB1997Enum: name: EthnicityOMB1997Enum definition_uri: https://w3id.org/valuesets/EthnicityOMB1997Enum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Ethnicity categories following OMB 1997 standards used by NIH and federal agencies + title: Ethnicity OMB1997 from_schema: https://w3id.org/linkml/valuesets/clinical/nih_demographics + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: HISPANIC_OR_LATINO: text: HISPANIC_OR_LATINO @@ -37202,11 +39751,18 @@ enums: BiologicalSexEnum: name: BiologicalSexEnum definition_uri: https://w3id.org/valuesets/BiologicalSexEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: 'Biological sex assigned at birth based on anatomical and physiological traits. Required by NIH as a biological variable in research.' + title: Biological Sex from_schema: https://w3id.org/linkml/valuesets/clinical/nih_demographics + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: MALE: text: MALE @@ -37246,9 +39802,16 @@ enums: AgeGroupEnum: name: AgeGroupEnum definition_uri: https://w3id.org/valuesets/AgeGroupEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Standard age groups used in NIH clinical research, particularly NINDS CDEs + title: Age Group from_schema: https://w3id.org/linkml/valuesets/clinical/nih_demographics + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: NEONATE: text: NEONATE @@ -37348,8 +39911,15 @@ enums: ParticipantVitalStatusEnum: name: ParticipantVitalStatusEnum definition_uri: https://w3id.org/valuesets/ParticipantVitalStatusEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Vital status of a research participant in clinical studies + title: Participant Vital Status from_schema: https://w3id.org/linkml/valuesets/clinical/nih_demographics + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: ALIVE: text: ALIVE @@ -37371,8 +39941,15 @@ enums: RecruitmentStatusEnum: name: RecruitmentStatusEnum definition_uri: https://w3id.org/valuesets/RecruitmentStatusEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Clinical trial or study recruitment status per NIH/ClinicalTrials.gov + title: Recruitment Status from_schema: https://w3id.org/linkml/valuesets/clinical/nih_demographics + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: NOT_YET_RECRUITING: text: NOT_YET_RECRUITING @@ -37416,8 +39993,15 @@ enums: StudyPhaseEnum: name: StudyPhaseEnum definition_uri: https://w3id.org/valuesets/StudyPhaseEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Clinical trial phases per FDA and NIH definitions + title: Study Phase from_schema: https://w3id.org/linkml/valuesets/clinical/nih_demographics + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: EARLY_PHASE_1: text: EARLY_PHASE_1 @@ -37485,8 +40069,22 @@ enums: KaryotypicSexEnum: name: KaryotypicSexEnum definition_uri: https://w3id.org/valuesets/KaryotypicSexEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinitionWithStewardship + annotations: + stewards: + tag: stewards + value: https://phenopackets.org + publishers: + tag: publishers + value: https://ga4gh.org description: Karyotypic sex of an individual based on chromosome composition + title: Karyotypic Sex from_schema: https://w3id.org/linkml/valuesets/clinical/phenopackets + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: STANDARD permissible_values: XX: text: XX @@ -37611,10 +40209,24 @@ enums: PhenotypicSexEnum: name: PhenotypicSexEnum definition_uri: https://w3id.org/valuesets/PhenotypicSexEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinitionWithStewardship + annotations: + stewards: + tag: stewards + value: https://phenopackets.org + publishers: + tag: publishers + value: https://ga4gh.org description: 'Phenotypic sex of an individual based on observable characteristics. FHIR mapping: AdministrativeGender' + title: Phenotypic Sex from_schema: https://w3id.org/linkml/valuesets/clinical/phenopackets + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: STANDARD permissible_values: MALE: text: MALE @@ -37645,8 +40257,22 @@ enums: AllelicStateEnum: name: AllelicStateEnum definition_uri: https://w3id.org/valuesets/AllelicStateEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinitionWithStewardship + annotations: + stewards: + tag: stewards + value: https://phenopackets.org + publishers: + tag: publishers + value: https://ga4gh.org description: Allelic state/zygosity of a variant or genetic feature + title: Allelic State from_schema: https://w3id.org/linkml/valuesets/clinical/phenopackets + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: STANDARD permissible_values: HETEROZYGOUS: text: HETEROZYGOUS @@ -37704,8 +40330,22 @@ enums: LateralityEnum: name: LateralityEnum definition_uri: https://w3id.org/valuesets/LateralityEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinitionWithStewardship + annotations: + stewards: + tag: stewards + value: https://phenopackets.org + publishers: + tag: publishers + value: https://ga4gh.org description: Laterality/sidedness of a finding or anatomical structure + title: Laterality from_schema: https://w3id.org/linkml/valuesets/clinical/phenopackets + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: STANDARD permissible_values: RIGHT: text: RIGHT @@ -37749,8 +40389,22 @@ enums: OnsetTimingEnum: name: OnsetTimingEnum definition_uri: https://w3id.org/valuesets/OnsetTimingEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinitionWithStewardship + annotations: + stewards: + tag: stewards + value: https://phenopackets.org + publishers: + tag: publishers + value: https://ga4gh.org description: Timing of disease or phenotype onset relative to developmental stages + title: Onset Timing from_schema: https://w3id.org/linkml/valuesets/clinical/phenopackets + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: STANDARD permissible_values: ANTENATAL_ONSET: text: ANTENATAL_ONSET @@ -37843,8 +40497,22 @@ enums: ACMGPathogenicityEnum: name: ACMGPathogenicityEnum definition_uri: https://w3id.org/valuesets/ACMGPathogenicityEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinitionWithStewardship + annotations: + stewards: + tag: stewards + value: https://phenopackets.org + publishers: + tag: publishers + value: https://ga4gh.org description: ACMG/AMP variant pathogenicity classification for clinical genetics + title: ACMG Pathogenicity from_schema: https://w3id.org/linkml/valuesets/clinical/phenopackets + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: STANDARD permissible_values: PATHOGENIC: text: PATHOGENIC @@ -37909,8 +40577,22 @@ enums: TherapeuticActionabilityEnum: name: TherapeuticActionabilityEnum definition_uri: https://w3id.org/valuesets/TherapeuticActionabilityEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinitionWithStewardship + annotations: + stewards: + tag: stewards + value: https://phenopackets.org + publishers: + tag: publishers + value: https://ga4gh.org description: Clinical actionability of a genetic finding for treatment decisions + title: Therapeutic Actionability from_schema: https://w3id.org/linkml/valuesets/clinical/phenopackets + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: STANDARD permissible_values: ACTIONABLE: text: ACTIONABLE @@ -37938,8 +40620,22 @@ enums: InterpretationProgressEnum: name: InterpretationProgressEnum definition_uri: https://w3id.org/valuesets/InterpretationProgressEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinitionWithStewardship + annotations: + stewards: + tag: stewards + value: https://phenopackets.org + publishers: + tag: publishers + value: https://ga4gh.org description: Progress status of clinical interpretation or diagnosis + title: Interpretation Progress from_schema: https://w3id.org/linkml/valuesets/clinical/phenopackets + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: STANDARD permissible_values: SOLVED: text: SOLVED @@ -37981,8 +40677,22 @@ enums: RegimenStatusEnum: name: RegimenStatusEnum definition_uri: https://w3id.org/valuesets/RegimenStatusEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinitionWithStewardship + annotations: + stewards: + tag: stewards + value: https://phenopackets.org + publishers: + tag: publishers + value: https://ga4gh.org description: Status of a therapeutic regimen or treatment protocol + title: Regimen Status from_schema: https://w3id.org/linkml/valuesets/clinical/phenopackets + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: STANDARD permissible_values: NOT_STARTED: text: NOT_STARTED @@ -38035,8 +40745,22 @@ enums: DrugResponseEnum: name: DrugResponseEnum definition_uri: https://w3id.org/valuesets/DrugResponseEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinitionWithStewardship + annotations: + stewards: + tag: stewards + value: https://phenopackets.org + publishers: + tag: publishers + value: https://ga4gh.org description: Response categories for drug treatment outcomes + title: Drug Response from_schema: https://w3id.org/linkml/valuesets/clinical/phenopackets + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: STANDARD permissible_values: FAVORABLE: text: FAVORABLE @@ -38090,8 +40814,15 @@ enums: ProcessScaleEnum: name: ProcessScaleEnum definition_uri: https://w3id.org/valuesets/ProcessScaleEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Scale of bioprocessing operations from lab bench to commercial production + title: Process Scale from_schema: https://w3id.org/linkml/valuesets/bioprocessing/scale_up + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: BENCH_SCALE: text: BENCH_SCALE @@ -38165,8 +40896,15 @@ enums: BioreactorTypeEnum: name: BioreactorTypeEnum definition_uri: https://w3id.org/valuesets/BioreactorTypeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of bioreactors used in fermentation and cell culture + title: Bioreactor Type from_schema: https://w3id.org/linkml/valuesets/bioprocessing/scale_up + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: STIRRED_TANK: text: STIRRED_TANK @@ -38270,8 +41008,15 @@ enums: FermentationModeEnum: name: FermentationModeEnum definition_uri: https://w3id.org/valuesets/FermentationModeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Modes of fermentation operation + title: Fermentation Mode from_schema: https://w3id.org/linkml/valuesets/bioprocessing/scale_up + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: BATCH: text: BATCH @@ -38343,8 +41088,15 @@ enums: OxygenationStrategyEnum: name: OxygenationStrategyEnum definition_uri: https://w3id.org/valuesets/OxygenationStrategyEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Oxygen supply strategies for fermentation + title: Oxygenation Strategy from_schema: https://w3id.org/linkml/valuesets/bioprocessing/scale_up + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: AEROBIC: text: AEROBIC @@ -38393,8 +41145,15 @@ enums: AgitationTypeEnum: name: AgitationTypeEnum definition_uri: https://w3id.org/valuesets/AgitationTypeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of agitation/mixing in bioreactors + title: Agitation Type from_schema: https://w3id.org/linkml/valuesets/bioprocessing/scale_up + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: RUSHTON_TURBINE: text: RUSHTON_TURBINE @@ -38476,8 +41235,15 @@ enums: DownstreamProcessEnum: name: DownstreamProcessEnum definition_uri: https://w3id.org/valuesets/DownstreamProcessEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Downstream processing unit operations + title: Downstream Process from_schema: https://w3id.org/linkml/valuesets/bioprocessing/scale_up + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: CENTRIFUGATION: text: CENTRIFUGATION @@ -38559,8 +41325,15 @@ enums: FeedstockTypeEnum: name: FeedstockTypeEnum definition_uri: https://w3id.org/valuesets/FeedstockTypeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of feedstocks for bioprocessing + title: Feedstock Type from_schema: https://w3id.org/linkml/valuesets/bioprocessing/scale_up + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: GLUCOSE: text: GLUCOSE @@ -38661,8 +41434,15 @@ enums: ProductTypeEnum: name: ProductTypeEnum definition_uri: https://w3id.org/valuesets/ProductTypeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of products from bioprocessing + title: Product Type from_schema: https://w3id.org/linkml/valuesets/bioprocessing/scale_up + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: BIOFUEL: text: BIOFUEL @@ -38753,8 +41533,15 @@ enums: SterilizationMethodEnum: name: SterilizationMethodEnum definition_uri: https://w3id.org/valuesets/SterilizationMethodEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Methods for sterilization in bioprocessing + title: Sterilization Method from_schema: https://w3id.org/linkml/valuesets/bioprocessing/scale_up + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: STEAM_IN_PLACE: text: STEAM_IN_PLACE @@ -38831,8 +41618,15 @@ enums: LengthUnitEnum: name: LengthUnitEnum definition_uri: https://w3id.org/valuesets/LengthUnitEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Units of length/distance measurement + title: Length Unit from_schema: https://w3id.org/valuesets/units/measurements + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: METER: text: METER @@ -38988,8 +41782,15 @@ enums: MassUnitEnum: name: MassUnitEnum definition_uri: https://w3id.org/valuesets/MassUnitEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Units of mass measurement + title: Mass Unit from_schema: https://w3id.org/valuesets/units/measurements + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: KILOGRAM: text: KILOGRAM @@ -39121,8 +41922,15 @@ enums: VolumeUnitEnum: name: VolumeUnitEnum definition_uri: https://w3id.org/valuesets/VolumeUnitEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Units of volume measurement + title: Volume Unit from_schema: https://w3id.org/valuesets/units/measurements + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: LITER: text: LITER @@ -39302,8 +42110,15 @@ enums: TemperatureUnitEnum: name: TemperatureUnitEnum definition_uri: https://w3id.org/valuesets/TemperatureUnitEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Units of temperature measurement + title: Temperature Unit from_schema: https://w3id.org/valuesets/units/measurements + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: KELVIN: text: KELVIN @@ -39362,8 +42177,15 @@ enums: TimeUnitEnum: name: TimeUnitEnum definition_uri: https://w3id.org/valuesets/TimeUnitEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Units of time measurement + title: Time Unit from_schema: https://w3id.org/valuesets/units/measurements + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: SECOND: text: SECOND @@ -39485,8 +42307,15 @@ enums: PressureUnitEnum: name: PressureUnitEnum definition_uri: https://w3id.org/valuesets/PressureUnitEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Units of pressure measurement + title: Pressure Unit from_schema: https://w3id.org/valuesets/units/measurements + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: PASCAL: text: PASCAL @@ -39597,8 +42426,15 @@ enums: ConcentrationUnitEnum: name: ConcentrationUnitEnum definition_uri: https://w3id.org/valuesets/ConcentrationUnitEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Units of concentration measurement + title: Concentration Unit from_schema: https://w3id.org/valuesets/units/measurements + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: MOLAR: text: MOLAR @@ -39720,8 +42556,15 @@ enums: FrequencyUnitEnum: name: FrequencyUnitEnum definition_uri: https://w3id.org/valuesets/FrequencyUnitEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Units of frequency measurement + title: Frequency Unit from_schema: https://w3id.org/valuesets/units/measurements + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: HERTZ: text: HERTZ @@ -39792,8 +42635,15 @@ enums: AngleUnitEnum: name: AngleUnitEnum definition_uri: https://w3id.org/valuesets/AngleUnitEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Units of angle measurement + title: Angle Unit from_schema: https://w3id.org/valuesets/units/measurements + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: RADIAN: text: RADIAN @@ -39860,8 +42710,15 @@ enums: DataSizeUnitEnum: name: DataSizeUnitEnum definition_uri: https://w3id.org/valuesets/DataSizeUnitEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Units of digital data size + title: Data Size Unit from_schema: https://w3id.org/valuesets/units/measurements + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: BIT: text: BIT @@ -40006,8 +42863,15 @@ enums: ImageFileFormatEnum: name: ImageFileFormatEnum definition_uri: https://w3id.org/valuesets/ImageFileFormatEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Common image file formats + title: Image File Format from_schema: https://w3id.org/valuesets/computing/file_formats + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: JPEG: text: JPEG @@ -40148,8 +43012,15 @@ enums: DocumentFormatEnum: name: DocumentFormatEnum definition_uri: https://w3id.org/valuesets/DocumentFormatEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Document and text file formats + title: Document Format from_schema: https://w3id.org/valuesets/computing/file_formats + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: PDF: text: PDF @@ -40297,8 +43168,15 @@ enums: DataFormatEnum: name: DataFormatEnum definition_uri: https://w3id.org/valuesets/DataFormatEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Structured data file formats + title: Data Format from_schema: https://w3id.org/valuesets/computing/file_formats + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: JSON: text: JSON @@ -40467,8 +43345,15 @@ enums: ArchiveFormatEnum: name: ArchiveFormatEnum definition_uri: https://w3id.org/valuesets/ArchiveFormatEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Archive and compression formats + title: Archive Format from_schema: https://w3id.org/valuesets/computing/file_formats + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: ZIP: text: ZIP @@ -40597,8 +43482,15 @@ enums: VideoFormatEnum: name: VideoFormatEnum definition_uri: https://w3id.org/valuesets/VideoFormatEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Video file formats + title: Video Format from_schema: https://w3id.org/valuesets/computing/file_formats + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: MP4: text: MP4 @@ -40704,8 +43596,15 @@ enums: AudioFormatEnum: name: AudioFormatEnum definition_uri: https://w3id.org/valuesets/AudioFormatEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Audio file formats + title: Audio Format from_schema: https://w3id.org/valuesets/computing/file_formats + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: MP3: text: MP3 @@ -40827,8 +43726,15 @@ enums: ProgrammingLanguageFileEnum: name: ProgrammingLanguageFileEnum definition_uri: https://w3id.org/valuesets/ProgrammingLanguageFileEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Programming language source file extensions + title: Programming Language File from_schema: https://w3id.org/valuesets/computing/file_formats + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: PYTHON: text: PYTHON @@ -41003,8 +43909,15 @@ enums: NetworkProtocolEnum: name: NetworkProtocolEnum definition_uri: https://w3id.org/valuesets/NetworkProtocolEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Network communication protocols + title: Network Protocol from_schema: https://w3id.org/valuesets/computing/file_formats + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: HTTP: text: HTTP @@ -41222,11 +44135,17 @@ enums: name: TechnologyReadinessLevel definition_uri: https://w3id.org/valuesets/TechnologyReadinessLevel conforms_to: ISO-16290:2013 + instantiates: + - valuesets_meta:ReferenceEnumDefinition description: NASA's Technology Readiness Level scale for assessing the maturity of technologies from basic research through operational deployment title: Technology Readiness Level (TRL) from_schema: https://w3id.org/common-value-sets/computing/maturity_levels source: https://www.nasa.gov/directorates/heo/scan/engineering/technology/technology_readiness_level + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: STANDARD permissible_values: TRL_1: text: TRL_1 @@ -41269,9 +44188,15 @@ enums: SoftwareMaturityLevel: name: SoftwareMaturityLevel definition_uri: https://w3id.org/valuesets/SoftwareMaturityLevel + instantiates: + - valuesets_meta:ReferenceEnumDefinition description: General software maturity assessment levels title: Software Maturity Level from_schema: https://w3id.org/common-value-sets/computing/maturity_levels + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: STANDARD permissible_values: ALPHA: text: ALPHA @@ -41309,11 +44234,17 @@ enums: name: CapabilityMaturityLevel definition_uri: https://w3id.org/valuesets/CapabilityMaturityLevel conforms_to: CMMI Version 2.0 + instantiates: + - valuesets_meta:ReferenceEnumDefinition description: CMMI levels for assessing organizational process maturity in software development title: Capability Maturity Model Integration (CMMI) Level from_schema: https://w3id.org/common-value-sets/computing/maturity_levels source: https://cmmiinstitute.com/ + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: STANDARD permissible_values: LEVEL_1: text: LEVEL_1 @@ -41340,9 +44271,15 @@ enums: StandardsMaturityLevel: name: StandardsMaturityLevel definition_uri: https://w3id.org/valuesets/StandardsMaturityLevel + instantiates: + - valuesets_meta:ReferenceEnumDefinition description: Maturity levels for standards and specifications title: Standards Development Maturity Level from_schema: https://w3id.org/common-value-sets/computing/maturity_levels + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: STANDARD permissible_values: DRAFT: text: DRAFT @@ -41383,9 +44320,15 @@ enums: ProjectMaturityLevel: name: ProjectMaturityLevel definition_uri: https://w3id.org/valuesets/ProjectMaturityLevel + instantiates: + - valuesets_meta:ReferenceEnumDefinition description: General project development maturity assessment title: Project Maturity Level from_schema: https://w3id.org/common-value-sets/computing/maturity_levels + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: STANDARD permissible_values: CONCEPT: text: CONCEPT @@ -41422,9 +44365,15 @@ enums: DataMaturityLevel: name: DataMaturityLevel definition_uri: https://w3id.org/valuesets/DataMaturityLevel + instantiates: + - valuesets_meta:ReferenceEnumDefinition description: Levels of data quality, governance, and organizational maturity title: Data Maturity Level from_schema: https://w3id.org/common-value-sets/computing/maturity_levels + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: STANDARD permissible_values: RAW: text: RAW @@ -41457,9 +44406,15 @@ enums: OpenSourceMaturityLevel: name: OpenSourceMaturityLevel definition_uri: https://w3id.org/valuesets/OpenSourceMaturityLevel + instantiates: + - valuesets_meta:ReferenceEnumDefinition description: Maturity assessment for open source projects title: Open Source Project Maturity from_schema: https://w3id.org/common-value-sets/computing/maturity_levels + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: STANDARD permissible_values: EXPERIMENTAL: text: EXPERIMENTAL @@ -41488,9 +44443,16 @@ enums: OWLProfileEnum: name: OWLProfileEnum definition_uri: https://w3id.org/valuesets/OWLProfileEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: OWL 2 profiles that provide different tradeoffs between expressiveness and computational complexity + title: OWL Profile from_schema: https://w3id.org/valuesets/computing/ontologies + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: OWL_2_EL: text: OWL_2_EL @@ -41567,12 +44529,19 @@ enums: MLDataType: name: MLDataType definition_uri: https://w3id.org/valuesets/MLDataType + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: 'Data types used in Croissant ML for describing field types in datasets. Based on XSD (XML Schema Definition) and schema.org vocabulary. ' + title: ML Data Type from_schema: https://w3id.org/valuesets/computing/croissant_ml + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: TEXT: text: TEXT @@ -41627,13 +44596,20 @@ enums: DatasetEncodingFormat: name: DatasetEncodingFormat definition_uri: https://w3id.org/valuesets/DatasetEncodingFormat + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: 'Encoding formats (MIME types) commonly used for ML dataset files in Croissant. These specify how data is serialized and stored. ' + title: Dataset Encoding Format from_schema: https://w3id.org/valuesets/computing/croissant_ml + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: CSV: text: CSV @@ -41730,6 +44706,8 @@ enums: DatasetSplitType: name: DatasetSplitType definition_uri: https://w3id.org/valuesets/DatasetSplitType + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: 'Standard dataset split types used in machine learning for training, validation, and testing. These splits are fundamental to ML model @@ -41737,7 +44715,12 @@ enums: development and evaluation workflows. ' + title: Dataset Split Type from_schema: https://w3id.org/valuesets/computing/croissant_ml + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: TRAIN: text: TRAIN @@ -41778,12 +44761,19 @@ enums: MLLicenseType: name: MLLicenseType definition_uri: https://w3id.org/valuesets/MLLicenseType + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: 'Common open source and Creative Commons licenses used for ML datasets. These licenses specify terms of use, redistribution, and modification. ' + title: ML License Type from_schema: https://w3id.org/valuesets/computing/croissant_ml + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: CC_BY_4_0: text: CC_BY_4_0 @@ -41879,13 +44869,20 @@ enums: MLFieldRole: name: MLFieldRole definition_uri: https://w3id.org/valuesets/MLFieldRole + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: 'Semantic roles that fields play in ML datasets. These roles help understand the purpose and usage of different data columns or attributes. ' + title: ML Field Role from_schema: https://w3id.org/valuesets/computing/croissant_ml + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: FEATURE: text: FEATURE @@ -41918,10 +44915,17 @@ enums: CompressionFormat: name: CompressionFormat definition_uri: https://w3id.org/valuesets/CompressionFormat + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: 'Compression and archive formats commonly used for ML dataset distribution. ' + title: Compression Format from_schema: https://w3id.org/valuesets/computing/croissant_ml + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: ZIP: text: ZIP @@ -41972,12 +44976,19 @@ enums: MLMediaType: name: MLMediaType definition_uri: https://w3id.org/valuesets/MLMediaType + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: 'Media types (MIME types) for different modalities of ML data including images, audio, video, and text. ' + title: ML Media Type from_schema: https://w3id.org/valuesets/computing/croissant_ml + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: IMAGE_JPEG: text: IMAGE_JPEG @@ -42110,12 +45121,19 @@ enums: MLModalityType: name: MLModalityType definition_uri: https://w3id.org/valuesets/MLModalityType + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: 'High-level data modalities used in machine learning. These represent the fundamental types of input data that ML models process. ' + title: ML Modality Type from_schema: https://w3id.org/valuesets/computing/croissant_ml + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: TEXT: text: TEXT @@ -42177,8 +45195,15 @@ enums: LegalEntityTypeEnum: name: LegalEntityTypeEnum definition_uri: https://w3id.org/valuesets/LegalEntityTypeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Legal entity types for business organizations + title: Legal Entity Type from_schema: https://w3id.org/linkml/valuesets/business/organizational_structures + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: SOLE_PROPRIETORSHIP: text: SOLE_PROPRIETORSHIP @@ -42512,8 +45537,15 @@ enums: OrganizationalStructureEnum: name: OrganizationalStructureEnum definition_uri: https://w3id.org/valuesets/OrganizationalStructureEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of organizational hierarchy and reporting structures + title: Organizational Structure from_schema: https://w3id.org/linkml/valuesets/business/organizational_structures + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: HIERARCHICAL: text: HIERARCHICAL @@ -42699,8 +45731,15 @@ enums: ManagementLevelEnum: name: ManagementLevelEnum definition_uri: https://w3id.org/valuesets/ManagementLevelEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Hierarchical levels within organizational management structure + title: Management Level from_schema: https://w3id.org/linkml/valuesets/business/organizational_structures + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: BOARD_OF_DIRECTORS: text: BOARD_OF_DIRECTORS @@ -42892,8 +45931,15 @@ enums: CorporateGovernanceRoleEnum: name: CorporateGovernanceRoleEnum definition_uri: https://w3id.org/valuesets/CorporateGovernanceRoleEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Roles within corporate governance structure + title: Corporate Governance Role from_schema: https://w3id.org/linkml/valuesets/business/organizational_structures + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: CHAIRMAN_OF_BOARD: text: CHAIRMAN_OF_BOARD @@ -43085,8 +46131,15 @@ enums: BusinessOwnershipTypeEnum: name: BusinessOwnershipTypeEnum definition_uri: https://w3id.org/valuesets/BusinessOwnershipTypeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of business ownership structures + title: Business Ownership Type from_schema: https://w3id.org/linkml/valuesets/business/organizational_structures + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: PRIVATE_OWNERSHIP: text: PRIVATE_OWNERSHIP @@ -43227,8 +46280,15 @@ enums: BusinessSizeClassificationEnum: name: BusinessSizeClassificationEnum definition_uri: https://w3id.org/valuesets/BusinessSizeClassificationEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Size classifications for business entities + title: Business Size Classification from_schema: https://w3id.org/linkml/valuesets/business/organizational_structures + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: MICRO_BUSINESS: text: MICRO_BUSINESS @@ -43335,8 +46395,15 @@ enums: BusinessLifecycleStageEnum: name: BusinessLifecycleStageEnum definition_uri: https://w3id.org/valuesets/BusinessLifecycleStageEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Stages in business development lifecycle + title: Business Lifecycle Stage from_schema: https://w3id.org/linkml/valuesets/business/organizational_structures + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: CONCEPT_STAGE: text: CONCEPT_STAGE @@ -43477,9 +46544,16 @@ enums: NAICSSectorEnum: name: NAICSSectorEnum definition_uri: https://w3id.org/valuesets/NAICSSectorEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: NAICS two-digit sector codes (North American Industry Classification System) + title: NAICS Sector from_schema: https://w3id.org/linkml/valuesets/business/industry_classifications + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: SECTOR_11: text: SECTOR_11 @@ -43765,8 +46839,15 @@ enums: EconomicSectorEnum: name: EconomicSectorEnum definition_uri: https://w3id.org/valuesets/EconomicSectorEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Broad economic sector classifications + title: Economic Sector from_schema: https://w3id.org/linkml/valuesets/business/industry_classifications + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: PRIMARY_SECTOR: text: PRIMARY_SECTOR @@ -43856,8 +46937,15 @@ enums: BusinessActivityTypeEnum: name: BusinessActivityTypeEnum definition_uri: https://w3id.org/valuesets/BusinessActivityTypeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of primary business activities + title: Business Activity Type from_schema: https://w3id.org/linkml/valuesets/business/industry_classifications + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: PRODUCTION: text: PRODUCTION @@ -44032,8 +47120,15 @@ enums: IndustryMaturityEnum: name: IndustryMaturityEnum definition_uri: https://w3id.org/valuesets/IndustryMaturityEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Industry lifecycle and maturity stages + title: Industry Maturity from_schema: https://w3id.org/linkml/valuesets/business/industry_classifications + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: EMERGING: text: EMERGING @@ -44138,8 +47233,15 @@ enums: MarketStructureEnum: name: MarketStructureEnum definition_uri: https://w3id.org/valuesets/MarketStructureEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Competitive structure of industry markets + title: Market Structure from_schema: https://w3id.org/linkml/valuesets/business/industry_classifications + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: PERFECT_COMPETITION: text: PERFECT_COMPETITION @@ -44244,8 +47346,15 @@ enums: IndustryRegulationLevelEnum: name: IndustryRegulationLevelEnum definition_uri: https://w3id.org/valuesets/IndustryRegulationLevelEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Level of government regulation in different industries + title: Industry Regulation Level from_schema: https://w3id.org/linkml/valuesets/business/industry_classifications + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: HIGHLY_REGULATED: text: HIGHLY_REGULATED @@ -44350,8 +47459,15 @@ enums: ManagementMethodologyEnum: name: ManagementMethodologyEnum definition_uri: https://w3id.org/valuesets/ManagementMethodologyEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Management approaches and methodologies + title: Management Methodology from_schema: https://w3id.org/linkml/valuesets/business/management_operations + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: TRADITIONAL_MANAGEMENT: text: TRADITIONAL_MANAGEMENT @@ -44526,8 +47642,15 @@ enums: StrategicFrameworkEnum: name: StrategicFrameworkEnum definition_uri: https://w3id.org/valuesets/StrategicFrameworkEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Strategic planning and analysis frameworks + title: Strategic Framework from_schema: https://w3id.org/linkml/valuesets/business/management_operations + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: SWOT_ANALYSIS: text: SWOT_ANALYSIS @@ -44703,8 +47826,15 @@ enums: OperationalModelEnum: name: OperationalModelEnum definition_uri: https://w3id.org/valuesets/OperationalModelEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Business operational models and approaches + title: Operational Model from_schema: https://w3id.org/linkml/valuesets/business/management_operations + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: CENTRALIZED_OPERATIONS: text: CENTRALIZED_OPERATIONS @@ -44879,8 +48009,15 @@ enums: PerformanceMeasurementEnum: name: PerformanceMeasurementEnum definition_uri: https://w3id.org/valuesets/PerformanceMeasurementEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Performance measurement systems and approaches + title: Performance Measurement from_schema: https://w3id.org/linkml/valuesets/business/management_operations + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: KEY_PERFORMANCE_INDICATORS: text: KEY_PERFORMANCE_INDICATORS @@ -45055,8 +48192,15 @@ enums: DecisionMakingStyleEnum: name: DecisionMakingStyleEnum definition_uri: https://w3id.org/valuesets/DecisionMakingStyleEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Decision-making approaches and styles + title: Decision Making Style from_schema: https://w3id.org/linkml/valuesets/business/management_operations + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: AUTOCRATIC: text: AUTOCRATIC @@ -45231,8 +48375,15 @@ enums: LeadershipStyleEnum: name: LeadershipStyleEnum definition_uri: https://w3id.org/valuesets/LeadershipStyleEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Leadership approaches and styles + title: Leadership Style from_schema: https://w3id.org/linkml/valuesets/business/management_operations + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: TRANSFORMATIONAL: text: TRANSFORMATIONAL @@ -45407,8 +48558,15 @@ enums: BusinessProcessTypeEnum: name: BusinessProcessTypeEnum definition_uri: https://w3id.org/valuesets/BusinessProcessTypeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of business processes + title: Business Process Type from_schema: https://w3id.org/linkml/valuesets/business/management_operations + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: CORE_PROCESS: text: CORE_PROCESS @@ -45549,8 +48707,15 @@ enums: QualityStandardEnum: name: QualityStandardEnum definition_uri: https://w3id.org/valuesets/QualityStandardEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Quality management standards and frameworks + title: Quality Standard from_schema: https://w3id.org/linkml/valuesets/business/quality_management + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: ISO_9001: text: ISO_9001 @@ -45795,8 +48960,15 @@ enums: QualityMethodologyEnum: name: QualityMethodologyEnum definition_uri: https://w3id.org/valuesets/QualityMethodologyEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Quality improvement methodologies and approaches + title: Quality Methodology from_schema: https://w3id.org/linkml/valuesets/business/quality_management + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: DMAIC: text: DMAIC @@ -46001,8 +49173,15 @@ enums: QualityControlTechniqueEnum: name: QualityControlTechniqueEnum definition_uri: https://w3id.org/valuesets/QualityControlTechniqueEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Quality control techniques and tools + title: Quality Control Technique from_schema: https://w3id.org/linkml/valuesets/business/quality_management + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: CONTROL_CHARTS: text: CONTROL_CHARTS @@ -46207,8 +49386,15 @@ enums: QualityAssuranceLevelEnum: name: QualityAssuranceLevelEnum definition_uri: https://w3id.org/valuesets/QualityAssuranceLevelEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Levels of quality assurance implementation + title: Quality Assurance Level from_schema: https://w3id.org/linkml/valuesets/business/quality_management + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: BASIC_QA: text: BASIC_QA @@ -46313,8 +49499,15 @@ enums: ProcessImprovementApproachEnum: name: ProcessImprovementApproachEnum definition_uri: https://w3id.org/valuesets/ProcessImprovementApproachEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Process improvement methodologies and approaches + title: Process Improvement Approach from_schema: https://w3id.org/linkml/valuesets/business/quality_management + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: BUSINESS_PROCESS_REENGINEERING: text: BUSINESS_PROCESS_REENGINEERING @@ -46479,8 +49672,15 @@ enums: QualityMaturityLevelEnum: name: QualityMaturityLevelEnum definition_uri: https://w3id.org/valuesets/QualityMaturityLevelEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Organizational quality maturity levels + title: Quality Maturity Level from_schema: https://w3id.org/linkml/valuesets/business/quality_management + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: AD_HOC: text: AD_HOC @@ -46585,8 +49785,15 @@ enums: ProcurementTypeEnum: name: ProcurementTypeEnum definition_uri: https://w3id.org/valuesets/ProcurementTypeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of procurement activities and approaches + title: Procurement Type from_schema: https://w3id.org/linkml/valuesets/business/supply_chain + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: DIRECT_PROCUREMENT: text: DIRECT_PROCUREMENT @@ -46791,8 +49998,15 @@ enums: VendorCategoryEnum: name: VendorCategoryEnum definition_uri: https://w3id.org/valuesets/VendorCategoryEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Vendor classification categories + title: Vendor Category from_schema: https://w3id.org/linkml/valuesets/business/supply_chain + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: STRATEGIC_SUPPLIER: text: STRATEGIC_SUPPLIER @@ -46997,8 +50211,15 @@ enums: SupplyChainStrategyEnum: name: SupplyChainStrategyEnum definition_uri: https://w3id.org/valuesets/SupplyChainStrategyEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Supply chain strategic approaches + title: Supply Chain Strategy from_schema: https://w3id.org/linkml/valuesets/business/supply_chain + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: LEAN_SUPPLY_CHAIN: text: LEAN_SUPPLY_CHAIN @@ -47203,8 +50424,15 @@ enums: LogisticsOperationEnum: name: LogisticsOperationEnum definition_uri: https://w3id.org/valuesets/LogisticsOperationEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of logistics operations + title: Logistics Operation from_schema: https://w3id.org/linkml/valuesets/business/supply_chain + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: INBOUND_LOGISTICS: text: INBOUND_LOGISTICS @@ -47409,8 +50637,15 @@ enums: SourcingStrategyEnum: name: SourcingStrategyEnum definition_uri: https://w3id.org/valuesets/SourcingStrategyEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Sourcing strategy approaches + title: Sourcing Strategy from_schema: https://w3id.org/linkml/valuesets/business/supply_chain + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: SINGLE_SOURCING: text: SINGLE_SOURCING @@ -47615,8 +50850,15 @@ enums: SupplierRelationshipTypeEnum: name: SupplierRelationshipTypeEnum definition_uri: https://w3id.org/valuesets/SupplierRelationshipTypeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of supplier relationship management + title: Supplier Relationship Type from_schema: https://w3id.org/linkml/valuesets/business/supply_chain + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: TRANSACTIONAL: text: TRANSACTIONAL @@ -47821,8 +51063,15 @@ enums: InventoryManagementApproachEnum: name: InventoryManagementApproachEnum definition_uri: https://w3id.org/valuesets/InventoryManagementApproachEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Inventory management methodologies + title: Inventory Management Approach from_schema: https://w3id.org/linkml/valuesets/business/supply_chain + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: JUST_IN_TIME: text: JUST_IN_TIME @@ -48027,8 +51276,15 @@ enums: EmploymentTypeEnum: name: EmploymentTypeEnum definition_uri: https://w3id.org/valuesets/EmploymentTypeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of employment arrangements and contracts + title: Employment Type from_schema: https://w3id.org/linkml/valuesets/business/human_resources + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: FULL_TIME: text: FULL_TIME @@ -48213,8 +51469,15 @@ enums: JobLevelEnum: name: JobLevelEnum definition_uri: https://w3id.org/valuesets/JobLevelEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Organizational job levels and career progression + title: Job Level from_schema: https://w3id.org/linkml/valuesets/business/human_resources + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: ENTRY_LEVEL: text: ENTRY_LEVEL @@ -48399,8 +51662,15 @@ enums: HRFunctionEnum: name: HRFunctionEnum definition_uri: https://w3id.org/valuesets/HRFunctionEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Human resources functional areas and specializations + title: HR Function from_schema: https://w3id.org/linkml/valuesets/business/human_resources + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: TALENT_ACQUISITION: text: TALENT_ACQUISITION @@ -48585,8 +51855,15 @@ enums: CompensationTypeEnum: name: CompensationTypeEnum definition_uri: https://w3id.org/valuesets/CompensationTypeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of employee compensation structures + title: Compensation Type from_schema: https://w3id.org/linkml/valuesets/business/human_resources + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: BASE_SALARY: text: BASE_SALARY @@ -48751,8 +52028,15 @@ enums: PerformanceRatingEnum: name: PerformanceRatingEnum definition_uri: https://w3id.org/valuesets/PerformanceRatingEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Employee performance evaluation ratings + title: Performance Rating from_schema: https://w3id.org/linkml/valuesets/business/human_resources + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: EXCEEDS_EXPECTATIONS: text: EXCEEDS_EXPECTATIONS @@ -48857,8 +52141,15 @@ enums: RecruitmentSourceEnum: name: RecruitmentSourceEnum definition_uri: https://w3id.org/valuesets/RecruitmentSourceEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Sources for candidate recruitment and sourcing + title: Recruitment Source from_schema: https://w3id.org/linkml/valuesets/business/human_resources + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: INTERNAL_REFERRAL: text: INTERNAL_REFERRAL @@ -49023,8 +52314,15 @@ enums: TrainingTypeEnum: name: TrainingTypeEnum definition_uri: https://w3id.org/valuesets/TrainingTypeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of employee training and development programs + title: Training Type from_schema: https://w3id.org/linkml/valuesets/business/human_resources + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: ONBOARDING: text: ONBOARDING @@ -49189,8 +52487,15 @@ enums: EmployeeStatusEnum: name: EmployeeStatusEnum definition_uri: https://w3id.org/valuesets/EmployeeStatusEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Current employment status classifications + title: Employee Status from_schema: https://w3id.org/linkml/valuesets/business/human_resources + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: ACTIVE: text: ACTIVE @@ -49315,8 +52620,15 @@ enums: WorkArrangementEnum: name: WorkArrangementEnum definition_uri: https://w3id.org/valuesets/WorkArrangementEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Work location and arrangement types + title: Work Arrangement from_schema: https://w3id.org/linkml/valuesets/business/human_resources + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: ON_SITE: text: ON_SITE @@ -49421,8 +52733,15 @@ enums: BenefitsCategoryEnum: name: BenefitsCategoryEnum definition_uri: https://w3id.org/valuesets/BenefitsCategoryEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Categories of employee benefits and compensation + title: Benefits Category from_schema: https://w3id.org/linkml/valuesets/business/human_resources + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: HEALTH_INSURANCE: text: HEALTH_INSURANCE @@ -49587,8 +52906,15 @@ enums: MassSpectrometerFileFormat: name: MassSpectrometerFileFormat definition_uri: https://w3id.org/valuesets/MassSpectrometerFileFormat + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Standard file formats used in mass spectrometry + title: Mass Spectrometer File Format from_schema: https://w3id.org/valuesets/analytical_chemistry/mass_spectrometry + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: MZML: text: MZML @@ -49673,8 +52999,15 @@ enums: MassSpectrometerVendor: name: MassSpectrometerVendor definition_uri: https://w3id.org/valuesets/MassSpectrometerVendor + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Major mass spectrometer manufacturers + title: Mass Spectrometer Vendor from_schema: https://w3id.org/valuesets/analytical_chemistry/mass_spectrometry + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: THERMO_FISHER_SCIENTIFIC: text: THERMO_FISHER_SCIENTIFIC @@ -49714,8 +53047,15 @@ enums: ChromatographyType: name: ChromatographyType definition_uri: https://w3id.org/valuesets/ChromatographyType + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of chromatographic separation methods + title: Chromatography Type from_schema: https://w3id.org/valuesets/analytical_chemistry/mass_spectrometry + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: GAS_CHROMATOGRAPHY: text: GAS_CHROMATOGRAPHY @@ -49744,8 +53084,15 @@ enums: DerivatizationMethod: name: DerivatizationMethod definition_uri: https://w3id.org/valuesets/DerivatizationMethod + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Chemical derivatization methods for sample preparation + title: Derivatization Method from_schema: https://w3id.org/valuesets/analytical_chemistry/mass_spectrometry + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: SILYLATION: text: SILYLATION @@ -49774,8 +53121,15 @@ enums: MetabolomicsAssayType: name: MetabolomicsAssayType definition_uri: https://w3id.org/valuesets/MetabolomicsAssayType + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of metabolomics assays and profiling approaches + title: Metabolomics Assay Type from_schema: https://w3id.org/valuesets/analytical_chemistry/mass_spectrometry + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: TARGETED_METABOLITE_PROFILING: text: TARGETED_METABOLITE_PROFILING @@ -49795,8 +53149,15 @@ enums: AnalyticalControlType: name: AnalyticalControlType definition_uri: https://w3id.org/valuesets/AnalyticalControlType + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of control samples used in analytical chemistry + title: Analytical Control Type from_schema: https://w3id.org/valuesets/analytical_chemistry/mass_spectrometry + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: INTERNAL_STANDARD: text: INTERNAL_STANDARD @@ -49832,8 +53193,15 @@ enums: LaboratoryDeviceTypeEnum: name: LaboratoryDeviceTypeEnum definition_uri: https://w3id.org/valuesets/LaboratoryDeviceTypeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of automated laboratory devices and equipment + title: Laboratory Device Type from_schema: https://w3id.org/linkml/valuesets/lab_automation/devices + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: LIQUID_HANDLER: text: LIQUID_HANDLER @@ -49937,8 +53305,15 @@ enums: RoboticArmTypeEnum: name: RoboticArmTypeEnum definition_uri: https://w3id.org/valuesets/RoboticArmTypeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of robotic arms used in laboratory automation systems + title: Robotic Arm Type from_schema: https://w3id.org/linkml/valuesets/lab_automation/devices + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: FLEXIBLE_CHANNEL_ARM: text: FLEXIBLE_CHANNEL_ARM @@ -49974,8 +53349,15 @@ enums: LiquidHandlingOperationEnum: name: LiquidHandlingOperationEnum definition_uri: https://w3id.org/valuesets/LiquidHandlingOperationEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Operations for automated liquid handling in laboratory automation + title: Liquid Handling Operation from_schema: https://w3id.org/linkml/valuesets/lab_automation/operations + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: PICK_UP_TIPS: text: PICK_UP_TIPS @@ -50038,8 +53420,15 @@ enums: SampleProcessingOperationEnum: name: SampleProcessingOperationEnum definition_uri: https://w3id.org/valuesets/SampleProcessingOperationEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: General sample processing operations in automated laboratories + title: Sample Processing Operation from_schema: https://w3id.org/linkml/valuesets/lab_automation/operations + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: CENTRIFUGATION: text: CENTRIFUGATION @@ -50100,8 +53489,15 @@ enums: MicroplateFormatEnum: name: MicroplateFormatEnum definition_uri: https://w3id.org/valuesets/MicroplateFormatEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Standard microplate well configurations following ANSI/SLAS standards + title: Microplate Format from_schema: https://w3id.org/linkml/valuesets/lab_automation/labware + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: WELL_6: text: WELL_6 @@ -50157,8 +53553,15 @@ enums: ContainerTypeEnum: name: ContainerTypeEnum definition_uri: https://w3id.org/valuesets/ContainerTypeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of laboratory containers and labware + title: Container Type from_schema: https://w3id.org/linkml/valuesets/lab_automation/labware + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: MICROPLATE: text: MICROPLATE @@ -50219,8 +53622,15 @@ enums: PlateMaterialEnum: name: PlateMaterialEnum definition_uri: https://w3id.org/valuesets/PlateMaterialEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Material composition of laboratory microplates + title: Plate Material from_schema: https://w3id.org/linkml/valuesets/lab_automation/labware + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: POLYSTYRENE: text: POLYSTYRENE @@ -50239,8 +53649,15 @@ enums: PlateCoatingEnum: name: PlateCoatingEnum definition_uri: https://w3id.org/valuesets/PlateCoatingEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Surface treatment of microplates + title: Plate Coating from_schema: https://w3id.org/linkml/valuesets/lab_automation/labware + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: COATED: text: COATED @@ -50265,8 +53682,15 @@ enums: WorkflowOrchestrationTypeEnum: name: WorkflowOrchestrationTypeEnum definition_uri: https://w3id.org/valuesets/WorkflowOrchestrationTypeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of workflow orchestration in laboratory automation systems + title: Workflow Orchestration Type from_schema: https://w3id.org/linkml/valuesets/lab_automation/protocols + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: STATIC_ORCHESTRATION: text: STATIC_ORCHESTRATION @@ -50294,8 +53718,15 @@ enums: SchedulerTypeEnum: name: SchedulerTypeEnum definition_uri: https://w3id.org/valuesets/SchedulerTypeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of scheduling algorithms for laboratory automation + title: Scheduler Type from_schema: https://w3id.org/linkml/valuesets/lab_automation/protocols + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: STATIC_SCHEDULER: text: STATIC_SCHEDULER @@ -50325,8 +53756,15 @@ enums: ProtocolStateEnum: name: ProtocolStateEnum definition_uri: https://w3id.org/valuesets/ProtocolStateEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Execution states of laboratory protocols + title: Protocol State from_schema: https://w3id.org/linkml/valuesets/lab_automation/protocols + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: PENDING: text: PENDING @@ -50363,8 +53801,15 @@ enums: ExecutionModeEnum: name: ExecutionModeEnum definition_uri: https://w3id.org/valuesets/ExecutionModeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Modes of protocol execution + title: Execution Mode from_schema: https://w3id.org/linkml/valuesets/lab_automation/protocols + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: AUTOMATED: text: AUTOMATED @@ -50393,8 +53838,15 @@ enums: WorkflowErrorHandlingEnum: name: WorkflowErrorHandlingEnum definition_uri: https://w3id.org/valuesets/WorkflowErrorHandlingEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Error handling strategies in laboratory automation workflows + title: Workflow Error Handling from_schema: https://w3id.org/linkml/valuesets/lab_automation/protocols + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: ABORT_ON_ERROR: text: ABORT_ON_ERROR @@ -50423,8 +53875,15 @@ enums: IntegrationSystemEnum: name: IntegrationSystemEnum definition_uri: https://w3id.org/valuesets/IntegrationSystemEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of systems integrated with laboratory automation platforms + title: Integration System from_schema: https://w3id.org/linkml/valuesets/lab_automation/protocols + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: LIMS: text: LIMS @@ -50469,8 +53928,15 @@ enums: AutomationStandardEnum: name: AutomationStandardEnum definition_uri: https://w3id.org/valuesets/AutomationStandardEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Industry standards for laboratory automation systems + title: Automation Standard from_schema: https://w3id.org/linkml/valuesets/lab_automation/standards + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: SILA_2: text: SILA_2 @@ -50552,8 +54018,15 @@ enums: CommunicationProtocolEnum: name: CommunicationProtocolEnum definition_uri: https://w3id.org/valuesets/CommunicationProtocolEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Communication protocols for laboratory automation integration + title: Communication Protocol from_schema: https://w3id.org/linkml/valuesets/lab_automation/standards + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: GRPC: text: GRPC @@ -50602,8 +54075,15 @@ enums: LabwareStandardEnum: name: LabwareStandardEnum definition_uri: https://w3id.org/valuesets/LabwareStandardEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Standardization specifications for laboratory labware + title: Labware Standard from_schema: https://w3id.org/linkml/valuesets/lab_automation/standards + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: ANSI_SLAS_1_2004: text: ANSI_SLAS_1_2004 @@ -50669,8 +54149,15 @@ enums: IntegrationFeatureEnum: name: IntegrationFeatureEnum definition_uri: https://w3id.org/valuesets/IntegrationFeatureEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Integration features for laboratory automation systems + title: Integration Feature from_schema: https://w3id.org/linkml/valuesets/lab_automation/standards + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: BARCODE_TRACKING: text: BARCODE_TRACKING @@ -50707,8 +54194,15 @@ enums: ThermalCyclerTypeEnum: name: ThermalCyclerTypeEnum definition_uri: https://w3id.org/valuesets/ThermalCyclerTypeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of thermal cycling instruments + title: Thermal Cycler Type from_schema: https://w3id.org/linkml/valuesets/lab_automation/thermal_cycling + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: STANDARD_THERMAL_CYCLER: text: STANDARD_THERMAL_CYCLER @@ -50755,8 +54249,15 @@ enums: PCROperationTypeEnum: name: PCROperationTypeEnum definition_uri: https://w3id.org/valuesets/PCROperationTypeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of PCR operations and techniques + title: PCR Operation Type from_schema: https://w3id.org/linkml/valuesets/lab_automation/thermal_cycling + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: STANDARD_PCR: text: STANDARD_PCR @@ -50817,8 +54318,15 @@ enums: DetectionModeEnum: name: DetectionModeEnum definition_uri: https://w3id.org/valuesets/DetectionModeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Detection modes for real-time PCR instruments + title: Detection Mode from_schema: https://w3id.org/linkml/valuesets/lab_automation/thermal_cycling + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: SYBR_GREEN: text: SYBR_GREEN @@ -50855,8 +54363,15 @@ enums: PCRPlateTypeEnum: name: PCRPlateTypeEnum definition_uri: https://w3id.org/valuesets/PCRPlateTypeEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Types of plates used for PCR applications + title: PCR Plate Type from_schema: https://w3id.org/linkml/valuesets/lab_automation/thermal_cycling + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: PCR_96_WELL: text: PCR_96_WELL @@ -50889,8 +54404,15 @@ enums: ThermalCyclingStepEnum: name: ThermalCyclingStepEnum definition_uri: https://w3id.org/valuesets/ThermalCyclingStepEnum + instantiates: + - valuesets_meta:ValueSetEnumDefinition description: Steps in thermal cycling protocols + title: Thermal Cycling Step from_schema: https://w3id.org/linkml/valuesets/lab_automation/thermal_cycling + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + status: DRAFT permissible_values: INITIAL_DENATURATION: text: INITIAL_DENATURATION @@ -54307,7 +57829,7 @@ classes: class_uri: valuesets:Fake metamodel_version: 1.7.0 source_file: valuesets.yaml -source_file_date: '2025-11-05T11:51:39' -source_file_size: 2841 -generation_date: '2025-11-11T17:37:58' +source_file_date: '2025-11-25T10:16:53' +source_file_size: 2915 +generation_date: '2025-11-25T11:01:16' diff --git a/docs/slides/valuesets-slides.pdf b/docs/slides/valuesets-slides.pdf index d428a55a..d49aaacd 100644 Binary files a/docs/slides/valuesets-slides.pdf and b/docs/slides/valuesets-slides.pdf differ diff --git a/docs/slides/valuesets-slides.pptx b/docs/slides/valuesets-slides.pptx index 58a80c88..bf5b3ed1 100644 Binary files a/docs/slides/valuesets-slides.pptx and b/docs/slides/valuesets-slides.pptx differ diff --git a/justfile b/justfile index 7130f204..4cfec018 100644 --- a/justfile +++ b/justfile @@ -76,7 +76,7 @@ clean: _clean_project # (Re-)Generate project and documentation locally [group('model development')] -site: gen-project gen-doc +site: gen-project gen-doc gen-slides # Deploy documentation site to Github Pages [group('deployment')] diff --git a/project/jsonschema/valuesets.schema.json b/project/jsonschema/valuesets.schema.json index b49db73c..3f282e59 100644 --- a/project/jsonschema/valuesets.schema.json +++ b/project/jsonschema/valuesets.schema.json @@ -5934,7 +5934,7 @@ "type": "string" }, "PresenceEnum": { - "description": "", + "description": "Classification of whether an entity is present, absent, or at detection limits", "enum": [ "PRESENT", "ABSENT", @@ -6689,7 +6689,7 @@ "type": "string" }, "RelativeTimeEnum": { - "description": "", + "description": "Temporal relationships between events or time points", "enum": [ "BEFORE", "AFTER", diff --git a/src/valuesets/datamodel/valuesets.py b/src/valuesets/datamodel/valuesets.py index ab30c331..4798862f 100644 --- a/src/valuesets/datamodel/valuesets.py +++ b/src/valuesets/datamodel/valuesets.py @@ -55,6 +55,9 @@ def __contains__(self, key: str) -> bool: linkml_meta = LinkMLMeta({'default_prefix': 'valuesets', 'description': 'A collection of commonly used value sets', 'id': 'https://w3id.org/linkml/valuesets', 'name': 'valuesets', 'title': 'valuesets'}) class RelativeTimeEnum(RichEnum): + """ + Temporal relationships between events or time points + """ # Enum members BEFORE = "BEFORE" AFTER = "AFTER" @@ -62,9 +65,15 @@ class RelativeTimeEnum(RichEnum): # Set metadata after class creation to avoid it becoming an enum member RelativeTimeEnum._metadata = { + "BEFORE": {'description': 'Occurs before the reference time point'}, + "AFTER": {'description': 'Occurs after the reference time point'}, + "AT_SAME_TIME_AS": {'description': 'Occurs at the same time as the reference time point'}, } class PresenceEnum(RichEnum): + """ + Classification of whether an entity is present, absent, or at detection limits + """ # Enum members PRESENT = "PRESENT" ABSENT = "ABSENT" @@ -127,8 +136,8 @@ class DataAbsentEnum(RichEnum): "AS_TEXT": {'description': 'The content of the data is represented in the resource narrative.', 'meaning': 'fhir_data_absent_reason:as-text'}, "ERROR": {'description': 'Some system or workflow process error means that the information is not available.', 'meaning': 'fhir_data_absent_reason:error'}, "NOT_A_NUMBER": {'description': 'The numeric value is undefined or unrepresentable due to a floating point processing error.', 'meaning': 'fhir_data_absent_reason:not-a-number'}, - "NEGATIVE_INFINITY": {'description': 'The numeric value is excessively low and unrepresentable due to a floating point processing error.', 'meaning': 'fhir_data_absent_reason:negative-infinity'}, - "POSITIVE_INFINITY": {'description': 'The numeric value is excessively high and unrepresentable due to a floating point processing error.', 'meaning': 'fhir_data_absent_reason:positive-infinity'}, + "NEGATIVE_INFINITY": {'description': 'The numeric value is excessively low and unrepresentable due to a floating point processing error.', 'meaning': 'fhir_data_absent_reason:negative-infinity'}, + "POSITIVE_INFINITY": {'description': 'The numeric value is excessively high and unrepresentable due to a floating point processing error.', 'meaning': 'fhir_data_absent_reason:positive-infinity'}, "NOT_PERFORMED": {'description': 'The value is not available because the observation procedure (test, etc.) was not performed.', 'meaning': 'fhir_data_absent_reason:not-performed'}, "NOT_PERMITTED": {'description': 'The value is not permitted in this context (e.g. due to profiles, or the base data types).', 'meaning': 'fhir_data_absent_reason:not-permitted'}, } diff --git a/src/valuesets/datamodel/valuesets_dataclass.py b/src/valuesets/datamodel/valuesets_dataclass.py index 7c9ccaa8..cb73833f 100644 --- a/src/valuesets/datamodel/valuesets_dataclass.py +++ b/src/valuesets/datamodel/valuesets_dataclass.py @@ -1,5 +1,5 @@ # Auto generated from valuesets.yaml by pythongen.py version: 0.0.1 -# Generation date: 2025-11-05T18:09:57 +# Generation date: 2025-11-25T10:23:04 # Schema: valuesets # # id: https://w3id.org/linkml/valuesets @@ -62,7 +62,9 @@ version = None # Namespaces +ORCID = CurieNamespace('orcid', 'https://orcid.org/') VALUESETS = CurieNamespace('valuesets', 'https://w3id.org/valuesets/') +VALUESETS_META = CurieNamespace('valuesets_meta', 'https://w3id.org/valuesets/meta/') DEFAULT_ = VALUESETS @@ -83,17 +85,28 @@ class Fake(YAMLRoot): # Enumerations class RelativeTimeEnum(EnumDefinitionImpl): - - BEFORE = PermissibleValue(text="BEFORE") - AFTER = PermissibleValue(text="AFTER") - AT_SAME_TIME_AS = PermissibleValue(text="AT_SAME_TIME_AS") + """ + Temporal relationships between events or time points + """ + BEFORE = PermissibleValue( + text="BEFORE", + description="Occurs before the reference time point") + AFTER = PermissibleValue( + text="AFTER", + description="Occurs after the reference time point") + AT_SAME_TIME_AS = PermissibleValue( + text="AT_SAME_TIME_AS", + description="Occurs at the same time as the reference time point") _defn = EnumDefinition( name="RelativeTimeEnum", + description="Temporal relationships between events or time points", ) class PresenceEnum(EnumDefinitionImpl): - + """ + Classification of whether an entity is present, absent, or at detection limits + """ PRESENT = PermissibleValue( text="PRESENT", description="The entity is present") @@ -109,6 +122,7 @@ class PresenceEnum(EnumDefinitionImpl): _defn = EnumDefinition( name="PresenceEnum", + description="Classification of whether an entity is present, absent, or at detection limits", ) class ContributorType(EnumDefinitionImpl): @@ -207,13 +221,13 @@ def _addvals(cls): PermissibleValue( text="negative-infinity", title="Negative Infinity (NINF)", - description="""The numeric value is excessively low and unrepresentable due to a floating point processing error.""", + description="""The numeric value is excessively low and unrepresentable due to a floating point processing error.""", meaning=FHIR_DATA_ABSENT_REASON["negative-infinity"])) setattr(cls, "positive-infinity", PermissibleValue( text="positive-infinity", title="Positive Infinity (PINF)", - description="""The numeric value is excessively high and unrepresentable due to a floating point processing error.""", + description="""The numeric value is excessively high and unrepresentable due to a floating point processing error.""", meaning=FHIR_DATA_ABSENT_REASON["positive-infinity"])) setattr(cls, "not-performed", PermissibleValue( @@ -2691,6 +2705,133 @@ class ProcessingStatus(EnumDefinitionImpl): description="Status of data processing workflows", ) +class CoordinationGeometry(EnumDefinitionImpl): + """ + Coordination geometry of metal centers in protein structures + """ + LINEAR = PermissibleValue( + text="LINEAR", + description="Linear coordination geometry (2 ligands at 180°)") + TRIGONAL_PLANAR = PermissibleValue( + text="TRIGONAL_PLANAR", + description="Trigonal planar coordination geometry (3 ligands, 120° angles)") + TRIGONAL_PYRAMIDAL = PermissibleValue( + text="TRIGONAL_PYRAMIDAL", + description="Trigonal pyramidal coordination geometry") + T_SHAPED = PermissibleValue( + text="T_SHAPED", + description="T-shaped coordination geometry") + TETRAHEDRAL = PermissibleValue( + text="TETRAHEDRAL", + title="tetrahedral molecular geometry", + description="Tetrahedral coordination geometry (4 ligands, 109.5° angles)", + meaning=NCIT["C103215"]) + SQUARE_PLANAR = PermissibleValue( + text="SQUARE_PLANAR", + title="square planar molecular geometry", + description="Square planar coordination geometry (4 ligands in plane)") + TRIGONAL_BIPYRAMIDAL = PermissibleValue( + text="TRIGONAL_BIPYRAMIDAL", + description="Trigonal bipyramidal coordination geometry (5 ligands)") + SQUARE_PYRAMIDAL = PermissibleValue( + text="SQUARE_PYRAMIDAL", + description="Square pyramidal coordination geometry (5 ligands)") + PENTAGONAL_PLANAR = PermissibleValue( + text="PENTAGONAL_PLANAR", + description="Pentagonal planar coordination geometry (5 ligands in plane)") + OCTAHEDRAL = PermissibleValue( + text="OCTAHEDRAL", + title="octahedral molecular geometry", + description="Octahedral coordination geometry (6 ligands)") + TRIGONAL_PRISMATIC = PermissibleValue( + text="TRIGONAL_PRISMATIC", + description="Trigonal prismatic coordination geometry (6 ligands)") + PENTAGONAL_BIPYRAMIDAL = PermissibleValue( + text="PENTAGONAL_BIPYRAMIDAL", + description="Pentagonal bipyramidal coordination geometry (7 ligands)") + HEXAGONAL_BIPYRAMIDAL = PermissibleValue( + text="HEXAGONAL_BIPYRAMIDAL", + description="Hexagonal bipyramidal coordination geometry (8 ligands)") + SQUARE_ANTIPRISMATIC = PermissibleValue( + text="SQUARE_ANTIPRISMATIC", + description="Square antiprismatic coordination geometry (8 ligands)") + DODECAHEDRAL = PermissibleValue( + text="DODECAHEDRAL", + description="Dodecahedral coordination geometry (8 ligands)") + CUBIC = PermissibleValue( + text="CUBIC", + description="Cubic coordination geometry (8 ligands)") + BENT = PermissibleValue( + text="BENT", + description="Bent or angular coordination geometry") + SEE_SAW = PermissibleValue( + text="SEE_SAW", + description="See-saw coordination geometry (4 ligands)") + + _defn = EnumDefinition( + name="CoordinationGeometry", + description="Coordination geometry of metal centers in protein structures", + ) + +class MetalLigandType(EnumDefinitionImpl): + """ + Types of metal-containing chemical components + """ + METAL_CATION = PermissibleValue( + text="METAL_CATION", + description="Metal cation (e.g., Ca2+, Mg2+, Zn2+, Fe3+)") + METAL_CONTAINING_LIGAND = PermissibleValue( + text="METAL_CONTAINING_LIGAND", + description="Metal-containing ligand or cofactor") + + _defn = EnumDefinition( + name="MetalLigandType", + description="Types of metal-containing chemical components", + ) + +class ProteinModificationType(EnumDefinitionImpl): + """ + Types of protein modifications + """ + METAL_COORDINATION = PermissibleValue( + text="METAL_COORDINATION", + description="Metal coordination modification") + PHOSPHORYLATION = PermissibleValue( + text="PHOSPHORYLATION", + description="Phosphorylation modification") + GLYCOSYLATION = PermissibleValue( + text="GLYCOSYLATION", + description="Glycosylation modification") + ACETYLATION = PermissibleValue( + text="ACETYLATION", + description="Acetylation modification") + METHYLATION = PermissibleValue( + text="METHYLATION", + description="Methylation modification") + UBIQUITINATION = PermissibleValue( + text="UBIQUITINATION", + description="Ubiquitination modification") + SUMOYLATION = PermissibleValue( + text="SUMOYLATION", + description="SUMOylation modification") + HYDROXYLATION = PermissibleValue( + text="HYDROXYLATION", + description="Hydroxylation modification") + LIPIDATION = PermissibleValue( + text="LIPIDATION", + description="Lipidation modification") + PROTEOLYTIC_CLEAVAGE = PermissibleValue( + text="PROTEOLYTIC_CLEAVAGE", + description="Proteolytic cleavage") + CROSSLINKING = PermissibleValue( + text="CROSSLINKING", + description="Crosslinking modification") + + _defn = EnumDefinition( + name="ProteinModificationType", + description="Types of protein modifications", + ) + class BiosafetyLevelEnum(EnumDefinitionImpl): """ Biosafety levels (BSL) defining containment requirements for biological agents @@ -8859,6 +9000,30 @@ class MimeType(EnumDefinitionImpl): text="APPLICATION_LD_JSON", description="JSON-LD format", meaning=IANA["application/ld+json"]) + APPLICATION_N_QUADS = PermissibleValue( + text="APPLICATION_N_QUADS", + description="N-Quads RDF serialization format", + meaning=IANA["application/n-quads"]) + APPLICATION_N_TRIPLES = PermissibleValue( + text="APPLICATION_N_TRIPLES", + description="N-Triples RDF serialization format", + meaning=IANA["application/n-triples"]) + APPLICATION_RDF_XML = PermissibleValue( + text="APPLICATION_RDF_XML", + description="RDF/XML serialization format", + meaning=IANA["application/rdf+xml"]) + APPLICATION_SPARQL_RESULTS_JSON = PermissibleValue( + text="APPLICATION_SPARQL_RESULTS_JSON", + description="SPARQL 1.1 Query Results JSON format", + meaning=IANA["application/sparql-results+json"]) + APPLICATION_SPARQL_RESULTS_XML = PermissibleValue( + text="APPLICATION_SPARQL_RESULTS_XML", + description="SPARQL 1.1 Query Results XML format", + meaning=IANA["application/sparql-results+xml"]) + APPLICATION_TRIG = PermissibleValue( + text="APPLICATION_TRIG", + description="TriG RDF serialization format", + meaning=IANA["application/trig"]) APPLICATION_WASM = PermissibleValue( text="APPLICATION_WASM", description="WebAssembly binary format", @@ -15766,7 +15931,7 @@ class UniProtSpeciesCode(EnumDefinitionImpl): SP_9ANUR = PermissibleValue( text="SP_9ANUR", title="Leptobrachium leishanense", - description="Leptobrachium leishanense (Leishan spiny toad) - Proteome: UP000694569", + description="Leptobrachium leishanense - Proteome: UP000694569", meaning=NCBITAXON["445787"]) SP_9APHY = PermissibleValue( text="SP_9APHY", @@ -15821,7 +15986,7 @@ class UniProtSpeciesCode(EnumDefinitionImpl): SP_9AVES = PermissibleValue( text="SP_9AVES", title="Anser brachyrhynchus", - description="Anser brachyrhynchus (Pink-footed goose) - Proteome: UP000694426", + description="Anser brachyrhynchus - Proteome: UP000694426", meaning=NCBITAXON["132585"]) SP_9BACE = PermissibleValue( text="SP_9BACE", @@ -15936,22 +16101,22 @@ class UniProtSpeciesCode(EnumDefinitionImpl): SP_9CERV = PermissibleValue( text="SP_9CERV", title="Cervus hanglu yarkandensis", - description="Cervus hanglu yarkandensis (Yarkand deer) - Proteome: UP000631465", + description="Cervus hanglu yarkandensis - Proteome: UP000631465", meaning=NCBITAXON["84702"]) SP_9CETA = PermissibleValue( text="SP_9CETA", title="Catagonus wagneri", - description="Catagonus wagneri (Chacoan peccary) - Proteome: UP000694540", + description="Catagonus wagneri - Proteome: UP000694540", meaning=NCBITAXON["51154"]) SP_9CHAR = PermissibleValue( text="SP_9CHAR", title="Rostratula benghalensis", - description="Rostratula benghalensis (greater painted-snipe) - Proteome: UP000545435", + description="Rostratula benghalensis - Proteome: UP000545435", meaning=NCBITAXON["118793"]) SP_9CHIR = PermissibleValue( text="SP_9CHIR", title="Phyllostomus discolor", - description="Phyllostomus discolor (pale spear-nosed bat) - Proteome: UP000504628", + description="Phyllostomus discolor - Proteome: UP000504628", meaning=NCBITAXON["89673"]) SP_9CHLA = PermissibleValue( text="SP_9CHLA", @@ -15981,7 +16146,7 @@ class UniProtSpeciesCode(EnumDefinitionImpl): SP_9CICH = PermissibleValue( text="SP_9CICH", title="Maylandia zebra", - description="Maylandia zebra (zebra mbuna) - Proteome: UP000265160", + description="Maylandia zebra - Proteome: UP000265160", meaning=NCBITAXON["106582"]) SP_9CILI = PermissibleValue( text="SP_9CILI", @@ -16011,12 +16176,12 @@ class UniProtSpeciesCode(EnumDefinitionImpl): SP_9COLU = PermissibleValue( text="SP_9COLU", title="Pampusana beccarii", - description="Pampusana beccarii (Western bronze ground-dove) - Proteome: UP000541332", + description="Pampusana beccarii - Proteome: UP000541332", meaning=NCBITAXON["2953425"]) SP_9CORV = PermissibleValue( text="SP_9CORV", title="Cnemophilus loriae", - description="Cnemophilus loriae (Loria's bird-of-paradise) - Proteome: UP000517678", + description="Cnemophilus loriae - Proteome: UP000517678", meaning=NCBITAXON["254448"]) SP_9CORY = PermissibleValue( text="SP_9CORY", @@ -16041,7 +16206,7 @@ class UniProtSpeciesCode(EnumDefinitionImpl): SP_9CUCU = PermissibleValue( text="SP_9CUCU", title="Ceutorhynchus assimilis", - description="Ceutorhynchus assimilis (cabbage seed weevil) - Proteome: UP001152799", + description="Ceutorhynchus assimilis - Proteome: UP001152799", meaning=NCBITAXON["467358"]) SP_9CYAN = PermissibleValue( text="SP_9CYAN", @@ -16071,7 +16236,7 @@ class UniProtSpeciesCode(EnumDefinitionImpl): SP_9DEND = PermissibleValue( text="SP_9DEND", title="Xiphorhynchus elegans", - description="Xiphorhynchus elegans (elegant woodcreeper) - Proteome: UP000551443", + description="Xiphorhynchus elegans - Proteome: UP000551443", meaning=NCBITAXON["269412"]) SP_9DINO = PermissibleValue( text="SP_9DINO", @@ -16186,7 +16351,7 @@ class UniProtSpeciesCode(EnumDefinitionImpl): SP_9GALL = PermissibleValue( text="SP_9GALL", title="Odontophorus gujanensis", - description="Odontophorus gujanensis (marbled wood quail) - Proteome: UP000522663", + description="Odontophorus gujanensis - Proteome: UP000522663", meaning=NCBITAXON["886794"]) SP_9GAMA = PermissibleValue( text="SP_9GAMA", @@ -16201,12 +16366,12 @@ class UniProtSpeciesCode(EnumDefinitionImpl): SP_9GAMM = PermissibleValue( text="SP_9GAMM", title="Buchnera aphidicola", - description="Buchnera aphidicola (Cinara tujafilina) - Proteome: UP000006811", + description="Buchnera aphidicola (Buchnera aphidicola (Cinara tujafilina)) - Proteome: UP000006811", meaning=NCBITAXON["261317"]) SP_9GAST = PermissibleValue( text="SP_9GAST", title="Elysia crispata", - description="Elysia crispata (lettuce slug) - Proteome: UP001283361", + description="Elysia crispata - Proteome: UP001283361", meaning=NCBITAXON["231223"]) SP_9GEMI = PermissibleValue( text="SP_9GEMI", @@ -16221,12 +16386,12 @@ class UniProtSpeciesCode(EnumDefinitionImpl): SP_9GOBI = PermissibleValue( text="SP_9GOBI", title="Neogobius melanostomus", - description="Neogobius melanostomus (round goby) - Proteome: UP000694523", + description="Neogobius melanostomus - Proteome: UP000694523", meaning=NCBITAXON["47308"]) SP_9GRUI = PermissibleValue( text="SP_9GRUI", title="Atlantisia rogersi", - description="Atlantisia rogersi (Inaccessible Island rail) - Proteome: UP000518911", + description="Atlantisia rogersi - Proteome: UP000518911", meaning=NCBITAXON["2478892"]) SP_9HELI = PermissibleValue( text="SP_9HELI", @@ -16271,7 +16436,7 @@ class UniProtSpeciesCode(EnumDefinitionImpl): SP_9INFA = PermissibleValue( text="SP_9INFA", title="Influenza A virus (A/California/VRDL364/2009", - description="Influenza A virus (A/California/VRDL364/2009 (mixed) - Proteome: UP000109975", + description="""Influenza A virus (A/California/VRDL364/2009 (Influenza A virus (A/California/VRDL364/2009(mixed))) - Proteome: UP000109975""", meaning=NCBITAXON["1049605"]) SP_9INSE = PermissibleValue( text="SP_9INSE", @@ -16281,43 +16446,223 @@ class UniProtSpeciesCode(EnumDefinitionImpl): SP_9LABR = PermissibleValue( text="SP_9LABR", title="Labrus bergylta", - description="Labrus bergylta (ballan wrasse) - Proteome: UP000261660", + description="Labrus bergylta - Proteome: UP000261660", meaning=NCBITAXON["56723"]) + SP_ACIB2 = PermissibleValue( + text="SP_ACIB2", + title="Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / JCM 6841 / CCUG 19606 / CIP 70.34 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81)", + description="""Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / JCM 6841 / CCUG 19606 / CIP 70.34 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81) (A. baumannii ATCC 19606) - Proteome: UP000498640""", + meaning=NCBITAXON["575584"]) + SP_ANOCA = PermissibleValue( + text="SP_ANOCA", + title="Anolis carolinensis", + description="Anolis carolinensis (Green anole (American chameleon)) - Proteome: UP000001646", + meaning=NCBITAXON["28377"]) + SP_ANOGA = PermissibleValue( + text="SP_ANOGA", + title="Anopheles gambiae", + description="Anopheles gambiae (African malaria mosquito) - Proteome: UP000007062", + meaning=NCBITAXON["7165"]) + SP_AQUAE = PermissibleValue( + text="SP_AQUAE", + title="Aquifex aeolicus", + description="Aquifex aeolicus (aquaficae bacteria) - Proteome: UP000000798", + meaning=NCBITAXON["224324"]) SP_ARATH = PermissibleValue( text="SP_ARATH", title="Arabidopsis thaliana", - description="Arabidopsis thaliana (Thale cress) - Proteome: UP000006548", + description="Arabidopsis thaliana (Mouse-ear cress) - Proteome: UP000006548", meaning=NCBITAXON["3702"]) + SP_ASPFU = PermissibleValue( + text="SP_ASPFU", + title="Neosartorya fumigata", + description="Neosartorya fumigata (ascomycote fungus) - Proteome: UP000002530", + meaning=NCBITAXON["330879"]) + SP_BACAN = PermissibleValue( + text="SP_BACAN", + title="Bacillus anthracis", + description="Bacillus anthracis - Proteome: UP000000594", + meaning=NCBITAXON["1392"]) + SP_BACCR = PermissibleValue( + text="SP_BACCR", + title="Bacillus cereus", + description="Bacillus cereus (bacillus cereus) - Proteome: UP000001417", + meaning=NCBITAXON["226900"]) SP_BACSU = PermissibleValue( text="SP_BACSU", title="Bacillus subtilis subsp. subtilis str. 168", - description="Bacillus subtilis subsp. subtilis str. 168 - Proteome: UP000001570", + description="Bacillus subtilis subsp. subtilis str. 168 (b subtilis) - Proteome: UP000001570", meaning=NCBITAXON["224308"]) + SP_BACTN = PermissibleValue( + text="SP_BACTN", + title="Bacteroides thetaiotaomicron", + description="Bacteroides thetaiotaomicron (bacteroidetes bacteria) - Proteome: UP000001414", + meaning=NCBITAXON["226186"]) + SP_BATDJ = PermissibleValue( + text="SP_BATDJ", + title="Batrachochytrium dendrobatidis", + description="Batrachochytrium dendrobatidis (Frog chytrid fungus) - Proteome: UP000007241", + meaning=NCBITAXON["684364"]) SP_BOVIN = PermissibleValue( text="SP_BOVIN", title="Bos taurus", description="Bos taurus (Cattle) - Proteome: UP000009136", meaning=NCBITAXON["9913"]) + SP_BRACM = PermissibleValue( + text="SP_BRACM", + title="Brassica campestris", + description="Brassica campestris (Field mustard) - Proteome: UP000011750", + meaning=NCBITAXON["3711"]) + SP_BRADI = PermissibleValue( + text="SP_BRADI", + title="Brachypodium distachyon", + description="Brachypodium distachyon (Purple false brome) - Proteome: UP000008810", + meaning=NCBITAXON["15368"]) + SP_BRADU = PermissibleValue( + text="SP_BRADU", + title="Bradyrhizobium diazoefficiens", + description="Bradyrhizobium diazoefficiens (alphaproteobacteria) - Proteome: UP000002526", + meaning=NCBITAXON["224911"]) + SP_BRAFL = PermissibleValue( + text="SP_BRAFL", + title="Branchiostoma floridae", + description="Branchiostoma floridae (Florida lancelet (Amphioxus)) - Proteome: UP000001554", + meaning=NCBITAXON["7739"]) + SP_CAEBR = PermissibleValue( + text="SP_CAEBR", + title="Caenorhabditis briggsae", + description="Caenorhabditis briggsae (nematode worm) - Proteome: UP000008549", + meaning=NCBITAXON["6238"]) SP_CAEEL = PermissibleValue( text="SP_CAEEL", title="Caenorhabditis elegans", - description="Caenorhabditis elegans - Proteome: UP000001940", + description="Caenorhabditis elegans (nematode worm) - Proteome: UP000001940", meaning=NCBITAXON["6239"]) + SP_CAMJE = PermissibleValue( + text="SP_CAMJE", + title="Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)", + description="""Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168) - Proteome: UP000000799""", + meaning=NCBITAXON["192222"]) + SP_CANAL = PermissibleValue( + text="SP_CANAL", + title="Candida albicans", + description="Candida albicans (Yeast) - Proteome: UP000000559", + meaning=NCBITAXON["237561"]) + SP_CANCO = PermissibleValue( + text="SP_CANCO", + title="Candida orthopsilosis (strain 90-125) (Co 90-125)", + description="Candida orthopsilosis (strain 90-125) (Co 90-125) - Proteome: UP000005018", + meaning=NCBITAXON["1136231"]) + SP_CANDC = PermissibleValue( + text="SP_CANDC", + title="Candida dubliniensis (strain CD36 / ATCC MYA-646 / CBS 7987 / NCPF 3949 / NRRL Y-17841)", + description="""Candida dubliniensis (strain CD36 / ATCC MYA-646 / CBS 7987 / NCPF 3949 / NRRL Y-17841) - Proteome: UP000002605""", + meaning=NCBITAXON["573826"]) + SP_CANGB = PermissibleValue( + text="SP_CANGB", + title="Candida glabrata (strain ATCC 2001 / BCRC 20586 / JCM 3761 / NBRC 0622 / NRRL Y-65 / CBS 138) (Nakaseomyces glabratus)", + description="""Candida glabrata (strain ATCC 2001 / BCRC 20586 / JCM 3761 / NBRC 0622 / NRRL Y-65 / CBS 138) (Nakaseomyces glabratus) - Proteome: UP000002428""", + meaning=NCBITAXON["284593"]) SP_CANLF = PermissibleValue( text="SP_CANLF", title="Canis lupus familiaris", description="Canis lupus familiaris (Dog) - Proteome: UP000805418", meaning=NCBITAXON["9615"]) + SP_CANPA = PermissibleValue( + text="SP_CANPA", + title="Candida parapsilosis (strain CDC 317 / ATCC MYA-4646)", + description="Candida parapsilosis (strain CDC 317 / ATCC MYA-4646) - Proteome: UP000005221", + meaning=NCBITAXON["578454"]) + SP_CANTI = PermissibleValue( + text="SP_CANTI", + title="Candida tropicalis (strain ATCC MYA-3404 / T1)", + description="Candida tropicalis (strain ATCC MYA-3404 / T1) - Proteome: UP000002037", + meaning=NCBITAXON["294747"]) SP_CHICK = PermissibleValue( text="SP_CHICK", title="Gallus gallus", description="Gallus gallus (Chicken) - Proteome: UP000000539", meaning=NCBITAXON["9031"]) + SP_CHLAA = PermissibleValue( + text="SP_CHLAA", + title="Chloroflexus aurantiacus", + description="Chloroflexus aurantiacus (chloroflexi bacteria) - Proteome: UP000002008", + meaning=NCBITAXON["324602"]) + SP_CHLRE = PermissibleValue( + text="SP_CHLRE", + title="Chlamydomonas reinhardtii", + description="Chlamydomonas reinhardtii (green algae) - Proteome: UP000006906", + meaning=NCBITAXON["3055"]) + SP_CHLTR = PermissibleValue( + text="SP_CHLTR", + title="Chlamydia trachomatis", + description="Chlamydia trachomatis (chlamydia) - Proteome: UP000000431", + meaning=NCBITAXON["272561"]) + SP_CIOIN = PermissibleValue( + text="SP_CIOIN", + title="Ciona intestinalis", + description="Ciona intestinalis (Transparent sea squirt) - Proteome: UP000008144", + meaning=NCBITAXON["7719"]) + SP_CITK8 = PermissibleValue( + text="SP_CITK8", + title="Citrobacter koseri (strain ATCC BAA-895 / CDC 4225-83 / SGSC4696)", + description="Citrobacter koseri (strain ATCC BAA-895 / CDC 4225-83 / SGSC4696) - Proteome: UP000008148", + meaning=NCBITAXON["290338"]) + SP_CLALU = PermissibleValue( + text="SP_CLALU", + title="Clavispora lusitaniae (strain ATCC 42720)", + description="Clavispora lusitaniae (strain ATCC 42720) - Proteome: UP000007703", + meaning=NCBITAXON["306902"]) + SP_CLOBH = PermissibleValue( + text="SP_CLOBH", + title="Clostridium botulinum", + description="Clostridium botulinum (firmicutes bacteria) - Proteome: UP000001986", + meaning=NCBITAXON["441771"]) + SP_COXBU = PermissibleValue( + text="SP_COXBU", + title="Coxiella burnetii", + description="Coxiella burnetii (gammaproteobacteria) - Proteome: UP000002671", + meaning=NCBITAXON["227377"]) + SP_CRYD1 = PermissibleValue( + text="SP_CRYD1", + title="Cryptococcus neoformans var. neoformans serotype D (Filobasidiella neoformans)", + description="""Cryptococcus neoformans var. neoformans serotype D (Filobasidiella neoformans) (C. neoformans) - Proteome: UP000002149""", + meaning=NCBITAXON["214684"]) SP_DANRE = PermissibleValue( text="SP_DANRE", title="Danio rerio", description="Danio rerio (Zebrafish) - Proteome: UP000000437", meaning=NCBITAXON["7955"]) + SP_DAPPU = PermissibleValue( + text="SP_DAPPU", + title="Daphnia pulex", + description="Daphnia pulex (Water flea) - Proteome: UP000000305", + meaning=NCBITAXON["6669"]) + SP_DEBHA = PermissibleValue( + text="SP_DEBHA", + title="Debaryomyces hansenii (strain ATCC 36239 / CBS 767 / BCRC 21394 / JCM 1990 / NBRC 0083 / IGC 2968) (Torulaspora hansenii)", + description="""Debaryomyces hansenii (strain ATCC 36239 / CBS 767 / BCRC 21394 / JCM 1990 / NBRC 0083 / IGC 2968) (Torulaspora hansenii) - Proteome: UP000000599""", + meaning=NCBITAXON["284592"]) + SP_DEIRA = PermissibleValue( + text="SP_DEIRA", + title="Deinococcus radiodurans", + description="Deinococcus radiodurans (deinococcus bacteria) - Proteome: UP000002524", + meaning=NCBITAXON["243230"]) + SP_DICDI = PermissibleValue( + text="SP_DICDI", + title="Dictyostelium discoideum", + description="Dictyostelium discoideum (Social amoeba) - Proteome: UP000002195", + meaning=NCBITAXON["44689"]) + SP_DICPU = PermissibleValue( + text="SP_DICPU", + title="Dictyostelium purpureum", + description="Dictyostelium purpureum (Slime mold) - Proteome: UP000001064", + meaning=NCBITAXON["5786"]) + SP_DICTD = PermissibleValue( + text="SP_DICTD", + title="Dictyoglomus turgidum", + description="Dictyoglomus turgidum (dictyoglomi bacteria) - Proteome: UP000007719", + meaning=NCBITAXON["515635"]) SP_DROME = PermissibleValue( text="SP_DROME", title="Drosophila melanogaster", @@ -16326,28 +16671,218 @@ class UniProtSpeciesCode(EnumDefinitionImpl): SP_ECOLI = PermissibleValue( text="SP_ECOLI", title="Escherichia coli K-12", - description="Escherichia coli K-12 - Proteome: UP000000625", + description="Escherichia coli K-12 (E. coli) - Proteome: UP000000625", meaning=NCBITAXON["83333"]) + SP_EMENI = PermissibleValue( + text="SP_EMENI", + title="Emericella nidulans", + description="Emericella nidulans (ascomycote fungus) - Proteome: UP000000560", + meaning=NCBITAXON["227321"]) + SP_ENTCA = PermissibleValue( + text="SP_ENTCA", + title="Enterococcus casseliflavus EC20", + description="Enterococcus casseliflavus EC20 - Proteome: UP000012675", + meaning=NCBITAXON["565655"]) + SP_ENTFA = PermissibleValue( + text="SP_ENTFA", + title="Enterococcus faecalis (strain ATCC 700802 / V583)", + description="Enterococcus faecalis (strain ATCC 700802 / V583) - Proteome: UP000001415", + meaning=NCBITAXON["226185"]) + SP_ENTGA = PermissibleValue( + text="SP_ENTGA", + title="Enterococcus gallinarum", + description="Enterococcus gallinarum - Proteome: UP000254807", + meaning=NCBITAXON["1353"]) + SP_ENTH1 = PermissibleValue( + text="SP_ENTH1", + title="Entamoeba histolytica", + description="Entamoeba histolytica (amoeba) - Proteome: UP000001926", + meaning=NCBITAXON["294381"]) + SP_EREGS = PermissibleValue( + text="SP_EREGS", + title="Eremothecium gossypii", + description="Eremothecium gossypii (Yeast) - Proteome: UP000000591", + meaning=NCBITAXON["284811"]) SP_FELCA = PermissibleValue( text="SP_FELCA", title="Felis catus", description="Felis catus (Cat) - Proteome: UP000011712", meaning=NCBITAXON["9685"]) + SP_FMDVO = PermissibleValue( + text="SP_FMDVO", + title="Foot-and-mouth disease virus serotype O (FMDV)", + description="Foot-and-mouth disease virus serotype O (FMDV) (FMDV) - Proteome: UP000008765", + meaning=NCBITAXON["12118"]) + SP_FUSNN = PermissibleValue( + text="SP_FUSNN", + title="Fusobacterium nucleatum (strain ATCC 25586)", + description="Fusobacterium nucleatum (strain ATCC 25586) (F. nucleatum ATCC 25586) - Proteome: UP000241660", + meaning=NCBITAXON["190304"]) + SP_GEOSL = PermissibleValue( + text="SP_GEOSL", + title="Geobacter sulfurreducens", + description="Geobacter sulfurreducens (deltaproteobacteria) - Proteome: UP000000577", + meaning=NCBITAXON["243231"]) + SP_GIAIC = PermissibleValue( + text="SP_GIAIC", + title="Giardia intestinalis", + description="Giardia intestinalis (giardia) - Proteome: UP000001548", + meaning=NCBITAXON["184922"]) + SP_GLOVI = PermissibleValue( + text="SP_GLOVI", + title="Gloeobacter violaceus", + description="Gloeobacter violaceus (cyanobacteria) - Proteome: UP000000557", + meaning=NCBITAXON["251221"]) SP_GORGO = PermissibleValue( text="SP_GORGO", title="Gorilla gorilla gorilla", description="Gorilla gorilla gorilla (Western lowland gorilla) - Proteome: UP000001519", meaning=NCBITAXON["9593"]) + SP_GOSHI = PermissibleValue( + text="SP_GOSHI", + title="Gossypium hirsutum", + description="Gossypium hirsutum (Upland cotton) - Proteome: UP000189702", + meaning=NCBITAXON["3635"]) + SP_HAEIN = PermissibleValue( + text="SP_HAEIN", + title="Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)", + description="""Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) (H. influenzae strain ATCC 51907) - Proteome: UP000000579""", + meaning=NCBITAXON["71421"]) + SP_HALH5 = PermissibleValue( + text="SP_HALH5", + title="Halalkalibacterium halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125) (Bacillus halodurans)", + description="""Halalkalibacterium halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125) (Bacillus halodurans) - Proteome: UP000001258""", + meaning=NCBITAXON["272558"]) + SP_HALSA = PermissibleValue( + text="SP_HALSA", + title="Halobacterium salinarum", + description="Halobacterium salinarum (euryarchaea) - Proteome: UP000000554", + meaning=NCBITAXON["64091"]) + SP_HBVCJ = PermissibleValue( + text="SP_HBVCJ", + title="Hepatitis B virus genotype C subtype ayr (isolate Human/Japan/Okamoto/-)", + description="""Hepatitis B virus genotype C subtype ayr (isolate Human/Japan/Okamoto/-) (HBV-C) - Proteome: UP000008591""", + meaning=NCBITAXON["928302"]) + SP_HCMVA = PermissibleValue( + text="SP_HCMVA", + title="Human cytomegalovirus (strain AD169)", + description="Human cytomegalovirus (strain AD169) (Human herpesvirus 5 (HHV-5)) - Proteome: UP000008992", + meaning=NCBITAXON["10360"]) + SP_HCMVM = PermissibleValue( + text="SP_HCMVM", + title="Human cytomegalovirus (Human herpesvirus 5) strain Merlin", + description="""Human cytomegalovirus (Human herpesvirus 5) strain Merlin (HHV-5 Merlin) - Proteome: UP000000938""", + meaning=NCBITAXON["295027"]) + SP_HCV77 = PermissibleValue( + text="SP_HCV77", + title="Hepatitis C virus genotype 1a (isolate H77)", + description="Hepatitis C virus genotype 1a (isolate H77) (HCV) - Proteome: UP000000518", + meaning=NCBITAXON["63746"]) + SP_HELAN = PermissibleValue( + text="SP_HELAN", + title="Helianthus annuus", + description="Helianthus annuus (Common sunflower) - Proteome: UP000215914", + meaning=NCBITAXON["4232"]) + SP_HELPY = PermissibleValue( + text="SP_HELPY", + title="Helicobacter pylori (Campylobacter pylori) strain ATCC 700392 / 26695", + description="""Helicobacter pylori (Campylobacter pylori) strain ATCC 700392 / 26695 (H. pylori) - Proteome: UP000000429""", + meaning=NCBITAXON["85962"]) + SP_HELRO = PermissibleValue( + text="SP_HELRO", + title="Helobdella robusta", + description="Helobdella robusta (Californian leech) - Proteome: UP000015101", + meaning=NCBITAXON["6412"]) + SP_HHV11 = PermissibleValue( + text="SP_HHV11", + title="Human herpesvirus 1 (strain 17)", + description="Human herpesvirus 1 (strain 17) (Human herpes simplex virus 1 (HHV-1)) - Proteome: UP000009294", + meaning=NCBITAXON["10299"]) SP_HORSE = PermissibleValue( text="SP_HORSE", title="Equus caballus", description="Equus caballus (Horse) - Proteome: UP000002281", meaning=NCBITAXON["9796"]) + SP_HORVV = PermissibleValue( + text="SP_HORVV", + title="Hordeum vulgare subsp. vulgare", + description="Hordeum vulgare subsp. vulgare (Domesticated barley) - Proteome: UP000011116", + meaning=NCBITAXON["112509"]) + SP_HPV16 = PermissibleValue( + text="SP_HPV16", + title="Human papillomavirus type 16", + description="Human papillomavirus type 16 - Proteome: UP000009251", + meaning=NCBITAXON["333760"]) SP_HUMAN = PermissibleValue( text="SP_HUMAN", title="Homo sapiens", description="Homo sapiens (Human) - Proteome: UP000005640", meaning=NCBITAXON["9606"]) + SP_HV1AN = PermissibleValue( + text="SP_HV1AN", + title="Human immunodeficiency virus type 1 group O (isolate ANT70)", + description="Human immunodeficiency virus type 1 group O (isolate ANT70) - Proteome: UP000007689", + meaning=NCBITAXON["327105"]) + SP_IXOSC = PermissibleValue( + text="SP_IXOSC", + title="Ixodes scapularis", + description="Ixodes scapularis (Deer tick) - Proteome: UP000001555", + meaning=NCBITAXON["6945"]) + SP_JUGRE = PermissibleValue( + text="SP_JUGRE", + title="Juglans regia", + description="Juglans regia (English walnut) - Proteome: UP000235220", + meaning=NCBITAXON["51240"]) + SP_KLENI = PermissibleValue( + text="SP_KLENI", + title="Klebsormidium nitens", + description="Klebsormidium nitens (Green alga) - Proteome: UP000054558", + meaning=NCBITAXON["105231"]) + SP_KLEPH = PermissibleValue( + text="SP_KLEPH", + title="Klebsiella pneumoniae subsp. pneumoniae (strain HS11286)", + description="Klebsiella pneumoniae subsp. pneumoniae (strain HS11286) - Proteome: UP000007841", + meaning=NCBITAXON["1125630"]) + SP_KLEPO = PermissibleValue( + text="SP_KLEPO", + title="Klebsiella pneumoniae subsp. ozaenae (subspecies)", + description="Klebsiella pneumoniae subsp. ozaenae (subspecies) - Proteome: UP000255382", + meaning=NCBITAXON["574"]) + SP_KORCO = PermissibleValue( + text="SP_KORCO", + title="Korarchaeum cryptofilum", + description="Korarchaeum cryptofilum (candidatus archaea) - Proteome: UP000001686", + meaning=NCBITAXON["374847"]) + SP_LACSA = PermissibleValue( + text="SP_LACSA", + title="Lactuca sativa", + description="Lactuca sativa (Garden lettuce) - Proteome: UP000235145", + meaning=NCBITAXON["4236"]) + SP_LEIMA = PermissibleValue( + text="SP_LEIMA", + title="Leishmania major strain Friedlin", + description="Leishmania major strain Friedlin (leishmania) - Proteome: UP000000542", + meaning=NCBITAXON["347515"]) + SP_LEPIN = PermissibleValue( + text="SP_LEPIN", + title="Leptospira interrogans", + description="Leptospira interrogans (spirochaetes bacteria) - Proteome: UP000001408", + meaning=NCBITAXON["189518"]) + SP_LEPOC = PermissibleValue( + text="SP_LEPOC", + title="Lepisosteus oculatus", + description="Lepisosteus oculatus (Spotted gar) - Proteome: UP000018468", + meaning=NCBITAXON["7918"]) + SP_LISMO = PermissibleValue( + text="SP_LISMO", + title="Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)", + description="Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) - Proteome: UP000000817", + meaning=NCBITAXON["169963"]) + SP_LODEL = PermissibleValue( + text="SP_LODEL", + title="Lodderomyces elongisporus (strain ATCC 11503 / CBS 2605 / JCM 1781 / NBRC 1676 / NRRL YB-4239) (Saccharomyces elongisporus)", + description="""Lodderomyces elongisporus (strain ATCC 11503 / CBS 2605 / JCM 1781 / NBRC 1676 / NRRL YB-4239) (Saccharomyces elongisporus) - Proteome: UP000001996""", + meaning=NCBITAXON["379508"]) SP_MACMU = PermissibleValue( text="SP_MACMU", title="Macaca mulatta", @@ -16358,11 +16893,116 @@ class UniProtSpeciesCode(EnumDefinitionImpl): title="Zea mays", description="Zea mays (Maize) - Proteome: UP000007305", meaning=NCBITAXON["4577"]) + SP_MANES = PermissibleValue( + text="SP_MANES", + title="Manihot esculenta", + description="Manihot esculenta (Cassava) - Proteome: UP000091857", + meaning=NCBITAXON["3983"]) + SP_MARPO = PermissibleValue( + text="SP_MARPO", + title="Marchantia polymorpha", + description="Marchantia polymorpha (Common liverwort) - Proteome: UP000244005", + meaning=NCBITAXON["3197"]) + SP_MEASC = PermissibleValue( + text="SP_MEASC", + title="Measles virus (Subacute sclerose panencephalitis virus) strain Ichinose-B95a", + description="""Measles virus (Subacute sclerose panencephalitis virus) strain Ichinose-B95a (MeV strain Ichinose-B95a) - Proteome: UP000008699""", + meaning=NCBITAXON["645098"]) + SP_MEDTR = PermissibleValue( + text="SP_MEDTR", + title="Medicago truncatula", + description="Medicago truncatula (Barrel medic) - Proteome: UP000002051", + meaning=NCBITAXON["3880"]) + SP_METAC = PermissibleValue( + text="SP_METAC", + title="Methanosarcina acetivorans", + description="Methanosarcina acetivorans (euryarchaea) - Proteome: UP000002487", + meaning=NCBITAXON["188937"]) + SP_METJA = PermissibleValue( + text="SP_METJA", + title="Methanocaldococcus jannaschii", + description="Methanocaldococcus jannaschii (methanococci archaea) - Proteome: UP000000805", + meaning=NCBITAXON["243232"]) + SP_MONBE = PermissibleValue( + text="SP_MONBE", + title="Monosiga brevicollis", + description="Monosiga brevicollis (sponge) - Proteome: UP000001357", + meaning=NCBITAXON["81824"]) + SP_MONDO = PermissibleValue( + text="SP_MONDO", + title="Monodelphis domestica", + description="Monodelphis domestica (Gray short-tailed opossum) - Proteome: UP000002280", + meaning=NCBITAXON["13616"]) SP_MOUSE = PermissibleValue( text="SP_MOUSE", title="Mus musculus", description="Mus musculus (Mouse) - Proteome: UP000000589", meaning=NCBITAXON["10090"]) + SP_MYCGE = PermissibleValue( + text="SP_MYCGE", + title="Mycoplasma genitalium", + description="Mycoplasma genitalium (mollicutes bacteria) - Proteome: UP000000807", + meaning=NCBITAXON["243273"]) + SP_MYCMD = PermissibleValue( + text="SP_MYCMD", + title="Mycosarcoma maydis (Ustilago maydis)", + description="Mycosarcoma maydis (Ustilago maydis) (Corn smut fungus) - Proteome: UP000000561", + meaning=NCBITAXON["5270"]) + SP_MYCPN = PermissibleValue( + text="SP_MYCPN", + title="Mycoplasma pneumoniae strain ATCC 29342 / M129 / Subtype 1", + description="Mycoplasma pneumoniae strain ATCC 29342 / M129 / Subtype 1 - Proteome: UP000000808", + meaning=NCBITAXON["272634"]) + SP_MYCTA = PermissibleValue( + text="SP_MYCTA", + title="Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra)", + description="Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra) - Proteome: UP000001988", + meaning=NCBITAXON["419947"]) + SP_MYCTU = PermissibleValue( + text="SP_MYCTU", + title="Mycobacterium tuberculosis H37Rv", + description="Mycobacterium tuberculosis H37Rv (actinobacteria) - Proteome: UP000001584", + meaning=NCBITAXON["83332"]) + SP_NEIMB = PermissibleValue( + text="SP_NEIMB", + title="Neisseria meningitidis serogroup B (strain ATCC BAA-335 / MC58)", + description="""Neisseria meningitidis serogroup B (strain ATCC BAA-335 / MC58) (betaproteobacteria) - Proteome: UP000000425""", + meaning=NCBITAXON["122586"]) + SP_NEIME = PermissibleValue( + text="SP_NEIME", + title="Neisseria meningitidis MC58", + description="Neisseria meningitidis MC58 - Proteome: UP000000425", + meaning=NCBITAXON["122586"]) + SP_NELNU = PermissibleValue( + text="SP_NELNU", + title="Nelumbo nucifera", + description="Nelumbo nucifera (Sacred lotus) - Proteome: UP000189703", + meaning=NCBITAXON["4432"]) + SP_NEMVE = PermissibleValue( + text="SP_NEMVE", + title="Nematostella vectensis", + description="Nematostella vectensis (Starlet sea anemone) - Proteome: UP000001593", + meaning=NCBITAXON["45351"]) + SP_NEUCR = PermissibleValue( + text="SP_NEUCR", + title="Neurospora crassa", + description="Neurospora crassa (ascomycote fungus) - Proteome: UP000001805", + meaning=NCBITAXON["367110"]) + SP_NITMS = PermissibleValue( + text="SP_NITMS", + title="Nitrosopumilus maritimus", + description="Nitrosopumilus maritimus (thaumarchaea) - Proteome: UP000000792", + meaning=NCBITAXON["436308"]) + SP_ORNAN = PermissibleValue( + text="SP_ORNAN", + title="Ornithorhynchus anatinus", + description="Ornithorhynchus anatinus (Duckbill platypus) - Proteome: UP000002279", + meaning=NCBITAXON["9258"]) + SP_ORYLA = PermissibleValue( + text="SP_ORYLA", + title="Oryzias latipes", + description="Oryzias latipes (Japanese rice fish) - Proteome: UP000001038", + meaning=NCBITAXON["8090"]) SP_ORYSJ = PermissibleValue( text="SP_ORYSJ", title="Oryza sativa subsp. japonica", @@ -16373,11 +17013,76 @@ class UniProtSpeciesCode(EnumDefinitionImpl): title="Pan troglodytes", description="Pan troglodytes (Chimpanzee) - Proteome: UP000002277", meaning=NCBITAXON["9598"]) + SP_PARTE = PermissibleValue( + text="SP_PARTE", + title="Paramecium tetraurelia", + description="Paramecium tetraurelia (alveolate) - Proteome: UP000000600", + meaning=NCBITAXON["5888"]) + SP_PEA = PermissibleValue( + text="SP_PEA", + title="Pisum sativum", + description="Pisum sativum (Garden pea) - Proteome: UP001058974", + meaning=NCBITAXON["3888"]) + SP_PHANO = PermissibleValue( + text="SP_PHANO", + title="Phaeosphaeria nodorum", + description="Phaeosphaeria nodorum (Glume blotch fungus) - Proteome: UP000663193", + meaning=NCBITAXON["321614"]) + SP_PHYPA = PermissibleValue( + text="SP_PHYPA", + title="Physcomitrella patens", + description="Physcomitrella patens (Spreading-leaved earth moss) - Proteome: UP000006727", + meaning=NCBITAXON["3218"]) + SP_PHYRM = PermissibleValue( + text="SP_PHYRM", + title="Phytophthora ramorum", + description="Phytophthora ramorum (Sudden oak death agent) - Proteome: UP000005238", + meaning=NCBITAXON["164328"]) + SP_PICGU = PermissibleValue( + text="SP_PICGU", + title="Meyerozyma guilliermondii (strain ATCC 6260 / CBS 566 / DSM 6381 / JCM 1539 / NBRC 10279 / NRRL Y-324) (Candida guilliermondii)", + description="""Meyerozyma guilliermondii (strain ATCC 6260 / CBS 566 / DSM 6381 / JCM 1539 / NBRC 10279 / NRRL Y-324) (Candida guilliermondii) - Proteome: UP000001997""", + meaning=NCBITAXON["294746"]) SP_PIG = PermissibleValue( text="SP_PIG", title="Sus scrofa", description="Sus scrofa (Pig) - Proteome: UP000008227", meaning=NCBITAXON["9823"]) + SP_PLAF7 = PermissibleValue( + text="SP_PLAF7", + title="Plasmodium falciparum 3D7", + description="Plasmodium falciparum 3D7 (Malaria parasite) - Proteome: UP000001450", + meaning=NCBITAXON["36329"]) + SP_POPTR = PermissibleValue( + text="SP_POPTR", + title="Populus trichocarpa", + description="Populus trichocarpa (Western balsam poplar) - Proteome: UP000006729", + meaning=NCBITAXON["3694"]) + SP_PRIPA = PermissibleValue( + text="SP_PRIPA", + title="Pristionchus pacificus", + description="Pristionchus pacificus (Parasitic nematode) - Proteome: UP000005239", + meaning=NCBITAXON["54126"]) + SP_PRUPE = PermissibleValue( + text="SP_PRUPE", + title="Prunus persica", + description="Prunus persica (Peach) - Proteome: UP000006882", + meaning=NCBITAXON["3760"]) + SP_PSEAE = PermissibleValue( + text="SP_PSEAE", + title="Pseudomonas aeruginosa PAO1", + description="Pseudomonas aeruginosa PAO1 (gammaproteobacteria) - Proteome: UP000002438", + meaning=NCBITAXON["208964"]) + SP_PUCGT = PermissibleValue( + text="SP_PUCGT", + title="Puccinia graminis", + description="Puccinia graminis (Black stem rust fungus) - Proteome: UP000008783", + meaning=NCBITAXON["418459"]) + SP_PYRAE = PermissibleValue( + text="SP_PYRAE", + title="Pyrobaculum aerophilum", + description="Pyrobaculum aerophilum (crenarchaea) - Proteome: UP000002439", + meaning=NCBITAXON["178306"]) SP_RABIT = PermissibleValue( text="SP_RABIT", title="Oryctolagus cuniculus", @@ -16388,117 +17093,256 @@ class UniProtSpeciesCode(EnumDefinitionImpl): title="Rattus norvegicus", description="Rattus norvegicus (Rat) - Proteome: UP000002494", meaning=NCBITAXON["10116"]) + SP_RHOBA = PermissibleValue( + text="SP_RHOBA", + title="Rhodopirellula baltica", + description="Rhodopirellula baltica (planctomycetes bacteria) - Proteome: UP000001025", + meaning=NCBITAXON["243090"]) + SP_SACS2 = PermissibleValue( + text="SP_SACS2", + title="Sulfolobus solfataricus", + description="Sulfolobus solfataricus (crenarchaea) - Proteome: UP000001974", + meaning=NCBITAXON["273057"]) + SP_SALTY = PermissibleValue( + text="SP_SALTY", + title="Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)", + description="""Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (S. typhimurium LT2) - Proteome: UP000001014""", + meaning=NCBITAXON["99287"]) + SP_SCHJY = PermissibleValue( + text="SP_SCHJY", + title="Schizosaccharomyces japonicus", + description="Schizosaccharomyces japonicus (Fission yeast) - Proteome: UP000001744", + meaning=NCBITAXON["402676"]) SP_SCHPO = PermissibleValue( text="SP_SCHPO", title="Schizosaccharomyces pombe 972h-", description="Schizosaccharomyces pombe 972h- (Fission yeast) - Proteome: UP000002485", meaning=NCBITAXON["284812"]) + SP_SCLS1 = PermissibleValue( + text="SP_SCLS1", + title="Sclerotinia sclerotiorum", + description="Sclerotinia sclerotiorum (White mold) - Proteome: UP000001312", + meaning=NCBITAXON["665079"]) SP_SHEEP = PermissibleValue( text="SP_SHEEP", title="Ovis aries", description="Ovis aries (Sheep) - Proteome: UP000002356", meaning=NCBITAXON["9940"]) - SP_XENLA = PermissibleValue( - text="SP_XENLA", - title="Xenopus laevis", - description="Xenopus laevis (African clawed frog) - Proteome: UP000186698", - meaning=NCBITAXON["8355"]) - SP_XENTR = PermissibleValue( - text="SP_XENTR", - title="Xenopus tropicalis", - description="Xenopus tropicalis (Western clawed frog) - Proteome: UP000008143", - meaning=NCBITAXON["8364"]) - SP_YEAST = PermissibleValue( - text="SP_YEAST", - title="Saccharomyces cerevisiae S288C", - description="Saccharomyces cerevisiae S288C (Baker's yeast) - Proteome: UP000002311", - meaning=NCBITAXON["559292"]) - SP_DICDI = PermissibleValue( - text="SP_DICDI", - title="Dictyostelium discoideum", - description="Dictyostelium discoideum (Slime mold) - Proteome: UP000002195", - meaning=NCBITAXON["44689"]) - SP_HELPY = PermissibleValue( - text="SP_HELPY", - title="Helicobacter pylori 26695", - description="Helicobacter pylori 26695 - Proteome: UP000000429", - meaning=NCBITAXON["85962"]) - SP_LEIMA = PermissibleValue( - text="SP_LEIMA", - title="Leishmania major strain Friedlin", - description="Leishmania major strain Friedlin", - meaning=NCBITAXON["347515"]) - SP_MEDTR = PermissibleValue( - text="SP_MEDTR", - title="Medicago truncatula", - description="Medicago truncatula (Barrel medic) - Proteome: UP000002051", - meaning=NCBITAXON["3880"]) - SP_MYCTU = PermissibleValue( - text="SP_MYCTU", - title="Mycobacterium tuberculosis H37Rv", - description="Mycobacterium tuberculosis H37Rv - Proteome: UP000001584", - meaning=NCBITAXON["83332"]) - SP_NEIME = PermissibleValue( - text="SP_NEIME", - title="Neisseria meningitidis MC58", - description="Neisseria meningitidis MC58 - Proteome: UP000000425", - meaning=NCBITAXON["122586"]) - SP_PLAF7 = PermissibleValue( - text="SP_PLAF7", - title="Plasmodium falciparum 3D7", - description="Plasmodium falciparum 3D7 (Malaria parasite) - Proteome: UP000001450", - meaning=NCBITAXON["36329"]) - SP_PSEAE = PermissibleValue( - text="SP_PSEAE", - title="Pseudomonas aeruginosa PAO1", - description="Pseudomonas aeruginosa PAO1 - Proteome: UP000002438", - meaning=NCBITAXON["208964"]) + SP_SHEON = PermissibleValue( + text="SP_SHEON", + title="Shewanella oneidensis", + description="Shewanella oneidensis (shewanella) - Proteome: UP000008186", + meaning=NCBITAXON["211586"]) + SP_SHIFL = PermissibleValue( + text="SP_SHIFL", + title="Shigella flexneri", + description="Shigella flexneri - Proteome: UP000001006", + meaning=NCBITAXON["623"]) + SP_SOLLC = PermissibleValue( + text="SP_SOLLC", + title="Solanum lycopersicum", + description="Solanum lycopersicum (Tomato) - Proteome: UP000004994", + meaning=NCBITAXON["4081"]) + SP_SORBI = PermissibleValue( + text="SP_SORBI", + title="Sorghum bicolor", + description="Sorghum bicolor (Sorghum) - Proteome: UP000000768", + meaning=NCBITAXON["4558"]) SP_SOYBN = PermissibleValue( text="SP_SOYBN", title="Glycine max", description="Glycine max (Soybean) - Proteome: UP000008827", meaning=NCBITAXON["3847"]) + SP_SPIOL = PermissibleValue( + text="SP_SPIOL", + title="Spinacia oleracea", + description="Spinacia oleracea (Spinach) - Proteome: UP001155700", + meaning=NCBITAXON["3562"]) + SP_STAA8 = PermissibleValue( + text="SP_STAA8", + title="Staphylococcus aureus (strain NCTC 8325 / PS 47)", + description="Staphylococcus aureus (strain NCTC 8325 / PS 47) (S. aureus NCTC 8325) - Proteome: UP000008816", + meaning=NCBITAXON["93061"]) SP_STAAU = PermissibleValue( text="SP_STAAU", title="Staphylococcus aureus subsp. aureus NCTC 8325", description="Staphylococcus aureus subsp. aureus NCTC 8325 - Proteome: UP000008816", meaning=NCBITAXON["93061"]) + SP_STRCL = PermissibleValue( + text="SP_STRCL", + title="Streptomyces clavuligerus", + description="Streptomyces clavuligerus - Proteome: UP000002357", + meaning=NCBITAXON["1901"]) + SP_STRCO = PermissibleValue( + text="SP_STRCO", + title="Streptomyces coelicolor", + description="Streptomyces coelicolor (actinobacteria) - Proteome: UP000001973", + meaning=NCBITAXON["100226"]) + SP_STRP1 = PermissibleValue( + text="SP_STRP1", + title="Streptococcus pyogenes serotype M1 (Strain: ATCC 700294 / SF370 / Serotype M1)", + description="""Streptococcus pyogenes serotype M1 (Strain: ATCC 700294 / SF370 / Serotype M1) - Proteome: UP000000750""", + meaning=NCBITAXON["301447"]) + SP_STRP2 = PermissibleValue( + text="SP_STRP2", + title="Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466)", + description="Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) - Proteome: UP000001452", + meaning=NCBITAXON["373153"]) SP_STRPN = PermissibleValue( text="SP_STRPN", - title="Streptococcus pneumoniae R6", - description="Streptococcus pneumoniae R6 - Proteome: UP000000586", + title="Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)", + description="Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4) - Proteome: UP000000586", meaning=NCBITAXON["171101"]) + SP_STRPU = PermissibleValue( + text="SP_STRPU", + title="Strongylocentrotus purpuratus", + description="Strongylocentrotus purpuratus (Purple sea urchin) - Proteome: UP000007110", + meaning=NCBITAXON["7668"]) + SP_STRR6 = PermissibleValue( + text="SP_STRR6", + title="Streptococcus pneumoniae", + description="Streptococcus pneumoniae (strep) - Proteome: UP000000586", + meaning=NCBITAXON["171101"]) + SP_SYNY3 = PermissibleValue( + text="SP_SYNY3", + title="Synechocystis sp.", + description="Synechocystis sp. (cyanobacteria) - Proteome: UP000001425", + meaning=NCBITAXON["1111708"]) + SP_THAPS = PermissibleValue( + text="SP_THAPS", + title="Thalassiosira pseudonana", + description="Thalassiosira pseudonana (Marine diatom) - Proteome: UP000001449", + meaning=NCBITAXON["35128"]) + SP_THECC = PermissibleValue( + text="SP_THECC", + title="Theobroma cacao", + description="Theobroma cacao (Cacao) - Proteome: UP000026915", + meaning=NCBITAXON["3641"]) + SP_THEKO = PermissibleValue( + text="SP_THEKO", + title="Thermococcus kodakaraensis", + description="Thermococcus kodakaraensis (euryarchaea) - Proteome: UP000000536", + meaning=NCBITAXON["69014"]) + SP_THEMA = PermissibleValue( + text="SP_THEMA", + title="Thermotoga maritima", + description="Thermotoga maritima (thermotogae bacteria) - Proteome: UP000008183", + meaning=NCBITAXON["243274"]) + SP_THEYD = PermissibleValue( + text="SP_THEYD", + title="Thermodesulfovibrio yellowstonii", + description="Thermodesulfovibrio yellowstonii (nitrospirae bacteria) - Proteome: UP000000718", + meaning=NCBITAXON["289376"]) + SP_TOBAC = PermissibleValue( + text="SP_TOBAC", + title="Nicotiana tabacum", + description="Nicotiana tabacum (Common tobacco) - Proteome: UP000084051", + meaning=NCBITAXON["4097"]) SP_TOXGO = PermissibleValue( text="SP_TOXGO", title="Toxoplasma gondii ME49", description="Toxoplasma gondii ME49 - Proteome: UP000001529", meaning=NCBITAXON["508771"]) + SP_TRIAD = PermissibleValue( + text="SP_TRIAD", + title="Trichoplax adhaerens", + description="Trichoplax adhaerens (placozoan) - Proteome: UP000009022", + meaning=NCBITAXON["10228"]) + SP_TRICA = PermissibleValue( + text="SP_TRICA", + title="Tribolium castaneum", + description="Tribolium castaneum (Red flour beetle) - Proteome: UP000007266", + meaning=NCBITAXON["7070"]) + SP_TRIV3 = PermissibleValue( + text="SP_TRIV3", + title="Trichomonas vaginalis", + description="Trichomonas vaginalis (excavate) - Proteome: UP000001542", + meaning=NCBITAXON["412133"]) SP_TRYB2 = PermissibleValue( text="SP_TRYB2", title="Trypanosoma brucei brucei TREU927", - description="Trypanosoma brucei brucei TREU927 - Proteome: UP000008524", + description="Trypanosoma brucei brucei TREU927 (excavate) - Proteome: UP000008524", meaning=NCBITAXON["185431"]) + SP_VACCW = PermissibleValue( + text="SP_VACCW", + title="Vaccinia virus (strain Western Reserve)", + description="Vaccinia virus (strain Western Reserve) (VACV strain WR) - Proteome: UP000000344", + meaning=NCBITAXON["10254"]) + SP_VAR67 = PermissibleValue( + text="SP_VAR67", + title="Variola virus (Smallpox virus) (isolate Human/India/Ind3/1967)", + description="Variola virus (Smallpox virus) (isolate Human/India/Ind3/1967) (VARV) - Proteome: UP000002060", + meaning=NCBITAXON["587200"]) + SP_VIBCH = PermissibleValue( + text="SP_VIBCH", + title="Vibrio cholerae", + description="Vibrio cholerae (cholera) - Proteome: UP000000584", + meaning=NCBITAXON["243277"]) + SP_VITVI = PermissibleValue( + text="SP_VITVI", + title="Vitis vinifera", + description="Vitis vinifera (Grape) - Proteome: UP000009183", + meaning=NCBITAXON["29760"]) + SP_VZVD = PermissibleValue( + text="SP_VZVD", + title="Varicella-zoster virus (Human herpesvirus 3) strain Dumas", + description="""Varicella-zoster virus (Human herpesvirus 3) strain Dumas (HHV-3 strain Dumas) - Proteome: UP000002602""", + meaning=NCBITAXON["10338"]) SP_WHEAT = PermissibleValue( text="SP_WHEAT", title="Triticum aestivum", description="Triticum aestivum (Wheat) - Proteome: UP000019116", meaning=NCBITAXON["4565"]) - SP_PEA = PermissibleValue( - text="SP_PEA", - title="Pisum sativum", - description="Pisum sativum (Garden pea) - Proteome: UP001058974", - meaning=NCBITAXON["3888"]) - SP_TOBAC = PermissibleValue( - text="SP_TOBAC", - title="Nicotiana tabacum", - description="Nicotiana tabacum (Common tobacco) - Proteome: UP000084051", - meaning=NCBITAXON["4097"]) + SP_XANCP = PermissibleValue( + text="SP_XANCP", + title="Xanthomonas campestris", + description="Xanthomonas campestris (xanthomonas) - Proteome: UP000001010", + meaning=NCBITAXON["190485"]) + SP_XENLA = PermissibleValue( + text="SP_XENLA", + title="Xenopus laevis", + description="Xenopus laevis (African clawed frog) - Proteome: UP000186698", + meaning=NCBITAXON["8355"]) + SP_XENTR = PermissibleValue( + text="SP_XENTR", + title="Xenopus tropicalis", + description="Xenopus tropicalis (Western clawed frog) - Proteome: UP000008143", + meaning=NCBITAXON["8364"]) + SP_YARLI = PermissibleValue( + text="SP_YARLI", + title="Yarrowia lipolytica", + description="Yarrowia lipolytica (Yeast) - Proteome: UP000001300", + meaning=NCBITAXON["284591"]) + SP_YEAST = PermissibleValue( + text="SP_YEAST", + title="Saccharomyces cerevisiae S288C", + description="Saccharomyces cerevisiae S288C (Baker's yeast) - Proteome: UP000002311", + meaning=NCBITAXON["559292"]) + SP_YERPE = PermissibleValue( + text="SP_YERPE", + title="Yersinia pestis", + description="Yersinia pestis (plague bacteria) - Proteome: UP000000815", + meaning=NCBITAXON["632"]) + SP_ZIKV = PermissibleValue( + text="SP_ZIKV", + title="Zika virus", + description="Zika virus (ZIKV) - Proteome: UP000054557", + meaning=NCBITAXON["64320"]) _defn = EnumDefinition( name="UniProtSpeciesCode", description="UniProt species mnemonic codes for reference proteomes with associated metadata", ) + @classmethod + def _addvals(cls): + setattr(cls, "SP_E. coli ECO57", + PermissibleValue( + text="SP_E. coli ECO57", + title="Escherichia coli O157:H7", + description="Escherichia coli O157:H7 - Proteome: UP000000558", + meaning=NCBITAXON["83334"])) + class LipidCategory(EnumDefinitionImpl): """ Major categories of lipids based on SwissLipids classification @@ -19369,6 +20213,364 @@ class FMRIParadigmTypeEnum(EnumDefinitionImpl): description="fMRI experimental paradigm types", ) +class FamilyRelationship(EnumDefinitionImpl): + """ + Family relationships used in pedigree and family history documentation + """ + PARENT = PermissibleValue( + text="PARENT", + description="""The player of the role is one who begets, gives birth to, or nurtures and raises the scoping entity (child)""", + meaning=HL7["v3-RoleCode#PRN"]) + MOTHER = PermissibleValue( + text="MOTHER", + description="""The player of the role is a female who conceives, gives birth to, or raises and nurtures the scoping entity (child)""", + meaning=HL7["v3-RoleCode#MTH"]) + FATHER = PermissibleValue( + text="FATHER", + description="The player of the role is a male who begets or raises or nurtures the scoping entity (child)", + meaning=HL7["v3-RoleCode#FTH"]) + NATURAL_MOTHER = PermissibleValue( + text="NATURAL_MOTHER", + description="The player of the role is a female who conceives or gives birth to the scoping entity (child)", + meaning=HL7["v3-RoleCode#NMTH"]) + NATURAL_FATHER = PermissibleValue( + text="NATURAL_FATHER", + description="The player of the role is a male who begets the scoping entity (child)", + meaning=HL7["v3-RoleCode#NFTH"]) + ADOPTIVE_PARENT = PermissibleValue( + text="ADOPTIVE_PARENT", + description="""The player of the role (parent) has taken the scoper (child) into their family through legal means and raises them as his or her own child""", + meaning=HL7["v3-RoleCode#ADOPTP"]) + ADOPTIVE_MOTHER = PermissibleValue( + text="ADOPTIVE_MOTHER", + description="""The player of the role (mother) is a female who has taken the scoper (child) into their family through legal means and raises them as her own child""", + meaning=HL7["v3-RoleCode#ADOPTM"]) + ADOPTIVE_FATHER = PermissibleValue( + text="ADOPTIVE_FATHER", + description="""The player of the role (father) is a male who has taken the scoper (child) into their family through legal means and raises them as his own child""", + meaning=HL7["v3-RoleCode#ADOPTF"]) + STEP_PARENT = PermissibleValue( + text="STEP_PARENT", + description="""The player of the role is the spouse of the scoping person's parent and not the scoping person's natural parent""", + meaning=HL7["v3-RoleCode#STPPRN"]) + STEP_MOTHER = PermissibleValue( + text="STEP_MOTHER", + description="""The player of the role is the female spouse of the scoping person's parent and not the scoping person's natural mother""", + meaning=HL7["v3-RoleCode#STPMTH"]) + STEP_FATHER = PermissibleValue( + text="STEP_FATHER", + description="""The player of the role is the male spouse of the scoping person's parent and not the scoping person's natural father""", + meaning=HL7["v3-RoleCode#STPFTH"]) + FOSTER_PARENT = PermissibleValue( + text="FOSTER_PARENT", + description="""The player of the role (parent) who is a state-certified caregiver responsible for the scoper (child)""", + meaning=HL7["v3-RoleCode#PRNFOST"]) + GESTATIONAL_MOTHER = PermissibleValue( + text="GESTATIONAL_MOTHER", + description="The player is a female whose womb carries the fetus of the scoper", + meaning=HL7["v3-RoleCode#GESTM"]) + SIBLING = PermissibleValue( + text="SIBLING", + description="The player of the role shares one or both parents in common with the scoping entity", + meaning=HL7["v3-RoleCode#SIB"]) + BROTHER = PermissibleValue( + text="BROTHER", + description="The player of the role is a male sharing one or both parents with the scoping entity", + meaning=HL7["v3-RoleCode#BRO"]) + SISTER = PermissibleValue( + text="SISTER", + description="The player of the role is a female sharing one or both parents with the scoping entity", + meaning=HL7["v3-RoleCode#SIS"]) + NATURAL_BROTHER = PermissibleValue( + text="NATURAL_BROTHER", + description="""The player of the role is a male related to the scoping entity by sharing only the same natural parents""", + meaning=HL7["v3-RoleCode#NBRO"]) + NATURAL_SISTER = PermissibleValue( + text="NATURAL_SISTER", + description="""The player of the role is a female related to the scoping entity by sharing only the same natural parents""", + meaning=HL7["v3-RoleCode#NSIS"]) + HALF_BROTHER = PermissibleValue( + text="HALF_BROTHER", + description="""The player of the role is a male related to the scoping entity by sharing only one biological parent""", + meaning=HL7["v3-RoleCode#HBRO"]) + HALF_SISTER = PermissibleValue( + text="HALF_SISTER", + description="""The player of the role is a female related to the scoping entity by sharing only one biological parent""", + meaning=HL7["v3-RoleCode#HSIS"]) + STEP_BROTHER = PermissibleValue( + text="STEP_BROTHER", + description="The player of the role is a male child of the scoping person's stepparent", + meaning=HL7["v3-RoleCode#STPBRO"]) + STEP_SISTER = PermissibleValue( + text="STEP_SISTER", + description="The player of the role is a female child of the scoping person's stepparent", + meaning=HL7["v3-RoleCode#STPSIS"]) + TWIN = PermissibleValue( + text="TWIN", + description="The scoper and player were carried in the same womb and delivered in the same birth", + meaning=HL7["v3-RoleCode#TWIN"]) + TWIN_BROTHER = PermissibleValue( + text="TWIN_BROTHER", + description="The player of the role is a male born from the same pregnancy as the scoping entity", + meaning=HL7["v3-RoleCode#TWINBRO"]) + TWIN_SISTER = PermissibleValue( + text="TWIN_SISTER", + description="The player of the role is a female born from the same pregnancy as the scoping entity", + meaning=HL7["v3-RoleCode#TWINSIS"]) + FRATERNAL_TWIN = PermissibleValue( + text="FRATERNAL_TWIN", + description="""The player of the role is born from the same pregnancy as the scoping entity but does not share the same genotype""", + meaning=HL7["v3-RoleCode#FTWIN"]) + IDENTICAL_TWIN = PermissibleValue( + text="IDENTICAL_TWIN", + description="""The player of the role is born from the same pregnancy as the scoping entity and shares the same genotype""", + meaning=HL7["v3-RoleCode#ITWIN"]) + CHILD = PermissibleValue( + text="CHILD", + description="The player of the role is a child of the scoping entity", + meaning=HL7["v3-RoleCode#CHILD"]) + SON = PermissibleValue( + text="SON", + description="The player of the role is a male offspring of the scoping entity (parent)", + meaning=HL7["v3-RoleCode#SON"]) + DAUGHTER = PermissibleValue( + text="DAUGHTER", + description="The player of the role is a female offspring of the scoping entity (parent)", + meaning=HL7["v3-RoleCode#DAU"]) + NATURAL_CHILD = PermissibleValue( + text="NATURAL_CHILD", + description="The player of the role is an offspring of the scoping entity as determined by birth", + meaning=HL7["v3-RoleCode#NCHILD"]) + ADOPTIVE_CHILD = PermissibleValue( + text="ADOPTIVE_CHILD", + description="""The player of the role is a child taken into a family through legal means and raised by the scoping person (parent) as his or her own child""", + meaning=HL7["v3-RoleCode#CHLDADOPT"]) + FOSTER_CHILD = PermissibleValue( + text="FOSTER_CHILD", + description="""The player of the role is a child receiving parental care and nurture from the scoping person (parent) but not related to him or her through legal or blood relationship""", + meaning=HL7["v3-RoleCode#CHLDFOST"]) + STEP_CHILD = PermissibleValue( + text="STEP_CHILD", + description="The player of the role is a child of the scoping person's spouse by a previous union", + meaning=HL7["v3-RoleCode#STPCHLD"]) + GRANDPARENT = PermissibleValue( + text="GRANDPARENT", + description="The player of the role is a parent of the scoping person's mother or father", + meaning=HL7["v3-RoleCode#GRPRN"]) + GRANDMOTHER = PermissibleValue( + text="GRANDMOTHER", + description="The player of the role is the mother of the scoping person's mother or father", + meaning=HL7["v3-RoleCode#GRMTH"]) + GRANDFATHER = PermissibleValue( + text="GRANDFATHER", + description="The player of the role is the father of the scoping person's mother or father", + meaning=HL7["v3-RoleCode#GRFTH"]) + MATERNAL_GRANDMOTHER = PermissibleValue( + text="MATERNAL_GRANDMOTHER", + description="The player of the role is the mother of the scoping person's mother", + meaning=HL7["v3-RoleCode#MGRMTH"]) + MATERNAL_GRANDFATHER = PermissibleValue( + text="MATERNAL_GRANDFATHER", + description="The player of the role is the father of the scoping person's mother", + meaning=HL7["v3-RoleCode#MGRFTH"]) + PATERNAL_GRANDMOTHER = PermissibleValue( + text="PATERNAL_GRANDMOTHER", + description="The player of the role is the mother of the scoping person's father", + meaning=HL7["v3-RoleCode#PGRMTH"]) + PATERNAL_GRANDFATHER = PermissibleValue( + text="PATERNAL_GRANDFATHER", + description="The player of the role is the father of the scoping person's father", + meaning=HL7["v3-RoleCode#PGRFTH"]) + GRANDCHILD = PermissibleValue( + text="GRANDCHILD", + description="The player of the role is a child of the scoping person's son or daughter", + meaning=HL7["v3-RoleCode#GRNDCHILD"]) + GRANDSON = PermissibleValue( + text="GRANDSON", + description="The player of the role is a son of the scoping person's son or daughter", + meaning=HL7["v3-RoleCode#GRNDSN"]) + GRANDDAUGHTER = PermissibleValue( + text="GRANDDAUGHTER", + description="The player of the role is a daughter of the scoping person's son or daughter", + meaning=HL7["v3-RoleCode#GRNDDAU"]) + AUNT = PermissibleValue( + text="AUNT", + description="The player of the role is a sister of the scoping person's mother or father", + meaning=HL7["v3-RoleCode#AUNT"]) + UNCLE = PermissibleValue( + text="UNCLE", + description="The player of the role is a brother of the scoping person's mother or father", + meaning=HL7["v3-RoleCode#UNCLE"]) + MATERNAL_AUNT = PermissibleValue( + text="MATERNAL_AUNT", + description="The player of the role is a sister of the scoping person's mother", + meaning=HL7["v3-RoleCode#MAUNT"]) + MATERNAL_UNCLE = PermissibleValue( + text="MATERNAL_UNCLE", + description="The player of the role is a brother of the scoping person's mother", + meaning=HL7["v3-RoleCode#MUNCLE"]) + PATERNAL_AUNT = PermissibleValue( + text="PATERNAL_AUNT", + description="The player of the role is a sister of the scoping person's father", + meaning=HL7["v3-RoleCode#PAUNT"]) + PATERNAL_UNCLE = PermissibleValue( + text="PATERNAL_UNCLE", + description="The player of the role is a brother of the scoping person's father", + meaning=HL7["v3-RoleCode#PUNCLE"]) + COUSIN = PermissibleValue( + text="COUSIN", + description="""The player of the role is a relative descended from a common ancestor, such as a grandparent, by two or more steps in a diverging line""", + meaning=HL7["v3-RoleCode#COUSN"]) + MATERNAL_COUSIN = PermissibleValue( + text="MATERNAL_COUSIN", + description="The player of the role is a child of a maternal aunt or uncle of the scoping person", + meaning=HL7["v3-RoleCode#MCOUSN"]) + PATERNAL_COUSIN = PermissibleValue( + text="PATERNAL_COUSIN", + description="The player of the role is a child of a paternal aunt or uncle of the scoping person", + meaning=HL7["v3-RoleCode#PCOUSN"]) + NIECE = PermissibleValue( + text="NIECE", + description="""The player of the role is a daughter of the scoping person's brother or sister or of the brother or sister of the scoping person's spouse""", + meaning=HL7["v3-RoleCode#NIECE"]) + NEPHEW = PermissibleValue( + text="NEPHEW", + description="""The player of the role is a son of the scoping person's brother or sister or of the brother or sister of the scoping person's spouse""", + meaning=HL7["v3-RoleCode#NEPHEW"]) + SPOUSE = PermissibleValue( + text="SPOUSE", + description="The player of the role is a marriage partner of the scoping person", + meaning=HL7["v3-RoleCode#SPS"]) + HUSBAND = PermissibleValue( + text="HUSBAND", + description="The player of the role is a man joined to a woman (scoping person) in marriage", + meaning=HL7["v3-RoleCode#HUSB"]) + WIFE = PermissibleValue( + text="WIFE", + description="The player of the role is a woman joined to a man (scoping person) in marriage", + meaning=HL7["v3-RoleCode#WIFE"]) + DOMESTIC_PARTNER = PermissibleValue( + text="DOMESTIC_PARTNER", + description="The player of the role cohabits with the scoping person but is not the scoping person's spouse", + meaning=HL7["v3-RoleCode#DOMPART"]) + GREAT_GRANDPARENT = PermissibleValue( + text="GREAT_GRANDPARENT", + description="The player of the role is a grandparent of the scoping person's mother or father", + meaning=HL7["v3-RoleCode#GGRPRN"]) + GREAT_GRANDMOTHER = PermissibleValue( + text="GREAT_GRANDMOTHER", + description="The player of the role is a grandmother of the scoping person's mother or father", + meaning=HL7["v3-RoleCode#GGRMTH"]) + GREAT_GRANDFATHER = PermissibleValue( + text="GREAT_GRANDFATHER", + description="The player of the role is a grandfather of the scoping person's mother or father", + meaning=HL7["v3-RoleCode#GGRFTH"]) + MOTHER_IN_LAW = PermissibleValue( + text="MOTHER_IN_LAW", + description="The player of the role is the mother of the scoping person's spouse", + meaning=HL7["v3-RoleCode#MTHINLAW"]) + FATHER_IN_LAW = PermissibleValue( + text="FATHER_IN_LAW", + description="The player of the role is the father of the scoping person's spouse", + meaning=HL7["v3-RoleCode#FTHINLAW"]) + DAUGHTER_IN_LAW = PermissibleValue( + text="DAUGHTER_IN_LAW", + description="The player of the role is the wife of scoping person's son", + meaning=HL7["v3-RoleCode#DAUINLAW"]) + SON_IN_LAW = PermissibleValue( + text="SON_IN_LAW", + description="The player of the role is the husband of scoping person's daughter", + meaning=HL7["v3-RoleCode#SONINLAW"]) + BROTHER_IN_LAW = PermissibleValue( + text="BROTHER_IN_LAW", + description="""The player of the role is a brother of the scoping person's spouse, or the husband of the scoping person's sister, or the husband of a sister of the scoping person's spouse""", + meaning=HL7["v3-RoleCode#BROINLAW"]) + SISTER_IN_LAW = PermissibleValue( + text="SISTER_IN_LAW", + description="""The player of the role is a sister of the scoping person's spouse, or the wife of the scoping person's brother, or the wife of a brother of the scoping person's spouse""", + meaning=HL7["v3-RoleCode#SISINLAW"]) + FAMILY_MEMBER = PermissibleValue( + text="FAMILY_MEMBER", + description="A relationship between two people characterizing their \"familial\" relationship", + meaning=HL7["v3-RoleCode#FAMMEMB"]) + EXTENDED_FAMILY_MEMBER = PermissibleValue( + text="EXTENDED_FAMILY_MEMBER", + description="Description of an extended family member", + meaning=HL7["v3-RoleCode#EXT"]) + SIGNIFICANT_OTHER = PermissibleValue( + text="SIGNIFICANT_OTHER", + description="""A person who is important to one's well being; especially a spouse or one in a similar relationship""", + meaning=HL7["v3-RoleCode#SIGOTHR"]) + + _defn = EnumDefinition( + name="FamilyRelationship", + description="Family relationships used in pedigree and family history documentation", + ) + +class FamilyHistoryStatus(EnumDefinitionImpl): + """ + Status of family history information availability + """ + COMPLETED = PermissibleValue( + text="COMPLETED", + description="All relevant family history information has been obtained", + meaning=HL7["observation-status#final"]) + PARTIAL = PermissibleValue( + text="PARTIAL", + description="Some family history information is available but not complete", + meaning=HL7["observation-status#preliminary"]) + UNKNOWN = PermissibleValue( + text="UNKNOWN", + description="Family history status is unknown", + meaning=FHIR_DATA_ABSENT_REASON["#unknown"]) + UNABLE_TO_OBTAIN = PermissibleValue( + text="UNABLE_TO_OBTAIN", + description="Information could not be obtained due to patient/family constraints", + meaning=FHIR_DATA_ABSENT_REASON["#patient-refused"]) + NOT_ASKED = PermissibleValue( + text="NOT_ASKED", + description="Family history information was not requested", + meaning=FHIR_DATA_ABSENT_REASON["#not-asked"]) + + _defn = EnumDefinition( + name="FamilyHistoryStatus", + description="Status of family history information availability", + ) + +class GeneticRelationship(EnumDefinitionImpl): + """ + Genetic relationship types for pedigree analysis + """ + BIOLOGICAL = PermissibleValue( + text="BIOLOGICAL", + description="Genetic relationship through biological inheritance", + meaning=SNOMED["444018008"]) + FULL_SIBLING = PermissibleValue( + text="FULL_SIBLING", + description="Siblings sharing both biological parents", + meaning=SNOMED["444301002"]) + HALF_SIBLING = PermissibleValue( + text="HALF_SIBLING", + description="Siblings sharing one biological parent", + meaning=SNOMED["445295006"]) + ADOPTIVE = PermissibleValue( + text="ADOPTIVE", + description="Relationship established through adoption", + meaning=SNOMED["160499008"]) + NO_GENETIC_RELATIONSHIP = PermissibleValue( + text="NO_GENETIC_RELATIONSHIP", + description="No genetic relationship exists", + meaning=SNOMED["373068000"]) + UNKNOWN_GENETIC_RELATIONSHIP = PermissibleValue( + text="UNKNOWN_GENETIC_RELATIONSHIP", + description="Genetic relationship status is unknown", + meaning=SNOMED["261665006"]) + + _defn = EnumDefinition( + name="GeneticRelationship", + description="Genetic relationship types for pedigree analysis", + ) + class RaceOMB1997Enum(EnumDefinitionImpl): """ Race categories following OMB 1997 standards used by NIH and federal agencies. @@ -25287,6 +26489,15 @@ class slots: slots.processing_status = Slot(uri=VALUESETS.processing_status, name="processing_status", curie=VALUESETS.curie('processing_status'), model_uri=VALUESETS.processing_status, domain=None, range=Optional[Union[str, "ProcessingStatus"]]) +slots.coordination_geometry = Slot(uri=VALUESETS.coordination_geometry, name="coordination_geometry", curie=VALUESETS.curie('coordination_geometry'), + model_uri=VALUESETS.coordination_geometry, domain=None, range=Optional[Union[str, "CoordinationGeometry"]]) + +slots.metal_ligand_type = Slot(uri=VALUESETS.metal_ligand_type, name="metal_ligand_type", curie=VALUESETS.curie('metal_ligand_type'), + model_uri=VALUESETS.metal_ligand_type, domain=None, range=Optional[Union[str, "MetalLigandType"]]) + +slots.protein_modification = Slot(uri=VALUESETS.protein_modification, name="protein_modification", curie=VALUESETS.curie('protein_modification'), + model_uri=VALUESETS.protein_modification, domain=None, range=Optional[Union[str, "ProteinModificationType"]]) + slots.biosafety_level = Slot(uri=VALUESETS.biosafety_level, name="biosafety_level", curie=VALUESETS.curie('biosafety_level'), model_uri=VALUESETS.biosafety_level, domain=None, range=Optional[Union[str, "BiosafetyLevelEnum"]]) @@ -26133,6 +27344,15 @@ class slots: slots.fmri_paradigm_type = Slot(uri=VALUESETS.fmri_paradigm_type, name="fmri_paradigm_type", curie=VALUESETS.curie('fmri_paradigm_type'), model_uri=VALUESETS.fmri_paradigm_type, domain=None, range=Optional[Union[str, "FMRIParadigmTypeEnum"]]) +slots.family_relationship = Slot(uri=VALUESETS.family_relationship, name="family_relationship", curie=VALUESETS.curie('family_relationship'), + model_uri=VALUESETS.family_relationship, domain=None, range=Optional[Union[str, "FamilyRelationship"]]) + +slots.family_history_status = Slot(uri=VALUESETS.family_history_status, name="family_history_status", curie=VALUESETS.curie('family_history_status'), + model_uri=VALUESETS.family_history_status, domain=None, range=Optional[Union[str, "FamilyHistoryStatus"]]) + +slots.genetic_relationship = Slot(uri=VALUESETS.genetic_relationship, name="genetic_relationship", curie=VALUESETS.curie('genetic_relationship'), + model_uri=VALUESETS.genetic_relationship, domain=None, range=Optional[Union[str, "GeneticRelationship"]]) + slots.race_omb1997 = Slot(uri=VALUESETS.race_omb1997, name="race_omb1997", curie=VALUESETS.curie('race_omb1997'), model_uri=VALUESETS.race_omb1997, domain=None, range=Optional[Union[str, "RaceOMB1997Enum"]]) diff --git a/src/valuesets/datamodel/valuesets_pydantic.py b/src/valuesets/datamodel/valuesets_pydantic.py index ab30c331..4798862f 100644 --- a/src/valuesets/datamodel/valuesets_pydantic.py +++ b/src/valuesets/datamodel/valuesets_pydantic.py @@ -55,6 +55,9 @@ def __contains__(self, key: str) -> bool: linkml_meta = LinkMLMeta({'default_prefix': 'valuesets', 'description': 'A collection of commonly used value sets', 'id': 'https://w3id.org/linkml/valuesets', 'name': 'valuesets', 'title': 'valuesets'}) class RelativeTimeEnum(RichEnum): + """ + Temporal relationships between events or time points + """ # Enum members BEFORE = "BEFORE" AFTER = "AFTER" @@ -62,9 +65,15 @@ class RelativeTimeEnum(RichEnum): # Set metadata after class creation to avoid it becoming an enum member RelativeTimeEnum._metadata = { + "BEFORE": {'description': 'Occurs before the reference time point'}, + "AFTER": {'description': 'Occurs after the reference time point'}, + "AT_SAME_TIME_AS": {'description': 'Occurs at the same time as the reference time point'}, } class PresenceEnum(RichEnum): + """ + Classification of whether an entity is present, absent, or at detection limits + """ # Enum members PRESENT = "PRESENT" ABSENT = "ABSENT" @@ -127,8 +136,8 @@ class DataAbsentEnum(RichEnum): "AS_TEXT": {'description': 'The content of the data is represented in the resource narrative.', 'meaning': 'fhir_data_absent_reason:as-text'}, "ERROR": {'description': 'Some system or workflow process error means that the information is not available.', 'meaning': 'fhir_data_absent_reason:error'}, "NOT_A_NUMBER": {'description': 'The numeric value is undefined or unrepresentable due to a floating point processing error.', 'meaning': 'fhir_data_absent_reason:not-a-number'}, - "NEGATIVE_INFINITY": {'description': 'The numeric value is excessively low and unrepresentable due to a floating point processing error.', 'meaning': 'fhir_data_absent_reason:negative-infinity'}, - "POSITIVE_INFINITY": {'description': 'The numeric value is excessively high and unrepresentable due to a floating point processing error.', 'meaning': 'fhir_data_absent_reason:positive-infinity'}, + "NEGATIVE_INFINITY": {'description': 'The numeric value is excessively low and unrepresentable due to a floating point processing error.', 'meaning': 'fhir_data_absent_reason:negative-infinity'}, + "POSITIVE_INFINITY": {'description': 'The numeric value is excessively high and unrepresentable due to a floating point processing error.', 'meaning': 'fhir_data_absent_reason:positive-infinity'}, "NOT_PERFORMED": {'description': 'The value is not available because the observation procedure (test, etc.) was not performed.', 'meaning': 'fhir_data_absent_reason:not-performed'}, "NOT_PERMITTED": {'description': 'The value is not permitted in this context (e.g. due to profiles, or the base data types).', 'meaning': 'fhir_data_absent_reason:not-permitted'}, } diff --git a/src/valuesets/enums/__init__.py b/src/valuesets/enums/__init__.py index 886fd6fe..c2c7bf63 100644 --- a/src/valuesets/enums/__init__.py +++ b/src/valuesets/enums/__init__.py @@ -89,6 +89,7 @@ from .investigation import CaseOrControlEnum from .mining_processing import RelativeTimeEnum, PresenceEnum, MineralogyFeedstockClass, BeneficiationPathway, InSituChemistryRegime, ExtractableTargetElement, SensorWhileDrillingFeature, ProcessPerformanceMetric, BioleachOrganism, BioleachMode, AutonomyLevel, RegulatoryConstraint from .statistics import PredictionOutcomeType +from .stewardship import ValueSetStewardEnum # Data domain from .data.data_absent_reason import DataAbsentEnum @@ -103,6 +104,7 @@ # Earth_Science domain from .earth_science.collection_methods import SESARCollectionMethod +from .earth_science.fao_soil import FAOSoilType from .earth_science.material_types import SESARMaterialType from .earth_science.physiographic_features import SESARPhysiographicFeature from .earth_science.sample_types import SESARSampleType @@ -332,6 +334,7 @@ "ExtractiveIndustryFacilityTypeEnum", "ExtractiveIndustryProductTypeEnum", "EyeColorEnum", + "FAOSoilType", "FMRIParadigmTypeEnum", "FamilyHistoryStatus", "FamilyRelationship", @@ -637,6 +640,7 @@ "VaccinationStatusEnum", "VaccineCategoryEnum", "VaccineTypeEnum", + "ValueSetStewardEnum", "VendorCategoryEnum", "VideoFormatEnum", "ViralGenomeTypeEnum", diff --git a/src/valuesets/enums/analytical_chemistry/mass_spectrometry.py b/src/valuesets/enums/analytical_chemistry/mass_spectrometry.py index 711cac2f..a888bfce 100644 --- a/src/valuesets/enums/analytical_chemistry/mass_spectrometry.py +++ b/src/valuesets/enums/analytical_chemistry/mass_spectrometry.py @@ -11,6 +11,9 @@ from valuesets.generators.rich_enum import RichEnum class RelativeTimeEnum(RichEnum): + """ + Temporal relationships between events or time points + """ # Enum members BEFORE = "BEFORE" AFTER = "AFTER" @@ -18,9 +21,15 @@ class RelativeTimeEnum(RichEnum): # Set metadata after class creation RelativeTimeEnum._metadata = { + "BEFORE": {'description': 'Occurs before the reference time point'}, + "AFTER": {'description': 'Occurs after the reference time point'}, + "AT_SAME_TIME_AS": {'description': 'Occurs at the same time as the reference time point'}, } class PresenceEnum(RichEnum): + """ + Classification of whether an entity is present, absent, or at detection limits + """ # Enum members PRESENT = "PRESENT" ABSENT = "ABSENT" diff --git a/src/valuesets/enums/bio/lipid_categories.py b/src/valuesets/enums/bio/lipid_categories.py index f280d380..fbbbf56d 100644 --- a/src/valuesets/enums/bio/lipid_categories.py +++ b/src/valuesets/enums/bio/lipid_categories.py @@ -11,6 +11,9 @@ from valuesets.generators.rich_enum import RichEnum class RelativeTimeEnum(RichEnum): + """ + Temporal relationships between events or time points + """ # Enum members BEFORE = "BEFORE" AFTER = "AFTER" @@ -18,9 +21,15 @@ class RelativeTimeEnum(RichEnum): # Set metadata after class creation RelativeTimeEnum._metadata = { + "BEFORE": {'description': 'Occurs before the reference time point'}, + "AFTER": {'description': 'Occurs after the reference time point'}, + "AT_SAME_TIME_AS": {'description': 'Occurs at the same time as the reference time point'}, } class PresenceEnum(RichEnum): + """ + Classification of whether an entity is present, absent, or at detection limits + """ # Enum members PRESENT = "PRESENT" ABSENT = "ABSENT" diff --git a/src/valuesets/enums/bio/proteomics_standards.py b/src/valuesets/enums/bio/proteomics_standards.py index 42ca25be..f1ddfd56 100644 --- a/src/valuesets/enums/bio/proteomics_standards.py +++ b/src/valuesets/enums/bio/proteomics_standards.py @@ -11,6 +11,9 @@ from valuesets.generators.rich_enum import RichEnum class RelativeTimeEnum(RichEnum): + """ + Temporal relationships between events or time points + """ # Enum members BEFORE = "BEFORE" AFTER = "AFTER" @@ -18,9 +21,15 @@ class RelativeTimeEnum(RichEnum): # Set metadata after class creation RelativeTimeEnum._metadata = { + "BEFORE": {'description': 'Occurs before the reference time point'}, + "AFTER": {'description': 'Occurs after the reference time point'}, + "AT_SAME_TIME_AS": {'description': 'Occurs at the same time as the reference time point'}, } class PresenceEnum(RichEnum): + """ + Classification of whether an entity is present, absent, or at detection limits + """ # Enum members PRESENT = "PRESENT" ABSENT = "ABSENT" diff --git a/src/valuesets/enums/chemistry/reaction_directionality.py b/src/valuesets/enums/chemistry/reaction_directionality.py index 7f1ae6e9..668ff220 100644 --- a/src/valuesets/enums/chemistry/reaction_directionality.py +++ b/src/valuesets/enums/chemistry/reaction_directionality.py @@ -11,6 +11,9 @@ from valuesets.generators.rich_enum import RichEnum class RelativeTimeEnum(RichEnum): + """ + Temporal relationships between events or time points + """ # Enum members BEFORE = "BEFORE" AFTER = "AFTER" @@ -18,9 +21,15 @@ class RelativeTimeEnum(RichEnum): # Set metadata after class creation RelativeTimeEnum._metadata = { + "BEFORE": {'description': 'Occurs before the reference time point'}, + "AFTER": {'description': 'Occurs after the reference time point'}, + "AT_SAME_TIME_AS": {'description': 'Occurs at the same time as the reference time point'}, } class PresenceEnum(RichEnum): + """ + Classification of whether an entity is present, absent, or at detection limits + """ # Enum members PRESENT = "PRESENT" ABSENT = "ABSENT" diff --git a/src/valuesets/enums/confidence_levels.py b/src/valuesets/enums/confidence_levels.py index a0ef40b6..2d8576f9 100644 --- a/src/valuesets/enums/confidence_levels.py +++ b/src/valuesets/enums/confidence_levels.py @@ -11,6 +11,9 @@ from valuesets.generators.rich_enum import RichEnum class RelativeTimeEnum(RichEnum): + """ + Temporal relationships between events or time points + """ # Enum members BEFORE = "BEFORE" AFTER = "AFTER" @@ -18,9 +21,15 @@ class RelativeTimeEnum(RichEnum): # Set metadata after class creation RelativeTimeEnum._metadata = { + "BEFORE": {'description': 'Occurs before the reference time point'}, + "AFTER": {'description': 'Occurs after the reference time point'}, + "AT_SAME_TIME_AS": {'description': 'Occurs at the same time as the reference time point'}, } class PresenceEnum(RichEnum): + """ + Classification of whether an entity is present, absent, or at detection limits + """ # Enum members PRESENT = "PRESENT" ABSENT = "ABSENT" diff --git a/src/valuesets/enums/core.py b/src/valuesets/enums/core.py index fd1405cf..f6c1a57a 100644 --- a/src/valuesets/enums/core.py +++ b/src/valuesets/enums/core.py @@ -11,6 +11,9 @@ from valuesets.generators.rich_enum import RichEnum class RelativeTimeEnum(RichEnum): + """ + Temporal relationships between events or time points + """ # Enum members BEFORE = "BEFORE" AFTER = "AFTER" @@ -18,9 +21,15 @@ class RelativeTimeEnum(RichEnum): # Set metadata after class creation RelativeTimeEnum._metadata = { + "BEFORE": {'description': 'Occurs before the reference time point'}, + "AFTER": {'description': 'Occurs after the reference time point'}, + "AT_SAME_TIME_AS": {'description': 'Occurs at the same time as the reference time point'}, } class PresenceEnum(RichEnum): + """ + Classification of whether an entity is present, absent, or at detection limits + """ # Enum members PRESENT = "PRESENT" ABSENT = "ABSENT" diff --git a/src/valuesets/enums/data/data_absent_reason.py b/src/valuesets/enums/data/data_absent_reason.py index 3f3eb560..539ff6bd 100644 --- a/src/valuesets/enums/data/data_absent_reason.py +++ b/src/valuesets/enums/data/data_absent_reason.py @@ -41,8 +41,8 @@ class DataAbsentEnum(RichEnum): "AS_TEXT": {'description': 'The content of the data is represented in the resource narrative.', 'meaning': 'fhir_data_absent_reason:as-text'}, "ERROR": {'description': 'Some system or workflow process error means that the information is not available.', 'meaning': 'fhir_data_absent_reason:error'}, "NOT_A_NUMBER": {'description': 'The numeric value is undefined or unrepresentable due to a floating point processing error.', 'meaning': 'fhir_data_absent_reason:not-a-number'}, - "NEGATIVE_INFINITY": {'description': 'The numeric value is excessively low and unrepresentable due to a floating point processing error.', 'meaning': 'fhir_data_absent_reason:negative-infinity'}, - "POSITIVE_INFINITY": {'description': 'The numeric value is excessively high and unrepresentable due to a floating point processing error.', 'meaning': 'fhir_data_absent_reason:positive-infinity'}, + "NEGATIVE_INFINITY": {'description': 'The numeric value is excessively low and unrepresentable due to a floating point processing error.', 'meaning': 'fhir_data_absent_reason:negative-infinity'}, + "POSITIVE_INFINITY": {'description': 'The numeric value is excessively high and unrepresentable due to a floating point processing error.', 'meaning': 'fhir_data_absent_reason:positive-infinity'}, "NOT_PERFORMED": {'description': 'The value is not available because the observation procedure (test, etc.) was not performed.', 'meaning': 'fhir_data_absent_reason:not-performed'}, "NOT_PERMITTED": {'description': 'The value is not permitted in this context (e.g. due to profiles, or the base data types).', 'meaning': 'fhir_data_absent_reason:not-permitted'}, } diff --git a/src/valuesets/enums/ecological_interactions.py b/src/valuesets/enums/ecological_interactions.py index daef2f49..5025ee0b 100644 --- a/src/valuesets/enums/ecological_interactions.py +++ b/src/valuesets/enums/ecological_interactions.py @@ -12,6 +12,9 @@ from valuesets.generators.rich_enum import RichEnum class RelativeTimeEnum(RichEnum): + """ + Temporal relationships between events or time points + """ # Enum members BEFORE = "BEFORE" AFTER = "AFTER" @@ -19,9 +22,15 @@ class RelativeTimeEnum(RichEnum): # Set metadata after class creation RelativeTimeEnum._metadata = { + "BEFORE": {'description': 'Occurs before the reference time point'}, + "AFTER": {'description': 'Occurs after the reference time point'}, + "AT_SAME_TIME_AS": {'description': 'Occurs at the same time as the reference time point'}, } class PresenceEnum(RichEnum): + """ + Classification of whether an entity is present, absent, or at detection limits + """ # Enum members PRESENT = "PRESENT" ABSENT = "ABSENT" diff --git a/src/valuesets/enums/mining_processing.py b/src/valuesets/enums/mining_processing.py index 8e7ed584..c3ea12bb 100644 --- a/src/valuesets/enums/mining_processing.py +++ b/src/valuesets/enums/mining_processing.py @@ -11,6 +11,9 @@ from valuesets.generators.rich_enum import RichEnum class RelativeTimeEnum(RichEnum): + """ + Temporal relationships between events or time points + """ # Enum members BEFORE = "BEFORE" AFTER = "AFTER" @@ -18,9 +21,15 @@ class RelativeTimeEnum(RichEnum): # Set metadata after class creation RelativeTimeEnum._metadata = { + "BEFORE": {'description': 'Occurs before the reference time point'}, + "AFTER": {'description': 'Occurs after the reference time point'}, + "AT_SAME_TIME_AS": {'description': 'Occurs at the same time as the reference time point'}, } class PresenceEnum(RichEnum): + """ + Classification of whether an entity is present, absent, or at detection limits + """ # Enum members PRESENT = "PRESENT" ABSENT = "ABSENT" diff --git a/src/valuesets/metamodel/valuesets_meta.yaml b/src/valuesets/metamodel/valuesets_meta.yaml new file mode 100644 index 00000000..48c8a8e4 --- /dev/null +++ b/src/valuesets/metamodel/valuesets_meta.yaml @@ -0,0 +1,301 @@ +name: valuesets_meta +title: Valuesets Metamodel +description: >- + Custom metamodel for the valuesets schema. Defines metaclasses that constrain + LinkML elements to enforce metadata standards for value set enums. + + This metamodel is NOT imported by the main schema - it is used declaratively + via the `instantiates` slot to indicate conformance intent. + +id: https://w3id.org/valuesets/meta + +prefixes: + linkml: https://w3id.org/linkml/ + valuesets_meta: https://w3id.org/valuesets/meta/ + orcid: https://orcid.org/ + dcterms: http://purl.org/dc/terms/ + fhir: http://hl7.org/fhir/ + +default_prefix: valuesets_meta +default_range: string + +imports: + - linkml:types + +# ============================================================================= +# Metaclasses for Enum Definitions +# ============================================================================= +# These classes define constraints on EnumDefinition elements in the main schema. +# Enums that `instantiates` these metaclasses are expected to conform to the +# slot requirements defined here. +# +# Note: As of LinkML 1.x, `instantiates` declares conformance intent but +# validation enforcement is limited. This metamodel documents the standard +# and enables future validation support. +# ============================================================================= + +classes: + + # --------------------------------------------------------------------------- + # ValueSetEnumDefinition + # --------------------------------------------------------------------------- + # The primary metaclass for all value set enums in this repository. + # Requires complete metadata: title, description, status, and contributors. + # --------------------------------------------------------------------------- + ValueSetEnumDefinition: + class_uri: valuesets_meta:ValueSetEnumDefinition + description: >- + A metaclass for enum definitions in the valuesets schema. + Enums instantiating this class MUST provide complete metadata + including title, description, status, and contributors. + slot_usage: + title: + required: true + description: >- + Human-readable display name for the enum. + Should be Title Case and clearly describe the value set. + description: + required: true + description: >- + Detailed explanation of the enum's purpose, scope, and usage. + Should be at least one complete sentence. + status: + required: true + description: >- + Maturity status of the enum. Must be a value from StandardsMaturityLevel: + DRAFT, WORKING_DRAFT, COMMITTEE_DRAFT, CANDIDATE_RECOMMENDATION, + PROPOSED_STANDARD, STANDARD, MATURE_STANDARD, SUPERSEDED, WITHDRAWN + contributors: + required: true + multivalued: true + description: >- + List of contributor identifiers (ORCIDs or URIs) who created or + maintain this enum. Should include at least one human contributor. + attributes: + title: + range: string + required: true + description: + range: string + required: true + status: + range: string + required: true + contributors: + range: uriorcurie + multivalued: true + required: true + + # --------------------------------------------------------------------------- + # ValueSetEnumDefinitionWithSource + # --------------------------------------------------------------------------- + # Extended metaclass for enums derived from external sources. + # Adds requirement for source provenance. + # --------------------------------------------------------------------------- + ValueSetEnumDefinitionWithSource: + class_uri: valuesets_meta:ValueSetEnumDefinitionWithSource + is_a: ValueSetEnumDefinition + description: >- + A metaclass for enum definitions derived from external standards or ontologies. + Requires all base metadata plus source provenance. + slot_usage: + source: + required: true + description: >- + URL or URI of the external resource this enum is derived from. + Maps to dcterms:source / prov:wasDerivedFrom. + attributes: + source: + range: uriorcurie + required: true + + # --------------------------------------------------------------------------- + # ValueSetEnumDefinitionWithConformance + # --------------------------------------------------------------------------- + # Extended metaclass for enums that conform to formal standards. + # Adds requirement for conforms_to. + # --------------------------------------------------------------------------- + ValueSetEnumDefinitionWithConformance: + class_uri: valuesets_meta:ValueSetEnumDefinitionWithConformance + is_a: ValueSetEnumDefinitionWithSource + description: >- + A metaclass for enum definitions that formally conform to external standards. + Requires source and explicit conformance declaration. + slot_usage: + conforms_to: + required: true + description: >- + The standard or specification this enum conforms to. + E.g., "ISO-16290:2013", "HL7 FHIR R4", etc. + attributes: + conforms_to: + range: string + required: true + + # --------------------------------------------------------------------------- + # ValueSetEnumDefinitionWithStewardship + # --------------------------------------------------------------------------- + # Extended metaclass for enums with explicit organizational stewardship. + # Requires at least one steward or publisher to be identified. + # Based on FHIR MetadataResource stewardship patterns. + # --------------------------------------------------------------------------- + ValueSetEnumDefinitionWithStewardship: + class_uri: valuesets_meta:ValueSetEnumDefinitionWithStewardship + is_a: ValueSetEnumDefinition + description: >- + A metaclass for enum definitions with explicit organizational stewardship. + Requires identification of stewards and/or publishers responsible for + maintaining the value set. Endorsers are optional but recommended for + value sets intended for broad adoption. + slot_usage: + stewards: + recommended: true + description: >- + Organizations or individuals responsible for ongoing curation. + At least one steward OR publisher should be specified. + publishers: + recommended: true + description: >- + Organizations or individuals responsible for release and maintenance. + At least one steward OR publisher should be specified. + endorsers: + description: >- + Organizations that officially endorse this value set. + Recommended for value sets intended for broad adoption. + attributes: + stewards: + range: uriorcurie + multivalued: true + publishers: + range: uriorcurie + multivalued: true + endorsers: + range: uriorcurie + multivalued: true + + # --------------------------------------------------------------------------- + # ReferenceEnumDefinition + # --------------------------------------------------------------------------- + # Metaclass for "reference" enums that define values used by other parts + # of the schema (like StandardsMaturityLevel used for status values). + # These should have STANDARD status and complete documentation. + # --------------------------------------------------------------------------- + ReferenceEnumDefinition: + class_uri: valuesets_meta:ReferenceEnumDefinition + is_a: ValueSetEnumDefinition + description: >- + A metaclass for reference enums that define values used elsewhere in the schema. + These are authoritative definitions and should have STANDARD status. + slot_usage: + status: + required: true + description: >- + Reference enums should typically have status STANDARD or MATURE_STANDARD + since they define authoritative values used by other schema elements. + +# ============================================================================= +# Slots +# ============================================================================= +# These slots are used in the metaclass definitions above. +# They mirror the LinkML metamodel slots but with valuesets-specific constraints. +# ============================================================================= + +slots: + title: + description: Human-readable display name + range: string + + description: + description: Detailed explanation of purpose and usage + range: string + + status: + description: >- + Maturity status using StandardsMaturityLevel values. + Valid values: DRAFT, WORKING_DRAFT, COMMITTEE_DRAFT, CANDIDATE_RECOMMENDATION, + PROPOSED_STANDARD, STANDARD, MATURE_STANDARD, SUPERSEDED, WITHDRAWN + range: string + + contributors: + description: List of contributor ORCIDs or URIs + range: uriorcurie + multivalued: true + + source: + description: External resource this element is derived from + range: uriorcurie + + conforms_to: + description: Standard or specification this element conforms to + range: string + + # --------------------------------------------------------------------------- + # Stewardship Slots (FHIR-inspired) + # --------------------------------------------------------------------------- + # These slots define organizational responsibility for value sets. + # Based on HL7 FHIR MetadataResource patterns. + # --------------------------------------------------------------------------- + + publishers: + description: >- + Organizations or individuals responsible for the release and ongoing + maintenance of this value set. The publisher is the authoritative source + for the content. Maps to dcterms:publisher / fhir:publisher. + range: uriorcurie + multivalued: true + slot_uri: dcterms:publisher + see_also: + - https://build.fhir.org/metadataresource.html + + stewards: + description: >- + Organizations or individuals responsible for the ongoing curation and + maintenance of this value set. Stewards ensure the value set remains + accurate, up-to-date, and fit for purpose. Unlike publishers, stewards + may not have release authority but are responsible for content quality. + range: uriorcurie + multivalued: true + slot_uri: valuesets_meta:stewards + + endorsers: + description: >- + Organizations that officially endorse this value set for use within + their domain or jurisdiction. Endorsement indicates that the organization + has reviewed the value set and recommends it for adoption. + Maps to fhir:endorser. + range: uriorcurie + multivalued: true + slot_uri: valuesets_meta:endorsers + see_also: + - https://build.fhir.org/metadataresource.html + +# ============================================================================= +# Enums +# ============================================================================= +# Define the valid values for status to enable future validation. +# ============================================================================= + +enums: + StandardsMaturityLevelEnum: + description: >- + Valid values for the status slot, mirroring StandardsMaturityLevel + from computing/maturity_levels.yaml + permissible_values: + DRAFT: + description: Initial draft under development + WORKING_DRAFT: + description: Work in progress by working group + COMMITTEE_DRAFT: + description: Draft reviewed by committee + CANDIDATE_RECOMMENDATION: + description: Mature draft ready for implementation testing + PROPOSED_STANDARD: + description: Stable specification ready for adoption + STANDARD: + description: Approved and published standard + MATURE_STANDARD: + description: Well-established standard with wide adoption + SUPERSEDED: + description: Replaced by a newer version + WITHDRAWN: + description: No longer valid or recommended diff --git a/src/valuesets/schema/academic/organizations.yaml b/src/valuesets/schema/academic/organizations.yaml index a90d3bc4..6a1b2847 100644 --- a/src/valuesets/schema/academic/organizations.yaml +++ b/src/valuesets/schema/academic/organizations.yaml @@ -18,10 +18,13 @@ id: https://w3id.org/linkml/valuesets/academic/organizations imports: - linkml:types prefixes: + linkml: https://w3id.org/linkml/ valuesets: https://w3id.org/valuesets/ ROR: https://ror.org/ GRID: https://www.grid.ac/institutes/ ISNI: https://isni.org/isni/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: @@ -43,6 +46,7 @@ slots: enums: USDOENationalLaboratoryEnum: + title: USDOE National Laboratory description: | United States Department of Energy National Laboratories. @@ -51,9 +55,15 @@ enums: These laboratories are managed by contractors and stewarded by various DOE program offices, with the Office of Science stewarding 10 of the 17 laboratories. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition comments: - - All organization names mapped to ROR (Research Organization Registry) identifiers - - See https://www.energy.gov/national-laboratories for official information + - All organization names mapped to ROR (Research Organization Registry) identifiers + - See https://www.energy.gov/national-laboratories for official information permissible_values: AMES_LABORATORY: title: Ames National Laboratory @@ -87,7 +97,7 @@ enums: description: Particle physics and accelerator research laboratory meaning: ROR:020hgte69 aliases: - - Fermilab + - Fermilab annotations: location: Batavia, Illinois established: 1967 @@ -107,8 +117,8 @@ enums: description: Multidisciplinary research laboratory meaning: ROR:02jbv0t02 aliases: - - Berkeley Lab - - LBNL + - Berkeley Lab + - LBNL annotations: location: Berkeley, California established: 1931 @@ -119,7 +129,7 @@ enums: description: National security laboratory focused on nuclear weapons and advanced technology meaning: ROR:041nk4h53 aliases: - - LLNL + - LLNL annotations: location: Livermore, California established: 1952 @@ -130,7 +140,7 @@ enums: description: Multidisciplinary research institution for national security meaning: ROR:01e41cf67 aliases: - - LANL + - LANL annotations: location: Los Alamos, New Mexico established: 1943 @@ -141,7 +151,7 @@ enums: description: Federal research laboratory focused on energy and environmental technology meaning: ROR:01x26mz03 aliases: - - NETL + - NETL annotations: location: Pittsburgh, Pennsylvania and Morgantown, West Virginia established: 1910 @@ -152,7 +162,7 @@ enums: description: Research and development laboratory focused on renewable energy and energy efficiency meaning: ROR:036266993 aliases: - - NREL + - NREL annotations: location: Golden, Colorado established: 1977 @@ -163,7 +173,7 @@ enums: description: Multidisciplinary science and technology laboratory meaning: ROR:01qz5mb56 aliases: - - ORNL + - ORNL annotations: location: Oak Ridge, Tennessee established: 1943 @@ -174,7 +184,7 @@ enums: description: Research laboratory focused on energy, environment, and national security meaning: ROR:05h992307 aliases: - - PNNL + - PNNL annotations: location: Richland, Washington established: 1965 @@ -185,7 +195,7 @@ enums: description: Plasma physics and fusion energy research laboratory meaning: ROR:03vn1ts68 aliases: - - PPPL + - PPPL annotations: location: Princeton, New Jersey established: 1951 @@ -196,8 +206,8 @@ enums: description: Multimission laboratory for national security and technology innovation meaning: ROR:01apwpt12 aliases: - - Sandia - - SNL + - Sandia + - SNL annotations: location: Albuquerque, New Mexico and Livermore, California established: 1949 @@ -208,7 +218,7 @@ enums: description: Applied research laboratory for environmental and national security missions meaning: ROR:05vc7qy59 aliases: - - SRNL + - SRNL annotations: location: Aiken, South Carolina established: 1951 @@ -219,7 +229,7 @@ enums: description: Particle physics and photon science research laboratory meaning: ROR:05gzmn429 aliases: - - SLAC + - SLAC annotations: location: Menlo Park, California established: 1962 @@ -230,8 +240,8 @@ enums: description: Nuclear physics research laboratory with particle accelerator meaning: ROR:02vwzrd76 aliases: - - Jefferson Lab - - JLab + - Jefferson Lab + - JLab annotations: location: Newport News, Virginia established: 1984 @@ -239,21 +249,28 @@ enums: website: https://www.jlab.org/ USFederalFundingAgencyEnum: + title: US Federal Funding Agency description: | Major United States Federal Research Funding Agencies. These agencies provide funding for basic and applied research across various scientific disciplines, supporting universities, national laboratories, and other research institutions. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition comments: - - All agency names mapped to ROR (Research Organization Registry) identifiers - - Includes primary research funding agencies + - All agency names mapped to ROR (Research Organization Registry) identifiers + - Includes primary research funding agencies permissible_values: NIH: title: National Institutes of Health description: Primary federal agency for biomedical and public health research meaning: ROR:01cwqze88 aliases: - - National Institutes of Health + - National Institutes of Health annotations: parent_department: Department of Health and Human Services website: https://www.nih.gov/ @@ -263,7 +280,7 @@ enums: description: Federal agency supporting fundamental research and education in non-medical fields meaning: ROR:021nxhr62 aliases: - - National Science Foundation + - National Science Foundation annotations: website: https://www.nsf.gov/ established: 1950 @@ -272,8 +289,8 @@ enums: description: Federal department overseeing energy policy and nuclear weapons program meaning: ROR:01bj3aw27 aliases: - - Department of Energy - - U.S. Department of Energy + - Department of Energy + - U.S. Department of Energy annotations: website: https://www.energy.gov/ established: 1977 @@ -289,7 +306,7 @@ enums: description: Federal agency protecting human health and the environment meaning: ROR:03tns0030 aliases: - - U.S. Environmental Protection Agency + - U.S. Environmental Protection Agency annotations: website: https://www.epa.gov/ established: 1970 @@ -314,7 +331,7 @@ enums: description: Principal research agency of the U.S. Department of Agriculture meaning: ROR:02d2m2044 aliases: - - USDA ARS + - USDA ARS annotations: parent_department: Department of Agriculture website: https://www.ars.usda.gov/ @@ -324,8 +341,8 @@ enums: description: Federal department responsible for military research and development meaning: ROR:0447fe631 aliases: - - Department of Defense - - U.S. Department of Defense + - Department of Defense + - U.S. Department of Defense annotations: website: https://www.defense.gov/ established: 1947 @@ -339,21 +356,28 @@ enums: established: 1879 NIHInstituteCenterEnum: + title: NIH Institute Center description: | National Institutes of Health (NIH) Institutes and Centers. NIH comprises 27 Institutes and Centers, each with a specific research agenda focused on particular diseases or body systems. These are the major NIH ICs that fund extramural research. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition comments: - - All mapped to ROR (Research Organization Registry) identifiers - - Focuses on major funding institutes + - All mapped to ROR (Research Organization Registry) identifiers + - Focuses on major funding institutes permissible_values: NCI: title: National Cancer Institute description: NIH institute for cancer research and training meaning: ROR:02t771148 aliases: - - National Cancer Institute + - National Cancer Institute annotations: parent_organization: National Institutes of Health website: https://www.cancer.gov/ @@ -363,7 +387,7 @@ enums: description: NIH institute for heart, lung, and blood diseases research meaning: ROR:012pb6c26 aliases: - - National Heart, Lung, and Blood Institute + - National Heart, Lung, and Blood Institute annotations: parent_organization: National Institutes of Health website: https://www.nhlbi.nih.gov/ @@ -445,21 +469,28 @@ enums: description: World's largest biomedical library and NIH component meaning: ROR:0060t0j89 aliases: - - National Library of Medicine + - National Library of Medicine annotations: parent_organization: National Institutes of Health website: https://www.nlm.nih.gov/ established: 1956 StandardsOrganizationEnum: + title: Standards Organization description: | Major International Standards Development Organizations. These organizations develop technical standards, specifications, and guidelines used globally across various industries including information technology, healthcare, and engineering. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition comments: - - All mapped to ROR (Research Organization Registry) identifiers where available - - Includes standards bodies commonly referenced in research + - All mapped to ROR (Research Organization Registry) identifiers where available + - Includes standards bodies commonly referenced in research permissible_values: ISO: title: International Organization for Standardization @@ -490,21 +521,28 @@ enums: description: Standards development organization for healthcare information exchange meaning: ROR:029ga8k16 aliases: - - Health Level Seven + - Health Level Seven annotations: website: https://www.hl7.org/ established: 1987 headquarters: Ann Arbor, Michigan UNSpecializedAgencyEnum: + title: UN Specialized Agency description: | United Nations Specialized Agencies. UN specialized agencies are autonomous international organizations that coordinate their work with the UN through negotiated agreements. They address international issues in their respective fields. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition comments: - - All mapped to ROR (Research Organization Registry) identifiers - - Includes major UN agencies relevant to research and development + - All mapped to ROR (Research Organization Registry) identifiers + - Includes major UN agencies relevant to research and development permissible_values: WHO: title: World Health Organization @@ -519,7 +557,7 @@ enums: description: UN Educational, Scientific and Cultural Organization meaning: ROR:04h4z8k05 aliases: - - United Nations Educational, Scientific and Cultural Organization + - United Nations Educational, Scientific and Cultural Organization annotations: website: https://www.unesco.org/ established: 1945 diff --git a/src/valuesets/schema/academic/research.yaml b/src/valuesets/schema/academic/research.yaml index 7a95f22a..54071487 100644 --- a/src/valuesets/schema/academic/research.yaml +++ b/src/valuesets/schema/academic/research.yaml @@ -5,6 +5,7 @@ id: https://w3id.org/linkml/valuesets/academic/research imports: - linkml:types prefixes: + linkml: https://w3id.org/linkml/ valuesets: https://w3id.org/valuesets/ DCMITYPE: http://purl.org/dc/dcmitype/ FABIO: http://purl.org/spar/fabio/ @@ -16,6 +17,8 @@ prefixes: SIO: http://semanticscience.org/resource/SIO_ CRediT: https://credit.niso.org/contributor-roles/ MS: http://purl.obolibrary.org/obo/MS_ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: publication: @@ -52,6 +55,12 @@ enums: PublicationType: title: Publication Type description: Types of academic and research publications + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: JOURNAL_ARTICLE: description: Peer-reviewed journal article @@ -200,7 +209,14 @@ enums: description: Annotation or scholarly note meaning: FABIO:Annotation PeerReviewStatus: + title: Peer Review Status description: Status of peer review process + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: NOT_PEER_REVIEWED: description: Not peer reviewed @@ -231,7 +247,14 @@ enums: description: Published after review meaning: IAO:0000311 AcademicDegree: + title: Academic Degree description: Academic degrees and qualifications + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: BA: title: Bachelor of Arts @@ -399,7 +422,14 @@ enums: annotations: level: postdoctoral LicenseType: + title: License Type description: Common software and content licenses + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: MIT: description: MIT License @@ -460,7 +490,14 @@ enums: CUSTOM: description: Custom license terms ResearchField: + title: Research Field description: Major research fields and disciplines + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: PHYSICS: description: Physics @@ -545,7 +582,14 @@ enums: PUBLIC_HEALTH: description: Public health FundingType: + title: Funding Type description: Types of research funding + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: GRANT: description: Research grant @@ -570,7 +614,14 @@ enums: CROWDFUNDING: description: Crowdfunded research ManuscriptSection: + title: Manuscript Section description: Sections of a scientific manuscript or publication + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: TITLE: title: document title @@ -800,7 +851,14 @@ enums: annotations: catch_all: true ResearchRole: + title: Research Role description: Roles in research and authorship + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: CONCEPTUALIZATION: description: Ideas; formulation of research goals @@ -868,7 +926,14 @@ enums: title: Collaborator meaning: NCIT:C84336 OpenAccessType: + title: Open Access Type description: Types of open access publishing + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: GOLD: description: Gold open access (published OA) @@ -885,7 +950,14 @@ enums: EMBARGO: description: Under embargo period CitationStyle: + title: Citation Style description: Common citation and reference styles + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: APA: description: American Psychological Association diff --git a/src/valuesets/schema/analytical_chemistry/mass_spectrometry.yaml b/src/valuesets/schema/analytical_chemistry/mass_spectrometry.yaml index e528f895..6fc38cf5 100644 --- a/src/valuesets/schema/analytical_chemistry/mass_spectrometry.yaml +++ b/src/valuesets/schema/analytical_chemistry/mass_spectrometry.yaml @@ -11,14 +11,23 @@ prefixes: MS: http://purl.obolibrary.org/obo/MS_ MSIO: http://purl.obolibrary.org/obo/MSIO_ CHMO: http://purl.obolibrary.org/obo/CHMO_ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets imports: - - linkml:types - - ../core +- linkml:types +- ../core enums: MassSpectrometerFileFormat: + title: Mass Spectrometer File Format description: Standard file formats used in mass spectrometry + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: MZML: title: mzML format @@ -86,7 +95,14 @@ enums: meaning: MS:1002531 MassSpectrometerVendor: + title: Mass Spectrometer Vendor description: Major mass spectrometer manufacturers + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: THERMO_FISHER_SCIENTIFIC: title: Thermo Fisher Scientific instrument model @@ -118,7 +134,14 @@ enums: meaning: MS:1001800 ChromatographyType: + title: Chromatography Type description: Types of chromatographic separation methods + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: GAS_CHROMATOGRAPHY: description: Gas chromatography @@ -140,7 +163,14 @@ enums: meaning: CHMO:0000506 DerivatizationMethod: + title: Derivatization Method description: Chemical derivatization methods for sample preparation + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: SILYLATION: description: Addition of silyl groups for improved volatility @@ -162,7 +192,14 @@ enums: meaning: MSIO:0000116 MetabolomicsAssayType: + title: Metabolomics Assay Type description: Types of metabolomics assays and profiling approaches + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: TARGETED_METABOLITE_PROFILING: title: targeted metabolite profiling @@ -178,7 +215,14 @@ enums: meaning: MSIO:0000099 AnalyticalControlType: + title: Analytical Control Type description: Types of control samples used in analytical chemistry + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: INTERNAL_STANDARD: title: internal standard role @@ -203,4 +247,4 @@ enums: BLANK: description: Sample containing only solvent/matrix without analyte QUALITY_CONTROL: - description: Sample with known composition for system performance monitoring \ No newline at end of file + description: Sample with known composition for system performance monitoring diff --git a/src/valuesets/schema/bio/bio_entities.yaml b/src/valuesets/schema/bio/bio_entities.yaml index c8e3d71f..d0c780b0 100644 --- a/src/valuesets/schema/bio/bio_entities.yaml +++ b/src/valuesets/schema/bio/bio_entities.yaml @@ -9,6 +9,7 @@ id: https://w3id.org/linkml/valuesets/bio/bio_entities imports: - linkml:types prefixes: + linkml: https://w3id.org/linkml/ valuesets: https://w3id.org/valuesets/ UBERON: http://purl.obolibrary.org/obo/UBERON_ CL: http://purl.obolibrary.org/obo/CL_ @@ -24,6 +25,8 @@ prefixes: SO: http://purl.obolibrary.org/obo/SO_ PATO: http://purl.obolibrary.org/obo/PATO_ RO: http://purl.obolibrary.org/obo/RO_ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: metazoan_anatomical_structure: @@ -111,9 +114,16 @@ slots: range: PhysicalQuality enums: MetazoanAnatomicalStructure: + title: Metazoan Anatomical Structure description: 'Any anatomical structure found in metazoan organisms, including organs, tissues, and body parts' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_ontology: obo:uberon source_nodes: @@ -122,7 +132,14 @@ enums: relationship_types: - rdfs:subClassOf HumanAnatomicalStructure: + title: Human Anatomical Structure description: Anatomical structures specific to humans (Homo sapiens) + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_ontology: obo:uberon source_nodes: @@ -131,7 +148,14 @@ enums: relationship_types: - rdfs:subClassOf PlantAnatomicalStructure: + title: Plant Anatomical Structure description: Any anatomical structure found in plant organisms + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_ontology: obo:po source_nodes: @@ -140,9 +164,16 @@ enums: relationship_types: - rdfs:subClassOf CellType: + title: Cell Type description: 'Any cell type from the Cell Ontology (CL), including native and experimentally modified cells' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_ontology: obo:cl source_nodes: @@ -151,7 +182,14 @@ enums: relationship_types: - rdfs:subClassOf NeuronType: + title: Neuron Type description: Neuron cell types from the Cell Ontology + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_ontology: obo:cl source_nodes: @@ -160,7 +198,14 @@ enums: relationship_types: - rdfs:subClassOf ImmuneCell: + title: Immune Cell description: Immune system cell types (leukocytes and their subtypes) + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_ontology: obo:cl source_nodes: @@ -169,7 +214,14 @@ enums: relationship_types: - rdfs:subClassOf StemCell: + title: Stem Cell description: Stem cell types and progenitor cells + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_ontology: obo:cl source_nodes: @@ -179,7 +231,14 @@ enums: relationship_types: - rdfs:subClassOf Disease: + title: Disease description: Human diseases from the Mondo Disease Ontology + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_ontology: obo:mondo source_nodes: @@ -188,7 +247,14 @@ enums: relationship_types: - rdfs:subClassOf InfectiousDisease: + title: Infectious Disease description: Infectious diseases caused by pathogenic organisms + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_ontology: obo:mondo source_nodes: @@ -197,7 +263,14 @@ enums: relationship_types: - rdfs:subClassOf Cancer: + title: Cancer description: Neoplastic and cancerous diseases + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_ontology: obo:mondo source_nodes: @@ -207,7 +280,14 @@ enums: relationship_types: - rdfs:subClassOf GeneticDisease: + title: Genetic Disease description: Hereditary and genetic diseases + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_ontology: obo:mondo source_nodes: @@ -217,7 +297,14 @@ enums: relationship_types: - rdfs:subClassOf ChemicalEntity: + title: Chemical Entity description: Any chemical entity from ChEBI ontology + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_ontology: obo:chebi source_nodes: @@ -226,7 +313,14 @@ enums: relationship_types: - rdfs:subClassOf Drug: + title: Drug description: Pharmaceutical drugs and medications + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_ontology: obo:chebi source_nodes: @@ -236,7 +330,14 @@ enums: - rdfs:subClassOf - RO:0000087 Metabolite: + title: Metabolite description: Metabolites and metabolic intermediates + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_ontology: obo:chebi source_nodes: @@ -245,7 +346,14 @@ enums: relationship_types: - rdfs:subClassOf Protein: + title: Protein description: Proteins and protein complexes + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_ontology: obo:pr source_nodes: @@ -254,7 +362,14 @@ enums: relationship_types: - rdfs:subClassOf Phenotype: + title: Phenotype description: Phenotypic abnormalities from Human Phenotype Ontology + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_ontology: obo:hp source_nodes: @@ -263,7 +378,14 @@ enums: relationship_types: - rdfs:subClassOf ClinicalFinding: + title: Clinical Finding description: Clinical findings and observations + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_ontology: obo:hp source_nodes: @@ -272,7 +394,14 @@ enums: relationship_types: - rdfs:subClassOf BiologicalProcess: + title: Biological Process description: Biological processes from Gene Ontology + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_ontology: obo:go source_nodes: @@ -281,7 +410,14 @@ enums: relationship_types: - rdfs:subClassOf MetabolicProcess: + title: Metabolic Process description: Metabolic processes and pathways + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_ontology: obo:go source_nodes: @@ -290,7 +426,14 @@ enums: relationship_types: - rdfs:subClassOf MolecularFunction: + title: Molecular Function description: Molecular functions from Gene Ontology + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_ontology: obo:go source_nodes: @@ -299,7 +442,14 @@ enums: relationship_types: - rdfs:subClassOf CellularComponent: + title: Cellular Component description: Cellular components and locations from Gene Ontology + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_ontology: obo:go source_nodes: @@ -308,7 +458,14 @@ enums: relationship_types: - rdfs:subClassOf SequenceFeature: + title: Sequence Feature description: Sequence features from the Sequence Ontology + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_ontology: obo:so source_nodes: @@ -317,7 +474,14 @@ enums: relationship_types: - rdfs:subClassOf GeneFeature: + title: Gene Feature description: Gene-related sequence features + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_ontology: obo:so source_nodes: @@ -326,7 +490,14 @@ enums: relationship_types: - rdfs:subClassOf Environment: + title: Environment description: Environmental systems and biomes + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_ontology: obo:envo source_nodes: @@ -336,7 +507,14 @@ enums: relationship_types: - rdfs:subClassOf EnvironmentalMaterial: + title: Environmental Material description: Environmental materials and substances + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_ontology: obo:envo source_nodes: @@ -345,7 +523,14 @@ enums: relationship_types: - rdfs:subClassOf Quality: + title: Quality description: Phenotypic qualities and attributes from PATO + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_ontology: obo:pato source_nodes: @@ -354,7 +539,14 @@ enums: relationship_types: - rdfs:subClassOf PhysicalQuality: + title: Physical Quality description: Physical qualities like size, shape, color + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_ontology: obo:pato source_nodes: diff --git a/src/valuesets/schema/bio/biological_colors.yaml b/src/valuesets/schema/bio/biological_colors.yaml index 0451f448..c5deadf1 100644 --- a/src/valuesets/schema/bio/biological_colors.yaml +++ b/src/valuesets/schema/bio/biological_colors.yaml @@ -15,6 +15,8 @@ prefixes: TO: http://purl.obolibrary.org/obo/TO_ VT: http://purl.obolibrary.org/obo/VT_ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: eye_color: @@ -37,7 +39,14 @@ slots: range: PlantLeafColorEnum enums: EyeColorEnum: + title: Eye Color description: Human eye color phenotypes + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: BROWN: description: Brown eyes @@ -89,7 +98,14 @@ enums: hex_range: 8B7AB8-9370DB prevalence: extremely rare HairColorEnum: + title: Hair Color description: Human hair color phenotypes + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: BLACK: description: Black hair @@ -162,7 +178,14 @@ enums: annotations: hex: C0C0C0 FlowerColorEnum: + title: Flower Color description: Common flower colors + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: RED: description: Red flowers @@ -243,7 +266,14 @@ enums: annotations: note: flowers with more than two colors AnimalCoatColorEnum: + title: Animal Coat Color description: Animal coat/fur colors + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: BLACK: description: Black coat @@ -332,7 +362,14 @@ enums: annotations: species: horses SkinToneEnum: + title: Skin Tone description: Human skin tone classifications (Fitzpatrick scale based) + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: TYPE_I: description: Very pale white skin @@ -371,7 +408,14 @@ enums: hex_range: 5C3A1E-3D2314 sun_reaction: never burns, always tans darkly PlantLeafColorEnum: + title: Plant Leaf Color description: Plant leaf colors (including seasonal changes) + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: GREEN: description: Green leaves (healthy/summer) diff --git a/src/valuesets/schema/bio/biosafety.yaml b/src/valuesets/schema/bio/biosafety.yaml index 54afbcd8..963156d9 100644 --- a/src/valuesets/schema/bio/biosafety.yaml +++ b/src/valuesets/schema/bio/biosafety.yaml @@ -4,6 +4,8 @@ prefixes: SNOMED: http://snomed.info/id/ METPO: https://w3id.org/metpo/ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: biosafety_level: @@ -11,29 +13,37 @@ slots: range: BiosafetyLevelEnum enums: BiosafetyLevelEnum: + title: Biosafety Level description: Biosafety levels (BSL) defining containment requirements for biological agents + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: BSL1: description: Suitable for well-characterized agents not known to consistently cause disease in healthy adults meaning: SNOMED:409600007 exact_mappings: - - METPO:1001102 + - METPO:1001102 title: biosafety level 1 BSL2: description: Suitable for agents that pose moderate hazards to personnel and the environment meaning: SNOMED:409603009 exact_mappings: - - METPO:1001103 + - METPO:1001103 title: biosafety level 2 BSL3: - description: Suitable for indigenous or exotic agents that may cause serious or potentially lethal disease through inhalation + description: Suitable for indigenous or exotic agents that may cause serious or potentially lethal disease + through inhalation meaning: SNOMED:409604003 exact_mappings: - - METPO:1001104 + - METPO:1001104 title: biosafety level 3 BSL4: description: Suitable for dangerous and exotic agents that pose high risk of life-threatening disease meaning: SNOMED:409605002 exact_mappings: - - METPO:1001105 + - METPO:1001105 title: biosafety level 4 diff --git a/src/valuesets/schema/bio/cell_cycle.yaml b/src/valuesets/schema/bio/cell_cycle.yaml index 9131b1b5..69a714ff 100644 --- a/src/valuesets/schema/bio/cell_cycle.yaml +++ b/src/valuesets/schema/bio/cell_cycle.yaml @@ -5,8 +5,11 @@ id: https://w3id.org/linkml/valuesets/bio/cell_cycle imports: - linkml:types prefixes: + linkml: https://w3id.org/linkml/ valuesets: https://w3id.org/valuesets/ GO: http://purl.obolibrary.org/obo/GO_ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: cell_cycle_phase: @@ -32,7 +35,14 @@ slots: range: DNADamageResponse enums: CellCyclePhase: + title: Cell Cycle Phase description: Major phases of the eukaryotic cell cycle + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: G0: description: G0 phase (quiescent/resting phase) @@ -74,7 +84,14 @@ enums: annotations: includes: G1, S, G2 MitoticPhase: + title: Mitotic Phase description: Stages of mitosis (M phase) + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: PROPHASE: description: Prophase @@ -114,7 +131,14 @@ enums: order: 6 features: cytoplasmic division CellCycleCheckpoint: + title: Cell Cycle Checkpoint description: Cell cycle checkpoints that regulate progression + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: G1_S_CHECKPOINT: description: G1/S checkpoint (Restriction point) @@ -146,7 +170,14 @@ enums: function: ensures proper chromosome attachment regulator: MAD2, BubR1 MeioticPhase: + title: Meiotic Phase description: Phases specific to meiotic cell division + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: MEIOSIS_I: description: Meiosis I (reductional division) @@ -199,7 +230,14 @@ enums: meaning: GO:0007139 title: meiotic telophase II CellCycleRegulator: + title: Cell Cycle Regulator description: Types of cell cycle regulatory molecules + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: CYCLIN: description: Cyclin proteins @@ -234,8 +272,8 @@ enums: E3_UBIQUITIN_LIGASE: description: E3 ubiquitin ligase (cell cycle) meaning: GO:0051437 - title: obsolete positive regulation of ubiquitin-protein ligase activity involved in regulation of mitotic cell cycle - transition + title: obsolete positive regulation of ubiquitin-protein ligase activity involved in regulation of mitotic cell + cycle transition annotations: examples: APC/C, SCF PHOSPHATASE: @@ -245,7 +283,14 @@ enums: annotations: examples: CDC25A, CDC25B, CDC25C CellProliferationState: + title: Cell Proliferation State description: Cell proliferation and growth states + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: PROLIFERATING: description: Actively proliferating cells @@ -284,7 +329,14 @@ enums: annotations: type: uncontrolled cell death DNADamageResponse: + title: DNA Damage Response description: DNA damage response pathways during cell cycle + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: CELL_CYCLE_ARREST: description: Cell cycle arrest diff --git a/src/valuesets/schema/bio/currency_chemicals.yaml b/src/valuesets/schema/bio/currency_chemicals.yaml index 51c20dc5..7dcff9ae 100644 --- a/src/valuesets/schema/bio/currency_chemicals.yaml +++ b/src/valuesets/schema/bio/currency_chemicals.yaml @@ -9,16 +9,25 @@ prefixes: linkml: https://w3id.org/linkml/ CHEBI: http://purl.obolibrary.org/obo/CHEBI_ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: currency_chemical: - description: Common metabolic currency molecules and cofactors that serve as energy carriers, electron donors/acceptors, - and group transfer agents in cellular metabolism + description: Common metabolic currency molecules and cofactors that serve as energy carriers, electron + donors/acceptors, and group transfer agents in cellular metabolism range: CurrencyChemical enums: CurrencyChemical: - description: Common metabolic currency molecules and cofactors that serve as energy carriers, electron donors/acceptors, - and group transfer agents in cellular metabolism. + title: Currency Chemical + description: Common metabolic currency molecules and cofactors that serve as energy carriers, electron + donors/acceptors, and group transfer agents in cellular metabolism. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ATP: description: Adenosine triphosphate - primary energy currency molecule in cells diff --git a/src/valuesets/schema/bio/developmental_stages.yaml b/src/valuesets/schema/bio/developmental_stages.yaml index b71aaee8..7ad82467 100644 --- a/src/valuesets/schema/bio/developmental_stages.yaml +++ b/src/valuesets/schema/bio/developmental_stages.yaml @@ -1,7 +1,7 @@ name: developmental_stages title: Developmental Stages Value Sets -description: Ontology-mapped developmental stages for human and mouse organisms. Human stages use HsapDv (Human Developmental - Stages) ontology. Mouse stages use MmusDv (Mouse Developmental Stages) ontology. +description: Ontology-mapped developmental stages for human and mouse organisms. Human stages use HsapDv (Human + Developmental Stages) ontology. Mouse stages use MmusDv (Mouse Developmental Stages) ontology. id: https://w3id.org/valuesets/bio/developmental_stages imports: - linkml:types @@ -11,6 +11,8 @@ prefixes: MmusDv: http://purl.obolibrary.org/obo/MmusDv_ UBERON: http://purl.obolibrary.org/obo/UBERON_ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: human_developmental_stage: @@ -21,54 +23,62 @@ slots: range: MouseDevelopmentalStage enums: HumanDevelopmentalStage: + title: Human Developmental Stage + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ZYGOTE_STAGE: text: ZYGOTE_STAGE title: Carnegie stage 01 meaning: HsapDv:0000003 - description: Embryonic stage defined by a fertilized oocyte and presence of pronuclei. Starts at day 1 post-fertilization. + description: Embryonic stage defined by a fertilized oocyte and presence of pronuclei. Starts at day 1 + post-fertilization. CLEAVAGE_STAGE: text: CLEAVAGE_STAGE title: Carnegie stage 02 meaning: HsapDv:0000005 - description: Embryonic stage during which cell division occurs with reduction in cytoplasmic volume, and formation - of inner and outer cell mass. 2-8 cells. Usually starts between day 2-3 post-fertilization. + description: Embryonic stage during which cell division occurs with reduction in cytoplasmic volume, and + formation of inner and outer cell mass. 2-8 cells. Usually starts between day 2-3 post-fertilization. MORULA_STAGE: text: MORULA_STAGE title: morula stage meaning: HsapDv:0000205 - description: The later part of Carnegie stage 02 when the cells have coalesced into a mass but the blastocystic cavity - has not formed. + description: The later part of Carnegie stage 02 when the cells have coalesced into a mass but the blastocystic + cavity has not formed. BLASTOCYST_STAGE: text: BLASTOCYST_STAGE title: Carnegie stage 03 meaning: HsapDv:0000007 - description: Blastula stage with the loss of the zona pellucida and the definition of a free blastocyst. Usually starts - between day 4-5 post-fertilization. + description: Blastula stage with the loss of the zona pellucida and the definition of a free blastocyst. Usually + starts between day 4-5 post-fertilization. GASTRULA_STAGE: text: GASTRULA_STAGE title: gastrula stage meaning: HsapDv:0000010 - description: Embryonic stage defined by a complex and coordinated series of cellular movements that occurs at the - end of cleavage. + description: Embryonic stage defined by a complex and coordinated series of cellular movements that occurs at + the end of cleavage. NEURULA_STAGE: text: NEURULA_STAGE title: neurula stage meaning: HsapDv:0000012 - description: Embryonic stage defined by the formation of a tube from the flat layer of ectodermal cells known as the - neural plate. This stage starts the emergence of the central nervous system. + description: Embryonic stage defined by the formation of a tube from the flat layer of ectodermal cells known as + the neural plate. This stage starts the emergence of the central nervous system. ORGANOGENESIS_STAGE: text: ORGANOGENESIS_STAGE title: organogenesis stage meaning: HsapDv:0000015 - description: Embryonic stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the - organism. + description: Embryonic stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of + the organism. FETAL_STAGE: text: FETAL_STAGE title: fetal stage meaning: HsapDv:0000037 - description: Prenatal stage that starts with the fully formed embryo and ends at birth. Generally from 8 weeks post-fertilization - until birth. + description: Prenatal stage that starts with the fully formed embryo and ends at birth. Generally from 8 weeks + post-fertilization until birth. NEONATAL_STAGE: text: NEONATAL_STAGE title: newborn stage (0-28 days) @@ -83,57 +93,64 @@ enums: text: TODDLER_STAGE title: child stage (1-4 yo) meaning: HsapDv:0000265 - description: Human stage that refers to a child who is over 12 months and under 5 years old. Often divided into early - toddler (1-2 years) and late toddler (2-3 years). + description: Human stage that refers to a child who is over 12 months and under 5 years old. Often divided into + early toddler (1-2 years) and late toddler (2-3 years). CHILD_STAGE: text: CHILD_STAGE title: juvenile stage (5-14 yo) meaning: HsapDv:0000271 - description: Pediatric stage that refers to a human who is over 5 and under 15 years old. Covers elementary and middle - school ages. + description: Pediatric stage that refers to a human who is over 5 and under 15 years old. Covers elementary and + middle school ages. ADOLESCENT_STAGE: text: ADOLESCENT_STAGE title: 15-19 year-old meaning: HsapDv:0000268 - description: A young adult stage that refers to an individual who is over 15 and under 20 years old. Period of transition - from childhood to adulthood. + description: A young adult stage that refers to an individual who is over 15 and under 20 years old. Period of + transition from childhood to adulthood. ADULT_STAGE: text: ADULT_STAGE title: adult stage meaning: HsapDv:0000258 - description: Human developmental stage that refers to a sexually mature human. Starts at approximately 15 years according - to HPO definitions. + description: Human developmental stage that refers to a sexually mature human. Starts at approximately 15 years + according to HPO definitions. AGED_STAGE: text: AGED_STAGE title: late adult stage meaning: HsapDv:0000227 - description: Late adult stage that refers to an individual who is over 60 and starts to have some age-related impairments. - Often subdivided into young-old (60-79) and old-old (80+). + description: Late adult stage that refers to an individual who is over 60 and starts to have some age-related + impairments. Often subdivided into young-old (60-79) and old-old (80+). EMBRYONIC_STAGE: text: EMBRYONIC_STAGE title: embryonic stage meaning: HsapDv:0000002 - description: Prenatal stage that starts with fertilization and ends with a fully formed embryo, before undergoing - last development during the fetal stage. Up to 8 weeks post-fertilization. + description: Prenatal stage that starts with fertilization and ends with a fully formed embryo, before + undergoing last development during the fetal stage. Up to 8 weeks post-fertilization. PRENATAL_STAGE: text: PRENATAL_STAGE title: prenatal stage meaning: HsapDv:0000045 - description: Prenatal stage that starts with fertilization and ends at birth. Encompasses both embryonic and fetal - stages. + description: Prenatal stage that starts with fertilization and ends at birth. Encompasses both embryonic and + fetal stages. POSTNATAL_STAGE: text: POSTNATAL_STAGE title: postnatal stage meaning: HsapDv:0010000 description: Human developmental stage that covers the whole of human life post birth. MouseDevelopmentalStage: + title: Mouse Developmental Stage + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ZYGOTE_STAGE: text: ZYGOTE_STAGE title: Theiler stage 01 meaning: MmusDv:0000003 - description: Embryonic stage defined by a one-cell embryo (fertilised egg) with zona pellucida present. Embryonic - age 0-0.9 dpc (days post coitum). + description: Embryonic stage defined by a one-cell embryo (fertilised egg) with zona pellucida present. + Embryonic age 0-0.9 dpc (days post coitum). TWO_CELL_STAGE: text: TWO_CELL_STAGE title: Theiler stage 02 @@ -153,31 +170,32 @@ enums: text: MORULA_STAGE title: Theiler stage 03 meaning: MmusDv:0000006 - description: Embryonic cleavage stage defined by a dividing 4-16 cells egg, early to fully compacted morula. Embryonic - age 2 dpc. + description: Embryonic cleavage stage defined by a dividing 4-16 cells egg, early to fully compacted morula. + Embryonic age 2 dpc. BLASTOCYST_STAGE: text: BLASTOCYST_STAGE title: Theiler stage 05 meaning: MmusDv:0000009 - description: Embryonic blastula stage defined by a zona free blastocyst (zona pellucida absent). Embryonic age 4 dpc. + description: Embryonic blastula stage defined by a zona free blastocyst (zona pellucida absent). Embryonic age 4 + dpc. GASTRULA_STAGE: text: GASTRULA_STAGE title: gastrula stage meaning: MmusDv:0000013 - description: Embryonic stage defined by complex and coordinated series of cellular movements that occurs at the end - of cleavage. + description: Embryonic stage defined by complex and coordinated series of cellular movements that occurs at the + end of cleavage. NEURULA_STAGE: text: NEURULA_STAGE title: Theiler stage 11 meaning: MmusDv:0000017 - description: Embryonic stage called presomite stage and defined by the formation of the neural plate. This stage starts - the emergence of the central nervous system at embryonic age 7.5 dpc. + description: Embryonic stage called presomite stage and defined by the formation of the neural plate. This stage + starts the emergence of the central nervous system at embryonic age 7.5 dpc. ORGANOGENESIS_STAGE: text: ORGANOGENESIS_STAGE title: organogenesis stage meaning: MmusDv:0000018 - description: Embryonic stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the - organism. + description: Embryonic stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of + the organism. E0_5: text: E0_5 title: Theiler stage 01 @@ -187,12 +205,14 @@ enums: text: E9_5 title: Theiler stage 16 meaning: MmusDv:0000023 - description: Embryonic day 9.5 - organogenesis stage with visible hind limb buds. Between Theiler stages 15 and 16. + description: Embryonic day 9.5 - organogenesis stage with visible hind limb buds. Between Theiler stages 15 and + 16. E14_5: text: E14_5 title: Theiler stage 22 meaning: MmusDv:0000029 - description: Embryonic day 14.5 - late organogenesis with clearly visible fingers and long bones of the limbs present. + description: Embryonic day 14.5 - late organogenesis with clearly visible fingers and long bones of the limbs + present. P0_NEWBORN: text: P0_NEWBORN title: Theiler stage 27 @@ -220,7 +240,7 @@ enums: description: Middle aged stage for mice over 10 and under 18 months old. Shows progressive age-related changes. THEILER_STAGE: text: THEILER_STAGE - description: Reference to any Theiler stage (TS1-TS28) which provides standardized morphological staging for mouse - development. + description: Reference to any Theiler stage (TS1-TS28) which provides standardized morphological staging for + mouse development. license: Apache-2.0 default_range: string diff --git a/src/valuesets/schema/bio/genome_features.yaml b/src/valuesets/schema/bio/genome_features.yaml index 334e95f6..26fbb567 100644 --- a/src/valuesets/schema/bio/genome_features.yaml +++ b/src/valuesets/schema/bio/genome_features.yaml @@ -9,8 +9,11 @@ id: https://w3id.org/linkml/valuesets/bio/genome_features imports: - linkml:types prefixes: + linkml: https://w3id.org/linkml/ valuesets: https://w3id.org/valuesets/ SO: http://purl.obolibrary.org/obo/SO_ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: genome_feature: @@ -19,11 +22,18 @@ slots: multivalued: true enums: GenomeFeatureType: + title: Genome Feature Type description: 'Genome feature types from SOFA (Sequence Ontology Feature Annotation). This is the subset of Sequence Ontology terms used in GFF3 files. Organized hierarchically following the Sequence Ontology structure.' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: REGION: description: A sequence feature with an extent greater than zero @@ -33,7 +43,8 @@ enums: meaning: SO:0001411 is_a: REGION GENE: - description: A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript + description: A region (or regions) that includes all of the sequence elements necessary to encode a functional + transcript meaning: SO:0000704 is_a: BIOLOGICAL_REGION TRANSCRIPT: @@ -49,16 +60,18 @@ enums: meaning: SO:0000234 is_a: TRANSCRIPT EXON: - description: A region of the transcript sequence within a gene which is not removed from the primary RNA transcript - by RNA splicing + description: A region of the transcript sequence within a gene which is not removed from the primary RNA + transcript by RNA splicing meaning: SO:0000147 is_a: BIOLOGICAL_REGION CDS: - description: Coding sequence; sequence of nucleotides that corresponds with the sequence of amino acids in a protein + description: Coding sequence; sequence of nucleotides that corresponds with the sequence of amino acids in a + protein meaning: SO:0000316 is_a: BIOLOGICAL_REGION INTRON: - description: A region of a primary transcript that is transcribed, but removed from within the transcript by splicing + description: A region of a primary transcript that is transcribed, but removed from within the transcript by + splicing meaning: SO:0000188 is_a: BIOLOGICAL_REGION FIVE_PRIME_UTR: @@ -133,8 +146,8 @@ enums: meaning: SO:0000625 is_a: REGULATORY_REGION TERMINATOR: - description: The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate - transcription + description: The sequence of DNA located either at the end of the transcript that causes RNA polymerase to + terminate transcription meaning: SO:0000141 is_a: REGULATORY_REGION ATTENUATOR: diff --git a/src/valuesets/schema/bio/genomics.yaml b/src/valuesets/schema/bio/genomics.yaml index 4e0543bb..5f3a3db7 100644 --- a/src/valuesets/schema/bio/genomics.yaml +++ b/src/valuesets/schema/bio/genomics.yaml @@ -9,11 +9,13 @@ prefixes: linkml: https://w3id.org/linkml/ mixs: http://purl.obolibrary.org/obo/MIXS_ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: cds_phase: - description: For features of type CDS (coding sequence), the phase indicates where the feature begins with reference to - the reading frame + description: For features of type CDS (coding sequence), the phase indicates where the feature begins with reference + to the reading frame range: CdsPhaseType contig_collection: description: The type of the contig set; the type of the 'omics data set @@ -26,9 +28,16 @@ slots: range: SequenceType enums: CdsPhaseType: - description: For features of type CDS (coding sequence), the phase indicates where the feature begins with reference to - the reading frame. The phase is one of the integers 0, 1, or 2, indicating the number of bases that should be removed - from the beginning of this feature to reach the first base of the next codon. + title: Cds Phase Type + description: For features of type CDS (coding sequence), the phase indicates where the feature begins with reference + to the reading frame. The phase is one of the integers 0, 1, or 2, indicating the number of bases that should be + removed from the beginning of this feature to reach the first base of the next codon. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: PHASE_0: description: Zero bases from reading frame to feature start. @@ -40,17 +49,24 @@ enums: description: Two bases from reading frame to feature start. title: '2' ContigCollectionType: - description: The type of the contig set; the type of the 'omics data set. Terms are taken from the Genomics Standards - Consortium where possible. See the GSC checklists at https://genomicsstandardsconsortium.github.io/mixs/ for the controlled - vocabularies used. + title: Contig Collection Type + description: The type of the contig set; the type of the 'omics data set. Terms are taken from the Genomics + Standards Consortium where possible. See the GSC checklists at https://genomicsstandardsconsortium.github.io/mixs/ + for the controlled vocabularies used. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ISOLATE: description: 'Sequences assembled from DNA of isolated organism. Bacteria/Archaea: https://genomicsstandardsconsortium.github.io/mixs/0010003/ Euk: https://genomicsstandardsconsortium.github.io/mixs/0010002/ Virus: https://genomicsstandardsconsortium.github.io/mixs/0010005/ Organelle: https://genomicsstandardsconsortium.github.io/mixs/0010006/ Plasmid: https://genomicsstandardsconsortium.github.io/mixs/0010004/' MAG: - description: Sequences assembled from DNA of mixed community and binned. MAGs are likely to represent a single taxonomic - origin. See checkm2 scores for quality assessment. + description: Sequences assembled from DNA of mixed community and binned. MAGs are likely to represent a single + taxonomic origin. See checkm2 scores for quality assessment. meaning: mixs:0010011 title: Mimag aliases: @@ -75,7 +91,15 @@ enums: description: 'Sequences from targeted region of DNA; see protocol for information on targeted region. specimen: https://genomicsstandardsconsortium.github.io/mixs/0010009/ survey: https://genomicsstandardsconsortium.github.io/mixs/0010008/' StrandType: - description: The strand that a feature appears on relative to a landmark. Also encompasses unknown or irrelevant strandedness. + title: Strand Type + description: The strand that a feature appears on relative to a landmark. Also encompasses unknown or irrelevant + strandedness. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: NEGATIVE: description: Represented by "-" in a GFF file; the strand is negative wrt the landmark. @@ -90,7 +114,14 @@ enums: description: Represented by "." in a GFF file; the feature is not stranded. title: unstranded SequenceType: + title: Sequence Type description: The type of sequence being represented. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: NUCLEIC_ACID: description: A nucleic acid sequence, as found in an FNA file. diff --git a/src/valuesets/schema/bio/go_aspect.yaml b/src/valuesets/schema/bio/go_aspect.yaml index 81120e4f..5ba3d302 100644 --- a/src/valuesets/schema/bio/go_aspect.yaml +++ b/src/valuesets/schema/bio/go_aspect.yaml @@ -5,8 +5,11 @@ id: https://w3id.org/linkml/valuesets/bio/go_aspect imports: - linkml:types prefixes: + linkml: https://w3id.org/linkml/ valuesets: https://w3id.org/valuesets/ GO: http://purl.obolibrary.org/obo/GO_ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: go_aspect: @@ -14,7 +17,17 @@ slots: range: GOAspect enums: GOAspect: + title: GO Aspect description: The three main aspects (namespaces) of Gene Ontology + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + stewards: https://geneontology.org + publishers: https://geneontology.org permissible_values: F: title: Molecular Function @@ -36,4 +49,4 @@ enums: aliases: - cellular_component - CC - meaning: GO:0005575 \ No newline at end of file + meaning: GO:0005575 diff --git a/src/valuesets/schema/bio/go_causality.yaml b/src/valuesets/schema/bio/go_causality.yaml index 65ea4e72..fbbe28f6 100644 --- a/src/valuesets/schema/bio/go_causality.yaml +++ b/src/valuesets/schema/bio/go_causality.yaml @@ -1,6 +1,7 @@ name: go_causality title: Gene Ontology Causality Value Sets -description: Value sets for GO causal relationships and predicates used in gene ontology annotations and pathway analysis +description: Value sets for GO causal relationships and predicates used in gene ontology annotations and pathway + analysis id: https://w3id.org/valuesets/bio/go_causality imports: - linkml:types @@ -8,6 +9,8 @@ prefixes: linkml: https://w3id.org/linkml/ RO: http://purl.obolibrary.org/obo/RO_ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: causal_predicate: @@ -15,8 +18,18 @@ slots: range: CausalPredicateEnum enums: CausalPredicateEnum: - description: A term describing the causal relationship between two activities. All terms are drawn from - the "causally upstream or within" (RO:0002418) branch of the Relation Ontology (RO). + title: Causal Predicate + description: A term describing the causal relationship between two activities. All terms are drawn from the + "causally upstream or within" (RO:0002418) branch of the Relation Ontology (RO). + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + stewards: https://geneontology.org + publishers: https://geneontology.org permissible_values: CONSTITUTIVELY_UPSTREAM_OF: title: constitutively upstream of @@ -116,4 +129,4 @@ enums: is_a: IS_SMALL_MOLECULE_REGULATOR_OF meaning: RO:0012006 annotations: - direction: NEGATIVE \ No newline at end of file + direction: NEGATIVE diff --git a/src/valuesets/schema/bio/go_evidence.yaml b/src/valuesets/schema/bio/go_evidence.yaml index 3095d2b8..131ff0c6 100644 --- a/src/valuesets/schema/bio/go_evidence.yaml +++ b/src/valuesets/schema/bio/go_evidence.yaml @@ -5,9 +5,12 @@ id: https://w3id.org/linkml/valuesets/bio/go_evidence imports: - linkml:types prefixes: + linkml: https://w3id.org/linkml/ valuesets: https://w3id.org/valuesets/ ECO: http://purl.obolibrary.org/obo/ECO_ GO_REF: http://purl.obolibrary.org/obo/GO_REF_ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: go_evidence: @@ -18,7 +21,17 @@ slots: range: GOElectronicMethods enums: GOEvidenceCode: + title: GO Evidence Code description: Gene Ontology evidence codes mapped to Evidence and Conclusion Ontology (ECO) terms + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + stewards: https://geneontology.org + publishers: https://geneontology.org permissible_values: EXP: title: Inferred from Experiment @@ -151,7 +164,17 @@ enums: - evidence used in automatic assertion meaning: ECO:0000501 GOElectronicMethods: + title: GO Electronic Methods description: Electronic annotation methods used in Gene Ontology, identified by GO_REF codes + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + stewards: https://geneontology.org + publishers: https://geneontology.org permissible_values: INTERPRO2GO: title: Gene Ontology annotation based on InterPro classification diff --git a/src/valuesets/schema/bio/insdc_geographic_locations.yaml b/src/valuesets/schema/bio/insdc_geographic_locations.yaml index ecb98945..f21943aa 100644 --- a/src/valuesets/schema/bio/insdc_geographic_locations.yaml +++ b/src/valuesets/schema/bio/insdc_geographic_locations.yaml @@ -14,6 +14,8 @@ prefixes: iso3166loc: http://id.loc.gov/vocabulary/countries/ geonames: http://sws.geonames.org/ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: insdc_geographic_location: @@ -21,11 +23,21 @@ slots: range: InsdcGeographicLocationEnum enums: InsdcGeographicLocationEnum: + title: Insdc Geographic Location description: 'INSDC controlled vocabulary for geographic locations of collected samples. Includes countries, oceans, seas, and other geographic regions as defined by INSDC. Countries use ISO 3166-1 alpha-2 codes from Library of Congress as canonical identifiers.' + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + stewards: https://gensc.org + publishers: https://www.insdc.org permissible_values: AFGHANISTAN: description: Afghanistan diff --git a/src/valuesets/schema/bio/insdc_missing_values.yaml b/src/valuesets/schema/bio/insdc_missing_values.yaml index 9b310874..5bc57d18 100644 --- a/src/valuesets/schema/bio/insdc_missing_values.yaml +++ b/src/valuesets/schema/bio/insdc_missing_values.yaml @@ -7,20 +7,32 @@ prefixes: SIO: http://semanticscience.org/resource/SIO_ insdc: https://www.insdc.org/controlled-vocabulary/missing-value/ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: insdc_missing_value: - description: INSDC (International Nucleotide Sequence Database Collaboration) controlled vocabulary for missing values - in sequence records + description: INSDC (International Nucleotide Sequence Database Collaboration) controlled vocabulary for missing + values in sequence records range: InsdcMissingValueEnum enums: InsdcMissingValueEnum: - description: INSDC (International Nucleotide Sequence Database Collaboration) controlled vocabulary for missing values - in sequence records + title: Insdc Missing Value + description: INSDC (International Nucleotide Sequence Database Collaboration) controlled vocabulary for missing + values in sequence records + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + stewards: https://gensc.org + publishers: https://www.insdc.org permissible_values: NOT_APPLICABLE: - description: Information is inappropriate to report, can indicate that the standard itself fails to model or represent - the information appropriately + description: Information is inappropriate to report, can indicate that the standard itself fails to model or + represent the information appropriately meaning: NCIT:C48660 title: not applicable MISSING: @@ -46,13 +58,13 @@ enums: annotations: note: NCIT:C67110 represents Data Not Releasable due to confidentiality MISSING_CONTROL_SAMPLE: - description: Information is not applicable to control samples, negative control samples (e.g. blank sample or clear - sample) + description: Information is not applicable to control samples, negative control samples (e.g. blank sample or + clear sample) annotations: note: No specific ontology term found for missing control sample data MISSING_SAMPLE_GROUP: - description: Information can not be provided for a sample group where a selection of samples is used to represent - a species, location or some other attribute/metric + description: Information can not be provided for a sample group where a selection of samples is used to + represent a species, location or some other attribute/metric annotations: note: No specific ontology term found for missing sample group data MISSING_SYNTHETIC_CONSTRUCT: @@ -60,8 +72,8 @@ enums: annotations: note: No specific ontology term found for missing synthetic construct data MISSING_LAB_STOCK: - description: Information is not collected for a lab stock and its cultivation, e.g. stock centers, culture collections, - seed banks + description: Information is not collected for a lab stock and its cultivation, e.g. stock centers, culture + collections, seed banks annotations: note: No specific ontology term found for missing lab stock data MISSING_THIRD_PARTY_DATA: @@ -71,8 +83,8 @@ enums: annotations: note: NCIT:C67329 represents Source Data Not Available MISSING_DATA_AGREEMENT_ESTABLISHED_PRE_2023: - description: Information can not be reported due to a data agreement established before metadata standards were introduced - in 2023 + description: Information can not be reported due to a data agreement established before metadata standards were + introduced in 2023 annotations: note: No specific ontology term for data missing due to pre-2023 agreements MISSING_ENDANGERED_SPECIES: diff --git a/src/valuesets/schema/bio/lipid_categories.yaml b/src/valuesets/schema/bio/lipid_categories.yaml index 84308ef7..b92167c9 100644 --- a/src/valuesets/schema/bio/lipid_categories.yaml +++ b/src/valuesets/schema/bio/lipid_categories.yaml @@ -9,6 +9,8 @@ prefixes: SLM: https://swisslipids.org/rdf/SLM_ CHEBI: http://purl.obolibrary.org/obo/CHEBI_ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: lipid_category: @@ -18,6 +20,12 @@ enums: LipidCategory: title: Lipid Category description: Major categories of lipids based on SwissLipids classification + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: LIPID: description: Lipid diff --git a/src/valuesets/schema/bio/plant_biology.yaml b/src/valuesets/schema/bio/plant_biology.yaml index febd45c7..5d50ea30 100644 --- a/src/valuesets/schema/bio/plant_biology.yaml +++ b/src/valuesets/schema/bio/plant_biology.yaml @@ -7,23 +7,33 @@ id: https://w3id.org/linkml/valuesets/bio/plant_biology imports: - linkml:types prefixes: + linkml: https://w3id.org/linkml/ valuesets: https://w3id.org/valuesets/ GSSO: http://purl.obolibrary.org/obo/GSSO_ PATO: http://purl.obolibrary.org/obo/PATO_ PO: http://purl.obolibrary.org/obo/PO_ TO: http://purl.obolibrary.org/obo/TO_ ECOCORE: http://purl.obolibrary.org/obo/ECOCORE_ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: plant_sexual_system: - description: Sexual systems in plants, describing the distribution and types of reproductive organs (flowers) within and - among individual plants + description: Sexual systems in plants, describing the distribution and types of reproductive organs (flowers) within + and among individual plants range: PlantSexualSystem enums: PlantSexualSystem: + title: Plant Sexual System description: 'Sexual systems in plants, describing the distribution and types of reproductive organs (flowers) within and among individual plants.' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ANDRODIOECIOUS: text: ANDRODIOECIOUS diff --git a/src/valuesets/schema/bio/plant_developmental_stages.yaml b/src/valuesets/schema/bio/plant_developmental_stages.yaml index d9f4eceb..530e3608 100644 --- a/src/valuesets/schema/bio/plant_developmental_stages.yaml +++ b/src/valuesets/schema/bio/plant_developmental_stages.yaml @@ -9,6 +9,8 @@ prefixes: linkml: https://w3id.org/linkml/ PO: http://purl.obolibrary.org/obo/PO_ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: plant_developmental_stage: @@ -16,8 +18,15 @@ slots: range: PlantDevelopmentalStage enums: PlantDevelopmentalStage: - description: Major developmental stages in the plant life cycle, from seed germination through senescence. Based on the - Plant Ontology (PO) standardized stages. + title: Plant Developmental Stage + description: Major developmental stages in the plant life cycle, from seed germination through senescence. Based on + the Plant Ontology (PO) standardized stages. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: SEED_GERMINATION_STAGE: description: Stage beginning with seed imbibition and ending with radicle emergence diff --git a/src/valuesets/schema/bio/plant_sex.yaml b/src/valuesets/schema/bio/plant_sex.yaml index 18376d59..04b88a5d 100644 --- a/src/valuesets/schema/bio/plant_sex.yaml +++ b/src/valuesets/schema/bio/plant_sex.yaml @@ -7,6 +7,8 @@ prefixes: ECOCORE: http://purl.obolibrary.org/obo/ECOCORE_ mixs: https://genomicsstandardsconsortium.github.io/mixs/ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: plant_sex: @@ -14,7 +16,14 @@ slots: range: PlantSexEnum enums: PlantSexEnum: + title: Plant Sex description: Plant reproductive and sexual system types + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ANDRODIOECIOUS: description: Having male and hermaphrodite flowers on separate plants diff --git a/src/valuesets/schema/bio/protein_evidence.yaml b/src/valuesets/schema/bio/protein_evidence.yaml index a7c570b2..db04d421 100644 --- a/src/valuesets/schema/bio/protein_evidence.yaml +++ b/src/valuesets/schema/bio/protein_evidence.yaml @@ -8,6 +8,8 @@ prefixes: CVS: https://w3id.org/common-value-sets/ linkml: https://w3id.org/linkml/ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: protein_evidence_for_existence: @@ -18,46 +20,61 @@ slots: range: RefSeqStatusType enums: ProteinEvidenceForExistence: - description: The evidence for the existence of a biological entity. See https://www.uniprot.org/help/protein_existence - and https://www.ncbi.nlm.nih.gov/genbank/evidence/. + title: Protein Evidence For Existence + description: The evidence for the existence of a biological entity. See + https://www.uniprot.org/help/protein_existence and https://www.ncbi.nlm.nih.gov/genbank/evidence/. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: EXPERIMENTAL_EVIDENCE_AT_PROTEIN_LEVEL: - description: Indicates that there is clear experimental evidence for the existence of the protein. The criteria include - partial or complete Edman sequencing, clear identification by mass spectrometry, X-ray or NMR structure, good quality - protein-protein interaction or detection of the protein by antibodies. + description: Indicates that there is clear experimental evidence for the existence of the protein. The criteria + include partial or complete Edman sequencing, clear identification by mass spectrometry, X-ray or NMR + structure, good quality protein-protein interaction or detection of the protein by antibodies. EXPERIMENTAL_EVIDENCE_AT_TRANSCRIPT_LEVEL: - description: Indicates that the existence of a protein has not been strictly proven but that expression data (such - as existence of cDNA(s), RT-PCR or Northern blots) indicate the existence of a transcript. + description: Indicates that the existence of a protein has not been strictly proven but that expression data + (such as existence of cDNA(s), RT-PCR or Northern blots) indicate the existence of a transcript. PROTEIN_INFERRED_BY_HOMOLOGY: - description: Indicates that the existence of a protein is probable because clear orthologs exist in closely related - species. + description: Indicates that the existence of a protein is probable because clear orthologs exist in closely + related species. PROTEIN_PREDICTED: description: Used for entries without evidence at protein, transcript, or homology levels. PROTEIN_UNCERTAIN: description: Indicates that the existence of the protein is unsure. RefSeqStatusType: + title: Ref Seq Status Type description: RefSeq status codes, taken from https://www.ncbi.nlm.nih.gov/genbank/evidence/. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: MODEL: - description: The RefSeq record is provided by the NCBI Genome Annotation pipeline and is not subject to individual - review or revision between annotation runs. + description: The RefSeq record is provided by the NCBI Genome Annotation pipeline and is not subject to + individual review or revision between annotation runs. INFERRED: - description: The RefSeq record has been predicted by genome sequence analysis, but it is not yet supported by experimental - evidence. The record may be partially supported by homology data. + description: The RefSeq record has been predicted by genome sequence analysis, but it is not yet supported by + experimental evidence. The record may be partially supported by homology data. PREDICTED: - description: The RefSeq record has not yet been subject to individual review, and some aspect of the RefSeq record - is predicted. + description: The RefSeq record has not yet been subject to individual review, and some aspect of the RefSeq + record is predicted. PROVISIONAL: - description: The RefSeq record has not yet been subject to individual review. The initial sequence-to-gene association - has been established by outside collaborators or NCBI staff. + description: The RefSeq record has not yet been subject to individual review. The initial sequence-to-gene + association has been established by outside collaborators or NCBI staff. REVIEWED: - description: The RefSeq record has been reviewed by NCBI staff or by a collaborator. The NCBI review process includes - assessing available sequence data and the literature. Some RefSeq records may incorporate expanded sequence and - annotation information. + description: The RefSeq record has been reviewed by NCBI staff or by a collaborator. The NCBI review process + includes assessing available sequence data and the literature. Some RefSeq records may incorporate expanded + sequence and annotation information. VALIDATED: - description: The RefSeq record has undergone an initial review to provide the preferred sequence standard. The record - has not yet been subject to final review at which time additional functional information may be provided. + description: The RefSeq record has undergone an initial review to provide the preferred sequence standard. The + record has not yet been subject to final review at which time additional functional information may be + provided. WGS: - description: The RefSeq record is provided to represent a collection of whole genome shotgun sequences. These records - are not subject to individual review or revisions between genome updates. + description: The RefSeq record is provided to represent a collection of whole genome shotgun sequences. These + records are not subject to individual review or revisions between genome updates. default_range: string diff --git a/src/valuesets/schema/bio/proteomics_standards.yaml b/src/valuesets/schema/bio/proteomics_standards.yaml index 150b3e86..42318470 100644 --- a/src/valuesets/schema/bio/proteomics_standards.yaml +++ b/src/valuesets/schema/bio/proteomics_standards.yaml @@ -12,6 +12,8 @@ prefixes: UO: http://purl.obolibrary.org/obo/UO_ cvs: https://w3id.org/common-value-sets/ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: peak_annotation_series_label: @@ -27,6 +29,12 @@ enums: PeakAnnotationSeriesLabel: title: Peak Annotation Series Label description: Types of peak annotations in mass spectrometry data + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: PEPTIDE: description: Peptide fragment ion @@ -57,6 +65,12 @@ enums: PeptideIonSeries: title: Peptide Ion Series description: Types of peptide fragment ion series in mass spectrometry + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: B: description: B ion series - N-terminal fragment with CO @@ -101,6 +115,12 @@ enums: MassErrorUnit: title: Mass Error Unit description: Units for expressing mass error in mass spectrometry + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: PPM: description: Parts per million - relative mass error diff --git a/src/valuesets/schema/bio/psi_mi.yaml b/src/valuesets/schema/bio/psi_mi.yaml index c0dc5fe6..d605a5e8 100644 --- a/src/valuesets/schema/bio/psi_mi.yaml +++ b/src/valuesets/schema/bio/psi_mi.yaml @@ -1,7 +1,7 @@ name: psi_mi title: PSI-MI (Molecular Interactions) Value Sets -description: Common value sets from the PSI-MI (Molecular Interactions) controlled vocabulary used for annotating protein-protein - interaction experiments. +description: Common value sets from the PSI-MI (Molecular Interactions) controlled vocabulary used for annotating + protein-protein interaction experiments. id: https://w3id.org/common-value-sets/bio/psi_mi imports: - linkml:types @@ -10,6 +10,8 @@ prefixes: linkml: https://w3id.org/linkml/ OBI: http://purl.obolibrary.org/obo/OBI_ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: interaction_detection_method: @@ -44,6 +46,12 @@ enums: InteractionDetectionMethod: title: Interaction Detection Method description: Methods used to detect molecular interactions + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinitionWithConformance source: http://purl.obolibrary.org/obo/mi.owl conforms_to: HUPO-PSI annotations: @@ -110,6 +118,12 @@ enums: InteractionType: title: Interaction Type description: Types of molecular interactions + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinitionWithConformance source: http://purl.obolibrary.org/obo/mi.owl conforms_to: HUPO-PSI permissible_values: @@ -157,6 +171,12 @@ enums: ExperimentalRole: title: Experimental Role description: Role played by a participant in the experiment + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinitionWithConformance source: http://purl.obolibrary.org/obo/mi.owl conforms_to: HUPO-PSI permissible_values: @@ -199,6 +219,12 @@ enums: BiologicalRole: title: Biological Role description: Physiological role of an interactor + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinitionWithConformance source: http://purl.obolibrary.org/obo/mi.owl conforms_to: HUPO-PSI permissible_values: @@ -237,6 +263,12 @@ enums: ParticipantIdentificationMethod: title: Participant Identification Method description: Methods to identify interaction participants + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: MASS_SPECTROMETRY: description: MS-based protein identification @@ -269,6 +301,12 @@ enums: FeatureType: title: Feature Type description: Molecular features affecting interactions + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: BINDING_SITE: description: Region involved in binding @@ -312,6 +350,12 @@ enums: InteractorType: title: Interactor Type description: Types of molecular species in interactions + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: PROTEIN: description: Polypeptide molecule @@ -358,6 +402,12 @@ enums: ConfidenceScore: title: Confidence Score Types description: Types of confidence scoring methods + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: INTACT_MISCORE: description: IntAct molecular interaction score @@ -373,6 +423,12 @@ enums: ExperimentalPreparation: title: Experimental Preparation description: Sample preparation methods + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: RECOMBINANT_EXPRESSION: description: Expressed in heterologous system diff --git a/src/valuesets/schema/bio/relationship_to_oxygen.yaml b/src/valuesets/schema/bio/relationship_to_oxygen.yaml index 7951b0d6..33313f8f 100644 --- a/src/valuesets/schema/bio/relationship_to_oxygen.yaml +++ b/src/valuesets/schema/bio/relationship_to_oxygen.yaml @@ -6,6 +6,8 @@ prefixes: MICRO: http://purl.obolibrary.org/obo/MICRO_ mixs: https://genomicsstandardsconsortium.github.io/mixs/ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: rel_to_oxygen: @@ -13,7 +15,14 @@ slots: range: RelToOxygenEnum enums: RelToOxygenEnum: + title: Rel To Oxygen description: Organism's relationship to oxygen for growth and survival + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: AEROBE: description: Organism that can survive and grow in an oxygenated environment diff --git a/src/valuesets/schema/bio/sequence_alphabets.yaml b/src/valuesets/schema/bio/sequence_alphabets.yaml index d9dbd2b9..38ec5552 100644 --- a/src/valuesets/schema/bio/sequence_alphabets.yaml +++ b/src/valuesets/schema/bio/sequence_alphabets.yaml @@ -14,6 +14,8 @@ prefixes: EDAM: http://edamontology.org/ GENO: http://purl.obolibrary.org/obo/GENO_ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: dna_base: @@ -45,7 +47,14 @@ slots: range: SequenceQualityEnum enums: DNABaseEnum: + title: DNA Base description: Standard DNA nucleotide bases (canonical) + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: A: title: Adenine @@ -84,7 +93,14 @@ enums: pyrimidine: 'true' chemical_formula: C5H6N2O2 DNABaseExtendedEnum: + title: DNA Base Extended description: Extended DNA alphabet with IUPAC ambiguity codes + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: A: title: Adenine @@ -177,7 +193,14 @@ enums: symbol: '-' represents: gap RNABaseEnum: + title: RNA Base description: Standard RNA nucleotide bases (canonical) + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: A: title: Adenine @@ -216,7 +239,14 @@ enums: pyrimidine: 'true' chemical_formula: C4H4N2O2 RNABaseExtendedEnum: + title: RNA Base Extended description: Extended RNA alphabet with IUPAC ambiguity codes + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: A: title: Adenine @@ -307,7 +337,14 @@ enums: symbol: '-' represents: gap AminoAcidEnum: + title: Amino Acid description: Standard amino acid single letter codes + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: A: title: Alanine @@ -529,7 +566,14 @@ enums: aromatic: 'true' hydroxyl: 'true' AminoAcidExtendedEnum: + title: Amino Acid Extended description: Extended amino acid alphabet with ambiguity codes and special characters + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: A: title: Alanine @@ -731,7 +775,14 @@ enums: special: 22nd amino acid codon: UAG in certain archaea/bacteria CodonEnum: + title: Codon description: Standard genetic code codons (DNA) + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: TTT: title: Phenylalanine codon @@ -1058,7 +1109,14 @@ enums: amino_acid: G amino_acid_name: Glycine NucleotideModificationEnum: + title: Nucleotide Modification description: Common nucleotide modifications + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: FIVE_METHYL_C: title: 5-methylcytosine @@ -1122,7 +1180,14 @@ enums: type: oxidative damage pairs_with: A or C SequenceQualityEnum: + title: Sequence Quality description: Sequence quality indicators (Phred scores) + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: Q0: description: Phred quality 0 (100% error probability) diff --git a/src/valuesets/schema/bio/sequence_chemistry.yaml b/src/valuesets/schema/bio/sequence_chemistry.yaml index 995f6eca..f5e4be8d 100644 --- a/src/valuesets/schema/bio/sequence_chemistry.yaml +++ b/src/valuesets/schema/bio/sequence_chemistry.yaml @@ -7,10 +7,13 @@ id: https://w3id.org/linkml/valuesets/bio/sequence_chemistry imports: - linkml:types prefixes: + linkml: https://w3id.org/linkml/ valuesets: https://w3id.org/valuesets/ IUPAC: http://purl.obolibrary.org/obo/IUPAC_ SO: http://purl.obolibrary.org/obo/SO_ CHEBI: http://purl.obolibrary.org/obo/CHEBI_ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: iupac_nucleotide: @@ -46,6 +49,12 @@ enums: description: 'Complete IUPAC nucleotide codes including ambiguous bases for DNA/RNA sequences. Used in FASTA and other sequence formats to represent uncertain nucleotides.' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: A: title: A @@ -92,6 +101,12 @@ enums: StandardAminoAcid: title: Standard Amino Acids description: The 20 standard proteinogenic amino acids with IUPAC single-letter codes + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: A: title: A @@ -158,6 +173,12 @@ enums: description: 'Complete IUPAC amino acid codes including standard amino acids, rare amino acids, and ambiguity codes' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: A: title: A @@ -246,6 +267,12 @@ enums: SequenceAlphabet: title: Sequence Alphabet Types description: Types of sequence alphabets used in bioinformatics + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: DNA: description: Deoxyribonucleic acid alphabet (A, T, G, C) @@ -270,6 +297,12 @@ enums: description: 'Quality score encoding standards used in FASTQ files and sequencing data. Different platforms and software versions use different ASCII offsets.' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: SANGER: description: Sanger/Phred+33 (PHRED scores, ASCII offset 33) @@ -306,6 +339,12 @@ enums: description: 'NCBI genetic code translation tables for different organisms. Table 1 is the universal genetic code used by most organisms.' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: TABLE_1: description: Standard genetic code (universal) @@ -430,6 +469,12 @@ enums: SequenceStrand: title: DNA/RNA Strand Orientation description: Strand orientation for nucleic acid sequences + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: PLUS: title: PLUS @@ -444,6 +489,12 @@ enums: SequenceTopology: title: Sequence Topology description: Topological structure of nucleic acid molecules + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: LINEAR: description: Linear sequence molecule @@ -458,6 +509,12 @@ enums: SequenceModality: title: Sequence Data Modality description: Types of sequence data based on experimental method + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: SINGLE_CELL: description: Single-cell sequencing data diff --git a/src/valuesets/schema/bio/sequencing_platforms.yaml b/src/valuesets/schema/bio/sequencing_platforms.yaml index 65ad91e5..81a72bdb 100644 --- a/src/valuesets/schema/bio/sequencing_platforms.yaml +++ b/src/valuesets/schema/bio/sequencing_platforms.yaml @@ -5,10 +5,13 @@ id: https://w3id.org/linkml/valuesets/bio/sequencing_platforms imports: - linkml:types prefixes: + linkml: https://w3id.org/linkml/ valuesets: https://w3id.org/valuesets/ OBI: http://purl.obolibrary.org/obo/OBI_ SO: http://purl.obolibrary.org/obo/SO_ EDAM: http://edamontology.org/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: sequencing_platform: @@ -36,6 +39,12 @@ enums: SequencingPlatform: title: Sequencing Platforms and Instruments description: Major DNA/RNA sequencing platforms and instruments used in genomics research + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ILLUMINA_HISEQ_2000: description: Illumina HiSeq 2000 @@ -245,6 +254,12 @@ enums: SequencingChemistry: title: Sequencing Chemistry Methods description: Fundamental chemical methods used for DNA/RNA sequencing + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: SEQUENCING_BY_SYNTHESIS: title: SEQUENCING_BY_SYNTHESIS @@ -282,6 +297,12 @@ enums: LibraryPreparation: title: Library Preparation Methods description: Methods for preparing sequencing libraries from nucleic acid samples + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: GENOMIC_DNA: description: Genomic DNA library preparation @@ -324,6 +345,12 @@ enums: SequencingApplication: title: Sequencing Applications description: Primary applications or assays using DNA/RNA sequencing + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: WHOLE_GENOME_SEQUENCING: title: WHOLE_GENOME_SEQUENCING @@ -382,6 +409,12 @@ enums: ReadType: title: Sequencing Read Types description: Configuration of sequencing reads generated by different platforms + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: SINGLE_END: title: SINGLE_END @@ -400,6 +433,12 @@ enums: SequenceFileFormat: title: Sequence File Formats description: Standard file formats used for storing sequence data + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: FASTA: description: FASTA sequence format @@ -492,6 +531,12 @@ enums: DataProcessingLevel: title: Sequence Data Processing Levels description: Levels of processing applied to raw sequencing data + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: RAW: description: Raw unprocessed sequencing reads diff --git a/src/valuesets/schema/bio/structural_biology.yaml b/src/valuesets/schema/bio/structural_biology.yaml index 9c5f44c7..f3cfc66d 100644 --- a/src/valuesets/schema/bio/structural_biology.yaml +++ b/src/valuesets/schema/bio/structural_biology.yaml @@ -15,6 +15,8 @@ prefixes: NCIT: http://purl.obolibrary.org/obo/NCIT_ MOP: http://purl.obolibrary.org/obo/MOP_ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: sample: @@ -64,7 +66,14 @@ slots: range: ProteinModificationType enums: SampleType: + title: Sample Type description: Types of biological samples used in structural biology + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: PROTEIN: description: Purified protein sample @@ -83,7 +92,14 @@ enums: TISSUE: description: Tissue sample StructuralBiologyTechnique: + title: Structural Biology Technique description: Structural biology experimental techniques + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: CRYO_EM: title: cryogenic electron microscopy @@ -136,7 +152,14 @@ enums: annotations: resolution_range: 15-30 Å typical CryoEMPreparationType: + title: Cryo EM Preparation Type description: Types of cryo-EM sample preparation + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: VITREOUS_ICE: description: Sample embedded in vitreous ice @@ -147,7 +170,14 @@ enums: HIGH_PRESSURE_FREEZING: description: High-pressure frozen sample CryoEMGridType: + title: Cryo EM Grid Type description: Types of electron microscopy grids + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: C_FLAT: description: C-flat holey carbon grid @@ -176,7 +206,14 @@ enums: annotations: advantages: atomically thin, good contrast VitrificationMethod: + title: Vitrification Method description: Methods for sample vitrification + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: PLUNGE_FREEZING: description: Plunge freezing in liquid ethane @@ -197,7 +234,14 @@ enums: annotations: applications: large samples, tissues CrystallizationMethod: + title: Crystallization Method description: Methods for protein crystallization + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: VAPOR_DIFFUSION_HANGING: description: Vapor diffusion hanging drop method @@ -227,7 +271,14 @@ enums: applications: membrane proteins lipid: monoolein most common XRaySource: + title: X Ray Source description: Types of X-ray sources + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: SYNCHROTRON: description: Synchrotron radiation source @@ -250,7 +301,14 @@ enums: advantages: higher power density, longer lifetime metals: gallium, indium Detector: + title: Detector description: Types of detectors for structural biology + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: DIRECT_ELECTRON: description: Direct electron detector (DED) @@ -275,7 +333,14 @@ enums: annotations: applications: legacy crystallography WorkflowType: + title: Workflow Type description: Types of computational processing workflows + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: MOTION_CORRECTION: description: Motion correction for cryo-EM movies @@ -327,7 +392,14 @@ enums: annotations: software: PRIMUS, CRYSOL, FoXS FileFormat: + title: File Format description: File formats used in structural biology + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: MRC: description: MRC format for EM density maps @@ -380,7 +452,14 @@ enums: extension: .ser applications: FEI movie stacks DataType: + title: Data Type description: Types of structural biology data + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: MICROGRAPH: description: Electron micrograph image @@ -419,7 +498,14 @@ enums: annotations: formats: STAR, XML, JSON ProcessingStatus: + title: Processing Status description: Status of data processing workflows + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: RAW: description: Raw unprocessed data @@ -438,7 +524,14 @@ enums: CANCELLED: description: Processing cancelled by user CoordinationGeometry: + title: Coordination Geometry description: Coordination geometry of metal centers in protein structures + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: LINEAR: description: Linear coordination geometry (2 ligands at 180°) @@ -519,7 +612,14 @@ enums: annotations: coordination_number: '4' MetalLigandType: + title: Metal Ligand Type description: Types of metal-containing chemical components + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: METAL_CATION: description: Metal cation (e.g., Ca2+, Mg2+, Zn2+, Fe3+) @@ -530,7 +630,14 @@ enums: annotations: examples: heme, chlorophyll, cobalamin, Fe-S cluster ProteinModificationType: + title: Protein Modification Type description: Types of protein modifications + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: METAL_COORDINATION: description: Metal coordination modification diff --git a/src/valuesets/schema/bio/taxonomy.yaml b/src/valuesets/schema/bio/taxonomy.yaml index 8a2aacd9..f96abc77 100644 --- a/src/valuesets/schema/bio/taxonomy.yaml +++ b/src/valuesets/schema/bio/taxonomy.yaml @@ -5,9 +5,12 @@ id: https://w3id.org/linkml/valuesets/bio/taxonomy imports: - linkml:types prefixes: + linkml: https://w3id.org/linkml/ valuesets: https://w3id.org/valuesets/ NCBITaxon: http://purl.obolibrary.org/obo/NCBITaxon_ TAXRANK: http://purl.obolibrary.org/obo/TAXRANK_ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: organism_taxon: @@ -24,6 +27,13 @@ slots: range: BiologicalKingdom enums: OrganismTaxonEnum: + title: Organism Taxon + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_nodes: - NCBITaxon:1 @@ -31,7 +41,14 @@ enums: relationship_types: - rdfs:subClassOf CommonOrganismTaxaEnum: + title: Common Organism Taxa description: Common model organisms used in biological research, mapped to NCBI Taxonomy IDs + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: BACTERIA: description: Bacteria domain @@ -380,7 +397,14 @@ enums: meaning: NCBITaxon:2697049 is_a: VIRUSES TaxonomicRank: + title: Taxonomic Rank description: Standard taxonomic ranks used in biological classification + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: DOMAIN: description: Domain (highest rank) @@ -424,7 +448,14 @@ enums: description: Cultivar (cultivated variety) meaning: TAXRANK:0000034 BiologicalKingdom: + title: Biological Kingdom description: Major kingdoms/domains of life + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: BACTERIA: description: Bacteria domain diff --git a/src/valuesets/schema/bio/trophic_levels.yaml b/src/valuesets/schema/bio/trophic_levels.yaml index 613bea8f..9c2a31d6 100644 --- a/src/valuesets/schema/bio/trophic_levels.yaml +++ b/src/valuesets/schema/bio/trophic_levels.yaml @@ -6,6 +6,8 @@ prefixes: BTO: http://purl.obolibrary.org/obo/BTO_ mixs: https://genomicsstandardsconsortium.github.io/mixs/ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: trophic_level: @@ -13,7 +15,14 @@ slots: range: TrophicLevelEnum enums: TrophicLevelEnum: + title: Trophic Level description: Trophic levels are the feeding position in a food chain + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: AUTOTROPH: description: Organism capable of synthesizing its own food from inorganic substances diff --git a/src/valuesets/schema/bio/uniprot_species.yaml b/src/valuesets/schema/bio/uniprot_species.yaml index c12e527c..508d0d0e 100644 --- a/src/valuesets/schema/bio/uniprot_species.yaml +++ b/src/valuesets/schema/bio/uniprot_species.yaml @@ -1,7 +1,6 @@ name: uniprot_species title: UniProt Species Codes Value Sets -description: Value sets for UniProt species mnemonic codes with associated proteome - IDs +description: Value sets for UniProt species mnemonic codes with associated proteome IDs id: https://w3id.org/common-value-sets/uniprot_species imports: - linkml:types @@ -11,16 +10,23 @@ prefixes: NCBITaxon: http://purl.obolibrary.org/obo/NCBITaxon_ uniprot.proteome: http://purl.uniprot.org/proteomes/ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: uni_prot_species: - description: UniProt species mnemonic codes for reference proteomes with associated - metadata + description: UniProt species mnemonic codes for reference proteomes with associated metadata range: UniProtSpeciesCode enums: UniProtSpeciesCode: - description: UniProt species mnemonic codes for reference proteomes with associated - metadata + title: Uni Prot Species Code + description: UniProt species mnemonic codes for reference proteomes with associated metadata + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: SP_9ABAC: description: 'Lambdina fiscellaria nucleopolyhedrovirus - Proteome: UP000201190' @@ -923,8 +929,7 @@ enums: annotations: sources: existing SP_9GAMM: - description: 'Buchnera aphidicola (Buchnera aphidicola (Cinara tujafilina)) - - Proteome: UP000006811' + description: 'Buchnera aphidicola (Buchnera aphidicola (Cinara tujafilina)) - Proteome: UP000006811' meaning: NCBITaxon:261317 title: Buchnera aphidicola exact_mappings: @@ -1052,8 +1057,8 @@ enums: annotations: sources: existing SP_9INFA: - description: 'Influenza A virus (A/California/VRDL364/2009 (Influenza A virus - (A/California/VRDL364/2009(mixed))) - Proteome: UP000109975' + description: 'Influenza A virus (A/California/VRDL364/2009 (Influenza A virus (A/California/VRDL364/2009(mixed))) + - Proteome: UP000109975' meaning: NCBITaxon:1049605 title: Influenza A virus (A/California/VRDL364/2009 exact_mappings: @@ -1082,12 +1087,11 @@ enums: annotations: sources: existing SP_ACIB2: - description: 'Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / JCM - 6841 / CCUG 19606 / CIP 70.34 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / - 81) (A. baumannii ATCC 19606) - Proteome: UP000498640' + description: 'Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / JCM 6841 / CCUG 19606 / CIP 70.34 / NBRC 109757 + / NCIMB 12457 / NCTC 12156 / 81) (A. baumannii ATCC 19606) - Proteome: UP000498640' meaning: NCBITaxon:575584 - title: Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / JCM 6841 / - CCUG 19606 / CIP 70.34 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81) + title: Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / JCM 6841 / CCUG 19606 / CIP 70.34 / NBRC 109757 + / NCIMB 12457 / NCTC 12156 / 81) exact_mappings: - NCBITaxon:575584 - uniprot.proteome:UP000498640 @@ -1096,8 +1100,7 @@ enums: annotations: sources: GO SP_ANOCA: - description: 'Anolis carolinensis (Green anole (American chameleon)) - Proteome: - UP000001646' + description: 'Anolis carolinensis (Green anole (American chameleon)) - Proteome: UP000001646' meaning: NCBITaxon:28377 title: Anolis carolinensis exact_mappings: @@ -1172,8 +1175,7 @@ enums: annotations: sources: GO SP_BACSU: - description: 'Bacillus subtilis subsp. subtilis str. 168 (b subtilis) - Proteome: - UP000001570' + description: 'Bacillus subtilis subsp. subtilis str. 168 (b subtilis) - Proteome: UP000001570' meaning: NCBITaxon:224308 title: Bacillus subtilis subsp. subtilis str. 168 exact_mappings: @@ -1184,8 +1186,7 @@ enums: annotations: sources: common, GO SP_BACTN: - description: 'Bacteroides thetaiotaomicron (bacteroidetes bacteria) - Proteome: - UP000001414' + description: 'Bacteroides thetaiotaomicron (bacteroidetes bacteria) - Proteome: UP000001414' meaning: NCBITaxon:226186 title: Bacteroides thetaiotaomicron exact_mappings: @@ -1196,8 +1197,7 @@ enums: annotations: sources: GO SP_BATDJ: - description: 'Batrachochytrium dendrobatidis (Frog chytrid fungus) - Proteome: - UP000007241' + description: 'Batrachochytrium dendrobatidis (Frog chytrid fungus) - Proteome: UP000007241' meaning: NCBITaxon:684364 title: Batrachochytrium dendrobatidis exact_mappings: @@ -1241,8 +1241,7 @@ enums: annotations: sources: GO SP_BRADU: - description: 'Bradyrhizobium diazoefficiens (alphaproteobacteria) - Proteome: - UP000002526' + description: 'Bradyrhizobium diazoefficiens (alphaproteobacteria) - Proteome: UP000002526' meaning: NCBITaxon:224911 title: Bradyrhizobium diazoefficiens exact_mappings: @@ -1253,8 +1252,7 @@ enums: annotations: sources: GO SP_BRAFL: - description: 'Branchiostoma floridae (Florida lancelet (Amphioxus)) - Proteome: - UP000001554' + description: 'Branchiostoma floridae (Florida lancelet (Amphioxus)) - Proteome: UP000001554' meaning: NCBITaxon:7739 title: Branchiostoma floridae exact_mappings: @@ -1287,11 +1285,9 @@ enums: annotations: sources: common, GO SP_CAMJE: - description: 'Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC - 700819 / NCTC 11168) - Proteome: UP000000799' + description: 'Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168) - Proteome: UP000000799' meaning: NCBITaxon:192222 - title: Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 - / NCTC 11168) + title: Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168) exact_mappings: - NCBITaxon:192222 - uniprot.proteome:UP000000799 @@ -1309,8 +1305,7 @@ enums: annotations: sources: GO SP_CANCO: - description: 'Candida orthopsilosis (strain 90-125) (Co 90-125) - Proteome: - UP000005018' + description: 'Candida orthopsilosis (strain 90-125) (Co 90-125) - Proteome: UP000005018' meaning: NCBITaxon:1136231 title: Candida orthopsilosis (strain 90-125) (Co 90-125) exact_mappings: @@ -1319,22 +1314,21 @@ enums: annotations: sources: GO SP_CANDC: - description: 'Candida dubliniensis (strain CD36 / ATCC MYA-646 / CBS 7987 - / NCPF 3949 / NRRL Y-17841) - Proteome: UP000002605' + description: 'Candida dubliniensis (strain CD36 / ATCC MYA-646 / CBS 7987 / NCPF 3949 / NRRL Y-17841) - Proteome: + UP000002605' meaning: NCBITaxon:573826 - title: Candida dubliniensis (strain CD36 / ATCC MYA-646 / CBS 7987 / NCPF - 3949 / NRRL Y-17841) + title: Candida dubliniensis (strain CD36 / ATCC MYA-646 / CBS 7987 / NCPF 3949 / NRRL Y-17841) exact_mappings: - NCBITaxon:573826 - uniprot.proteome:UP000002605 annotations: sources: GO SP_CANGB: - description: 'Candida glabrata (strain ATCC 2001 / BCRC 20586 / JCM 3761 / - NBRC 0622 / NRRL Y-65 / CBS 138) (Nakaseomyces glabratus) - Proteome: UP000002428' + description: 'Candida glabrata (strain ATCC 2001 / BCRC 20586 / JCM 3761 / NBRC 0622 / NRRL Y-65 / CBS 138) (Nakaseomyces + glabratus) - Proteome: UP000002428' meaning: NCBITaxon:284593 - title: Candida glabrata (strain ATCC 2001 / BCRC 20586 / JCM 3761 / NBRC 0622 - / NRRL Y-65 / CBS 138) (Nakaseomyces glabratus) + title: Candida glabrata (strain ATCC 2001 / BCRC 20586 / JCM 3761 / NBRC 0622 / NRRL Y-65 / CBS 138) + (Nakaseomyces glabratus) exact_mappings: - NCBITaxon:284593 - uniprot.proteome:UP000002428 @@ -1352,8 +1346,7 @@ enums: annotations: sources: common, GO SP_CANPA: - description: 'Candida parapsilosis (strain CDC 317 / ATCC MYA-4646) - Proteome: - UP000005221' + description: 'Candida parapsilosis (strain CDC 317 / ATCC MYA-4646) - Proteome: UP000005221' meaning: NCBITaxon:578454 title: Candida parapsilosis (strain CDC 317 / ATCC MYA-4646) exact_mappings: @@ -1382,8 +1375,7 @@ enums: annotations: sources: common, GO SP_CHLAA: - description: 'Chloroflexus aurantiacus (chloroflexi bacteria) - Proteome: - UP000002008' + description: 'Chloroflexus aurantiacus (chloroflexi bacteria) - Proteome: UP000002008' meaning: NCBITaxon:324602 title: Chloroflexus aurantiacus exact_mappings: @@ -1427,8 +1419,7 @@ enums: annotations: sources: GO SP_CITK8: - description: 'Citrobacter koseri (strain ATCC BAA-895 / CDC 4225-83 / SGSC4696) - - Proteome: UP000008148' + description: 'Citrobacter koseri (strain ATCC BAA-895 / CDC 4225-83 / SGSC4696) - Proteome: UP000008148' meaning: NCBITaxon:290338 title: Citrobacter koseri (strain ATCC BAA-895 / CDC 4225-83 / SGSC4696) exact_mappings: @@ -1468,11 +1459,10 @@ enums: annotations: sources: GO SP_CRYD1: - description: 'Cryptococcus neoformans var. neoformans serotype D (Filobasidiella - neoformans) (C. neoformans) - Proteome: UP000002149' + description: 'Cryptococcus neoformans var. neoformans serotype D (Filobasidiella neoformans) (C. neoformans) - Proteome: + UP000002149' meaning: NCBITaxon:214684 - title: Cryptococcus neoformans var. neoformans serotype D (Filobasidiella - neoformans) + title: Cryptococcus neoformans var. neoformans serotype D (Filobasidiella neoformans) exact_mappings: - NCBITaxon:214684 - uniprot.proteome:UP000002149 @@ -1503,11 +1493,11 @@ enums: annotations: sources: GO SP_DEBHA: - description: 'Debaryomyces hansenii (strain ATCC 36239 / CBS 767 / BCRC 21394 - / JCM 1990 / NBRC 0083 / IGC 2968) (Torulaspora hansenii) - Proteome: UP000000599' + description: 'Debaryomyces hansenii (strain ATCC 36239 / CBS 767 / BCRC 21394 / JCM 1990 / NBRC 0083 / IGC 2968) (Torulaspora + hansenii) - Proteome: UP000000599' meaning: NCBITaxon:284592 - title: Debaryomyces hansenii (strain ATCC 36239 / CBS 767 / BCRC 21394 / JCM - 1990 / NBRC 0083 / IGC 2968) (Torulaspora hansenii) + title: Debaryomyces hansenii (strain ATCC 36239 / CBS 767 / BCRC 21394 / JCM 1990 / NBRC 0083 / IGC 2968) + (Torulaspora hansenii) exact_mappings: - NCBITaxon:284592 - uniprot.proteome:UP000000599 @@ -1609,8 +1599,7 @@ enums: annotations: sources: GO SP_ENTFA: - description: 'Enterococcus faecalis (strain ATCC 700802 / V583) - Proteome: - UP000001415' + description: 'Enterococcus faecalis (strain ATCC 700802 / V583) - Proteome: UP000001415' meaning: NCBITaxon:226185 title: Enterococcus faecalis (strain ATCC 700802 / V583) exact_mappings: @@ -1661,8 +1650,7 @@ enums: annotations: sources: common, GO SP_FMDVO: - description: 'Foot-and-mouth disease virus serotype O (FMDV) (FMDV) - Proteome: - UP000008765' + description: 'Foot-and-mouth disease virus serotype O (FMDV) (FMDV) - Proteome: UP000008765' meaning: NCBITaxon:12118 title: Foot-and-mouth disease virus serotype O (FMDV) exact_mappings: @@ -1673,8 +1661,7 @@ enums: annotations: sources: GO SP_FUSNN: - description: 'Fusobacterium nucleatum (strain ATCC 25586) (F. nucleatum ATCC - 25586) - Proteome: UP000241660' + description: 'Fusobacterium nucleatum (strain ATCC 25586) (F. nucleatum ATCC 25586) - Proteome: UP000241660' meaning: NCBITaxon:190304 title: Fusobacterium nucleatum (strain ATCC 25586) exact_mappings: @@ -1718,8 +1705,7 @@ enums: annotations: sources: GO SP_GORGO: - description: 'Gorilla gorilla gorilla (Western lowland gorilla) - Proteome: - UP000001519' + description: 'Gorilla gorilla gorilla (Western lowland gorilla) - Proteome: UP000001519' meaning: NCBITaxon:9593 title: Gorilla gorilla gorilla exact_mappings: @@ -1741,8 +1727,8 @@ enums: annotations: sources: GO SP_HAEIN: - description: 'Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 - / Rd) (H. influenzae strain ATCC 51907) - Proteome: UP000000579' + description: 'Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) (H. influenzae strain ATCC 51907) + - Proteome: UP000000579' meaning: NCBITaxon:71421 title: Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) exact_mappings: @@ -1753,11 +1739,11 @@ enums: annotations: sources: GO SP_HALH5: - description: 'Halalkalibacterium halodurans (strain ATCC BAA-125 / DSM 18197 - / FERM 7344 / JCM 9153 / C-125) (Bacillus halodurans) - Proteome: UP000001258' + description: 'Halalkalibacterium halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125) (Bacillus + halodurans) - Proteome: UP000001258' meaning: NCBITaxon:272558 - title: Halalkalibacterium halodurans (strain ATCC BAA-125 / DSM 18197 / FERM - 7344 / JCM 9153 / C-125) (Bacillus halodurans) + title: Halalkalibacterium halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125) (Bacillus + halodurans) exact_mappings: - NCBITaxon:272558 - uniprot.proteome:UP000001258 @@ -1775,8 +1761,7 @@ enums: annotations: sources: GO SP_HBVCJ: - description: 'Hepatitis B virus genotype C subtype ayr (isolate Human/Japan/Okamoto/-) - (HBV-C) - Proteome: UP000008591' + description: 'Hepatitis B virus genotype C subtype ayr (isolate Human/Japan/Okamoto/-) (HBV-C) - Proteome: UP000008591' meaning: NCBITaxon:928302 title: Hepatitis B virus genotype C subtype ayr (isolate Human/Japan/Okamoto/-) exact_mappings: @@ -1787,8 +1772,7 @@ enums: annotations: sources: GO SP_HCMVA: - description: 'Human cytomegalovirus (strain AD169) (Human herpesvirus 5 (HHV-5)) - - Proteome: UP000008992' + description: 'Human cytomegalovirus (strain AD169) (Human herpesvirus 5 (HHV-5)) - Proteome: UP000008992' meaning: NCBITaxon:10360 title: Human cytomegalovirus (strain AD169) exact_mappings: @@ -1799,8 +1783,7 @@ enums: annotations: sources: GO SP_HCMVM: - description: 'Human cytomegalovirus (Human herpesvirus 5) strain Merlin (HHV-5 - Merlin) - Proteome: UP000000938' + description: 'Human cytomegalovirus (Human herpesvirus 5) strain Merlin (HHV-5 Merlin) - Proteome: UP000000938' meaning: NCBITaxon:295027 title: Human cytomegalovirus (Human herpesvirus 5) strain Merlin exact_mappings: @@ -1811,8 +1794,7 @@ enums: annotations: sources: GO SP_HCV77: - description: 'Hepatitis C virus genotype 1a (isolate H77) (HCV) - Proteome: - UP000000518' + description: 'Hepatitis C virus genotype 1a (isolate H77) (HCV) - Proteome: UP000000518' meaning: NCBITaxon:63746 title: Hepatitis C virus genotype 1a (isolate H77) exact_mappings: @@ -1834,8 +1816,7 @@ enums: annotations: sources: GO SP_HELPY: - description: 'Helicobacter pylori (Campylobacter pylori) strain ATCC 700392 - / 26695 (H. pylori) - Proteome: UP000000429' + description: 'Helicobacter pylori (Campylobacter pylori) strain ATCC 700392 / 26695 (H. pylori) - Proteome: UP000000429' meaning: NCBITaxon:85962 title: Helicobacter pylori (Campylobacter pylori) strain ATCC 700392 / 26695 exact_mappings: @@ -1857,8 +1838,7 @@ enums: annotations: sources: GO SP_HHV11: - description: 'Human herpesvirus 1 (strain 17) (Human herpes simplex virus - 1 (HHV-1)) - Proteome: UP000009294' + description: 'Human herpesvirus 1 (strain 17) (Human herpes simplex virus 1 (HHV-1)) - Proteome: UP000009294' meaning: NCBITaxon:10299 title: Human herpesvirus 1 (strain 17) exact_mappings: @@ -1880,8 +1860,7 @@ enums: annotations: sources: common, GO SP_HORVV: - description: 'Hordeum vulgare subsp. vulgare (Domesticated barley) - Proteome: - UP000011116' + description: 'Hordeum vulgare subsp. vulgare (Domesticated barley) - Proteome: UP000011116' meaning: NCBITaxon:112509 title: Hordeum vulgare subsp. vulgare exact_mappings: @@ -1912,8 +1891,7 @@ enums: annotations: sources: common, GO SP_HV1AN: - description: 'Human immunodeficiency virus type 1 group O (isolate ANT70) - - Proteome: UP000007689' + description: 'Human immunodeficiency virus type 1 group O (isolate ANT70) - Proteome: UP000007689' meaning: NCBITaxon:327105 title: Human immunodeficiency virus type 1 group O (isolate ANT70) exact_mappings: @@ -1955,8 +1933,7 @@ enums: annotations: sources: GO SP_KLEPH: - description: 'Klebsiella pneumoniae subsp. pneumoniae (strain HS11286) - Proteome: - UP000007841' + description: 'Klebsiella pneumoniae subsp. pneumoniae (strain HS11286) - Proteome: UP000007841' meaning: NCBITaxon:1125630 title: Klebsiella pneumoniae subsp. pneumoniae (strain HS11286) exact_mappings: @@ -1965,8 +1942,7 @@ enums: annotations: sources: GO SP_KLEPO: - description: 'Klebsiella pneumoniae subsp. ozaenae (subspecies) - Proteome: - UP000255382' + description: 'Klebsiella pneumoniae subsp. ozaenae (subspecies) - Proteome: UP000255382' meaning: NCBITaxon:574 title: Klebsiella pneumoniae subsp. ozaenae (subspecies) exact_mappings: @@ -2030,8 +2006,7 @@ enums: annotations: sources: GO SP_LISMO: - description: 'Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) - - Proteome: UP000000817' + description: 'Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) - Proteome: UP000000817' meaning: NCBITaxon:169963 title: Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) exact_mappings: @@ -2040,12 +2015,11 @@ enums: annotations: sources: GO SP_LODEL: - description: 'Lodderomyces elongisporus (strain ATCC 11503 / CBS 2605 / JCM - 1781 / NBRC 1676 / NRRL YB-4239) (Saccharomyces elongisporus) - Proteome: - UP000001996' + description: 'Lodderomyces elongisporus (strain ATCC 11503 / CBS 2605 / JCM 1781 / NBRC 1676 / NRRL YB-4239) (Saccharomyces + elongisporus) - Proteome: UP000001996' meaning: NCBITaxon:379508 - title: Lodderomyces elongisporus (strain ATCC 11503 / CBS 2605 / JCM 1781 - / NBRC 1676 / NRRL YB-4239) (Saccharomyces elongisporus) + title: Lodderomyces elongisporus (strain ATCC 11503 / CBS 2605 / JCM 1781 / NBRC 1676 / NRRL YB-4239) + (Saccharomyces elongisporus) exact_mappings: - NCBITaxon:379508 - uniprot.proteome:UP000001996 @@ -2096,8 +2070,8 @@ enums: annotations: sources: GO SP_MEASC: - description: 'Measles virus (Subacute sclerose panencephalitis virus) strain - Ichinose-B95a (MeV strain Ichinose-B95a) - Proteome: UP000008699' + description: 'Measles virus (Subacute sclerose panencephalitis virus) strain Ichinose-B95a (MeV strain Ichinose-B95a) + - Proteome: UP000008699' meaning: NCBITaxon:645098 title: Measles virus (Subacute sclerose panencephalitis virus) strain Ichinose-B95a exact_mappings: @@ -2130,8 +2104,7 @@ enums: annotations: sources: GO SP_METJA: - description: 'Methanocaldococcus jannaschii (methanococci archaea) - Proteome: - UP000000805' + description: 'Methanocaldococcus jannaschii (methanococci archaea) - Proteome: UP000000805' meaning: NCBITaxon:243232 title: Methanocaldococcus jannaschii exact_mappings: @@ -2153,8 +2126,7 @@ enums: annotations: sources: GO SP_MONDO: - description: 'Monodelphis domestica (Gray short-tailed opossum) - Proteome: - UP000002280' + description: 'Monodelphis domestica (Gray short-tailed opossum) - Proteome: UP000002280' meaning: NCBITaxon:13616 title: Monodelphis domestica exact_mappings: @@ -2187,8 +2159,7 @@ enums: annotations: sources: GO SP_MYCMD: - description: 'Mycosarcoma maydis (Ustilago maydis) (Corn smut fungus) - Proteome: - UP000000561' + description: 'Mycosarcoma maydis (Ustilago maydis) (Corn smut fungus) - Proteome: UP000000561' meaning: NCBITaxon:5270 title: Mycosarcoma maydis (Ustilago maydis) exact_mappings: @@ -2199,8 +2170,7 @@ enums: annotations: sources: GO SP_MYCPN: - description: 'Mycoplasma pneumoniae strain ATCC 29342 / M129 / Subtype 1 - - Proteome: UP000000808' + description: 'Mycoplasma pneumoniae strain ATCC 29342 / M129 / Subtype 1 - Proteome: UP000000808' meaning: NCBITaxon:272634 title: Mycoplasma pneumoniae strain ATCC 29342 / M129 / Subtype 1 exact_mappings: @@ -2209,8 +2179,7 @@ enums: annotations: sources: GO SP_MYCTA: - description: 'Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra) - Proteome: - UP000001988' + description: 'Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra) - Proteome: UP000001988' meaning: NCBITaxon:419947 title: Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra) exact_mappings: @@ -2219,8 +2188,7 @@ enums: annotations: sources: GO SP_MYCTU: - description: 'Mycobacterium tuberculosis H37Rv (actinobacteria) - Proteome: - UP000001584' + description: 'Mycobacterium tuberculosis H37Rv (actinobacteria) - Proteome: UP000001584' meaning: NCBITaxon:83332 title: Mycobacterium tuberculosis H37Rv exact_mappings: @@ -2231,8 +2199,7 @@ enums: annotations: sources: GO SP_NEIMB: - description: 'Neisseria meningitidis serogroup B (strain ATCC BAA-335 / MC58) - (betaproteobacteria) - Proteome: UP000000425' + description: 'Neisseria meningitidis serogroup B (strain ATCC BAA-335 / MC58) (betaproteobacteria) - Proteome: UP000000425' meaning: NCBITaxon:122586 title: Neisseria meningitidis serogroup B (strain ATCC BAA-335 / MC58) exact_mappings: @@ -2373,8 +2340,7 @@ enums: annotations: sources: GO SP_PHYPA: - description: 'Physcomitrella patens (Spreading-leaved earth moss) - Proteome: - UP000006727' + description: 'Physcomitrella patens (Spreading-leaved earth moss) - Proteome: UP000006727' meaning: NCBITaxon:3218 title: Physcomitrella patens exact_mappings: @@ -2396,12 +2362,11 @@ enums: annotations: sources: GO SP_PICGU: - description: 'Meyerozyma guilliermondii (strain ATCC 6260 / CBS 566 / DSM - 6381 / JCM 1539 / NBRC 10279 / NRRL Y-324) (Candida guilliermondii) - Proteome: - UP000001997' + description: 'Meyerozyma guilliermondii (strain ATCC 6260 / CBS 566 / DSM 6381 / JCM 1539 / NBRC 10279 / NRRL Y-324) + (Candida guilliermondii) - Proteome: UP000001997' meaning: NCBITaxon:294746 - title: Meyerozyma guilliermondii (strain ATCC 6260 / CBS 566 / DSM 6381 / - JCM 1539 / NBRC 10279 / NRRL Y-324) (Candida guilliermondii) + title: Meyerozyma guilliermondii (strain ATCC 6260 / CBS 566 / DSM 6381 / JCM 1539 / NBRC 10279 / NRRL Y-324) + (Candida guilliermondii) exact_mappings: - NCBITaxon:294746 - uniprot.proteome:UP000001997 @@ -2463,8 +2428,7 @@ enums: annotations: sources: GO SP_PSEAE: - description: 'Pseudomonas aeruginosa PAO1 (gammaproteobacteria) - Proteome: - UP000002438' + description: 'Pseudomonas aeruginosa PAO1 (gammaproteobacteria) - Proteome: UP000002438' meaning: NCBITaxon:208964 title: Pseudomonas aeruginosa PAO1 exact_mappings: @@ -2519,8 +2483,7 @@ enums: annotations: sources: common, GO SP_RHOBA: - description: 'Rhodopirellula baltica (planctomycetes bacteria) - Proteome: - UP000001025' + description: 'Rhodopirellula baltica (planctomycetes bacteria) - Proteome: UP000001025' meaning: NCBITaxon:243090 title: Rhodopirellula baltica exact_mappings: @@ -2542,8 +2505,7 @@ enums: annotations: sources: GO SP_SALTY: - description: 'Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) - (S. typhimurium LT2) - Proteome: UP000001014' + description: 'Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (S. typhimurium LT2) - Proteome: UP000001014' meaning: NCBITaxon:99287 title: Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) exact_mappings: @@ -2565,8 +2527,7 @@ enums: annotations: sources: GO SP_SCHPO: - description: 'Schizosaccharomyces pombe 972h- (Fission yeast) - Proteome: - UP000002485' + description: 'Schizosaccharomyces pombe 972h- (Fission yeast) - Proteome: UP000002485' meaning: NCBITaxon:284812 title: Schizosaccharomyces pombe 972h- exact_mappings: @@ -2663,8 +2624,7 @@ enums: annotations: sources: GO SP_STAA8: - description: 'Staphylococcus aureus (strain NCTC 8325 / PS 47) (S. aureus - NCTC 8325) - Proteome: UP000008816' + description: 'Staphylococcus aureus (strain NCTC 8325 / PS 47) (S. aureus NCTC 8325) - Proteome: UP000008816' meaning: NCBITaxon:93061 title: Staphylococcus aureus (strain NCTC 8325 / PS 47) exact_mappings: @@ -2704,19 +2664,16 @@ enums: annotations: sources: GO SP_STRP1: - description: 'Streptococcus pyogenes serotype M1 (Strain: ATCC 700294 / SF370 - / Serotype M1) - Proteome: UP000000750' + description: 'Streptococcus pyogenes serotype M1 (Strain: ATCC 700294 / SF370 / Serotype M1) - Proteome: UP000000750' meaning: NCBITaxon:301447 - title: 'Streptococcus pyogenes serotype M1 (Strain: ATCC 700294 / SF370 / - Serotype M1)' + title: 'Streptococcus pyogenes serotype M1 (Strain: ATCC 700294 / SF370 / Serotype M1)' exact_mappings: - NCBITaxon:301447 - uniprot.proteome:UP000000750 annotations: sources: GO SP_STRP2: - description: 'Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) - - Proteome: UP000001452' + description: 'Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) - Proteome: UP000001452' meaning: NCBITaxon:373153 title: Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) exact_mappings: @@ -2725,8 +2682,7 @@ enums: annotations: sources: GO SP_STRPN: - description: 'Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4) - - Proteome: UP000000586' + description: 'Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4) - Proteome: UP000000586' meaning: NCBITaxon:171101 title: Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4) exact_mappings: @@ -2735,8 +2691,7 @@ enums: annotations: sources: GO SP_STRPU: - description: 'Strongylocentrotus purpuratus (Purple sea urchin) - Proteome: - UP000007110' + description: 'Strongylocentrotus purpuratus (Purple sea urchin) - Proteome: UP000007110' meaning: NCBITaxon:7668 title: Strongylocentrotus purpuratus exact_mappings: @@ -2813,8 +2768,7 @@ enums: annotations: sources: GO SP_THEYD: - description: 'Thermodesulfovibrio yellowstonii (nitrospirae bacteria) - Proteome: - UP000000718' + description: 'Thermodesulfovibrio yellowstonii (nitrospirae bacteria) - Proteome: UP000000718' meaning: NCBITaxon:289376 title: Thermodesulfovibrio yellowstonii exact_mappings: @@ -2889,8 +2843,7 @@ enums: annotations: sources: GO SP_VACCW: - description: 'Vaccinia virus (strain Western Reserve) (VACV strain WR) - Proteome: - UP000000344' + description: 'Vaccinia virus (strain Western Reserve) (VACV strain WR) - Proteome: UP000000344' meaning: NCBITaxon:10254 title: Vaccinia virus (strain Western Reserve) exact_mappings: @@ -2901,8 +2854,7 @@ enums: annotations: sources: GO SP_VAR67: - description: 'Variola virus (Smallpox virus) (isolate Human/India/Ind3/1967) - (VARV) - Proteome: UP000002060' + description: 'Variola virus (Smallpox virus) (isolate Human/India/Ind3/1967) (VARV) - Proteome: UP000002060' meaning: NCBITaxon:587200 title: Variola virus (Smallpox virus) (isolate Human/India/Ind3/1967) exact_mappings: @@ -2935,8 +2887,7 @@ enums: annotations: sources: GO SP_VZVD: - description: 'Varicella-zoster virus (Human herpesvirus 3) strain Dumas (HHV-3 - strain Dumas) - Proteome: UP000002602' + description: 'Varicella-zoster virus (Human herpesvirus 3) strain Dumas (HHV-3 strain Dumas) - Proteome: UP000002602' meaning: NCBITaxon:10338 title: Varicella-zoster virus (Human herpesvirus 3) strain Dumas exact_mappings: @@ -3002,8 +2953,7 @@ enums: annotations: sources: GO SP_YEAST: - description: 'Saccharomyces cerevisiae S288C (Baker''s yeast) - Proteome: - UP000002311' + description: 'Saccharomyces cerevisiae S288C (Baker''s yeast) - Proteome: UP000002311' meaning: NCBITaxon:559292 title: Saccharomyces cerevisiae S288C exact_mappings: diff --git a/src/valuesets/schema/bio/viral_genome_types.yaml b/src/valuesets/schema/bio/viral_genome_types.yaml index 4de49e00..4abb2ae7 100644 --- a/src/valuesets/schema/bio/viral_genome_types.yaml +++ b/src/valuesets/schema/bio/viral_genome_types.yaml @@ -6,6 +6,8 @@ prefixes: SO: http://purl.obolibrary.org/obo/SO_ mixs: https://genomicsstandardsconsortium.github.io/mixs/ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: viral_genome_type: @@ -13,7 +15,14 @@ slots: range: ViralGenomeTypeEnum enums: ViralGenomeTypeEnum: + title: Viral Genome Type description: Types of viral genomes based on Baltimore classification + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition conforms_to: https://en.wikipedia.org/wiki/Baltimore_classification permissible_values: DNA: @@ -81,7 +90,8 @@ enums: - Group VI - Retroviruses DSDNA_RT: - description: Double-stranded DNA viruses that replicate through a single-stranded RNA intermediate (pararetroviruses) + description: Double-stranded DNA viruses that replicate through a single-stranded RNA intermediate + (pararetroviruses) meaning: NCIT:C14349 title: Other Virus Grouping is_a: DSDNA diff --git a/src/valuesets/schema/bioprocessing/scale_up.yaml b/src/valuesets/schema/bioprocessing/scale_up.yaml index 789e21d3..e5287870 100644 --- a/src/valuesets/schema/bioprocessing/scale_up.yaml +++ b/src/valuesets/schema/bioprocessing/scale_up.yaml @@ -7,6 +7,7 @@ id: https://w3id.org/linkml/valuesets/bioprocessing/scale_up imports: - linkml:types prefixes: + linkml: https://w3id.org/linkml/ valuesets: https://w3id.org/valuesets/ NCIT: http://purl.obolibrary.org/obo/NCIT_ OBI: http://purl.obolibrary.org/obo/OBI_ @@ -19,6 +20,8 @@ prefixes: MSIO: http://purl.obolibrary.org/obo/MSIO_ mesh: http://id.nlm.nih.gov/mesh/ FOODON: http://purl.obolibrary.org/obo/FOODON_ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: process_scale: @@ -50,7 +53,14 @@ slots: range: SterilizationMethodEnum enums: ProcessScaleEnum: + title: Process Scale description: Scale of bioprocessing operations from lab bench to commercial production + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: BENCH_SCALE: description: Laboratory bench scale (typically < 10 L) @@ -87,7 +97,14 @@ enums: typical_volume: 1-1000 μL purpose: High-throughput screening BioreactorTypeEnum: + title: Bioreactor Type description: Types of bioreactors used in fermentation and cell culture + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: STIRRED_TANK: description: Stirred tank reactor (STR/CSTR) @@ -144,7 +161,14 @@ enums: light_source: Required organisms: Algae, cyanobacteria FermentationModeEnum: + title: Fermentation Mode description: Modes of fermentation operation + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: BATCH: title: batch cell culture @@ -184,7 +208,14 @@ enums: operation: Periodic harvest and refill advantage: Extended production OxygenationStrategyEnum: + title: Oxygenation Strategy description: Oxygen supply strategies for fermentation + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: AEROBIC: description: Aerobic with active aeration @@ -211,7 +242,14 @@ enums: oxygen: Optional flexibility: Organism-dependent AgitationTypeEnum: + title: Agitation Type description: Types of agitation/mixing in bioreactors + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: RUSHTON_TURBINE: description: Rushton turbine impeller @@ -253,7 +291,14 @@ enums: annotations: mixing: Gas sparging or static DownstreamProcessEnum: + title: Downstream Process description: Downstream processing unit operations + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: CENTRIFUGATION: title: analytical centrifugation @@ -304,7 +349,14 @@ enums: annotations: methods: High pressure, bead mill FeedstockTypeEnum: + title: Feedstock Type description: Types of feedstocks for bioprocessing + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: GLUCOSE: description: Glucose/dextrose @@ -358,7 +410,14 @@ enums: variable_composition: true sustainability: Circular economy ProductTypeEnum: + title: Product Type description: Types of products from bioprocessing + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: BIOFUEL: title: fuel @@ -417,7 +476,14 @@ enums: annotations: category: Specialty chemical SterilizationMethodEnum: + title: Sterilization Method description: Methods for sterilization in bioprocessing + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: STEAM_IN_PLACE: description: Steam in place (SIP) diff --git a/src/valuesets/schema/business/human_resources.yaml b/src/valuesets/schema/business/human_resources.yaml index 7e987184..8d06e078 100644 --- a/src/valuesets/schema/business/human_resources.yaml +++ b/src/valuesets/schema/business/human_resources.yaml @@ -1,17 +1,19 @@ name: human_resources title: Human Resources Management and Workforce Classifications -description: 'Employment types, HR functions, compensation structures, performance - management, and workforce development classifications. Based on labor standards, - HR best practices, and organizational development frameworks.' +description: 'Employment types, HR functions, compensation structures, performance management, and workforce development classifications. + Based on labor standards, HR best practices, and organizational development frameworks.' id: https://w3id.org/linkml/valuesets/business/human_resources imports: - linkml:types prefixes: + linkml: https://w3id.org/linkml/ valuesets: https://w3id.org/valuesets/ SHRM: https://www.shrm.org/ BLS: https://www.bls.gov/ FLSA: https://www.dol.gov/agencies/whd/flsa/ EEO: https://www.eeoc.gov/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: employment_type: @@ -46,7 +48,14 @@ slots: range: BenefitsCategoryEnum enums: EmploymentTypeEnum: + title: Employment Type description: Types of employment arrangements and contracts + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: FULL_TIME: title: Full-Time Employment @@ -130,7 +139,14 @@ enums: purpose: "mission-driven work" recognition: "non-monetary recognition" JobLevelEnum: + title: Job Level description: Organizational job levels and career progression + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ENTRY_LEVEL: title: Entry Level @@ -214,7 +230,14 @@ enums: stakeholders: "external stakeholder management" fiduciary: "fiduciary responsibility" HRFunctionEnum: + title: HR Function description: Human resources functional areas and specializations + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: TALENT_ACQUISITION: title: Talent Acquisition @@ -298,7 +321,14 @@ enums: integration: "system integration" security: "data security" CompensationTypeEnum: + title: Compensation Type description: Types of employee compensation structures + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: BASE_SALARY: title: Base Salary @@ -373,7 +403,14 @@ enums: supplemental: "supplemental income" categories: "interns, volunteers, board members" PerformanceRatingEnum: + title: Performance Rating description: Employee performance evaluation ratings + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: EXCEEDS_EXPECTATIONS: title: Exceeds Expectations @@ -421,7 +458,14 @@ enums: innovation: "innovation and excellence" rarity: "rare rating" RecruitmentSourceEnum: + title: Recruitment Source description: Sources for candidate recruitment and sourcing + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: INTERNAL_REFERRAL: title: Internal Employee Referral @@ -496,7 +540,14 @@ enums: confidential: "confidential searches" cost: "premium cost" TrainingTypeEnum: + title: Training Type description: Types of employee training and development programs + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ONBOARDING: title: New Employee Onboarding @@ -571,7 +622,14 @@ enums: understanding: "broader understanding" collaboration: "improved collaboration" EmployeeStatusEnum: + title: Employee Status description: Current employment status classifications + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ACTIVE: title: Active Employment @@ -628,7 +686,14 @@ enums: service: "completed service" transition: "career transition" WorkArrangementEnum: + title: Work Arrangement description: Work location and arrangement types + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ON_SITE: title: On-Site Work @@ -676,7 +741,14 @@ enums: work_life: "work-life integration" communication: "virtual team communication" BenefitsCategoryEnum: + title: Benefits Category description: Categories of employee benefits and compensation + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: HEALTH_INSURANCE: title: Health Insurance @@ -749,4 +821,4 @@ enums: family: "family support" childcare: "childcare assistance" elder_care: "elder care support" - balance: "life balance" \ No newline at end of file + balance: "life balance" diff --git a/src/valuesets/schema/business/industry_classifications.yaml b/src/valuesets/schema/business/industry_classifications.yaml index 5d62cae2..c67f90b5 100644 --- a/src/valuesets/schema/business/industry_classifications.yaml +++ b/src/valuesets/schema/business/industry_classifications.yaml @@ -1,17 +1,19 @@ name: industry_classifications title: Business Industry Classifications and Economic Sectors -description: 'Industry classification systems including NAICS codes, economic sectors, - and business activity categories. Based on official government classification systems - and international standards for economic analysis and business categorization.' +description: 'Industry classification systems including NAICS codes, economic sectors, and business activity categories. Based + on official government classification systems and international standards for economic analysis and business categorization.' id: https://w3id.org/linkml/valuesets/business/industry_classifications imports: - linkml:types prefixes: + linkml: https://w3id.org/linkml/ valuesets: https://w3id.org/valuesets/ NAICS: https://www.census.gov/naics/ SIC: https://www.osha.gov/data/sic-manual/ ISIC: https://unstats.un.org/unsd/classifications/Econ/ISIC BLS: https://www.bls.gov/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: naics_sector: @@ -34,7 +36,14 @@ slots: range: IndustryRegulationLevelEnum enums: NAICSSectorEnum: + title: NAICS Sector description: NAICS two-digit sector codes (North American Industry Classification System) + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: SECTOR_11: title: Agriculture, Forestry, Fishing and Hunting @@ -177,7 +186,14 @@ enums: activities: "executive, legislative, judicial, public safety" sector: "government sector" EconomicSectorEnum: + title: Economic Sector description: Broad economic sector classifications + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: PRIMARY_SECTOR: title: Primary Sector @@ -220,7 +236,14 @@ enums: characteristics: "elite services and leadership roles" scope: "limited to highest level activities" BusinessActivityTypeEnum: + title: Business Activity Type description: Types of primary business activities + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: PRODUCTION: title: Production/Manufacturing @@ -303,7 +326,14 @@ enums: examples: "law firms, consulting, accounting" expertise: "specialized professional expertise" IndustryMaturityEnum: + title: Industry Maturity description: Industry lifecycle and maturity stages + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: EMERGING: title: Emerging Industry @@ -351,7 +381,14 @@ enums: uncertainty: "high uncertainty about future structure" opportunity: "opportunities for innovation and disruption" MarketStructureEnum: + title: Market Structure description: Competitive structure of industry markets + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: PERFECT_COMPETITION: title: Perfect Competition @@ -399,7 +436,14 @@ enums: strategy: "strategic competition" examples: "aircraft manufacturing, some software markets" IndustryRegulationLevelEnum: + title: Industry Regulation Level description: Level of government regulation in different industries + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: HIGHLY_REGULATED: title: Highly Regulated @@ -445,4 +489,4 @@ enums: competition: "market-based competition" transition: "transition from regulation to competition" examples: "airlines, telecommunications, energy" - benefits: "increased competition and efficiency" \ No newline at end of file + benefits: "increased competition and efficiency" diff --git a/src/valuesets/schema/business/management_operations.yaml b/src/valuesets/schema/business/management_operations.yaml index fa69e0be..c28fbdb3 100644 --- a/src/valuesets/schema/business/management_operations.yaml +++ b/src/valuesets/schema/business/management_operations.yaml @@ -1,16 +1,18 @@ name: management_operations title: Business Management and Operations -description: 'Business management methodologies, operational frameworks, strategic planning - approaches, and performance management systems. Based on management theory, business - strategy frameworks, and operational excellence practices.' +description: 'Business management methodologies, operational frameworks, strategic planning approaches, and performance management + systems. Based on management theory, business strategy frameworks, and operational excellence practices.' id: https://w3id.org/linkml/valuesets/business/management_operations imports: - linkml:types prefixes: + linkml: https://w3id.org/linkml/ valuesets: https://w3id.org/valuesets/ ISO: https://www.iso.org/ PMI: https://www.pmi.org/ ITIL: https://www.itil-officialsite.com/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: management_methodology: @@ -36,7 +38,14 @@ slots: range: BusinessProcessTypeEnum enums: ManagementMethodologyEnum: + title: Management Methodology description: Management approaches and methodologies + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: TRADITIONAL_MANAGEMENT: title: Traditional Management @@ -119,7 +128,14 @@ enums: equality: "equal voice in decisions" transparency: "transparent processes" StrategicFrameworkEnum: + title: Strategic Framework description: Strategic planning and analysis frameworks + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: SWOT_ANALYSIS: title: SWOT Analysis @@ -202,7 +218,14 @@ enums: focus: "competency-based strategy" development: "capability development" OperationalModelEnum: + title: Operational Model description: Business operational models and approaches + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: CENTRALIZED_OPERATIONS: title: Centralized Operations @@ -285,7 +308,14 @@ enums: data_driven: "data-driven operations" scalability: "digital scalability" PerformanceMeasurementEnum: + title: Performance Measurement description: Performance measurement systems and approaches + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: KEY_PERFORMANCE_INDICATORS: title: Key Performance Indicators (KPIs) @@ -368,7 +398,14 @@ enums: social: "social responsibility" governance: "governance effectiveness" DecisionMakingStyleEnum: + title: Decision Making Style description: Decision-making approaches and styles + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: AUTOCRATIC: title: Autocratic Decision Making @@ -451,7 +488,14 @@ enums: speed: "rapid response required" risk: "high-risk decision making" LeadershipStyleEnum: + title: Leadership Style description: Leadership approaches and styles + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: TRANSFORMATIONAL: title: Transformational Leadership @@ -534,7 +578,14 @@ enums: growth: "personal and professional growth" support: "supportive leadership" BusinessProcessTypeEnum: + title: Business Process Type description: Types of business processes + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: CORE_PROCESS: title: Core Business Process @@ -599,4 +650,4 @@ enums: financial: "financial management" accounting: "accounting and reporting" control: "financial control" - compliance: "financial compliance" \ No newline at end of file + compliance: "financial compliance" diff --git a/src/valuesets/schema/business/organizational_structures.yaml b/src/valuesets/schema/business/organizational_structures.yaml index 6dd03dea..a07c1bb4 100644 --- a/src/valuesets/schema/business/organizational_structures.yaml +++ b/src/valuesets/schema/business/organizational_structures.yaml @@ -1,16 +1,19 @@ name: organizational_structures title: Business Organizational Structures and Legal Entities -description: 'Classifications of business organizational structures including legal entity types, - corporate hierarchies, management levels, and organizational frameworks. Based on business - law standards, corporate governance frameworks, and organizational behavior research.' +description: 'Classifications of business organizational structures including legal entity types, corporate hierarchies, management + levels, and organizational frameworks. Based on business law standards, corporate governance frameworks, and organizational + behavior research.' id: https://w3id.org/linkml/valuesets/business/organizational_structures imports: - linkml:types prefixes: + linkml: https://w3id.org/linkml/ valuesets: https://w3id.org/valuesets/ SBA: https://www.sba.gov/ IRS: https://www.irs.gov/ SEC: https://www.sec.gov/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: legal_entity_type: @@ -36,7 +39,14 @@ slots: range: BusinessLifecycleStageEnum enums: LegalEntityTypeEnum: + title: Legal Entity Type description: Legal entity types for business organizations + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: SOLE_PROPRIETORSHIP: title: Sole Proprietorship @@ -193,7 +203,14 @@ enums: regulation: government regulations and oversight funding: government funding sources OrganizationalStructureEnum: + title: Organizational Structure description: Types of organizational hierarchy and reporting structures + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: HIERARCHICAL: title: Hierarchical Structure @@ -277,7 +294,14 @@ enums: complexity: increased structural complexity customization: customized to organization needs ManagementLevelEnum: + title: Management Level description: Hierarchical levels within organizational management structure + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: BOARD_OF_DIRECTORS: title: Board of Directors @@ -368,7 +392,14 @@ enums: supervision: close supervision growth_potential: career growth opportunities CorporateGovernanceRoleEnum: + title: Corporate Governance Role description: Roles within corporate governance structure + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: CHAIRMAN_OF_BOARD: title: Chairman of the Board @@ -459,7 +490,14 @@ enums: meetings: board meeting coordination legal: legal compliance oversight BusinessOwnershipTypeEnum: + title: Business Ownership Type description: Types of business ownership structures + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: PRIVATE_OWNERSHIP: title: Private Ownership @@ -526,7 +564,14 @@ enums: governance: shared governance coordination: ownership coordination BusinessSizeClassificationEnum: + title: Business Size Classification description: Size classifications for business entities + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: MICRO_BUSINESS: title: Micro Business @@ -577,7 +622,14 @@ enums: market_position: "market leadership positions" recognition: "prestigious business recognition" BusinessLifecycleStageEnum: + title: Business Lifecycle Stage description: Stages in business development lifecycle + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: CONCEPT_STAGE: title: Concept Stage @@ -642,4 +694,4 @@ enums: focus: "exit strategy execution" activities: "sale, merger, or liquidation" valuation: "business valuation" - transition: "ownership transition" \ No newline at end of file + transition: "ownership transition" diff --git a/src/valuesets/schema/business/quality_management.yaml b/src/valuesets/schema/business/quality_management.yaml index 05feef79..12ef9716 100644 --- a/src/valuesets/schema/business/quality_management.yaml +++ b/src/valuesets/schema/business/quality_management.yaml @@ -1,16 +1,18 @@ name: quality_management title: Quality Management Systems and Standards -description: 'Quality management frameworks, ISO standards, process improvement methodologies, - and quality assurance systems. Based on international quality standards, continuous - improvement methodologies, and quality management best practices.' +description: 'Quality management frameworks, ISO standards, process improvement methodologies, and quality assurance systems. + Based on international quality standards, continuous improvement methodologies, and quality management best practices.' id: https://w3id.org/linkml/valuesets/business/quality_management imports: - linkml:types prefixes: + linkml: https://w3id.org/linkml/ valuesets: https://w3id.org/valuesets/ ISO: https://www.iso.org/ TQM: https://www.asq.org/ LEAN: https://www.lean.org/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: quality_standard: @@ -33,7 +35,14 @@ slots: range: QualityMaturityLevelEnum enums: QualityStandardEnum: + title: Quality Standard description: Quality management standards and frameworks + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ISO_9001: title: ISO 9001 Quality Management Systems @@ -144,7 +153,14 @@ enums: design_controls: "design controls" risk_management: "risk management" QualityMethodologyEnum: + title: Quality Methodology description: Quality improvement methodologies and approaches + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: DMAIC: title: DMAIC (Define, Measure, Analyze, Improve, Control) @@ -237,7 +253,14 @@ enums: external: "external benchmarking" internal: "internal benchmarking" QualityControlTechniqueEnum: + title: Quality Control Technique description: Quality control techniques and tools + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: CONTROL_CHARTS: title: Control Charts @@ -330,7 +353,14 @@ enums: variation: "measurement variation" capability: "measurement capability" QualityAssuranceLevelEnum: + title: Quality Assurance Level description: Levels of quality assurance implementation + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: BASIC_QA: title: Basic Quality Assurance @@ -378,7 +408,14 @@ enums: customer: "customer-focused" continuous: "continuous improvement" ProcessImprovementApproachEnum: + title: Process Improvement Approach description: Process improvement methodologies and approaches + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: BUSINESS_PROCESS_REENGINEERING: title: Business Process Reengineering (BPR) @@ -453,7 +490,14 @@ enums: responsive: "responsive to change" collaboration: "collaborative improvement" QualityMaturityLevelEnum: + title: Quality Maturity Level description: Organizational quality maturity levels + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: AD_HOC: title: Ad Hoc Quality Approach @@ -499,4 +543,4 @@ enums: leadership: "industry leadership" innovation: "quality innovation" excellence: "sustained excellence" - recognition: "external recognition" \ No newline at end of file + recognition: "external recognition" diff --git a/src/valuesets/schema/business/supply_chain.yaml b/src/valuesets/schema/business/supply_chain.yaml index c1e2c728..8d2503ee 100644 --- a/src/valuesets/schema/business/supply_chain.yaml +++ b/src/valuesets/schema/business/supply_chain.yaml @@ -1,16 +1,18 @@ name: supply_chain title: Supply Chain Management and Procurement -description: 'Supply chain management classifications including procurement types, vendor - management, logistics operations, and supply chain strategies. Based on supply chain - management best practices, procurement standards, and logistics frameworks.' +description: 'Supply chain management classifications including procurement types, vendor management, logistics operations, + and supply chain strategies. Based on supply chain management best practices, procurement standards, and logistics frameworks.' id: https://w3id.org/linkml/valuesets/business/supply_chain imports: - linkml:types prefixes: + linkml: https://w3id.org/linkml/ valuesets: https://w3id.org/valuesets/ SCOR: https://www.apics.org/apics-for-business/frameworks/scor CSCMP: https://cscmp.org/ ISM: https://www.ismworld.org/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: procurement_type: @@ -36,7 +38,14 @@ slots: range: InventoryManagementApproachEnum enums: ProcurementTypeEnum: + title: Procurement Type description: Types of procurement activities and approaches + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: DIRECT_PROCUREMENT: title: Direct Procurement @@ -129,7 +138,14 @@ enums: certification: "sustainability certifications" stakeholder: "stakeholder value" VendorCategoryEnum: + title: Vendor Category description: Vendor classification categories + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: STRATEGIC_SUPPLIER: title: Strategic Supplier @@ -222,7 +238,14 @@ enums: no_relationship: "no ongoing relationship" market_based: "market-based pricing" SupplyChainStrategyEnum: + title: Supply Chain Strategy description: Supply chain strategic approaches + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: LEAN_SUPPLY_CHAIN: title: Lean Supply Chain @@ -315,7 +338,14 @@ enums: responsiveness: "customer responsiveness" satisfaction: "customer satisfaction" LogisticsOperationEnum: + title: Logistics Operation description: Types of logistics operations + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: INBOUND_LOGISTICS: title: Inbound Logistics @@ -408,7 +438,14 @@ enums: coordination: "multi-modal coordination" compliance: "regulatory compliance" SourcingStrategyEnum: + title: Sourcing Strategy description: Sourcing strategy approaches + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: SINGLE_SOURCING: title: Single Sourcing @@ -501,7 +538,14 @@ enums: complexity: "coordination complexity" relationships: "multi-party relationships" SupplierRelationshipTypeEnum: + title: Supplier Relationship Type description: Types of supplier relationship management + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: TRANSACTIONAL: title: Transactional Relationship @@ -594,7 +638,14 @@ enums: outcomes: "shared outcomes" collaboration: "collaborative approach" InventoryManagementApproachEnum: + title: Inventory Management Approach description: Inventory management methodologies + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: JUST_IN_TIME: title: Just-in-Time (JIT) @@ -685,4 +736,4 @@ enums: variable: "variable order quantity" target: "target inventory level" aggregation: "order aggregation" - efficiency: "administrative efficiency" \ No newline at end of file + efficiency: "administrative efficiency" diff --git a/src/valuesets/schema/chemistry/chemical_entities.yaml b/src/valuesets/schema/chemistry/chemical_entities.yaml index 0d1c5261..3c45b5bf 100644 --- a/src/valuesets/schema/chemistry/chemical_entities.yaml +++ b/src/valuesets/schema/chemistry/chemical_entities.yaml @@ -17,6 +17,8 @@ prefixes: damlpt: http://www.daml.org/2003/01/periodictable/PeriodicTable# pdg: https://pdgapi.lbl.gov/summaries/ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: subatomic_particle: @@ -54,7 +56,14 @@ slots: range: NanostructureMorphologyEnum enums: SubatomicParticleEnum: + title: Subatomic Particle description: Fundamental and composite subatomic particles + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ELECTRON: description: Elementary particle with -1 charge, spin 1/2 @@ -252,7 +261,14 @@ enums: charge: '+1' composition: 1 proton, 2 neutrons BondTypeEnum: + title: Bond Type description: Types of chemical bonds + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: SINGLE: description: Single covalent bond @@ -319,7 +335,14 @@ enums: annotations: orbital_overlap: head-to-head PeriodicTableBlockEnum: + title: Periodic Table Block description: Blocks of the periodic table + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: S_BLOCK: title: s-block molecular entity @@ -350,7 +373,14 @@ enums: valence_orbital: f series: lanthanides, actinides ElementFamilyEnum: + title: Element Family description: Chemical element families/groups + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ALKALI_METALS: title: alkali metal atom @@ -422,7 +452,14 @@ enums: annotations: elements: H, C, N, O, F, P, S, Cl, Se, Br, I ElementMetallicClassificationEnum: + title: Element Metallic Classification description: Metallic character classification + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: METALLIC: description: Metallic elements @@ -440,7 +477,14 @@ enums: annotations: properties: intermediate properties HardOrSoftEnum: + title: Hard Or Soft description: HSAB (Hard Soft Acid Base) classification + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: HARD: description: Hard acids/bases (small, high charge density) @@ -458,7 +502,14 @@ enums: examples: Fe2+, Co2+, Ni2+, Cu2+, Zn2+ polarizability: intermediate BronstedAcidBaseRoleEnum: + title: Bronsted Acid Base Role description: Brønsted-Lowry acid-base roles + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ACID: title: Bronsted acid @@ -478,7 +529,14 @@ enums: definition: species that can donate or accept H+ examples: H2O, HSO4-, H2PO4- LewisAcidBaseRoleEnum: + title: Lewis Acid Base Role description: Lewis acid-base roles + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: LEWIS_ACID: description: Electron pair acceptor @@ -491,7 +549,14 @@ enums: definition: species that donates electron pair examples: NH3, OH-, H2O OxidationStateEnum: + title: Oxidation State description: Common oxidation states + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: MINUS_4: description: Oxidation state -4 @@ -559,7 +624,14 @@ enums: value: '+8' example: Os in OsO4 ChiralityEnum: + title: Chirality description: Chirality/stereochemistry descriptors + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: R: description: Rectus (right) configuration @@ -596,7 +668,14 @@ enums: annotations: geometric_isomer: 'true' NanostructureMorphologyEnum: + title: Nanostructure Morphology description: Types of nanostructure morphologies + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: NANOTUBE: description: Cylindrical nanostructure diff --git a/src/valuesets/schema/chemistry/reaction_directionality.yaml b/src/valuesets/schema/chemistry/reaction_directionality.yaml index 1c79ca99..fbadbfd4 100644 --- a/src/valuesets/schema/chemistry/reaction_directionality.yaml +++ b/src/valuesets/schema/chemistry/reaction_directionality.yaml @@ -10,6 +10,8 @@ prefixes: SBO: http://biomodels.net/SBO/ cvs: https://w3id.org/common-value-sets/ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: reaction_directionality: @@ -19,6 +21,12 @@ enums: ReactionDirectionality: title: Reaction Directionality description: The directionality of a chemical reaction or process + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: LEFT_TO_RIGHT: description: Reaction proceeds from left to right (forward direction) diff --git a/src/valuesets/schema/chemistry/reactions.yaml b/src/valuesets/schema/chemistry/reactions.yaml index b8298449..0dcc2945 100644 --- a/src/valuesets/schema/chemistry/reactions.yaml +++ b/src/valuesets/schema/chemistry/reactions.yaml @@ -15,6 +15,8 @@ prefixes: GO: http://purl.obolibrary.org/obo/GO_ EC: https://enzyme.expasy.org/EC/ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: reaction_type: @@ -43,7 +45,14 @@ slots: range: ThermodynamicParameterEnum enums: ReactionTypeEnum: + title: Reaction Type description: Types of chemical reactions + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: SYNTHESIS: description: Combination reaction (A + B → AB) @@ -138,7 +147,14 @@ enums: annotations: type: conjugate addition ReactionMechanismEnum: + title: Reaction Mechanism description: Reaction mechanism types + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: SN1: description: Unimolecular nucleophilic substitution @@ -183,7 +199,14 @@ enums: annotations: intermediate: tetrahedral CatalystTypeEnum: + title: Catalyst Type description: Types of catalysts + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: HOMOGENEOUS: description: Catalyst in same phase as reactants @@ -233,7 +256,14 @@ enums: annotations: sites: multiple ReactionConditionEnum: + title: Reaction Condition description: Reaction conditions + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ROOM_TEMPERATURE: description: Standard room temperature (20-25°C) @@ -285,7 +315,14 @@ enums: annotations: type: batch process ReactionRateOrderEnum: + title: Reaction Rate Order description: Reaction rate orders + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ZERO_ORDER: description: Rate independent of concentration @@ -315,7 +352,14 @@ enums: annotations: example: rate = k[A][B]² EnzymeClassEnum: + title: Enzyme Class description: EC enzyme classification + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: OXIDOREDUCTASE: title: Oxidoreductases @@ -367,7 +411,14 @@ enums: EC_class: '7' examples: ATPases, ion pumps SolventClassEnum: + title: Solvent Class description: Classes of solvents + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: PROTIC: description: Solvents with acidic hydrogen @@ -408,7 +459,14 @@ enums: property: low environmental impact examples: water, ethanol, scCO2 ThermodynamicParameterEnum: + title: Thermodynamic Parameter description: Thermodynamic parameters + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ENTHALPY: description: Heat content (ΔH) diff --git a/src/valuesets/schema/clinical/nih_demographics.yaml b/src/valuesets/schema/clinical/nih_demographics.yaml index 8397db60..f87b4711 100644 --- a/src/valuesets/schema/clinical/nih_demographics.yaml +++ b/src/valuesets/schema/clinical/nih_demographics.yaml @@ -7,6 +7,7 @@ id: https://w3id.org/linkml/valuesets/clinical/nih_demographics imports: - linkml:types prefixes: + linkml: https://w3id.org/linkml/ valuesets: https://w3id.org/valuesets/ NCIT: http://purl.obolibrary.org/obo/NCIT_ OMRSE: http://purl.obolibrary.org/obo/OMRSE_ @@ -15,6 +16,8 @@ prefixes: SIO: http://semanticscience.org/resource/SIO_ HP: http://purl.obolibrary.org/obo/HP_ ExO: http://purl.obolibrary.org/obo/ExO_ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: race_omb1997: @@ -40,13 +43,20 @@ slots: range: StudyPhaseEnum enums: RaceOMB1997Enum: + title: Race OMB1997 description: 'Race categories following OMB 1997 standards used by NIH and federal agencies. Respondents may select multiple races.' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: AMERICAN_INDIAN_OR_ALASKA_NATIVE: - description: A person having origins in any of the original peoples of North and South America (including Central - America), and who maintains tribal affiliation or community attachment + description: A person having origins in any of the original peoples of North and South America (including + Central America), and who maintains tribal affiliation or community attachment meaning: NCIT:C41259 annotations: omb_code: 1002-5 @@ -54,8 +64,8 @@ enums: - ExO:0000134 - ExO:0000133 ASIAN: - description: A person having origins in any of the original peoples of the Far East, Southeast Asia, or the Indian - subcontinent + description: A person having origins in any of the original peoples of the Far East, Southeast Asia, or the + Indian subcontinent meaning: NCIT:C41260 annotations: omb_code: 2028-9 @@ -76,7 +86,8 @@ enums: related_mappings: - ExO:0000132 NATIVE_HAWAIIAN_OR_OTHER_PACIFIC_ISLANDER: - description: A person having origins in any of the original peoples of Hawaii, Guam, Samoa, or other Pacific Islands + description: A person having origins in any of the original peoples of Hawaii, Guam, Samoa, or other Pacific + Islands meaning: NCIT:C41219 annotations: omb_code: 2076-8 @@ -105,11 +116,18 @@ enums: annotations: aliases: Unknown, Not Reported, Prefer not to answer EthnicityOMB1997Enum: + title: Ethnicity OMB1997 description: Ethnicity categories following OMB 1997 standards used by NIH and federal agencies + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: HISPANIC_OR_LATINO: - description: A person of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin, - regardless of race + description: A person of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or + origin, regardless of race meaning: NCIT:C17459 annotations: omb_code: 2135-2 @@ -136,9 +154,16 @@ enums: annotations: aliases: Unknown, Not Reported, Prefer not to answer BiologicalSexEnum: + title: Biological Sex description: 'Biological sex assigned at birth based on anatomical and physiological traits. Required by NIH as a biological variable in research.' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: MALE: description: Male sex assigned at birth @@ -167,7 +192,14 @@ enums: meaning: NCIT:C17998 title: Unknown AgeGroupEnum: + title: Age Group description: Standard age groups used in NIH clinical research, particularly NINDS CDEs + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: NEONATE: description: Birth to 28 days @@ -223,7 +255,14 @@ enums: min_age_years: 65 aliases: Geriatric, Elderly, Senior ParticipantVitalStatusEnum: + title: Participant Vital Status description: Vital status of a research participant in clinical studies + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ALIVE: description: Participant is living @@ -240,7 +279,14 @@ enums: description: Vital status unknown or lost to follow-up meaning: NCIT:C17998 RecruitmentStatusEnum: + title: Recruitment Status description: Clinical trial or study recruitment status per NIH/ClinicalTrials.gov + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: NOT_YET_RECRUITING: description: Study has not started recruiting participants @@ -274,7 +320,14 @@ enums: meaning: NCIT:C70758 title: Study Withdrawn StudyPhaseEnum: + title: Study Phase description: Clinical trial phases per FDA and NIH definitions + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: EARLY_PHASE_1: description: Exploratory trials before traditional Phase 1 diff --git a/src/valuesets/schema/clinical/phenopackets.yaml b/src/valuesets/schema/clinical/phenopackets.yaml index 6c4099ac..deeb6a0b 100644 --- a/src/valuesets/schema/clinical/phenopackets.yaml +++ b/src/valuesets/schema/clinical/phenopackets.yaml @@ -5,6 +5,7 @@ id: https://w3id.org/linkml/valuesets/clinical/phenopackets imports: - linkml:types prefixes: + linkml: https://w3id.org/linkml/ valuesets: https://w3id.org/valuesets/ NCIT: http://purl.obolibrary.org/obo/NCIT_ GENO: http://purl.obolibrary.org/obo/GENO_ @@ -13,6 +14,8 @@ prefixes: UBERON: http://purl.obolibrary.org/obo/UBERON_ UCUM: http://unitsofmeasure.org/ PATO: http://purl.obolibrary.org/obo/PATO_ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: karyotypic_sex: @@ -47,7 +50,17 @@ slots: range: DrugResponseEnum enums: KaryotypicSexEnum: + title: Karyotypic Sex description: Karyotypic sex of an individual based on chromosome composition + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + stewards: https://phenopackets.org + publishers: https://ga4gh.org permissible_values: XX: description: Female karyotype (46,XX) @@ -121,9 +134,19 @@ enums: meaning: NCIT:C17998 title: Unknown PhenotypicSexEnum: + title: Phenotypic Sex description: 'Phenotypic sex of an individual based on observable characteristics. FHIR mapping: AdministrativeGender' + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + stewards: https://phenopackets.org + publishers: https://ga4gh.org permissible_values: MALE: description: Male phenotypic sex @@ -146,7 +169,17 @@ enums: meaning: NCIT:C17998 title: Unknown AllelicStateEnum: + title: Allelic State description: Allelic state/zygosity of a variant or genetic feature + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + stewards: https://phenopackets.org + publishers: https://ga4gh.org permissible_values: HETEROZYGOUS: description: Different alleles at a locus @@ -182,7 +215,17 @@ enums: annotations: symbol: hom alt LateralityEnum: + title: Laterality description: Laterality/sidedness of a finding or anatomical structure + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + stewards: https://phenopackets.org + publishers: https://ga4gh.org permissible_values: RIGHT: description: Right side @@ -209,7 +252,17 @@ enums: annotations: note: Along the body's central axis OnsetTimingEnum: + title: Onset Timing description: Timing of disease or phenotype onset relative to developmental stages + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + stewards: https://phenopackets.org + publishers: https://ga4gh.org permissible_values: ANTENATAL_ONSET: description: Before birth (prenatal) @@ -267,7 +320,17 @@ enums: annotations: period: '>60 years' ACMGPathogenicityEnum: + title: ACMG Pathogenicity description: ACMG/AMP variant pathogenicity classification for clinical genetics + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + stewards: https://phenopackets.org + publishers: https://ga4gh.org permissible_values: PATHOGENIC: description: Pathogenic variant @@ -305,7 +368,17 @@ enums: abbreviation: B clinical_significance: Not disease-causing TherapeuticActionabilityEnum: + title: Therapeutic Actionability description: Clinical actionability of a genetic finding for treatment decisions + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + stewards: https://phenopackets.org + publishers: https://ga4gh.org permissible_values: ACTIONABLE: description: Finding has direct therapeutic implications @@ -324,7 +397,17 @@ enums: meaning: NCIT:C17998 title: Unknown InterpretationProgressEnum: + title: Interpretation Progress description: Progress status of clinical interpretation or diagnosis + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + stewards: https://phenopackets.org + publishers: https://ga4gh.org permissible_values: SOLVED: description: Diagnosis achieved/case solved @@ -353,7 +436,17 @@ enums: meaning: NCIT:C17998 title: Unknown RegimenStatusEnum: + title: Regimen Status description: Status of a therapeutic regimen or treatment protocol + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + stewards: https://phenopackets.org + publishers: https://ga4gh.org permissible_values: NOT_STARTED: description: Treatment not yet begun @@ -392,7 +485,17 @@ enums: meaning: NCIT:C17998 title: Unknown DrugResponseEnum: + title: Drug Response description: Response categories for drug treatment outcomes + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + stewards: https://phenopackets.org + publishers: https://ga4gh.org permissible_values: FAVORABLE: description: Favorable response to treatment diff --git a/src/valuesets/schema/computing/croissant_ml.yaml b/src/valuesets/schema/computing/croissant_ml.yaml index cfb11ccb..7bfae1ca 100644 --- a/src/valuesets/schema/computing/croissant_ml.yaml +++ b/src/valuesets/schema/computing/croissant_ml.yaml @@ -20,13 +20,22 @@ prefixes: schema: http://schema.org/ xsd: http://www.w3.org/2001/XMLSchema# spdx: https://spdx.org/licenses/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets enums: MLDataType: + title: ML Data Type description: | Data types used in Croissant ML for describing field types in datasets. Based on XSD (XML Schema Definition) and schema.org vocabulary. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: TEXT: description: Text or string data @@ -72,9 +81,16 @@ enums: - schema:URL DatasetEncodingFormat: + title: Dataset Encoding Format description: | Encoding formats (MIME types) commonly used for ML dataset files in Croissant. These specify how data is serialized and stored. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: CSV: description: Comma-separated values format for tabular data @@ -135,10 +151,17 @@ enums: mime_type: application/x-tar DatasetSplitType: + title: Dataset Split Type description: | Standard dataset split types used in machine learning for training, validation, and testing. These splits are fundamental to ML model development and evaluation workflows. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: TRAIN: description: Training split used for model learning @@ -160,9 +183,16 @@ enums: description: Complete dataset without splits MLLicenseType: + title: ML License Type description: | Common open source and Creative Commons licenses used for ML datasets. These licenses specify terms of use, redistribution, and modification. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: CC_BY_4_0: description: Creative Commons Attribution 4.0 International @@ -226,9 +256,16 @@ enums: copyleft: true MLFieldRole: + title: ML Field Role description: | Semantic roles that fields play in ML datasets. These roles help understand the purpose and usage of different data columns or attributes. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: FEATURE: description: Input features used for model prediction @@ -248,8 +285,15 @@ enums: also_known_as: ID, key, primary key CompressionFormat: + title: Compression Format description: | Compression and archive formats commonly used for ML dataset distribution. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ZIP: description: ZIP archive format with lossless data compression @@ -279,9 +323,16 @@ enums: typical_extension: .tar.gz MLMediaType: + title: ML Media Type description: | Media types (MIME types) for different modalities of ML data including images, audio, video, and text. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: # Images IMAGE_JPEG: @@ -357,9 +408,16 @@ enums: modality: text MLModalityType: + title: ML Modality Type description: | High-level data modalities used in machine learning. These represent the fundamental types of input data that ML models process. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: TEXT: description: Textual data (natural language, code, etc.) diff --git a/src/valuesets/schema/computing/file_formats.yaml b/src/valuesets/schema/computing/file_formats.yaml index 13af5c73..107e6946 100644 --- a/src/valuesets/schema/computing/file_formats.yaml +++ b/src/valuesets/schema/computing/file_formats.yaml @@ -12,6 +12,8 @@ prefixes: IAO: http://purl.obolibrary.org/obo/IAO_ SWO: http://purl.obolibrary.org/obo/SWO_ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: image_file_format: @@ -40,7 +42,14 @@ slots: range: NetworkProtocolEnum enums: ImageFileFormatEnum: + title: Image File Format description: Common image file formats + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: JPEG: description: Joint Photographic Experts Group @@ -111,7 +120,14 @@ enums: mime_type: image/x-icon use: favicons, app icons DocumentFormatEnum: + title: Document Format description: Document and text file formats + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: PDF: description: Portable Document Format @@ -188,7 +204,14 @@ enums: mime_type: application/epub+zip use: e-books DataFormatEnum: + title: Data Format description: Structured data file formats + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: JSON: description: JavaScript Object Notation @@ -272,7 +295,14 @@ enums: mime_type: application/x-sqlite3 type: embedded database ArchiveFormatEnum: + title: Archive Format description: Archive and compression formats + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ZIP: description: ZIP archive @@ -333,7 +363,14 @@ enums: mime_type: application/vnd.rar proprietary: 'true' VideoFormatEnum: + title: Video Format description: Video file formats + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: MP4: description: MPEG-4 Part 14 @@ -383,7 +420,14 @@ enums: extension: .mpeg, .mpg mime_type: video/mpeg AudioFormatEnum: + title: Audio Format description: Audio file formats + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: MP3: description: MPEG Audio Layer 3 @@ -440,7 +484,14 @@ enums: mime_type: audio/aiff creator: Apple ProgrammingLanguageFileEnum: + title: Programming Language File description: Programming language source file extensions + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: PYTHON: description: Python source file @@ -528,7 +579,14 @@ enums: extension: .sh, .bash mime_type: text/x-shellscript NetworkProtocolEnum: + title: Network Protocol description: Network communication protocols + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: HTTP: description: Hypertext Transfer Protocol diff --git a/src/valuesets/schema/computing/maturity_levels.yaml b/src/valuesets/schema/computing/maturity_levels.yaml index b28956eb..1f7963b6 100644 --- a/src/valuesets/schema/computing/maturity_levels.yaml +++ b/src/valuesets/schema/computing/maturity_levels.yaml @@ -1,18 +1,20 @@ name: maturity_levels title: Software and Technology Maturity Levels -description: Value sets for assessing maturity levels of software, technology, and standards across different frameworks and - domains. +description: Value sets for assessing maturity levels of software, technology, and standards across different frameworks + and domains. id: https://w3id.org/common-value-sets/computing/maturity_levels imports: - linkml:types prefixes: linkml: https://w3id.org/linkml/ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: technology_readiness_level: - description: NASA's Technology Readiness Level scale for assessing the maturity of technologies from basic research through - operational deployment + description: NASA's Technology Readiness Level scale for assessing the maturity of technologies from basic research + through operational deployment range: TechnologyReadinessLevel software_maturity_level: description: General software maturity assessment levels @@ -35,8 +37,14 @@ slots: enums: TechnologyReadinessLevel: title: Technology Readiness Level (TRL) - description: NASA's Technology Readiness Level scale for assessing the maturity of technologies from basic research through - operational deployment + description: NASA's Technology Readiness Level scale for assessing the maturity of technologies from basic research + through operational deployment + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ReferenceEnumDefinition source: https://www.nasa.gov/directorates/heo/scan/engineering/technology/technology_readiness_level conforms_to: ISO-16290:2013 permissible_values: @@ -70,6 +78,12 @@ enums: SoftwareMaturityLevel: title: Software Maturity Level description: General software maturity assessment levels + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ReferenceEnumDefinition permissible_values: ALPHA: description: Early development stage with basic functionality, may be unstable @@ -98,6 +112,12 @@ enums: CapabilityMaturityLevel: title: Capability Maturity Model Integration (CMMI) Level description: CMMI levels for assessing organizational process maturity in software development + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ReferenceEnumDefinition source: https://cmmiinstitute.com/ conforms_to: CMMI Version 2.0 permissible_values: @@ -119,6 +139,12 @@ enums: StandardsMaturityLevel: title: Standards Development Maturity Level description: Maturity levels for standards and specifications + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ReferenceEnumDefinition permissible_values: DRAFT: description: Initial draft under development @@ -150,6 +176,12 @@ enums: ProjectMaturityLevel: title: Project Maturity Level description: General project development maturity assessment + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ReferenceEnumDefinition permissible_values: CONCEPT: description: Initial idea or concept stage @@ -178,6 +210,12 @@ enums: DataMaturityLevel: title: Data Maturity Level description: Levels of data quality, governance, and organizational maturity + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ReferenceEnumDefinition permissible_values: RAW: description: Unprocessed, uncleaned data @@ -203,6 +241,12 @@ enums: OpenSourceMaturityLevel: title: Open Source Project Maturity description: Maturity assessment for open source projects + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ReferenceEnumDefinition permissible_values: EXPERIMENTAL: description: Early experimental project diff --git a/src/valuesets/schema/computing/mime_types.yaml b/src/valuesets/schema/computing/mime_types.yaml index 9d0091d5..6da5e0e9 100644 --- a/src/valuesets/schema/computing/mime_types.yaml +++ b/src/valuesets/schema/computing/mime_types.yaml @@ -1,7 +1,7 @@ name: mime_types title: MIME Types Value Sets -description: Common MIME (Multipurpose Internet Mail Extensions) types for various file formats and content types used in - web and application development. +description: Common MIME (Multipurpose Internet Mail Extensions) types for various file formats and content types used + in web and application development. id: https://w3id.org/linkml/valuesets/computing/mime_types imports: - linkml:types @@ -10,6 +10,8 @@ prefixes: cvs: https://w3id.org/linkml/valuesets/ iana: https://www.iana.org/assignments/media-types/ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: mime: @@ -26,7 +28,14 @@ slots: range: CompressionType enums: MimeType: + title: Mime Type description: Common MIME types for various file formats + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: APPLICATION_JSON: description: JSON format @@ -224,7 +233,14 @@ enums: description: Mixed multipart message meaning: iana:multipart/mixed MimeTypeCategory: + title: Mime Type Category description: Categories of MIME types + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: APPLICATION: description: Application data @@ -245,7 +261,14 @@ enums: MODEL: description: 3D models and similar TextCharset: + title: Text Charset description: Character encodings for text content + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: UTF_8: description: UTF-8 Unicode encoding @@ -270,7 +293,14 @@ enums: BIG5: description: Traditional Chinese encoding CompressionType: + title: Compression Type description: Compression types used with Content-Encoding + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: GZIP: description: GZIP compression diff --git a/src/valuesets/schema/computing/ontologies.yaml b/src/valuesets/schema/computing/ontologies.yaml index a339f389..199ee148 100644 --- a/src/valuesets/schema/computing/ontologies.yaml +++ b/src/valuesets/schema/computing/ontologies.yaml @@ -11,6 +11,8 @@ prefixes: owl: http://www.w3.org/2002/07/owl# valuesets: https://w3id.org/valuesets/ IAO: http://purl.obolibrary.org/obo/IAO_ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: owl_profile: @@ -18,12 +20,18 @@ slots: range: OWLProfileEnum enums: OWLProfileEnum: - description: OWL 2 profiles that provide different tradeoffs between expressiveness and computational - complexity + title: OWL Profile + description: OWL 2 profiles that provide different tradeoffs between expressiveness and computational complexity + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: OWL_2_EL: - description: OWL 2 EL (Existential Language) - optimized for applications using very large - ontologies with basic relationships. Provides polynomial time reasoning. + description: OWL 2 EL (Existential Language) - optimized for applications using very large ontologies with basic + relationships. Provides polynomial time reasoning. title: OWL 2 EL see_also: - https://www.w3.org/TR/owl2-profiles/#OWL_2_EL @@ -31,8 +39,8 @@ enums: complexity: polynomial time use_case: large biomedical ontologies, SNOMED CT OWL_2_QL: - description: OWL 2 QL (Query Language) - optimized for query answering over large data - repositories. Based on DL-Lite family. + description: OWL 2 QL (Query Language) - optimized for query answering over large data repositories. Based on + DL-Lite family. title: OWL 2 QL see_also: - https://www.w3.org/TR/owl2-profiles/#OWL_2_QL @@ -40,8 +48,8 @@ enums: complexity: LogSpace data complexity use_case: ontology-based data access, database integration OWL_2_RL: - description: OWL 2 RL (Rule Language) - optimized for rule-based reasoning and can be implemented - using rule engines. Compatible with RDF Schema. + description: OWL 2 RL (Rule Language) - optimized for rule-based reasoning and can be implemented using rule + engines. Compatible with RDF Schema. title: OWL 2 RL see_also: - https://www.w3.org/TR/owl2-profiles/#OWL_2_RL @@ -49,8 +57,8 @@ enums: complexity: polynomial time use_case: business rules, policy systems OWL_2_DL: - description: OWL 2 DL (Description Logic) - full expressiveness while maintaining computational - completeness and decidability. Maximum expressiveness without sacrificing decidability. + description: OWL 2 DL (Description Logic) - full expressiveness while maintaining computational completeness and + decidability. Maximum expressiveness without sacrificing decidability. title: OWL 2 DL see_also: - https://www.w3.org/TR/owl2-syntax/ @@ -58,8 +66,8 @@ enums: complexity: NExpTime use_case: general purpose ontologies requiring high expressiveness OWL_2_FULL: - description: OWL 2 Full - maximum expressiveness with no restrictions, but reasoning is - undecidable. Allows full RDF capabilities. + description: OWL 2 Full - maximum expressiveness with no restrictions, but reasoning is undecidable. Allows full + RDF capabilities. title: OWL 2 Full see_also: - https://www.w3.org/TR/owl2-syntax/ diff --git a/src/valuesets/schema/confidence_levels.yaml b/src/valuesets/schema/confidence_levels.yaml index 3b23c2a8..1adb4984 100644 --- a/src/valuesets/schema/confidence_levels.yaml +++ b/src/valuesets/schema/confidence_levels.yaml @@ -1,7 +1,7 @@ name: confidence_levels title: Confidence Level Value Sets -description: Value sets for expressing levels of confidence, certainty, and evidence strength in various contexts including - research, clinical, and data quality assessments. +description: Value sets for expressing levels of confidence, certainty, and evidence strength in various contexts + including research, clinical, and data quality assessments. id: https://w3id.org/valuesets/valuesets/confidence_levels imports: - linkml:types @@ -12,33 +12,43 @@ prefixes: NCIT: http://purl.obolibrary.org/obo/NCIT_ CIO: http://purl.obolibrary.org/obo/CIO_ OBCS: http://purl.obolibrary.org/obo/OBCS_ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: confidence_level: description: Standard confidence levels based on NCIT (NCI Thesaurus) definitions range: ConfidenceLevel cio_confidence_level: - description: Confidence levels from the Confidence Information Ontology (CIO), representing different levels of trust - in evidence + description: Confidence levels from the Confidence Information Ontology (CIO), representing different levels of + trust in evidence range: CIOConfidenceLevel obcs_certainty_level: description: Certainty levels from the Ontology of Biological and Clinical Statistics (OBCS) range: OBCSCertaintyLevel ipcc_likelihood_scale: - description: IPCC (Intergovernmental Panel on Climate Change) standardized likelihood scale used to communicate the assessed - probability of an outcome or result + description: IPCC (Intergovernmental Panel on Climate Change) standardized likelihood scale used to communicate the + assessed probability of an outcome or result range: IPCCLikelihoodScale ipcc_confidence_level: - description: IPCC confidence qualifiers used to express the degree of confidence in a finding based on the type, amount, - quality, and consistency of evidence and the degree of agreement + description: IPCC confidence qualifiers used to express the degree of confidence in a finding based on the type, + amount, quality, and consistency of evidence and the degree of agreement range: IPCCConfidenceLevel ncit_five_point_confidence_scale: - description: NCIT 5-point subjective confidence scale ranging from "Not at all confident" (1) to "Very confident" (5) + description: NCIT 5-point subjective confidence scale ranging from "Not at all confident" (1) to "Very confident" + (5) range: NCITFivePointConfidenceScale enums: ConfidenceLevel: - description: Standard confidence levels based on NCIT (NCI Thesaurus) definitions. Used to express the degree of confidence - in evidence, data, or assertions. + title: Confidence Level + description: Standard confidence levels based on NCIT (NCI Thesaurus) definitions. Used to express the degree of + confidence in evidence, data, or assertions. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinitionWithConformance source: http://purl.obolibrary.org/obo/ncit.owl conforms_to: NCI Thesaurus permissible_values: @@ -57,8 +67,15 @@ enums: aliases: - Very Low Confidence or No Confidence CIOConfidenceLevel: - description: Confidence levels from the Confidence Information Ontology (CIO), representing different levels of trust - in evidence. + title: CIO Confidence Level + description: Confidence levels from the Confidence Information Ontology (CIO), representing different levels of + trust in evidence. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: HIGH: description: A confidence level representing a high trust in an evidence. @@ -82,8 +99,15 @@ enums: exact_mappings: - NCIT:C129481 OBCSCertaintyLevel: - description: Certainty levels from the Ontology of Biological and Clinical Statistics (OBCS). These terms are used to - express degrees of certainty in statistical and clinical contexts. + title: OBCS Certainty Level + description: Certainty levels from the Ontology of Biological and Clinical Statistics (OBCS). These terms are used + to express degrees of certainty in statistical and clinical contexts. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: DEFINITIVE: description: Definitive certainty level - the highest degree of certainty. @@ -107,8 +131,15 @@ enums: exact_mappings: - NCIT:C129480 IPCCLikelihoodScale: - description: IPCC (Intergovernmental Panel on Climate Change) standardized likelihood scale used to communicate the assessed - probability of an outcome or result. Widely used in climate science and environmental assessments. + title: IPCC Likelihood Scale + description: IPCC (Intergovernmental Panel on Climate Change) standardized likelihood scale used to communicate the + assessed probability of an outcome or result. Widely used in climate science and environmental assessments. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: VIRTUALLY_CERTAIN: description: 99-100% probability of occurrence/truth. @@ -151,8 +182,15 @@ enums: annotations: probability_range: 0.00-0.01 IPCCConfidenceLevel: - description: IPCC confidence qualifiers used to express the degree of confidence in a finding based on the type, amount, - quality, and consistency of evidence and the degree of agreement. + title: IPCC Confidence Level + description: IPCC confidence qualifiers used to express the degree of confidence in a finding based on the type, + amount, quality, and consistency of evidence and the degree of agreement. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: VERY_HIGH_CONFIDENCE: description: Very high confidence in the validity of a finding. @@ -175,8 +213,15 @@ enums: exact_mappings: - NCIT:C129482 NCITFivePointConfidenceScale: - description: NCIT 5-point subjective confidence scale ranging from "Not at all confident" (1) to "Very confident" (5). - Used in clinical assessments and questionnaires. + title: NCIT Five Point Confidence Scale + description: NCIT 5-point subjective confidence scale ranging from "Not at all confident" (1) to "Very confident" + (5). Used in clinical assessments and questionnaires. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: NOT_AT_ALL_CONFIDENT: description: A subjective score of 1 - Not at all confident. diff --git a/src/valuesets/schema/contributor.yaml b/src/valuesets/schema/contributor.yaml index baa52346..6951f2ac 100644 --- a/src/valuesets/schema/contributor.yaml +++ b/src/valuesets/schema/contributor.yaml @@ -10,6 +10,8 @@ prefixes: NCIT: http://purl.obolibrary.org/obo/NCIT_ DataCite: https://purl.org/datacite/ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: contributor: @@ -17,7 +19,14 @@ slots: range: ContributorType enums: ContributorType: + title: Contributor Type description: The type of contributor being represented. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: PERSON: description: A person. diff --git a/src/valuesets/schema/core.yaml b/src/valuesets/schema/core.yaml index 74b6fdf2..28a214ee 100644 --- a/src/valuesets/schema/core.yaml +++ b/src/valuesets/schema/core.yaml @@ -26,6 +26,8 @@ prefixes: _base: http://example.org/ mixs: http://w3id.org/mixs/ ucum: http://unitsofmeasure.org/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: relative_time: @@ -36,11 +38,30 @@ slots: range: PresenceEnum enums: RelativeTimeEnum: + title: Relative Time + description: Temporal relationships between events or time points + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: - BEFORE: null - AFTER: null - AT_SAME_TIME_AS: null + BEFORE: + description: Occurs before the reference time point + AFTER: + description: Occurs after the reference time point + AT_SAME_TIME_AS: + description: Occurs at the same time as the reference time point PresenceEnum: + title: Presence Status + description: Classification of whether an entity is present, absent, or at detection limits + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: PRESENT: description: The entity is present diff --git a/src/valuesets/schema/data/data_absent_reason.yaml b/src/valuesets/schema/data/data_absent_reason.yaml index 681e0254..628c8d39 100644 --- a/src/valuesets/schema/data/data_absent_reason.yaml +++ b/src/valuesets/schema/data/data_absent_reason.yaml @@ -4,6 +4,8 @@ prefixes: fhir: http://hl7.org/fhir/ fhir_data_absent_reason: http://terminology.hl7.org/CodeSystem/data-absent-reason valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: data_absent: @@ -11,7 +13,14 @@ slots: range: DataAbsentEnum enums: DataAbsentEnum: + title: Data Absent description: Used to specify why the normally expected content of the data element is missing. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: unknown: description: The value is expected to exist but is not known. @@ -63,12 +72,12 @@ enums: is_a: error title: Not a Number (NaN) negative-infinity: - description: The numeric value is excessively low and unrepresentable due to a floating point processing error. + description: The numeric value is excessively low and unrepresentable due to a floating point processing error. meaning: fhir_data_absent_reason:negative-infinity is_a: error title: Negative Infinity (NINF) positive-infinity: - description: The numeric value is excessively high and unrepresentable due to a floating point processing error. + description: The numeric value is excessively high and unrepresentable due to a floating point processing error. meaning: fhir_data_absent_reason:positive-infinity is_a: error title: Positive Infinity (PINF) diff --git a/src/valuesets/schema/data_science/binary_classification.yaml b/src/valuesets/schema/data_science/binary_classification.yaml index cd4fb0f3..efb5663f 100644 --- a/src/valuesets/schema/data_science/binary_classification.yaml +++ b/src/valuesets/schema/data_science/binary_classification.yaml @@ -7,6 +7,8 @@ prefixes: PATO: http://purl.obolibrary.org/obo/PATO_ GSSO: http://purl.obolibrary.org/obo/GSSO_ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: binary_classification: @@ -26,7 +28,14 @@ slots: range: FraudDetectionEnum enums: BinaryClassificationEnum: + title: Binary Classification description: Generic binary classification labels + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: POSITIVE: description: Positive class @@ -47,7 +56,14 @@ enums: - 'no' - F SpamClassificationEnum: + title: Spam Classification description: Standard labels for spam/ham email classification + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: SPAM: description: Unwanted or unsolicited message @@ -65,7 +81,14 @@ enums: - legitimate - '0' AnomalyDetectionEnum: + title: Anomaly Detection description: Labels for anomaly detection tasks + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: NORMAL: description: Normal, expected behavior or pattern @@ -85,7 +108,14 @@ enums: - irregular - '1' ChurnClassificationEnum: + title: Churn Classification description: Customer churn prediction labels + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: RETAINED: description: Customer continues using the service @@ -105,7 +135,14 @@ enums: - attrited - '1' FraudDetectionEnum: + title: Fraud Detection description: Fraud detection classification labels + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: LEGITIMATE: description: Legitimate, non-fraudulent transaction or activity diff --git a/src/valuesets/schema/data_science/emotion_classification.yaml b/src/valuesets/schema/data_science/emotion_classification.yaml index 14b5ef30..f779501a 100644 --- a/src/valuesets/schema/data_science/emotion_classification.yaml +++ b/src/valuesets/schema/data_science/emotion_classification.yaml @@ -4,6 +4,8 @@ prefixes: # linkml_common: https://w3id.org/linkml-common/ MFOEM: http://purl.obolibrary.org/obo/MFOEM_ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: basic_emotion: @@ -14,7 +16,14 @@ slots: range: ExtendedEmotionEnum enums: BasicEmotionEnum: + title: Basic Emotion description: Ekman's six basic emotions commonly used in emotion recognition + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition conforms_to: https://en.wikipedia.org/wiki/Basic_emotions permissible_values: ANGER: @@ -61,7 +70,14 @@ enums: - surprised - shocked ExtendedEmotionEnum: + title: Extended Emotion description: Extended emotion set including complex emotions + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition conforms_to: https://en.wikipedia.org/wiki/Emotion_classification permissible_values: ANGER: diff --git a/src/valuesets/schema/data_science/priority_severity.yaml b/src/valuesets/schema/data_science/priority_severity.yaml index 96305678..49e8b043 100644 --- a/src/valuesets/schema/data_science/priority_severity.yaml +++ b/src/valuesets/schema/data_science/priority_severity.yaml @@ -5,6 +5,8 @@ prefixes: NCIT: http://purl.obolibrary.org/obo/NCIT_ STATO: http://purl.obolibrary.org/obo/STATO_ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: priority_level: @@ -18,7 +20,14 @@ slots: range: ConfidenceLevelEnum enums: PriorityLevelEnum: + title: Priority Level description: Standard priority levels for task/issue classification + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: CRITICAL: description: Highest priority, requires immediate attention @@ -57,7 +66,14 @@ enums: - cosmetic - '5' SeverityLevelEnum: + title: Severity Level description: Severity levels for incident/bug classification + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: CRITICAL: description: System is unusable, data loss possible @@ -88,7 +104,14 @@ enums: - cosmetic - low ConfidenceLevelEnum: + title: Confidence Level description: Confidence levels for predictions and classifications + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: VERY_HIGH: description: Very high confidence (>95%) diff --git a/src/valuesets/schema/data_science/quality_control.yaml b/src/valuesets/schema/data_science/quality_control.yaml index 66bbd778..e7c4660f 100644 --- a/src/valuesets/schema/data_science/quality_control.yaml +++ b/src/valuesets/schema/data_science/quality_control.yaml @@ -4,6 +4,8 @@ prefixes: # linkml_common: https://w3id.org/linkml-common/ NCIT: http://purl.obolibrary.org/obo/NCIT_ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: quality_control: @@ -14,7 +16,14 @@ slots: range: DefectClassificationEnum enums: QualityControlEnum: + title: Quality Control description: Quality control classification labels + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: PASS: description: Item meets quality standards @@ -35,7 +44,14 @@ enums: - defective - '0' DefectClassificationEnum: + title: Defect Classification description: Manufacturing defect classification + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: NO_DEFECT: description: No defect detected diff --git a/src/valuesets/schema/data_science/sentiment_analysis.yaml b/src/valuesets/schema/data_science/sentiment_analysis.yaml index 8dd13639..85b5948f 100644 --- a/src/valuesets/schema/data_science/sentiment_analysis.yaml +++ b/src/valuesets/schema/data_science/sentiment_analysis.yaml @@ -4,6 +4,8 @@ prefixes: # linkml_common: https://w3id.org/linkml-common/ NCIT: http://purl.obolibrary.org/obo/NCIT_ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: sentiment_classification: @@ -14,7 +16,14 @@ slots: range: FineSentimentClassificationEnum enums: SentimentClassificationEnum: + title: Sentiment Classification description: Standard labels for sentiment analysis classification tasks + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: POSITIVE: description: Positive sentiment or opinion @@ -40,7 +49,14 @@ enums: - neu - '2' FineSentimentClassificationEnum: + title: Fine Sentiment Classification description: Fine-grained sentiment analysis labels with intensity levels + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: VERY_POSITIVE: description: Strongly positive sentiment diff --git a/src/valuesets/schema/data_science/text_classification.yaml b/src/valuesets/schema/data_science/text_classification.yaml index 06b971d2..21d5dd00 100644 --- a/src/valuesets/schema/data_science/text_classification.yaml +++ b/src/valuesets/schema/data_science/text_classification.yaml @@ -5,6 +5,8 @@ prefixes: NCIT: http://purl.obolibrary.org/obo/NCIT_ SIO: http://semanticscience.org/resource/SIO_ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: news_topic_category: @@ -18,7 +20,14 @@ slots: range: IntentClassificationEnum enums: NewsTopicCategoryEnum: + title: News Topic Category description: Common news article topic categories + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: POLITICS: description: Political news and government affairs @@ -63,7 +72,14 @@ enums: aliases: - regional ToxicityClassificationEnum: + title: Toxicity Classification description: Text toxicity classification labels + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: NON_TOXIC: description: Text is appropriate and non-harmful @@ -101,7 +117,14 @@ enums: title: Identity Hate is_a: TOXIC IntentClassificationEnum: + title: Intent Classification description: Common chatbot/NLU intent categories + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: GREETING: description: User greeting or hello diff --git a/src/valuesets/schema/demographics.yaml b/src/valuesets/schema/demographics.yaml index 5992b24f..a0a02016 100644 --- a/src/valuesets/schema/demographics.yaml +++ b/src/valuesets/schema/demographics.yaml @@ -10,6 +10,8 @@ prefixes: HL7: http://terminology.hl7.org/CodeSystem/ SNOMED: http://snomed.info/id/ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: education_level: @@ -35,7 +37,14 @@ slots: range: OmbEthnicityCategory enums: EducationLevel: + title: Education Level description: Years of education that a person has completed + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinitionWithSource source: https://terminology.hl7.org/CodeSystem-v3-EducationLevel.html permissible_values: ELEM: @@ -66,7 +75,14 @@ enums: description: Doctoral or post graduate education meaning: HL7:v3-EducationLevel#POSTG MaritalStatus: + title: Marital Status description: The domestic partnership status of a person + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinitionWithSource source: https://www.hl7.org/fhir/valueset-marital-status.html permissible_values: ANNULLED: @@ -106,7 +122,14 @@ enums: description: A proper value is applicable, but not known meaning: HL7:marital-status#UNK EmploymentStatus: + title: Employment Status description: Employment status of a person + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinitionWithSource source: https://terminology.hl7.org/CodeSystem-v2-0066.html permissible_values: FULL_TIME_EMPLOYED: @@ -146,7 +169,14 @@ enums: description: Unknown meaning: HL7:v2-0066#9 HousingStatus: + title: Housing Status description: Housing status of patients per UDS Plus HRSA standards + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinitionWithSource source: https://www.fhir.org/guides/hrsa/uds-plus/CodeSystem-udsplus-housing-status-codes.html permissible_values: HOMELESS_SHELTER: @@ -171,7 +201,14 @@ enums: description: Patients with Unknown accommodation meaning: HL7:udsplus-housing-status-codes#unknown GenderIdentity: + title: Gender Identity description: Gender identity codes indicating an individual's personal sense of gender + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinitionWithSource source: https://terminology.hl7.org/ValueSet-gender-identity.html permissible_values: FEMALE: @@ -190,7 +227,14 @@ enums: description: A proper value is applicable, but not known meaning: HL7:UNK OmbRaceCategory: + title: Omb Race Category description: Office of Management and Budget (OMB) race category codes + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinitionWithSource source: https://www.hl7.org/fhir/us/core/ValueSet-omb-race-category.html permissible_values: AMERICAN_INDIAN_OR_ALASKA_NATIVE: @@ -218,7 +262,14 @@ enums: description: unknown meaning: HL7:UNK OmbEthnicityCategory: + title: Omb Ethnicity Category description: Office of Management and Budget (OMB) ethnicity category codes + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinitionWithSource source: https://www.hl7.org/fhir/us/core/ValueSet-omb-ethnicity-category.html permissible_values: HISPANIC_OR_LATINO: diff --git a/src/valuesets/schema/earth_science/collection_methods.yaml b/src/valuesets/schema/earth_science/collection_methods.yaml index bc9e52da..e9938e5d 100644 --- a/src/valuesets/schema/earth_science/collection_methods.yaml +++ b/src/valuesets/schema/earth_science/collection_methods.yaml @@ -6,6 +6,8 @@ prefixes: linkml: https://w3id.org/linkml/ OBI: http://purl.obolibrary.org/obo/OBI_ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: @@ -15,11 +17,18 @@ slots: enums: SESARCollectionMethod: + title: SESAR Collection Method description: >- Sample collection methods as defined by SESAR (System for Earth Sample Registration). These describe the method by which a sample was collected. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition see_also: - - https://www.geosamples.org/vocabularies + - https://www.geosamples.org/vocabularies permissible_values: BLASTING: description: Sample collected using blasting techniques @@ -126,5 +135,5 @@ enums: license: MIT see_also: - - https://linkml.github.io/valuesets - - https://www.geosamples.org/vocabularies +- https://linkml.github.io/valuesets +- https://www.geosamples.org/vocabularies diff --git a/src/valuesets/schema/earth_science/fao_soil.yaml b/src/valuesets/schema/earth_science/fao_soil.yaml index e669fa9e..241cacf4 100644 --- a/src/valuesets/schema/earth_science/fao_soil.yaml +++ b/src/valuesets/schema/earth_science/fao_soil.yaml @@ -6,6 +6,8 @@ prefixes: linkml: https://w3id.org/linkml/ ENVO: http://purl.obolibrary.org/obo/ENVO_ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: @@ -15,13 +17,20 @@ slots: enums: FAOSoilType: + title: FAO Soil Type description: >- FAO World Reference Base (WRB) soil classification system. Based on the Harmonized World Soil Database (HWSD) version 2. These represent the major soil groups according to the World Reference Base for Soil Resources. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition see_also: - - https://www.fao.org/soils-portal/data-hub/soil-classification/world-reference-base/en/ - - https://www.isric.org/explore/hwsd + - https://www.fao.org/soils-portal/data-hub/soil-classification/world-reference-base/en/ + - https://www.isric.org/explore/hwsd permissible_values: ACRISOLS: description: Acrisols - soils with subsurface accumulation of low-activity clays and low base saturation @@ -169,7 +178,8 @@ enums: fao_id: 24 color_rgb: "115,0,0" PODZOLS: - description: Podzols - soils with subsurface accumulation of aluminium and iron complexes with organic matter (spodic horizon) + description: Podzols - soils with subsurface accumulation of aluminium and iron complexes with organic matter + (spodic horizon) annotations: symbol: PZ fao_id: 25 @@ -240,6 +250,6 @@ enums: license: MIT see_also: - - https://linkml.github.io/valuesets - - https://www.fao.org/soils-portal/data-hub/soil-classification/world-reference-base/en/ - - https://www.isric.org/explore/hwsd \ No newline at end of file +- https://linkml.github.io/valuesets +- https://www.fao.org/soils-portal/data-hub/soil-classification/world-reference-base/en/ +- https://www.isric.org/explore/hwsd diff --git a/src/valuesets/schema/earth_science/material_types.yaml b/src/valuesets/schema/earth_science/material_types.yaml index 861af99b..dadeee64 100644 --- a/src/valuesets/schema/earth_science/material_types.yaml +++ b/src/valuesets/schema/earth_science/material_types.yaml @@ -8,6 +8,8 @@ prefixes: CHEBI: http://purl.obolibrary.org/obo/CHEBI_ PO: http://purl.obolibrary.org/obo/PO_ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: @@ -17,11 +19,18 @@ slots: enums: SESARMaterialType: + title: SESAR Material Type description: >- Material types as defined by SESAR (System for Earth Sample Registration). These describe what a sample consists of (e.g., rock, mineral, liquid). + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition see_also: - - https://www.geosamples.org/vocabularies + - https://www.geosamples.org/vocabularies permissible_values: BIOLOGY: description: Biological material or specimens @@ -79,5 +88,5 @@ enums: license: MIT see_also: - - https://linkml.github.io/valuesets - - https://www.geosamples.org/vocabularies +- https://linkml.github.io/valuesets +- https://www.geosamples.org/vocabularies diff --git a/src/valuesets/schema/earth_science/physiographic_features.yaml b/src/valuesets/schema/earth_science/physiographic_features.yaml index 3527ebed..2ae0bc39 100644 --- a/src/valuesets/schema/earth_science/physiographic_features.yaml +++ b/src/valuesets/schema/earth_science/physiographic_features.yaml @@ -1,11 +1,14 @@ name: valuesets-earth-science-physiographic-features title: Earth Science Physiographic Features -description: Physiographic features for earth sample collection sites, based on SESAR (System for Earth Sample Registration) vocabulary +description: Physiographic features for earth sample collection sites, based on SESAR (System for Earth Sample + Registration) vocabulary id: https://w3id.org/valuesets/earth_science/physiographic_features prefixes: linkml: https://w3id.org/linkml/ ENVO: http://purl.obolibrary.org/obo/ENVO_ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: @@ -15,11 +18,18 @@ slots: enums: SESARPhysiographicFeature: + title: SESAR Physiographic Feature description: >- Physiographic feature types as defined by SESAR (System for Earth Sample Registration). These describe the type of physical feature from which a sample was collected. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition see_also: - - https://www.geosamples.org/vocabularies + - https://www.geosamples.org/vocabularies permissible_values: ABYSSAL_FEATURE: description: Deep ocean floor feature @@ -180,5 +190,5 @@ enums: license: MIT see_also: - - https://linkml.github.io/valuesets - - https://www.geosamples.org/vocabularies +- https://linkml.github.io/valuesets +- https://www.geosamples.org/vocabularies diff --git a/src/valuesets/schema/earth_science/sample_types.yaml b/src/valuesets/schema/earth_science/sample_types.yaml index c5ef04c5..d1c08c23 100644 --- a/src/valuesets/schema/earth_science/sample_types.yaml +++ b/src/valuesets/schema/earth_science/sample_types.yaml @@ -7,6 +7,8 @@ prefixes: ENVO: http://purl.obolibrary.org/obo/ENVO_ OBI: http://purl.obolibrary.org/obo/OBI_ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: @@ -16,11 +18,18 @@ slots: enums: SESARSampleType: + title: SESAR Sample Type description: >- Sample object types as defined by SESAR (System for Earth Sample Registration). These describe the physical form and collection context of samples. + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition see_also: - - https://www.geosamples.org/vocabularies/sample-type-object + - https://www.geosamples.org/vocabularies/sample-type-object permissible_values: CORE: description: Long cylindrical cores @@ -75,5 +84,5 @@ enums: license: MIT see_also: - - https://linkml.github.io/valuesets - - https://www.geosamples.org/vocabularies/sample-type-object +- https://linkml.github.io/valuesets +- https://www.geosamples.org/vocabularies/sample-type-object diff --git a/src/valuesets/schema/ecological_interactions.yaml b/src/valuesets/schema/ecological_interactions.yaml index b5ec58e4..c2bd5223 100644 --- a/src/valuesets/schema/ecological_interactions.yaml +++ b/src/valuesets/schema/ecological_interactions.yaml @@ -15,6 +15,8 @@ prefixes: # cval: https://w3id.org/linkml-common/ RO: http://purl.obolibrary.org/obo/RO_ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets default_curi_maps: - semweb_context @@ -24,10 +26,17 @@ slots: range: BioticInteractionType enums: BioticInteractionType: + title: Biotic Interaction Type description: 'Types of biotic interactions between organisms, based on RO:0002437 (biotically interacts with). These represent ecological relationships where at least one partner is an organism. ' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: BIOTICALLY_INTERACTS_WITH: description: 'An interaction relationship in which at least one of the partners is an organism and the other is either diff --git a/src/valuesets/schema/energy/energy.yaml b/src/valuesets/schema/energy/energy.yaml index 373feedf..e65b0584 100644 --- a/src/valuesets/schema/energy/energy.yaml +++ b/src/valuesets/schema/energy/energy.yaml @@ -5,10 +5,13 @@ id: https://w3id.org/linkml/valuesets/energy/energy imports: - linkml:types prefixes: + linkml: https://w3id.org/linkml/ valuesets: https://w3id.org/valuesets/ QUDT: http://qudt.org/vocab/unit/ ENVO: http://purl.obolibrary.org/obo/ENVO_ CHEBI: http://purl.obolibrary.org/obo/CHEBI_ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: energy_source: @@ -43,7 +46,14 @@ slots: range: ElectricityMarket enums: EnergySource: + title: Energy Source description: Types of energy sources and generation methods + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: SOLAR: title: Solar energy (photovoltaic and thermal) @@ -184,7 +194,14 @@ enums: annotations: storage: true EnergyUnit: + title: Energy Unit description: Units for measuring energy + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: JOULE: description: Joule (J) @@ -298,7 +315,14 @@ enums: ucum: tce joules: 2.93e10 PowerUnit: + title: Power Unit description: Units for measuring power (energy per time) + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: WATT: description: Watt (W) @@ -349,7 +373,14 @@ enums: ucum: '[Btu_IT]/h' watts: 0.293 EnergyEfficiencyRating: + title: Energy Efficiency Rating description: Energy efficiency ratings and standards + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: A_PLUS_PLUS_PLUS: description: A+++ (highest efficiency) @@ -410,7 +441,14 @@ enums: annotations: region: US BuildingEnergyStandard: + title: Building Energy Standard description: Building energy efficiency standards and certifications + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: PASSIVE_HOUSE: description: Passive House (Passivhaus) standard @@ -439,7 +477,14 @@ enums: ZERO_CARBON: description: Zero Carbon Building GridType: + title: Grid Type description: Types of electrical grid systems + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: MAIN_GRID: description: Main utility grid @@ -454,7 +499,14 @@ enums: VIRTUAL_POWER_PLANT: description: Virtual power plant EnergyStorageType: + title: Energy Storage Type description: Types of energy storage systems + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: LITHIUM_ION_BATTERY: description: Lithium-ion battery @@ -521,7 +573,14 @@ enums: annotations: category: electrical EmissionScope: + title: Emission Scope description: Greenhouse gas emission scopes (GHG Protocol) + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: SCOPE_1: description: Direct emissions from owned or controlled sources @@ -544,7 +603,14 @@ enums: annotations: ghg_protocol: Scope 3 CarbonIntensity: + title: Carbon Intensity description: Carbon intensity levels for energy sources + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ZERO_CARBON: description: Zero carbon emissions @@ -571,7 +637,14 @@ enums: annotations: gCO2_per_kWh: 1000+ ElectricityMarket: + title: Electricity Market description: Types of electricity markets and pricing + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: SPOT_MARKET: description: Spot market/real-time pricing diff --git a/src/valuesets/schema/energy/fossil_fuels.yaml b/src/valuesets/schema/energy/fossil_fuels.yaml index 06e5c323..08c2a978 100644 --- a/src/valuesets/schema/energy/fossil_fuels.yaml +++ b/src/valuesets/schema/energy/fossil_fuels.yaml @@ -5,6 +5,8 @@ prefixes: ENVO: http://purl.obolibrary.org/obo/ENVO_ CHEBI: http://purl.obolibrary.org/obo/CHEBI_ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: fossil_fuel_type: @@ -12,7 +14,14 @@ slots: range: FossilFuelTypeEnum enums: FossilFuelTypeEnum: + title: Fossil Fuel Type description: Types of fossil fuels used for energy generation + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: COAL: description: Coal diff --git a/src/valuesets/schema/energy/nuclear/nuclear_facilities.yaml b/src/valuesets/schema/energy/nuclear/nuclear_facilities.yaml index 13a0e729..094edb94 100644 --- a/src/valuesets/schema/energy/nuclear/nuclear_facilities.yaml +++ b/src/valuesets/schema/energy/nuclear/nuclear_facilities.yaml @@ -1,16 +1,18 @@ name: nuclear_facilities title: Nuclear Facilities and Infrastructure Types -description: 'Classifications of nuclear facilities including power plants, research reactors, - fuel cycle facilities, waste management facilities, and nuclear infrastructure. - Based on IAEA classifications and nuclear industry standards.' +description: 'Classifications of nuclear facilities including power plants, research reactors, fuel cycle facilities, waste + management facilities, and nuclear infrastructure. Based on IAEA classifications and nuclear industry standards.' id: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_facilities imports: - linkml:types prefixes: + linkml: https://w3id.org/linkml/ valuesets: https://w3id.org/valuesets/ IAEA: https://www.iaea.org/ WNA: https://world-nuclear.org/ NRC: https://www.nrc.gov/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: nuclear_facility_type: @@ -33,7 +35,14 @@ slots: range: NuclearShipTypeEnum enums: NuclearFacilityTypeEnum: + title: Nuclear Facility Type description: Types of nuclear facilities and infrastructure + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: COMMERCIAL_POWER_PLANT: title: Commercial Nuclear Power Plant @@ -168,7 +177,14 @@ enums: production_methods: reactor irradiation, accelerator market: medical and industrial applications PowerPlantStatusEnum: + title: Power Plant Status description: Operational status of nuclear power plants + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: UNDER_CONSTRUCTION: title: Under Construction @@ -227,7 +243,14 @@ enums: site_condition: restored for unrestricted use radioactive_materials: removed ResearchReactorTypeEnum: + title: Research Reactor Type description: Types of research reactors + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: POOL_TYPE: title: Pool-Type Research Reactor @@ -279,7 +302,14 @@ enums: neutron_source: external source required applications: research, training, transmutation studies FuelCycleFacilityTypeEnum: + title: Fuel Cycle Facility Type description: Types of nuclear fuel cycle facilities + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: IN_SITU_LEACH_MINE: title: In-Situ Leach Mine @@ -345,7 +375,14 @@ enums: temperature: high temperature operation technology_status: under development WasteFacilityTypeEnum: + title: Waste Facility Type description: Types of nuclear waste management facilities + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: SPENT_FUEL_POOL: title: Spent Fuel Pool @@ -411,7 +448,14 @@ enums: materials: equipment, clothing, tools methods: chemical, physical decontamination NuclearShipTypeEnum: + title: Nuclear Ship Type description: Types of nuclear-powered vessels + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: AIRCRAFT_CARRIER: title: Nuclear Aircraft Carrier @@ -460,4 +504,4 @@ enums: propulsion: nuclear mission: scientific research duration: extended operations without refueling - examples: limited number built \ No newline at end of file + examples: limited number built diff --git a/src/valuesets/schema/energy/nuclear/nuclear_fuel_cycle.yaml b/src/valuesets/schema/energy/nuclear/nuclear_fuel_cycle.yaml index 775deea0..0fc81ee4 100644 --- a/src/valuesets/schema/energy/nuclear/nuclear_fuel_cycle.yaml +++ b/src/valuesets/schema/energy/nuclear/nuclear_fuel_cycle.yaml @@ -3,10 +3,12 @@ title: Nuclear Fuel Cycle Value Sets description: Value sets for nuclear fuel cycle processes and stages id: https://w3id.org/common-value-sets/nuclear_fuel_cycle imports: - - linkml:types +- linkml:types prefixes: linkml: https://w3id.org/linkml/ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: @@ -22,7 +24,14 @@ slots: enums: NuclearFuelCycleStageEnum: + title: Nuclear Fuel Cycle Stage description: Stages in the nuclear fuel cycle from mining to disposal + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: MINING: description: Uranium ore mining and extraction @@ -44,7 +53,14 @@ enums: description: Permanent disposal of nuclear waste NuclearFuelFormEnum: + title: Nuclear Fuel Form description: Different forms of nuclear fuel throughout the cycle + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: URANIUM_ORE: description: Natural uranium ore containing uranium minerals @@ -68,7 +84,14 @@ enums: description: MOX fuel containing plutonium and uranium oxides EnrichmentProcessEnum: + title: Enrichment Process description: Methods for enriching uranium to increase U-235 concentration + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: GAS_DIFFUSION: description: Gaseous diffusion enrichment process diff --git a/src/valuesets/schema/energy/nuclear/nuclear_fuels.yaml b/src/valuesets/schema/energy/nuclear/nuclear_fuels.yaml index 0c2a9c7f..37814055 100644 --- a/src/valuesets/schema/energy/nuclear/nuclear_fuels.yaml +++ b/src/valuesets/schema/energy/nuclear/nuclear_fuels.yaml @@ -1,16 +1,18 @@ name: nuclear_fuels title: Nuclear Fuel Types and Classifications -description: 'Classifications of nuclear fuel types including uranium enrichment levels, - fuel forms, and alternative fuel cycles. Based on IAEA classifications, nuclear - fuel cycle standards, and industry specifications.' +description: 'Classifications of nuclear fuel types including uranium enrichment levels, fuel forms, and alternative fuel + cycles. Based on IAEA classifications, nuclear fuel cycle standards, and industry specifications.' id: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_fuels imports: - linkml:types prefixes: + linkml: https://w3id.org/linkml/ valuesets: https://w3id.org/valuesets/ IAEA: https://www.iaea.org/ WNA: https://world-nuclear.org/ CHEBI: http://purl.obolibrary.org/obo/CHEBI_ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: nuclear_fuel_type: @@ -33,7 +35,14 @@ slots: range: FissileIsotopeEnum enums: NuclearFuelTypeEnum: + title: Nuclear Fuel Type description: Types of nuclear fuel materials and compositions + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: NATURAL_URANIUM: title: Natural Uranium @@ -168,7 +177,14 @@ enums: density: high typical_use: fast reactors UraniumEnrichmentLevelEnum: + title: Uranium Enrichment Level description: Standard uranium-235 enrichment level classifications + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: NATURAL: title: Natural Uranium @@ -213,7 +229,14 @@ enums: category: WGU proliferation_concern: extreme FuelFormEnum: + title: Fuel Form description: Physical forms of nuclear fuel + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: OXIDE_PELLETS: title: Oxide Pellets @@ -267,7 +290,14 @@ enums: geometry: long cylinders typical_use: commercial power reactors FuelAssemblyTypeEnum: + title: Fuel Assembly Type description: Types of fuel assembly configurations + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: PWR_ASSEMBLY: title: PWR Fuel Assembly @@ -316,7 +346,14 @@ enums: geometry: hexagonal wrapper coolant_flow: axial FuelCycleStageEnum: + title: Fuel Cycle Stage description: Stages in the nuclear fuel cycle + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: MINING: title: Uranium Mining @@ -373,7 +410,14 @@ enums: duration: permanent status: under development globally FissileIsotopeEnum: + title: Fissile Isotope description: Fissile isotopes used in nuclear fuel + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: URANIUM_233: title: Uranium-233 @@ -418,4 +462,4 @@ enums: mass_number: 241 half_life: 14.3 years thermal_fission: yes - decay_product: Am-241 \ No newline at end of file + decay_product: Am-241 diff --git a/src/valuesets/schema/energy/nuclear/nuclear_operations.yaml b/src/valuesets/schema/energy/nuclear/nuclear_operations.yaml index 1b0a90d1..36d3f67a 100644 --- a/src/valuesets/schema/energy/nuclear/nuclear_operations.yaml +++ b/src/valuesets/schema/energy/nuclear/nuclear_operations.yaml @@ -1,16 +1,18 @@ name: nuclear_operations title: Nuclear Operations and Reactor States -description: 'Classifications for nuclear reactor operational states, maintenance activities, - licensing stages, and operational procedures. Based on nuclear industry standards - and regulatory frameworks.' +description: 'Classifications for nuclear reactor operational states, maintenance activities, licensing stages, and operational + procedures. Based on nuclear industry standards and regulatory frameworks.' id: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_operations imports: - linkml:types prefixes: + linkml: https://w3id.org/linkml/ valuesets: https://w3id.org/valuesets/ IAEA: https://www.iaea.org/ NRC: https://www.nrc.gov/ WNA: https://world-nuclear.org/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: reactor_operating_state: @@ -33,7 +35,14 @@ slots: range: OperationalProcedureEnum enums: ReactorOperatingStateEnum: + title: Reactor Operating State description: Operational states of nuclear reactors + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: STARTUP: title: Startup @@ -132,7 +141,14 @@ enums: investigation: extensive post-event analysis recovery: detailed restart procedures MaintenanceTypeEnum: + title: Maintenance Type description: Types of nuclear facility maintenance activities + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: PREVENTIVE_MAINTENANCE: title: Preventive Maintenance @@ -199,7 +215,14 @@ enums: testing: extensive post-modification testing documentation: comprehensive documentation updates LicensingStageEnum: + title: Licensing Stage description: Nuclear facility licensing stages + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: SITE_PERMIT: title: Site Permit @@ -266,7 +289,14 @@ enums: release: site release for unrestricted use finality: end of regulatory oversight FuelCycleOperationEnum: + title: Fuel Cycle Operation description: Nuclear fuel cycle operational activities + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: URANIUM_EXPLORATION: title: Uranium Exploration @@ -361,7 +391,14 @@ enums: isolation: long-term containment safety: protect public and environment ReactorControlModeEnum: + title: Reactor Control Mode description: Reactor control and safety system operational modes + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: MANUAL_CONTROL: title: Manual Control @@ -412,7 +449,14 @@ enums: equipment: portable emergency equipment coordination: multi-unit considerations OperationalProcedureEnum: + title: Operational Procedure description: Standard nuclear facility operational procedures + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: STARTUP_PROCEDURE: title: Reactor Startup Procedure @@ -477,4 +521,4 @@ enums: access_control: personnel access authorization detection: intrusion detection systems response: security force response - coordination: with law enforcement \ No newline at end of file + coordination: with law enforcement diff --git a/src/valuesets/schema/energy/nuclear/nuclear_regulatory.yaml b/src/valuesets/schema/energy/nuclear/nuclear_regulatory.yaml index a94c29c9..16584d3c 100644 --- a/src/valuesets/schema/energy/nuclear/nuclear_regulatory.yaml +++ b/src/valuesets/schema/energy/nuclear/nuclear_regulatory.yaml @@ -3,10 +3,12 @@ title: Nuclear Regulatory Frameworks Value Sets description: Value sets for nuclear regulatory bodies, frameworks, and compliance standards id: https://w3id.org/common-value-sets/nuclear_regulatory imports: - - linkml:types +- linkml:types prefixes: linkml: https://w3id.org/linkml/ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: @@ -28,7 +30,14 @@ slots: enums: NuclearRegulatoryBodyEnum: + title: Nuclear Regulatory Body description: Nuclear regulatory authorities and international organizations + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: IAEA: description: International Atomic Energy Agency @@ -71,7 +80,14 @@ enums: title: Atomic Energy Regulatory Board (India) RegulatoryFrameworkEnum: + title: Regulatory Framework description: Nuclear regulatory frameworks and international conventions + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: NPT: description: Nuclear Non-Proliferation Treaty @@ -108,7 +124,14 @@ enums: title: IAEA Nuclear Security Series LicensingStageEnum: + title: Licensing Stage description: Stages in nuclear facility licensing process + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: PRE_APPLICATION: description: Pre-application consultation and preparation @@ -132,7 +155,14 @@ enums: description: Combined construction and operating license ComplianceStandardEnum: + title: Compliance Standard description: Nuclear safety and security compliance standards + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ISO_14001: description: Environmental Management Systems @@ -166,7 +196,14 @@ enums: title: WENRA Reference Levels InspectionTypeEnum: + title: Inspection Type description: Types of nuclear regulatory inspections and assessments + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ROUTINE_INSPECTION: description: Regularly scheduled inspection activities diff --git a/src/valuesets/schema/energy/nuclear/nuclear_safety.yaml b/src/valuesets/schema/energy/nuclear/nuclear_safety.yaml index 8005d588..42df935c 100644 --- a/src/valuesets/schema/energy/nuclear/nuclear_safety.yaml +++ b/src/valuesets/schema/energy/nuclear/nuclear_safety.yaml @@ -1,17 +1,19 @@ name: nuclear_safety title: Nuclear Safety Classifications and Emergency Levels -description: 'Nuclear safety classifications including INES scale, emergency action levels, - nuclear security categories, and safety system classifications. Based on IAEA standards, - NRC regulations, and international nuclear safety frameworks.' +description: 'Nuclear safety classifications including INES scale, emergency action levels, nuclear security categories, and + safety system classifications. Based on IAEA standards, NRC regulations, and international nuclear safety frameworks.' id: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_safety imports: - linkml:types prefixes: + linkml: https://w3id.org/linkml/ valuesets: https://w3id.org/valuesets/ IAEA: https://www.iaea.org/ NRC: https://www.nrc.gov/ INES: https://www.iaea.org/resources/databases/ines IEEE: https://standards.ieee.org/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: ines_level: @@ -37,7 +39,14 @@ slots: range: RadiationProtectionZoneEnum enums: INESLevelEnum: + title: INES Level description: International Nuclear and Radiological Event Scale (INES) levels + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: LEVEL_0: title: Level 0 - Below Scale/Deviation @@ -108,7 +117,14 @@ enums: examples: Chernobyl (1986), Fukushima (2011) consequences: long-term environmental contamination EmergencyClassificationEnum: + title: Emergency Classification description: Nuclear emergency action levels and classifications + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: NOTIFICATION_UNUSUAL_EVENT: title: Notification of Unusual Event (NOUE) @@ -151,7 +167,14 @@ enums: emergency_response: maximum response plant_status: core degradation or containment failure NuclearSecurityCategoryEnum: + title: Nuclear Security Category description: IAEA nuclear material security categories (INFCIRC/225) + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: CATEGORY_I: title: Category I Nuclear Material @@ -189,7 +212,14 @@ enums: protection_requirements: administrative examples: small quantities of natural uranium SafetySystemClassEnum: + title: Safety System Class description: Nuclear safety system classifications (based on IEEE and ASME standards) + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: CLASS_1E: title: Class 1E Safety Systems @@ -224,7 +254,14 @@ enums: quality_requirements: commercial standards failure_impact: minimal safety impact ReactorSafetyFunctionEnum: + title: Reactor Safety Function description: Fundamental nuclear reactor safety functions + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: REACTIVITY_CONTROL: title: Reactivity Control @@ -266,7 +303,14 @@ enums: systems: control systems, shutdown systems time_requirement: rapid response capability DefenseInDepthLevelEnum: + title: Defense In Depth Level description: Defense in depth barrier levels for nuclear safety + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: LEVEL_1: title: Level 1 - Prevention of Abnormal Operation @@ -304,7 +348,14 @@ enums: approach: emergency planning and response examples: evacuation plans, protective actions RadiationProtectionZoneEnum: + title: Radiation Protection Zone description: Radiation protection zone classifications for nuclear facilities + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: EXCLUSION_AREA: title: Exclusion Area @@ -349,4 +400,4 @@ enums: annotations: monitoring: periodic monitoring access_control: limited restrictions - training_required: basic radiation awareness \ No newline at end of file + training_required: basic radiation awareness diff --git a/src/valuesets/schema/energy/nuclear/nuclear_waste.yaml b/src/valuesets/schema/energy/nuclear/nuclear_waste.yaml index 4ee10136..fc657871 100644 --- a/src/valuesets/schema/energy/nuclear/nuclear_waste.yaml +++ b/src/valuesets/schema/energy/nuclear/nuclear_waste.yaml @@ -1,16 +1,18 @@ name: nuclear_waste title: Nuclear Waste Classifications -description: 'Classifications of radioactive waste based on IAEA standards, NRC 10 CFR 61 - classifications, and international waste management standards. Includes activity levels, - disposal requirements, and time scales.' +description: 'Classifications of radioactive waste based on IAEA standards, NRC 10 CFR 61 classifications, and international + waste management standards. Includes activity levels, disposal requirements, and time scales.' id: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_waste imports: - linkml:types prefixes: + linkml: https://w3id.org/linkml/ valuesets: https://w3id.org/valuesets/ IAEA: https://www.iaea.org/ NRC: https://www.nrc.gov/ CFR: https://www.ecfr.gov/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: waste_classification: @@ -36,7 +38,14 @@ slots: range: TransuranicWasteCategoryEnum enums: IAEAWasteClassificationEnum: + title: IAEA Waste Classification description: IAEA General Safety Requirements radioactive waste classification scheme + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: EXEMPT_WASTE: title: Exempt Waste (EW) @@ -102,7 +111,14 @@ enums: cooling: required shielding: heavy shielding required NRCWasteClassEnum: + title: NRC Waste Class description: US NRC 10 CFR 61 low-level radioactive waste classification + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: CLASS_A: title: Class A Low-Level Waste @@ -144,7 +160,14 @@ enums: nrc_evaluation: required concentration_limits: exceeds Class C WasteHeatGenerationEnum: + title: Waste Heat Generation description: Heat generation categories for radioactive waste + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: NEGLIGIBLE_HEAT: title: Negligible Heat Generation @@ -169,7 +192,14 @@ enums: thermal_consideration: major design factor typical_waste: spent nuclear fuel, HLW glass WasteHalfLifeCategoryEnum: + title: Waste Half Life Category description: Half-life categories for radioactive waste classification + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: VERY_SHORT_LIVED: title: Very Short-Lived @@ -194,7 +224,14 @@ enums: decay_significance: minimal over human timescales examples: actinides, some fission products WasteDisposalMethodEnum: + title: Waste Disposal Method description: Methods for radioactive waste disposal + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: CLEARANCE: title: Clearance for Unrestricted Use @@ -241,7 +278,14 @@ enums: waste_categories: long-lived actinides status: research and development WasteSourceEnum: + title: Waste Source description: Sources of radioactive waste generation + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: NUCLEAR_POWER_PLANTS: title: Nuclear Power Plants @@ -300,7 +344,14 @@ enums: classification: variable depending on process uranium_content: often contains enriched uranium TransuranicWasteCategoryEnum: + title: Transuranic Waste Category description: Transuranic waste classifications (US system) + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: CONTACT_HANDLED_TRU: title: Contact-Handled Transuranic Waste @@ -329,4 +380,4 @@ enums: regulation: both radiological and chemical hazard regulations treatment: may require chemical treatment before disposal disposal: geological repository after treatment - complexity: dual regulatory framework \ No newline at end of file + complexity: dual regulatory framework diff --git a/src/valuesets/schema/energy/nuclear/reactor_types.yaml b/src/valuesets/schema/energy/nuclear/reactor_types.yaml index 769c3808..7b288f72 100644 --- a/src/valuesets/schema/energy/nuclear/reactor_types.yaml +++ b/src/valuesets/schema/energy/nuclear/reactor_types.yaml @@ -1,16 +1,18 @@ name: nuclear_reactor_types title: Nuclear Reactor Types and Classifications -description: 'Classifications of nuclear reactor types based on coolant, moderator, neutron spectrum, - and generational designs. Based on World Nuclear Association classifications, IAEA reactor types, - and industry standards.' +description: 'Classifications of nuclear reactor types based on coolant, moderator, neutron spectrum, and generational designs. + Based on World Nuclear Association classifications, IAEA reactor types, and industry standards.' id: https://w3id.org/linkml/valuesets/energy/nuclear/reactor_types imports: - linkml:types prefixes: + linkml: https://w3id.org/linkml/ valuesets: https://w3id.org/valuesets/ IAEA: https://www.iaea.org/ WNA: https://world-nuclear.org/ IEEE: https://standards.ieee.org/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: reactor_type: @@ -33,7 +35,14 @@ slots: range: ReactorSizeCategoryEnum enums: ReactorTypeEnum: + title: Reactor Type description: Nuclear reactor types based on design and operational characteristics + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: PWR: title: Pressurized Water Reactor @@ -193,7 +202,14 @@ enums: coolant: supercritical water generation: IV ReactorGenerationEnum: + title: Reactor Generation description: Nuclear reactor generational classifications + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: GENERATION_I: title: Generation I @@ -235,7 +251,14 @@ enums: goals: sustainability, economics, safety, proliferation resistance examples: VHTR, SFR, LFR, GFR, SCWR, MSR ReactorCoolantEnum: + title: Reactor Coolant description: Primary coolant types used in nuclear reactors + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: LIGHT_WATER: title: Light Water (H2O) @@ -297,7 +320,14 @@ enums: pressure: ">221 bar" temperature: ">374°C" ReactorModeratorEnum: + title: Reactor Moderator description: Neutron moderator types used in nuclear reactors + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: LIGHT_WATER: title: Light Water (H2O) @@ -335,7 +365,14 @@ enums: neutron_spectrum: fast moderation: none ReactorNeutronSpectrumEnum: + title: Reactor Neutron Spectrum description: Neutron energy spectrum classifications + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: THERMAL: title: Thermal Neutron Spectrum @@ -358,7 +395,14 @@ enums: moderation: minimal or none breeding_capability: high ReactorSizeCategoryEnum: + title: Reactor Size Category description: Nuclear reactor size classifications + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: LARGE: title: Large Reactor @@ -391,4 +435,4 @@ enums: description: Small reactors for research and isotope production annotations: power_output: "<100 MWt" - primary_use: research, isotopes, training \ No newline at end of file + primary_use: research, isotopes, training diff --git a/src/valuesets/schema/environmental_health/exposures.yaml b/src/valuesets/schema/environmental_health/exposures.yaml index 97ba9d22..b19428e6 100644 --- a/src/valuesets/schema/environmental_health/exposures.yaml +++ b/src/valuesets/schema/environmental_health/exposures.yaml @@ -11,6 +11,8 @@ prefixes: ExO: http://purl.obolibrary.org/obo/ExO_ ECTO: http://purl.obolibrary.org/obo/ECTO_ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: air_pollutant: @@ -54,7 +56,14 @@ slots: range: StudyPopulationEnum enums: AirPollutantEnum: + title: Air Pollutant description: Common air pollutants and air quality indicators + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: PM2_5: description: Fine particulate matter with diameter less than 2.5 micrometers @@ -99,7 +108,14 @@ enums: meaning: CHEBI:33848 title: polycyclic arene PesticideTypeEnum: + title: Pesticide Type description: Categories of pesticides by target organism or chemical class + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: HERBICIDE: description: Chemical used to kill unwanted plants @@ -137,7 +153,14 @@ enums: description: Glyphosate herbicide meaning: CHEBI:27744 HeavyMetalEnum: + title: Heavy Metal description: Heavy metals of environmental health concern + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: LEAD: description: Lead (Pb) @@ -176,20 +199,27 @@ enums: meaning: CHEBI:27638 title: cobalt atom ExposureRouteEnum: + title: Exposure Route description: Routes by which exposure to environmental agents occurs + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: INHALATION: description: Exposure through breathing meaning: NCIT:C38284 title: Nasal Route of Administration related_mappings: - - ExO:0000057 + - ExO:0000057 INGESTION: description: Exposure through eating or drinking meaning: NCIT:C38288 title: Oral Route of Administration related_mappings: - - ExO:0000056 + - ExO:0000056 DERMAL: description: Exposure through skin contact meaning: NCIT:C38675 @@ -199,13 +229,13 @@ enums: meaning: NCIT:C38276 title: Intravenous Route of Administration related_mappings: - - ExO:0000060 + - ExO:0000060 TRANSPLACENTAL: description: Exposure through placental transfer meaning: NCIT:C38307 title: Transplacental Route of Administration related_mappings: - - ExO:0000159 + - ExO:0000159 OCULAR: description: Exposure through the eyes meaning: NCIT:C38287 @@ -244,35 +274,42 @@ enums: SUBCUTANEOUS: description: Exposure through subcutaneous tissue related_mappings: - - ExO:0000061 + - ExO:0000061 INTRAMUSCULAR: description: Exposure through muscle tissue related_mappings: - - ExO:0000062 + - ExO:0000062 INTRAVASCULAR: description: Exposure through blood vessels related_mappings: - - ExO:0000063 + - ExO:0000063 MULTIPLE_ROUTES: description: Exposure through multiple pathways ExposureSourceEnum: + title: Exposure Source description: Common sources of environmental exposures + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: AMBIENT_AIR: description: Outdoor air pollution related_mappings: - - ENVO:01000676 - - ExO:0000020 + - ENVO:01000676 + - ExO:0000020 INDOOR_AIR: description: Indoor air pollution related_mappings: - - ENVO:01000676 - - ExO:0000019 + - ENVO:01000676 + - ExO:0000019 DRINKING_WATER: description: Contaminated drinking water related_mappings: - - ENVO:00003064 - - ENVO:00002186 + - ENVO:00003064 + - ENVO:00002186 SOIL: description: Contaminated soil meaning: ENVO:00002116 @@ -280,33 +317,33 @@ enums: FOOD: description: Contaminated food related_mappings: - - CHEBI:33290 + - CHEBI:33290 OCCUPATIONAL: description: Workplace exposure meaning: ENVO:03501332 title: occupational environment related_mappings: - - ExO:0000093 + - ExO:0000093 CONSUMER_PRODUCTS: description: Household and consumer products related_mappings: - - ENVO:00003074 - - ENVO:03501339 + - ENVO:00003074 + - ENVO:03501339 INDUSTRIAL_EMISSIONS: description: Industrial facility emissions related_mappings: - - ENVO:03000092 - - ENVO:00003861 + - ENVO:03000092 + - ENVO:00003861 AGRICULTURAL: description: Agricultural activities related_mappings: - - ENVO:00000077 - - ENVO:01000311 + - ENVO:00000077 + - ENVO:01000311 TRAFFIC: description: Traffic-related pollution related_mappings: - - ENVO:00000064 - - ENVO:01000601 + - ENVO:00000064 + - ENVO:01000601 TOBACCO_SMOKE: description: Active or passive tobacco smoke exposure meaning: NCIT:C17140 @@ -314,13 +351,20 @@ enums: CONSTRUCTION: description: Construction-related exposure related_mappings: - - ENVO:01000996 + - ENVO:01000996 MINING: description: Mining-related exposure related_mappings: - - ENVO:01001437 + - ENVO:01001437 WaterContaminantEnum: + title: Water Contaminant description: Common water contaminants + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: LEAD: description: Lead contamination @@ -367,7 +411,14 @@ enums: meaning: CHEBI:25944 title: pesticide EndocrineDisruptorEnum: + title: Endocrine Disruptor description: Common endocrine disrupting chemicals + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: BPA: description: Bisphenol A @@ -404,7 +455,14 @@ enums: meaning: CHEBI:172368 title: brominated flame retardant ExposureDurationEnum: + title: Exposure Duration description: Duration categories for environmental exposures + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ACUTE: description: Single or short-term exposure (hours to days) @@ -423,7 +481,14 @@ enums: DEVELOPMENTAL: description: Exposure during critical developmental periods SmokingStatusEnum: + title: Smoking Status description: Tobacco and nicotine consumption status + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: CURRENT_SMOKER: description: Person who is currently smoking tobacco @@ -438,7 +503,14 @@ enums: description: Person who is not currently smoking meaning: ExO:0000118 ExposureStressorTypeEnum: + title: Exposure Stressor Type description: Types of exposure stressors by their origin or nature + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: BIOLOGICAL_AGENT: description: Agent of biological origin (e.g., bacteria, viruses, allergens) @@ -459,7 +531,14 @@ enums: description: Disruption to ecological systems (e.g., habitat degradation, climate change) meaning: ExO:0000007 ExposureTransportPathEnum: + title: Exposure Transport Path description: Transport medium through which exposure stressor reaches the recipient + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: AIR_TRANSPORT_PATH: description: Transport path allowing stressor to interact with recipient via air @@ -471,7 +550,14 @@ enums: description: Transport path involving interaction with stressor via soil meaning: ExO:0000029 ExposureFrequencyEnum: + title: Exposure Frequency description: Temporal pattern of exposure occurrence + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: INTERMITTENT: description: Exposure occurring at irregular intervals or periodically @@ -480,7 +566,14 @@ enums: description: Exposure occurring without interruption meaning: ExO:0000053 StudyPopulationEnum: + title: Study Population description: Specific population groups commonly studied in exposure research + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: CHILDREN: description: Human children (pediatric population) @@ -512,4 +605,4 @@ enums: title: controls for disease or phenotype license: MIT see_also: - - https://linkml.github.io/valuesets +- https://linkml.github.io/valuesets diff --git a/src/valuesets/schema/geography/geographic_codes.yaml b/src/valuesets/schema/geography/geographic_codes.yaml index 2018bd86..65debf79 100644 --- a/src/valuesets/schema/geography/geographic_codes.yaml +++ b/src/valuesets/schema/geography/geographic_codes.yaml @@ -9,6 +9,8 @@ prefixes: iso3166loc: http://id.loc.gov/vocabulary/countries/ geonames: http://sws.geonames.org/ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: country_code_iso2: @@ -49,7 +51,14 @@ slots: range: CurrencyCodeISO4217Enum enums: CountryCodeISO2Enum: + title: Country Code ISO2 description: ISO 3166-1 alpha-2 country codes (2-letter codes) + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: US: description: United States of America @@ -302,7 +311,14 @@ enums: exact_mappings: - GAZ:00003750 CountryCodeISO3Enum: + title: Country Code ISO3 description: ISO 3166-1 alpha-3 country codes (3-letter codes) + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: USA: description: United States of America @@ -455,7 +471,14 @@ enums: exact_mappings: - GAZ:00002929 USStateCodeEnum: + title: US State Code description: United States state and territory codes + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: AL: description: Alabama @@ -570,7 +593,14 @@ enums: MP: description: Northern Mariana Islands CanadianProvinceCodeEnum: + title: Canadian Province Code description: Canadian province and territory codes + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: AB: description: Alberta @@ -599,7 +629,14 @@ enums: YT: description: Yukon CompassDirection: + title: Compass Direction description: Cardinal and intercardinal compass directions + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: NORTH: description: North (0°/360°) @@ -682,7 +719,14 @@ enums: abbreviation: NNW degrees: 337.5 RelativeDirection: + title: Relative Direction description: Relative directional terms + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: FORWARD: description: Forward/Ahead @@ -726,7 +770,14 @@ enums: abbreviation: CCW aliases: anticlockwise WindDirection: + title: Wind Direction description: Wind direction nomenclature (named for where wind comes FROM) + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: NORTHERLY: description: Wind from the north @@ -773,7 +824,14 @@ enums: annotations: note: changing or inconsistent direction ContinentEnum: + title: Continent description: Continental regions + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: AFRICA: description: Africa @@ -790,7 +848,14 @@ enums: SOUTH_AMERICA: description: South America UNRegionEnum: + title: UN Region description: United Nations regional classifications + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: EASTERN_AFRICA: description: Eastern Africa @@ -837,7 +902,14 @@ enums: POLYNESIA: description: Polynesia LanguageCodeISO639_1Enum: + title: Language Code ISO639_1 description: ISO 639-1 two-letter language codes + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: EN: description: English @@ -900,7 +972,14 @@ enums: UK: description: Ukrainian TimeZoneEnum: + title: Time Zone description: Common time zones + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: UTC: description: Coordinated Universal Time @@ -947,7 +1026,14 @@ enums: NZDT: description: New Zealand Daylight Time (UTC+13) CurrencyCodeISO4217Enum: + title: Currency Code ISO4217 description: ISO 4217 currency codes + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: USD: description: United States Dollar diff --git a/src/valuesets/schema/health.yaml b/src/valuesets/schema/health.yaml index 164933cb..c4b9fde6 100644 --- a/src/valuesets/schema/health.yaml +++ b/src/valuesets/schema/health.yaml @@ -10,6 +10,8 @@ prefixes: NCIT: http://purl.obolibrary.org/obo/NCIT_ fhir: http://hl7.org/fhir/ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: vital_status: @@ -17,7 +19,14 @@ slots: range: VitalStatusEnum enums: VitalStatusEnum: + title: Vital Status description: The vital status of a person or organism + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ALIVE: description: The person is living diff --git a/src/valuesets/schema/health/vaccination.yaml b/src/valuesets/schema/health/vaccination.yaml index d45a4adc..6b35fb43 100644 --- a/src/valuesets/schema/health/vaccination.yaml +++ b/src/valuesets/schema/health/vaccination.yaml @@ -11,6 +11,8 @@ prefixes: NCIT: http://purl.obolibrary.org/obo/NCIT_ VO: http://purl.obolibrary.org/obo/VO_ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: vaccination_status: @@ -24,7 +26,14 @@ slots: range: VaccineCategoryEnum enums: VaccinationStatusEnum: + title: Vaccination Status description: The vaccination status of an individual + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: VACCINATED: description: A status indicating that an individual has received a vaccination @@ -48,7 +57,14 @@ enums: description: The vaccination status is not known meaning: NCIT:C17998 VaccinationPeriodicityEnum: + title: Vaccination Periodicity description: The periodicity or frequency of vaccination + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: SINGLE_DOSE: description: A vaccination regimen requiring only one dose @@ -69,7 +85,14 @@ enums: AS_NEEDED: description: Vaccination given as needed based on exposure risk or other factors VaccineCategoryEnum: + title: Vaccine Category description: The broad category or type of vaccine + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: LIVE_ATTENUATED_VACCINE: description: A vaccine made from microbes that have been weakened in the laboratory @@ -99,4 +122,4 @@ enums: description: A vaccine produced using recombinant DNA technology license: MIT see_also: -- https://linkml.github.io/valuesets \ No newline at end of file +- https://linkml.github.io/valuesets diff --git a/src/valuesets/schema/healthcare.yaml b/src/valuesets/schema/healthcare.yaml index 83c469b5..fbd38240 100644 --- a/src/valuesets/schema/healthcare.yaml +++ b/src/valuesets/schema/healthcare.yaml @@ -11,6 +11,8 @@ prefixes: fhir: http://hl7.org/fhir/ omopschema: http://example.org/omop/ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: healthcare_encounter_classification: @@ -18,22 +20,30 @@ slots: range: HealthcareEncounterClassification enums: HealthcareEncounterClassification: + title: Healthcare Encounter Classification + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: Inpatient Visit: - description: Person visiting hospital, at a Care Site, in bed, for duration of more than one day, with physicians - and other Providers permanently available to deliver service around the clock + description: Person visiting hospital, at a Care Site, in bed, for duration of more than one day, with + physicians and other Providers permanently available to deliver service around the clock Emergency Room Visit: - description: Person visiting dedicated healthcare institution for treating emergencies, at a Care Site, within one - day, with physicians and Providers permanently available to deliver service around the clock + description: Person visiting dedicated healthcare institution for treating emergencies, at a Care Site, within + one day, with physicians and Providers permanently available to deliver service around the clock Emergency Room and Inpatient Visit: - description: Person visiting ER followed by a subsequent Inpatient Visit, where Emergency department is part of hospital, - and transition from the ER to other hospital departments is undefined + description: Person visiting ER followed by a subsequent Inpatient Visit, where Emergency department is part of + hospital, and transition from the ER to other hospital departments is undefined Non-hospital institution Visit: - description: Person visiting dedicated institution for reasons of poor health, at a Care Site, long-term or permanently, - with no physician but possibly other Providers permanently available to deliver service around the clock + description: Person visiting dedicated institution for reasons of poor health, at a Care Site, long-term or + permanently, with no physician but possibly other Providers permanently available to deliver service around + the clock Outpatient Visit: - description: Person visiting dedicated ambulatory healthcare institution, at a Care Site, within one day, without - bed, with physicians or medical Providers delivering service during Visit + description: Person visiting dedicated ambulatory healthcare institution, at a Care Site, within one day, + without bed, with physicians or medical Providers delivering service during Visit Home Visit: description: Provider visiting Person, without a Care Site, within one day, delivering service Telehealth Visit: @@ -41,13 +51,14 @@ enums: Pharmacy Visit: description: Person visiting pharmacy for dispensing of Drug, at a Care Site, within one day Laboratory Visit: - description: Patient visiting dedicated institution, at a Care Site, within one day, for the purpose of a Measurement. + description: Patient visiting dedicated institution, at a Care Site, within one day, for the purpose of a + Measurement. Ambulance Visit: - description: Person using transportation service for the purpose of initiating one of the other Visits, without a - Care Site, within one day, potentially with Providers accompanying the Visit and delivering service + description: Person using transportation service for the purpose of initiating one of the other Visits, without + a Care Site, within one day, potentially with Providers accompanying the Visit and delivering service Case Management Visit: - description: Person interacting with healthcare system, without a Care Site, within a day, with no Providers involved, - for administrative purposes + description: Person interacting with healthcare system, without a Care Site, within a day, with no Providers + involved, for administrative purposes license: MIT see_also: - https://linkml.github.io/valuesets diff --git a/src/valuesets/schema/industry/extractive_industry.yaml b/src/valuesets/schema/industry/extractive_industry.yaml index 4fa10dfa..67c3e3fe 100644 --- a/src/valuesets/schema/industry/extractive_industry.yaml +++ b/src/valuesets/schema/industry/extractive_industry.yaml @@ -3,6 +3,8 @@ id: https://w3id.org/linkml/valuesets/industry/extractive_industry prefixes: # linkml_common: https://w3id.org/linkml-common/ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: extractive_industry_facility_type: @@ -19,7 +21,14 @@ slots: range: WellTypeEnum enums: ExtractiveIndustryFacilityTypeEnum: + title: Extractive Industry Facility Type description: Types of extractive industry facilities + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: MINING_FACILITY: description: A facility where mineral resources are extracted @@ -31,7 +40,14 @@ enums: description: A facility where stone, sand, or gravel are extracted title: Quarry Facility ExtractiveIndustryProductTypeEnum: + title: Extractive Industry Product Type description: Types of products extracted from extractive industry facilities + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: MINERAL: description: A solid inorganic substance @@ -58,7 +74,14 @@ enums: description: A loose aggregation of rock fragments title: Gravel MiningMethodEnum: + title: Mining Method description: Methods used for extracting minerals from the earth + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: UNDERGROUND: description: Extraction occurs beneath the earth's surface @@ -73,7 +96,14 @@ enums: description: Extraction without removing the ore from its original location title: In Situ WellTypeEnum: + title: Well Type description: Types of wells used for extracting fluid resources + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: OIL: description: A well that primarily extracts crude oil diff --git a/src/valuesets/schema/industry/mining.yaml b/src/valuesets/schema/industry/mining.yaml index d5089a3f..a9f0a1c1 100644 --- a/src/valuesets/schema/industry/mining.yaml +++ b/src/valuesets/schema/industry/mining.yaml @@ -5,11 +5,14 @@ id: https://w3id.org/linkml/valuesets/industry/mining imports: - linkml:types prefixes: + linkml: https://w3id.org/linkml/ valuesets: https://w3id.org/valuesets/ ENVO: http://purl.obolibrary.org/obo/ENVO_ CHEBI: http://purl.obolibrary.org/obo/CHEBI_ ExO: http://purl.obolibrary.org/obo/ExO_ MINMOD: https://minmod.isi.edu/resource/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: mining: @@ -19,8 +22,8 @@ slots: description: Categories of minerals and materials range: MineralCategory critical_mineral: - description: Critical minerals essential for economic and national security, particularly for clean energy, defense, and - technology applications + description: Critical minerals essential for economic and national security, particularly for clean energy, defense, + and technology applications range: CriticalMineral common_mineral: description: Common minerals extracted through mining @@ -42,7 +45,14 @@ slots: range: EnvironmentalImpact enums: MiningType: + title: Mining Type description: Types of mining operations + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: OPEN_PIT: description: Open-pit mining @@ -133,7 +143,14 @@ enums: category: marine depth: ocean floor MineralCategory: + title: Mineral Category description: Categories of minerals and materials + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: PRECIOUS_METALS: description: Precious metals @@ -177,11 +194,18 @@ enums: annotations: examples: phosphate, potash, sulfur CriticalMineral: + title: Critical Mineral description: 'Critical minerals essential for economic and national security, particularly for clean energy, defense, and technology applications. Based on US Geological Survey and EU critical raw materials lists.' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: LITHIUM: description: Lithium (Li) - essential for batteries @@ -539,7 +563,14 @@ enums: atomic_number: 38 applications: magnets, pyrotechnics, medical CommonMineral: + title: Common Mineral description: Common minerals extracted through mining + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: GOLD: description: Gold (Au) @@ -671,7 +702,14 @@ enums: formula: C use: gemstone, industrial MiningEquipment: + title: Mining Equipment description: Types of mining equipment + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: DRILL_RIG: description: Drilling rig @@ -738,7 +776,14 @@ enums: annotations: category: underground transport OreGrade: + title: Ore Grade description: Classification of ore grades + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: HIGH_GRADE: description: High-grade ore @@ -767,7 +812,14 @@ enums: annotations: concentration: below cutoff MiningPhase: + title: Mining Phase description: Phases of mining operations + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: EXPLORATION: description: Exploration phase @@ -798,7 +850,14 @@ enums: annotations: activities: long-term monitoring MiningHazard: + title: Mining Hazard description: Mining-related hazards and risks + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: CAVE_IN: description: Cave-in/roof collapse @@ -845,7 +904,14 @@ enums: annotations: type: mechanical EnvironmentalImpact: + title: Environmental Impact description: Environmental impacts of mining + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: HABITAT_DESTRUCTION: description: Habitat destruction diff --git a/src/valuesets/schema/industry/safety_colors.yaml b/src/valuesets/schema/industry/safety_colors.yaml index c786cbf9..0e9dd99a 100644 --- a/src/valuesets/schema/industry/safety_colors.yaml +++ b/src/valuesets/schema/industry/safety_colors.yaml @@ -14,6 +14,8 @@ prefixes: ANSI: https://www.ansi.org/ OSHA: https://www.osha.gov/ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: safety_color: @@ -39,7 +41,14 @@ slots: range: ElectricalWireColorEnum enums: SafetyColorEnum: + title: Safety Color description: ANSI/ISO standard safety colors + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: SAFETY_RED: description: Safety red - danger, stop, prohibition @@ -107,7 +116,14 @@ enums: annotations: usage: background color for signs TrafficLightColorEnum: + title: Traffic Light Color description: Traffic signal colors (international) + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: RED: description: Red - stop @@ -145,7 +161,14 @@ enums: annotations: usage: transit priority signals HazmatColorEnum: + title: Hazmat Color description: Hazardous materials placarding colors (DOT/UN) + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ORANGE: description: Orange - explosives (Class 1) @@ -196,7 +219,14 @@ enums: hazard: flammable solid pattern: white with red vertical stripes FireSafetyColorEnum: + title: Fire Safety Color description: Fire safety equipment and signage colors + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: FIRE_RED: description: Fire red - fire equipment @@ -226,7 +256,14 @@ enums: annotations: usage: mandatory fire safety equipment MaritimeSignalColorEnum: + title: Maritime Signal Color description: Maritime signal and navigation colors + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: PORT_RED: description: Port (left) red light @@ -267,7 +304,14 @@ enums: usage: law enforcement vessels pattern: flashing AviationLightColorEnum: + title: Aviation Light Color description: Aviation lighting colors + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: RED_BEACON: description: Red obstruction light @@ -317,7 +361,14 @@ enums: annotations: usage: runway end ElectricalWireColorEnum: + title: Electrical Wire Color description: Electrical wire color codes (US/International) + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: BLACK_HOT: description: Black - hot/live wire (US) diff --git a/src/valuesets/schema/investigation.yaml b/src/valuesets/schema/investigation.yaml index e8f55940..4740545e 100644 --- a/src/valuesets/schema/investigation.yaml +++ b/src/valuesets/schema/investigation.yaml @@ -14,6 +14,8 @@ prefixes: dcterms: http://purl.org/dc/terms/ fibo.commons.PartiesAndSituations: https://spec.edmcouncil.org/fibo/ontology/FBC/ommons/PartiesAndSituations/ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: case_or_control: @@ -30,6 +32,13 @@ slots: range: SampleProcessingEnum enums: CaseOrControlEnum: + title: Case Or Control + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: CASE: title: case role in case-control study @@ -38,6 +47,13 @@ enums: title: control role in case-control study meaning: OBI:0002493 StudyDesignEnum: + title: Study Design + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_nodes: - OBI:0500000 @@ -45,6 +61,13 @@ enums: relationship_types: - rdfs:subClassOf InvestigativeProtocolEnum: + title: Investigative Protocol + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_nodes: - OBI:0000272 @@ -52,6 +75,13 @@ enums: relationship_types: - rdfs:subClassOf SampleProcessingEnum: + title: Sample Processing + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition reachable_from: source_nodes: - OBI:0000094 diff --git a/src/valuesets/schema/lab_automation/devices.yaml b/src/valuesets/schema/lab_automation/devices.yaml index 57523dd4..755739fe 100644 --- a/src/valuesets/schema/lab_automation/devices.yaml +++ b/src/valuesets/schema/lab_automation/devices.yaml @@ -5,6 +5,8 @@ prefixes: SNOMED: http://snomed.info/id/ NCIT: http://purl.obolibrary.org/obo/NCIT_ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: laboratory_device_type: @@ -15,7 +17,14 @@ slots: range: RoboticArmTypeEnum enums: LaboratoryDeviceTypeEnum: + title: Laboratory Device Type description: Types of automated laboratory devices and equipment + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: LIQUID_HANDLER: description: A device that is used for automated liquid transfer and handling @@ -30,11 +39,13 @@ enums: meaning: OBI:0400106 title: centrifuge MICROCENTRIFUGE: - description: A type of centrifuge that is designed for small tubes (0.2 ml to 2.0 ml), has a compact design, and has a small footprint + description: A type of centrifuge that is designed for small tubes (0.2 ml to 2.0 ml), has a compact design, and + has a small footprint meaning: OBI:0001100 title: microcentrifuge INCUBATOR: - description: A device in which environmental conditions (light, photoperiod, temperature, humidity, etc.) can be controlled + description: A device in which environmental conditions (light, photoperiod, temperature, humidity, etc.) can be + controlled meaning: OBI:0000136 title: incubator INCUBATOR_SHAKER: @@ -42,7 +53,8 @@ enums: meaning: OBI:0001076 title: incubator shaker MICROPLATE_READER: - description: A measurement device that detects biological, chemical or physical events of samples in microtiter plates + description: A measurement device that detects biological, chemical or physical events of samples in microtiter + plates meaning: OBI:0001058 title: microplate reader ELISA_MICROPLATE_READER: @@ -54,7 +66,8 @@ enums: meaning: OBI:0001090 title: multimode microplate reader MICROPLATE_WASHER: - description: A device that is used to wash immunoassays in microwell strips and plates with professional accuracy + description: A device that is used to wash immunoassays in microwell strips and plates with professional + accuracy meaning: OBI:0001113 title: microplate washer ELISA_MICROPLATE_WASHER: @@ -62,7 +75,8 @@ enums: meaning: OBI:0001115 title: ELISA microplate washer MULTICHANNEL_PIPETTE: - description: A pipetting system that has a plurality of tip fittings and is used for multi-well plate applications + description: A pipetting system that has a plurality of tip fittings and is used for multi-well plate + applications meaning: OBI:0001118 title: multichannel pipette ROBOTIC_ARM: @@ -85,7 +99,14 @@ enums: description: A device for automated dispensing of reagents or samples title: dispenser RoboticArmTypeEnum: + title: Robotic Arm Type description: Types of robotic arms used in laboratory automation systems + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: FLEXIBLE_CHANNEL_ARM: description: Robotic arm with flexible channels for disposable tip handling and liquid handling @@ -98,7 +119,8 @@ enums: annotations: abbreviation: MCA ROBOTIC_GRIPPER_ARM: - description: Robotic arm used to pick and transfer objects within the working area, equipped with dedicated gripper fingers + description: Robotic arm used to pick and transfer objects within the working area, equipped with dedicated + gripper fingers title: robotic gripper arm annotations: abbreviation: RGA diff --git a/src/valuesets/schema/lab_automation/labware.yaml b/src/valuesets/schema/lab_automation/labware.yaml index f2e78a73..9afc1e6d 100644 --- a/src/valuesets/schema/lab_automation/labware.yaml +++ b/src/valuesets/schema/lab_automation/labware.yaml @@ -6,6 +6,8 @@ prefixes: OBI: http://purl.obolibrary.org/obo/OBI_ MSIO: http://purl.obolibrary.org/obo/MSIO_ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: microplate_format: @@ -22,7 +24,14 @@ slots: range: PlateCoatingEnum enums: MicroplateFormatEnum: + title: Microplate Format description: Standard microplate well configurations following ANSI/SLAS standards + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: WELL_6: description: Microplate with 6 wells @@ -56,13 +65,21 @@ enums: well_spacing: 2.25mm standard: ANSI/SLAS 4-2004 ContainerTypeEnum: + title: Container Type description: Types of laboratory containers and labware + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: MICROPLATE: - description: A flat dish with multiple individual wells that are arrayed in a standardized number, size, and arrangement + description: A flat dish with multiple individual wells that are arrayed in a standardized number, size, and + arrangement meaning: NCIT:C43377 exact_mappings: - - BAO:0000508 + - BAO:0000508 title: microplate DEEP_WELL_PLATE: description: A microplate with deeper wells for increased sample volume capacity @@ -99,7 +116,14 @@ enums: meaning: NCIT:C128793 title: microplate well PlateMaterialEnum: + title: Plate Material description: Material composition of laboratory microplates + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: POLYSTYRENE: description: Plates made from polystyrene, the most common material for standard applications @@ -111,10 +135,18 @@ enums: description: Plates with glass inserts for samples not suitable for plastic containers title: glass PlateCoatingEnum: + title: Plate Coating description: Surface treatment of microplates + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: COATED: - description: A microplate whose surface has been treated, for instance by covalently attaching proteins to favor cell growth + description: A microplate whose surface has been treated, for instance by covalently attaching proteins to favor + cell growth meaning: MSIO:0000164 title: coated microplate UNCOATED: diff --git a/src/valuesets/schema/lab_automation/operations.yaml b/src/valuesets/schema/lab_automation/operations.yaml index 8b424c55..cf11b1b4 100644 --- a/src/valuesets/schema/lab_automation/operations.yaml +++ b/src/valuesets/schema/lab_automation/operations.yaml @@ -5,6 +5,8 @@ prefixes: MMO: http://purl.obolibrary.org/obo/MMO_ OBI: http://purl.obolibrary.org/obo/OBI_ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: liquid_handling_operation: @@ -15,7 +17,14 @@ slots: range: SampleProcessingOperationEnum enums: LiquidHandlingOperationEnum: + title: Liquid Handling Operation description: Operations for automated liquid handling in laboratory automation + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: PICK_UP_TIPS: description: Operation to pick up pipette tips from a tip rack @@ -36,7 +45,8 @@ enums: description: Combined operation to aspirate from source and dispense to destination title: transfer PIPETTING: - description: A procedure or technique by which the size of the three dimensional space occupied by a liquid substance is ascertained using a pipette + description: A procedure or technique by which the size of the three dimensional space occupied by a liquid + substance is ascertained using a pipette meaning: MMO:0000392 title: pipette method MIXING: @@ -52,14 +62,23 @@ enums: description: Operation to transfer samples from one plate to another in the same well pattern title: plate stamping ACOUSTIC_TRANSFER: - description: Acoustic liquid handling that uses acoustics to fly individual droplets from a source container to a destination + description: Acoustic liquid handling that uses acoustics to fly individual droplets from a source container to + a destination title: acoustic transfer MOUTH_PIPETTING: - description: A method of using the researcher's mouth to apply small negative pressure to aspirate a volume into a pipette + description: A method of using the researcher's mouth to apply small negative pressure to aspirate a volume into + a pipette meaning: EFO:0010182 title: mouth pipetting SampleProcessingOperationEnum: + title: Sample Processing Operation description: General sample processing operations in automated laboratories + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: CENTRIFUGATION: description: Operation to separate components of a sample using centrifugal force diff --git a/src/valuesets/schema/lab_automation/protocols.yaml b/src/valuesets/schema/lab_automation/protocols.yaml index 291a4f0a..d17c11ec 100644 --- a/src/valuesets/schema/lab_automation/protocols.yaml +++ b/src/valuesets/schema/lab_automation/protocols.yaml @@ -2,6 +2,8 @@ name: lab_automation_protocols id: https://w3id.org/linkml/valuesets/lab_automation/protocols prefixes: valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: workflow_orchestration_type: @@ -18,7 +20,14 @@ slots: range: ExecutionModeEnum enums: WorkflowOrchestrationTypeEnum: + title: Workflow Orchestration Type description: Types of workflow orchestration in laboratory automation systems + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: STATIC_ORCHESTRATION: description: Pre-planned orchestration based on known constraints and fixed workflow @@ -36,7 +45,14 @@ enums: description: Orchestration that enables concurrent execution of independent tasks title: parallel processing SchedulerTypeEnum: + title: Scheduler Type description: Types of scheduling algorithms for laboratory automation + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: STATIC_SCHEDULER: description: Makes decisions based on known constraints requiring upfront planning @@ -57,7 +73,14 @@ enums: description: Schedules tasks to meet specified deadlines title: deadline-driven scheduler ProtocolStateEnum: + title: Protocol State description: Execution states of laboratory protocols + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: PENDING: description: Protocol is queued but not yet started @@ -84,7 +107,14 @@ enums: description: Protocol is waiting for required resources to become available title: waiting for resource ExecutionModeEnum: + title: Execution Mode description: Modes of protocol execution + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: AUTOMATED: description: Fully automated execution without human intervention @@ -105,7 +135,14 @@ enums: description: Test execution without actual operations title: dry run WorkflowErrorHandlingEnum: + title: Workflow Error Handling description: Error handling strategies in laboratory automation workflows + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ABORT_ON_ERROR: description: Terminate workflow immediately upon encountering an error @@ -126,7 +163,14 @@ enums: description: Switch to backup resource or alternative execution path title: failover IntegrationSystemEnum: + title: Integration System description: Types of systems integrated with laboratory automation platforms + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: LIMS: description: Laboratory Information Management System diff --git a/src/valuesets/schema/lab_automation/standards.yaml b/src/valuesets/schema/lab_automation/standards.yaml index d02fde4d..7ea17695 100644 --- a/src/valuesets/schema/lab_automation/standards.yaml +++ b/src/valuesets/schema/lab_automation/standards.yaml @@ -2,6 +2,8 @@ name: lab_automation_standards id: https://w3id.org/linkml/valuesets/lab_automation/standards prefixes: valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: automation_standard: @@ -15,10 +17,18 @@ slots: range: LabwareStandardEnum enums: AutomationStandardEnum: + title: Automation Standard description: Industry standards for laboratory automation systems + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: SILA_2: - description: Standardization in Lab Automation version 2 - international standard for open connectivity in lab automation + description: Standardization in Lab Automation version 2 - international standard for open connectivity in lab + automation title: SiLA 2 annotations: organization: Society for Laboratory Automation and Screening @@ -61,7 +71,14 @@ enums: annotations: organization: Clinical and Laboratory Standards Institute CommunicationProtocolEnum: + title: Communication Protocol description: Communication protocols for laboratory automation integration + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: GRPC: description: gRPC protocol used in SiLA 2 @@ -95,7 +112,14 @@ enums: description: Universal Serial Bus communication title: USB LabwareStandardEnum: + title: Labware Standard description: Standardization specifications for laboratory labware + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ANSI_SLAS_1_2004: description: Microplates - Footprint Dimensions @@ -132,7 +156,14 @@ enums: annotations: dimensions: 127.76mm x 85.5mm IntegrationFeatureEnum: + title: Integration Feature description: Integration features for laboratory automation systems + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: BARCODE_TRACKING: description: Integration feature for tracking samples via barcodes diff --git a/src/valuesets/schema/lab_automation/thermal_cycling.yaml b/src/valuesets/schema/lab_automation/thermal_cycling.yaml index 0903074a..dea8a929 100644 --- a/src/valuesets/schema/lab_automation/thermal_cycling.yaml +++ b/src/valuesets/schema/lab_automation/thermal_cycling.yaml @@ -4,6 +4,8 @@ prefixes: OBI: http://purl.obolibrary.org/obo/OBI_ NCIT: http://purl.obolibrary.org/obo/NCIT_ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: thermal_cycler_type: @@ -17,7 +19,14 @@ slots: range: DetectionModeEnum enums: ThermalCyclerTypeEnum: + title: Thermal Cycler Type description: Types of thermal cycling instruments + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: STANDARD_THERMAL_CYCLER: description: Standard thermal cycler for endpoint PCR @@ -47,7 +56,14 @@ enums: description: Thermal cycler designed for in situ PCR applications title: in situ thermal cycler PCROperationTypeEnum: + title: PCR Operation Type description: Types of PCR operations and techniques + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: STANDARD_PCR: description: Standard endpoint PCR amplification @@ -90,7 +106,14 @@ enums: description: Absolute quantification PCR using partitioning title: digital PCR DetectionModeEnum: + title: Detection Mode description: Detection modes for real-time PCR instruments + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: SYBR_GREEN: description: DNA-binding dye detection @@ -116,7 +139,14 @@ enums: description: Multi-channel fluorescence detection title: multi-channel PCRPlateTypeEnum: + title: PCR Plate Type description: Types of plates used for PCR applications + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: PCR_96_WELL: description: 96-well plate for PCR @@ -140,7 +170,14 @@ enums: description: PCR plate with partial skirt title: semi-skirted plate ThermalCyclingStepEnum: + title: Thermal Cycling Step description: Steps in thermal cycling protocols + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: INITIAL_DENATURATION: description: Initial high-temperature step to denature template DNA diff --git a/src/valuesets/schema/materials_science/characterization_methods.yaml b/src/valuesets/schema/materials_science/characterization_methods.yaml index cb3ab7bf..81467346 100644 --- a/src/valuesets/schema/materials_science/characterization_methods.yaml +++ b/src/valuesets/schema/materials_science/characterization_methods.yaml @@ -5,6 +5,8 @@ prefixes: CHMO: http://purl.obolibrary.org/obo/CHMO_ # linkml_common: https://w3id.org/linkml-common/ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: microscopy_method: @@ -21,7 +23,14 @@ slots: range: MechanicalTestingMethodEnum enums: MicroscopyMethodEnum: + title: Microscopy Method description: Microscopy techniques for material characterization + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: SEM: description: Scanning Electron Microscopy @@ -73,7 +82,14 @@ enums: - CONFOCAL - Confocal SpectroscopyMethodEnum: + title: Spectroscopy Method description: Spectroscopy techniques for material analysis + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: XRD: description: X-ray Diffraction @@ -132,7 +148,14 @@ enums: - X-ray Fluorescence - XRF ThermalAnalysisMethodEnum: + title: Thermal Analysis Method description: Thermal analysis techniques + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: DSC: description: Differential Scanning Calorimetry @@ -165,7 +188,14 @@ enums: - DMA - Dynamic Mechanical Analysis MechanicalTestingMethodEnum: + title: Mechanical Testing Method description: Mechanical testing methods + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: TENSILE: description: Tensile strength testing diff --git a/src/valuesets/schema/materials_science/crystal_structures.yaml b/src/valuesets/schema/materials_science/crystal_structures.yaml index e6ab3bc6..754277da 100644 --- a/src/valuesets/schema/materials_science/crystal_structures.yaml +++ b/src/valuesets/schema/materials_science/crystal_structures.yaml @@ -8,6 +8,8 @@ prefixes: PROCO: http://purl.obolibrary.org/obo/PROCO_ # linkml_common: https://w3id.org/linkml-common/ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: crystal_system: @@ -18,7 +20,14 @@ slots: range: BravaisLatticeEnum enums: CrystalSystemEnum: + title: Crystal System description: The seven crystal systems in crystallography + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition conforms_to: https://en.wikipedia.org/wiki/Crystal_system permissible_values: TRICLINIC: @@ -58,7 +67,14 @@ enums: aliases: - isometric BravaisLatticeEnum: + title: Bravais Lattice description: The 14 Bravais lattices describing all possible crystal lattices + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition conforms_to: https://en.wikipedia.org/wiki/Bravais_lattice permissible_values: PRIMITIVE_TRICLINIC: diff --git a/src/valuesets/schema/materials_science/material_properties.yaml b/src/valuesets/schema/materials_science/material_properties.yaml index 67e1ade7..1b157863 100644 --- a/src/valuesets/schema/materials_science/material_properties.yaml +++ b/src/valuesets/schema/materials_science/material_properties.yaml @@ -6,6 +6,8 @@ prefixes: PATO: http://purl.obolibrary.org/obo/PATO_ # linkml_common: https://w3id.org/linkml-common/ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: electrical_conductivity: @@ -25,7 +27,14 @@ slots: range: MechanicalBehaviorEnum enums: ElectricalConductivityEnum: + title: Electrical Conductivity description: Classification of materials by electrical conductivity + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: CONDUCTOR: description: Material with high electrical conductivity (resistivity < 10^-5 Ω·m) @@ -47,7 +56,14 @@ enums: description: Material with zero electrical resistance below critical temperature title: Superconductor MagneticPropertyEnum: + title: Magnetic Property description: Classification of materials by magnetic properties + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: DIAMAGNETIC: description: Weakly repelled by magnetic fields @@ -65,7 +81,14 @@ enums: description: Adjacent magnetic moments cancel each other title: Antiferromagnetic OpticalPropertyEnum: + title: Optical Property description: Optical properties of materials + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: TRANSPARENT: description: Allows light to pass through with minimal scattering @@ -91,7 +114,14 @@ enums: description: Continues to emit light after excitation stops title: Phosphorescent ThermalConductivityEnum: + title: Thermal Conductivity description: Classification by thermal conductivity + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: HIGH_THERMAL_CONDUCTOR: description: High thermal conductivity (>100 W/m·K) @@ -107,7 +137,14 @@ enums: aliases: - thermal barrier MechanicalBehaviorEnum: + title: Mechanical Behavior description: Mechanical behavior of materials under stress + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ELASTIC: description: Returns to original shape after stress removal diff --git a/src/valuesets/schema/materials_science/material_types.yaml b/src/valuesets/schema/materials_science/material_types.yaml index 5bc83afd..32d95e78 100644 --- a/src/valuesets/schema/materials_science/material_types.yaml +++ b/src/valuesets/schema/materials_science/material_types.yaml @@ -9,6 +9,8 @@ prefixes: SNOMED: http://snomed.info/id/ # linkml_common: https://w3id.org/linkml-common/ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: material_class: @@ -25,7 +27,14 @@ slots: range: CompositeTypeEnum enums: MaterialClassEnum: + title: Material Class description: Major classes of materials + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: METAL: description: Metallic materials with metallic bonding @@ -62,7 +71,14 @@ enums: title: Nanomaterial meaning: NCIT:C62371 PolymerTypeEnum: + title: Polymer Type description: Types of polymer materials + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: THERMOPLASTIC: description: Polymer that becomes moldable above specific temperature @@ -92,7 +108,14 @@ enums: aliases: - conducting polymer MetalTypeEnum: + title: Metal Type description: Types of metallic materials + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: FERROUS: description: Iron-based metals and alloys @@ -119,7 +142,14 @@ enums: title: Heavy Metal meaning: CHEBI:5631 CompositeTypeEnum: + title: Composite Type description: Types of composite materials + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: FIBER_REINFORCED: description: Composite with fiber reinforcement diff --git a/src/valuesets/schema/materials_science/pigments_dyes.yaml b/src/valuesets/schema/materials_science/pigments_dyes.yaml index f7033e9e..4dd1a61f 100644 --- a/src/valuesets/schema/materials_science/pigments_dyes.yaml +++ b/src/valuesets/schema/materials_science/pigments_dyes.yaml @@ -12,6 +12,8 @@ prefixes: CHEBI: http://purl.obolibrary.org/obo/CHEBI_ NCIt: http://purl.obolibrary.org/obo/NCIT_ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: traditional_pigment: @@ -28,7 +30,14 @@ slots: range: AutomobilePaintColorEnum enums: TraditionalPigmentEnum: + title: Traditional Pigment description: Traditional artist pigments and their colors + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: TITANIUM_WHITE: title: titanium dioxide nanoparticle @@ -222,7 +231,14 @@ enums: chemical: C source: soot IndustrialDyeEnum: + title: Industrial Dye description: Industrial and textile dyes + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: INDIGO: description: Indigo dye @@ -300,7 +316,14 @@ enums: hex: 002F5C use: cotton vat dyeing FoodColoringEnum: + title: Food Coloring description: Food coloring and natural food dyes + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: FD_C_RED_40: description: FD&C Red No. 40 (Allura Red) @@ -398,7 +421,14 @@ enums: source: spirulina algae natural: 'true' AutomobilePaintColorEnum: + title: Automobile Paint Color description: Common automobile paint colors + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ARCTIC_WHITE: description: Arctic White diff --git a/src/valuesets/schema/materials_science/synthesis_methods.yaml b/src/valuesets/schema/materials_science/synthesis_methods.yaml index dc71dedf..635eadd1 100644 --- a/src/valuesets/schema/materials_science/synthesis_methods.yaml +++ b/src/valuesets/schema/materials_science/synthesis_methods.yaml @@ -5,6 +5,8 @@ prefixes: CHMO: http://purl.obolibrary.org/obo/CHMO_ # linkml_common: https://w3id.org/linkml-common/ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: synthesis_method: @@ -18,7 +20,14 @@ slots: range: AdditiveManufacturingEnum enums: SynthesisMethodEnum: + title: Synthesis Method description: Common material synthesis and processing methods + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: SOL_GEL: description: Synthesis from solution through gel formation @@ -95,7 +104,14 @@ enums: description: Coating by spraying title: Spray Coating CrystalGrowthMethodEnum: + title: Crystal Growth Method description: Methods for growing single crystals + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: CZOCHRALSKI: description: Crystal pulling from melt @@ -143,7 +159,14 @@ enums: aliases: - MOVPE AdditiveManufacturingEnum: + title: Additive Manufacturing description: 3D printing and additive manufacturing methods + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: FDM: description: Fused Deposition Modeling diff --git a/src/valuesets/schema/medical/clinical.yaml b/src/valuesets/schema/medical/clinical.yaml index 523b25b6..88df9c38 100644 --- a/src/valuesets/schema/medical/clinical.yaml +++ b/src/valuesets/schema/medical/clinical.yaml @@ -19,6 +19,8 @@ prefixes: ICD10: http://purl.bioontology.org/ontology/ICD10/ RxNorm: http://purl.bioontology.org/ontology/RXNORM/ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: blood_type: @@ -53,7 +55,14 @@ slots: range: BMIClassificationEnum enums: BloodTypeEnum: + title: Blood Type description: ABO and Rh blood group classifications + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: A_POSITIVE: description: Blood type A, Rh positive @@ -122,7 +131,14 @@ enums: can_donate: all types special: universal donor AnatomicalSystemEnum: + title: Anatomical System description: Major anatomical systems of the body + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: CARDIOVASCULAR: title: Heart and blood vessels @@ -203,6 +219,12 @@ enums: components: blood, bone marrow, spleen MedicalSpecialtyEnum: title: Medical specialties and subspecialties + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ANESTHESIOLOGY: title: Anesthesia and perioperative medicine @@ -256,6 +278,12 @@ enums: title: Urinary and male reproductive system DrugRouteEnum: title: Routes of drug administration + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ORAL: title: By mouth @@ -361,6 +389,12 @@ enums: forms: drops VitalSignEnum: title: Standard vital signs + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: HEART_RATE: title: Heart beats per minute @@ -406,6 +440,12 @@ enums: type: subjective DiagnosticTestTypeEnum: title: Types of diagnostic tests + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: BLOOD_TEST: title: Blood sample analysis @@ -491,6 +531,12 @@ enums: types: karyotype, sequencing, PCR SymptomSeverityEnum: title: Severity levels for symptoms + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ABSENT: title: No symptoms @@ -525,6 +571,12 @@ enums: impact: urgent intervention required AllergyTypeEnum: title: Types of allergic reactions + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: DRUG: title: Drug allergy @@ -555,6 +607,12 @@ enums: severity: life-threatening VaccineTypeEnum: title: Types of vaccines + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: LIVE_ATTENUATED: title: Weakened live pathogen @@ -582,6 +640,12 @@ enums: examples: COVID-19 (J&J, AstraZeneca) BMIClassificationEnum: title: Body Mass Index classifications + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: UNDERWEIGHT: title: BMI less than 18.5 diff --git a/src/valuesets/schema/medical/family_history.yaml b/src/valuesets/schema/medical/family_history.yaml index c3b45384..22902368 100644 --- a/src/valuesets/schema/medical/family_history.yaml +++ b/src/valuesets/schema/medical/family_history.yaml @@ -11,6 +11,8 @@ prefixes: HL7: http://terminology.hl7.org/CodeSystem/ SNOMED: http://snomed.info/id/ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: @@ -26,15 +28,24 @@ slots: enums: FamilyRelationship: + title: Family Relationship description: Family relationships used in pedigree and family history documentation + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinitionWithSource source: https://terminology.hl7.org/2.1.0/ValueSet-v3-FamilyMember.html permissible_values: # Core Parent Relationships PARENT: - description: The player of the role is one who begets, gives birth to, or nurtures and raises the scoping entity (child) + description: The player of the role is one who begets, gives birth to, or nurtures and raises the scoping entity + (child) meaning: HL7:v3-RoleCode#PRN MOTHER: - description: The player of the role is a female who conceives, gives birth to, or raises and nurtures the scoping entity (child) + description: The player of the role is a female who conceives, gives birth to, or raises and nurtures the + scoping entity (child) meaning: HL7:v3-RoleCode#MTH FATHER: description: The player of the role is a male who begets or raises or nurtures the scoping entity (child) @@ -46,30 +57,37 @@ enums: description: The player of the role is a male who begets the scoping entity (child) meaning: HL7:v3-RoleCode#NFTH ADOPTIVE_PARENT: - description: The player of the role (parent) has taken the scoper (child) into their family through legal means and raises them as his or her own child + description: The player of the role (parent) has taken the scoper (child) into their family through legal means + and raises them as his or her own child meaning: HL7:v3-RoleCode#ADOPTP ADOPTIVE_MOTHER: - description: The player of the role (mother) is a female who has taken the scoper (child) into their family through legal means and raises them as her own child + description: The player of the role (mother) is a female who has taken the scoper (child) into their family + through legal means and raises them as her own child meaning: HL7:v3-RoleCode#ADOPTM ADOPTIVE_FATHER: - description: The player of the role (father) is a male who has taken the scoper (child) into their family through legal means and raises them as his own child + description: The player of the role (father) is a male who has taken the scoper (child) into their family + through legal means and raises them as his own child meaning: HL7:v3-RoleCode#ADOPTF STEP_PARENT: - description: The player of the role is the spouse of the scoping person's parent and not the scoping person's natural parent + description: The player of the role is the spouse of the scoping person's parent and not the scoping person's + natural parent meaning: HL7:v3-RoleCode#STPPRN STEP_MOTHER: - description: The player of the role is the female spouse of the scoping person's parent and not the scoping person's natural mother + description: The player of the role is the female spouse of the scoping person's parent and not the scoping + person's natural mother meaning: HL7:v3-RoleCode#STPMTH STEP_FATHER: - description: The player of the role is the male spouse of the scoping person's parent and not the scoping person's natural father + description: The player of the role is the male spouse of the scoping person's parent and not the scoping + person's natural father meaning: HL7:v3-RoleCode#STPFTH FOSTER_PARENT: - description: The player of the role (parent) who is a state-certified caregiver responsible for the scoper (child) + description: The player of the role (parent) who is a state-certified caregiver responsible for the scoper + (child) meaning: HL7:v3-RoleCode#PRNFOST GESTATIONAL_MOTHER: description: The player is a female whose womb carries the fetus of the scoper meaning: HL7:v3-RoleCode#GESTM - + # Sibling Relationships SIBLING: description: The player of the role shares one or both parents in common with the scoping entity @@ -81,16 +99,20 @@ enums: description: The player of the role is a female sharing one or both parents with the scoping entity meaning: HL7:v3-RoleCode#SIS NATURAL_BROTHER: - description: The player of the role is a male related to the scoping entity by sharing only the same natural parents + description: The player of the role is a male related to the scoping entity by sharing only the same natural + parents meaning: HL7:v3-RoleCode#NBRO NATURAL_SISTER: - description: The player of the role is a female related to the scoping entity by sharing only the same natural parents + description: The player of the role is a female related to the scoping entity by sharing only the same natural + parents meaning: HL7:v3-RoleCode#NSIS HALF_BROTHER: - description: The player of the role is a male related to the scoping entity by sharing only one biological parent + description: The player of the role is a male related to the scoping entity by sharing only one biological + parent meaning: HL7:v3-RoleCode#HBRO HALF_SISTER: - description: The player of the role is a female related to the scoping entity by sharing only one biological parent + description: The player of the role is a female related to the scoping entity by sharing only one biological + parent meaning: HL7:v3-RoleCode#HSIS STEP_BROTHER: description: The player of the role is a male child of the scoping person's stepparent @@ -108,12 +130,14 @@ enums: description: The player of the role is a female born from the same pregnancy as the scoping entity meaning: HL7:v3-RoleCode#TWINSIS FRATERNAL_TWIN: - description: The player of the role is born from the same pregnancy as the scoping entity but does not share the same genotype + description: The player of the role is born from the same pregnancy as the scoping entity but does not share the + same genotype meaning: HL7:v3-RoleCode#FTWIN IDENTICAL_TWIN: - description: The player of the role is born from the same pregnancy as the scoping entity and shares the same genotype + description: The player of the role is born from the same pregnancy as the scoping entity and shares the same + genotype meaning: HL7:v3-RoleCode#ITWIN - + # Child Relationships CHILD: description: The player of the role is a child of the scoping entity @@ -128,15 +152,17 @@ enums: description: The player of the role is an offspring of the scoping entity as determined by birth meaning: HL7:v3-RoleCode#NCHILD ADOPTIVE_CHILD: - description: The player of the role is a child taken into a family through legal means and raised by the scoping person (parent) as his or her own child + description: The player of the role is a child taken into a family through legal means and raised by the scoping + person (parent) as his or her own child meaning: HL7:v3-RoleCode#CHLDADOPT FOSTER_CHILD: - description: The player of the role is a child receiving parental care and nurture from the scoping person (parent) but not related to him or her through legal or blood relationship + description: The player of the role is a child receiving parental care and nurture from the scoping person + (parent) but not related to him or her through legal or blood relationship meaning: HL7:v3-RoleCode#CHLDFOST STEP_CHILD: description: The player of the role is a child of the scoping person's spouse by a previous union meaning: HL7:v3-RoleCode#STPCHLD - + # Grandparent Relationships GRANDPARENT: description: The player of the role is a parent of the scoping person's mother or father @@ -159,7 +185,7 @@ enums: PATERNAL_GRANDFATHER: description: The player of the role is the father of the scoping person's father meaning: HL7:v3-RoleCode#PGRFTH - + # Grandchild Relationships GRANDCHILD: description: The player of the role is a child of the scoping person's son or daughter @@ -170,7 +196,7 @@ enums: GRANDDAUGHTER: description: The player of the role is a daughter of the scoping person's son or daughter meaning: HL7:v3-RoleCode#GRNDDAU - + # Aunt/Uncle Relationships AUNT: description: The player of the role is a sister of the scoping person's mother or father @@ -190,10 +216,11 @@ enums: PATERNAL_UNCLE: description: The player of the role is a brother of the scoping person's father meaning: HL7:v3-RoleCode#PUNCLE - + # Cousin Relationships COUSIN: - description: The player of the role is a relative descended from a common ancestor, such as a grandparent, by two or more steps in a diverging line + description: The player of the role is a relative descended from a common ancestor, such as a grandparent, by + two or more steps in a diverging line meaning: HL7:v3-RoleCode#COUSN MATERNAL_COUSIN: description: The player of the role is a child of a maternal aunt or uncle of the scoping person @@ -201,15 +228,17 @@ enums: PATERNAL_COUSIN: description: The player of the role is a child of a paternal aunt or uncle of the scoping person meaning: HL7:v3-RoleCode#PCOUSN - + # Niece/Nephew Relationships NIECE: - description: The player of the role is a daughter of the scoping person's brother or sister or of the brother or sister of the scoping person's spouse + description: The player of the role is a daughter of the scoping person's brother or sister or of the brother or + sister of the scoping person's spouse meaning: HL7:v3-RoleCode#NIECE NEPHEW: - description: The player of the role is a son of the scoping person's brother or sister or of the brother or sister of the scoping person's spouse + description: The player of the role is a son of the scoping person's brother or sister or of the brother or + sister of the scoping person's spouse meaning: HL7:v3-RoleCode#NEPHEW - + # Spouse/Partner Relationships SPOUSE: description: The player of the role is a marriage partner of the scoping person @@ -223,7 +252,7 @@ enums: DOMESTIC_PARTNER: description: The player of the role cohabits with the scoping person but is not the scoping person's spouse meaning: HL7:v3-RoleCode#DOMPART - + # Great-Grandparent Relationships GREAT_GRANDPARENT: description: The player of the role is a grandparent of the scoping person's mother or father @@ -234,7 +263,7 @@ enums: GREAT_GRANDFATHER: description: The player of the role is a grandfather of the scoping person's mother or father meaning: HL7:v3-RoleCode#GGRFTH - + # In-Law Relationships MOTHER_IN_LAW: description: The player of the role is the mother of the scoping person's spouse @@ -249,12 +278,14 @@ enums: description: The player of the role is the husband of scoping person's daughter meaning: HL7:v3-RoleCode#SONINLAW BROTHER_IN_LAW: - description: The player of the role is a brother of the scoping person's spouse, or the husband of the scoping person's sister, or the husband of a sister of the scoping person's spouse + description: The player of the role is a brother of the scoping person's spouse, or the husband of the scoping + person's sister, or the husband of a sister of the scoping person's spouse meaning: HL7:v3-RoleCode#BROINLAW SISTER_IN_LAW: - description: The player of the role is a sister of the scoping person's spouse, or the wife of the scoping person's brother, or the wife of a brother of the scoping person's spouse + description: The player of the role is a sister of the scoping person's spouse, or the wife of the scoping + person's brother, or the wife of a brother of the scoping person's spouse meaning: HL7:v3-RoleCode#SISINLAW - + # Extended Family FAMILY_MEMBER: description: A relationship between two people characterizing their "familial" relationship @@ -265,9 +296,16 @@ enums: SIGNIFICANT_OTHER: description: A person who is important to one's well being; especially a spouse or one in a similar relationship meaning: HL7:v3-RoleCode#SIGOTHR - + FamilyHistoryStatus: + title: Family History Status description: Status of family history information availability + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: COMPLETED: description: All relevant family history information has been obtained @@ -284,9 +322,16 @@ enums: NOT_ASKED: description: Family history information was not requested meaning: HL7:data-absent-reason#not-asked - + GeneticRelationship: + title: Genetic Relationship description: Genetic relationship types for pedigree analysis + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: BIOLOGICAL: description: Genetic relationship through biological inheritance @@ -311,4 +356,4 @@ license: MIT see_also: - https://terminology.hl7.org/2.1.0/ValueSet-v3-FamilyMember.html - https://github.com/GA4GH-Pedigree-Standard/family_history_terminology -- https://www.healthit.gov/isp/representing-patient-family-health-history \ No newline at end of file +- https://www.healthit.gov/isp/representing-patient-family-health-history diff --git a/src/valuesets/schema/medical/neuroimaging.yaml b/src/valuesets/schema/medical/neuroimaging.yaml index 446b7b53..019266cc 100644 --- a/src/valuesets/schema/medical/neuroimaging.yaml +++ b/src/valuesets/schema/medical/neuroimaging.yaml @@ -1,6 +1,7 @@ name: neuroimaging title: Neuroimaging Value Sets -description: 'Value sets for neuroimaging including MRI modalities, fMRI paradigms, acquisition parameters, and image analysis methods.' +description: 'Value sets for neuroimaging including MRI modalities, fMRI paradigms, acquisition parameters, and image analysis + methods.' id: https://w3id.org/valuesets/medical/neuroimaging imports: - linkml:types @@ -14,6 +15,8 @@ prefixes: CHMO: http://purl.obolibrary.org/obo/CHMO_ STATO: http://purl.obolibrary.org/obo/STATO_ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: @@ -32,7 +35,14 @@ slots: enums: MRIModalityEnum: + title: MRI Modality description: MRI imaging modalities and techniques + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: STRUCTURAL_T1: title: T1-weighted structural MRI @@ -158,7 +168,14 @@ enums: metric: correlation coefficients MRISequenceTypeEnum: + title: MRI Sequence Type description: MRI pulse sequence types + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: GRADIENT_ECHO: title: Gradient echo sequence @@ -217,7 +234,14 @@ enums: signal: high MRIContrastTypeEnum: + title: MRI Contrast Type description: MRI image contrast mechanisms + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: T1_WEIGHTED: title: T1-weighted contrast @@ -273,7 +297,14 @@ enums: typical_use: stroke, tumor vascularity FMRIParadigmTypeEnum: + title: FMRI Paradigm Type description: fMRI experimental paradigm types + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: BLOCK_DESIGN: title: Block design paradigm @@ -322,4 +353,4 @@ enums: annotations: stimulus_type: complex, realistic advantage: ecological validity - analysis: inter-subject correlation \ No newline at end of file + analysis: inter-subject correlation diff --git a/src/valuesets/schema/mining_processing.yaml b/src/valuesets/schema/mining_processing.yaml index a751a7f7..6e31f6b5 100644 --- a/src/valuesets/schema/mining_processing.yaml +++ b/src/valuesets/schema/mining_processing.yaml @@ -1,7 +1,7 @@ name: mining_processing title: Mining and Mineral Processing Value Sets -description: Value sets for mining operations, mineral processing, beneficiation, and in-situ extraction, including bioleaching - and autonomous mining systems. +description: Value sets for mining operations, mineral processing, beneficiation, and in-situ extraction, including + bioleaching and autonomous mining systems. id: https://w3id.org/valuesets/mining-processing version: 1.0.0 status: release @@ -16,37 +16,40 @@ prefixes: OBI: http://purl.obolibrary.org/obo/OBI_ PATO: http://purl.obolibrary.org/obo/PATO_ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets default_curi_maps: - semweb_context slots: mineralogy_feedstock: - description: Types of mineral feedstock sources for extraction and processing operations, including primary and secondary - sources + description: Types of mineral feedstock sources for extraction and processing operations, including primary and + secondary sources range: MineralogyFeedstockClass required: true comments: - Required field for mining operation records - Manual customization - do not modify beneficiation_pathway: - description: Methods for mineral separation and concentration aligned with advanced ore processing initiatives (AOI-2) + description: Methods for mineral separation and concentration aligned with advanced ore processing initiatives + (AOI-2) range: BeneficiationPathway in_situ_chemistry_regime: - description: Chemical leaching systems for in-situ extraction with associated parameters including pH, Eh, temperature, - and ionic strength + description: Chemical leaching systems for in-situ extraction with associated parameters including pH, Eh, + temperature, and ionic strength range: InSituChemistryRegime extractable_target_element: description: Target elements for extraction, particularly rare earth elements (REE) and critical minerals range: ExtractableTargetElement multivalued: true sensor_while_drilling_feature: - description: Measurement while drilling (MWD) and logging while drilling (LWD) features for orebody ML and geosteering - applications + description: Measurement while drilling (MWD) and logging while drilling (LWD) features for orebody ML and + geosteering applications range: SensorWhileDrillingFeature multivalued: true process_performance_metric: - description: Key performance indicators for mining and processing operations tied to SMART milestones and sustainability - goals + description: Key performance indicators for mining and processing operations tied to SMART milestones and + sustainability goals range: ProcessPerformanceMetric multivalued: true bioleach_organism: @@ -56,20 +59,27 @@ slots: description: Mechanisms of bioleaching including indirect and direct bacterial action range: BioleachMode autonomy_level: - description: Levels of autonomy for mining systems including drilling, hauling, and sorting robots (relevant for Topic - 1 initiatives) + description: Levels of autonomy for mining systems including drilling, hauling, and sorting robots (relevant for + Topic 1 initiatives) range: AutonomyLevel regulatory_constraint: - description: Regulatory and community constraints affecting mining operations, particularly for in-situ extraction and - community engagement + description: Regulatory and community constraints affecting mining operations, particularly for in-situ extraction + and community engagement range: RegulatoryConstraint multivalued: true enums: MineralogyFeedstockClass: + title: Mineralogy Feedstock Class description: 'Types of mineral feedstock sources for extraction and processing operations, including primary and secondary sources. ' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: HARDROCK_PRIMARY: title: HARDROCK_PRIMARY @@ -90,9 +100,16 @@ enums: title: BRINES description: Saline water sources containing dissolved minerals BeneficiationPathway: + title: Beneficiation Pathway description: 'Methods for mineral separation and concentration aligned with advanced ore processing initiatives (AOI-2). ' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ORE_SORTING: description: Sensor-based sorting of ore particles @@ -113,10 +130,17 @@ enums: BIO_BENEFICIATION: description: Biological methods for mineral beneficiation InSituChemistryRegime: + title: In Situ Chemistry Regime description: 'Chemical leaching systems for in-situ extraction with associated parameters including pH, Eh, temperature, and ionic strength. ' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ACIDIC_SULFATE: title: ACIDIC_SULFATE @@ -134,9 +158,16 @@ enums: BIOLEACH_IRON_OXIDIZING: description: Bioleaching using iron-oxidizing bacteria ExtractableTargetElement: + title: Extractable Target Element description: 'Target elements for extraction, particularly rare earth elements (REE) and critical minerals. ' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: REE_LA: title: REE_LA @@ -196,10 +227,17 @@ enums: title: LI description: Lithium SensorWhileDrillingFeature: + title: Sensor While Drilling Feature description: 'Measurement while drilling (MWD) and logging while drilling (LWD) features for orebody ML and geosteering applications. ' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: WOB: description: Weight on bit measurement @@ -218,10 +256,17 @@ enums: RSS_ANGLE: description: Rotary steerable system angle ProcessPerformanceMetric: + title: Process Performance Metric description: 'Key performance indicators for mining and processing operations tied to SMART milestones and sustainability goals. ' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: RECOVERY_PCT: description: Percentage recovery of target material @@ -238,9 +283,16 @@ enums: TAILINGS_MASS_REDUCTION_PCT: description: Percentage reduction in tailings mass BioleachOrganism: + title: Bioleach Organism description: 'Microorganisms used in bioleaching and biomining operations, including engineered strains. ' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ACIDITHIOBACILLUS_FERROOXIDANS: description: Iron and sulfur oxidizing bacterium @@ -254,9 +306,16 @@ enums: ENGINEERED_STRAIN: description: Genetically modified organism for enhanced bioleaching BioleachMode: + title: Bioleach Mode description: 'Mechanisms of bioleaching including indirect and direct bacterial action. ' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: INDIRECT_BIOLEACH_ORGANIC_ACIDS: description: Indirect bioleaching through organic acid production @@ -265,10 +324,17 @@ enums: IRON_OXIDATION: description: Direct bacterial oxidation of iron compounds AutonomyLevel: + title: Autonomy Level description: 'Levels of autonomy for mining systems including drilling, hauling, and sorting robots (relevant for Topic 1 initiatives). ' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ASSISTIVE: description: Human operator with assistive technologies @@ -279,10 +345,17 @@ enums: FULLY_AUTONOMOUS: description: Complete autonomous operation without human intervention RegulatoryConstraint: + title: Regulatory Constraint description: 'Regulatory and community constraints affecting mining operations, particularly for in-situ extraction and community engagement. ' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: AQUIFER_PROTECTION: title: AQUIFER_PROTECTION diff --git a/src/valuesets/schema/physics/states_of_matter.yaml b/src/valuesets/schema/physics/states_of_matter.yaml index df744b44..1bccfa25 100644 --- a/src/valuesets/schema/physics/states_of_matter.yaml +++ b/src/valuesets/schema/physics/states_of_matter.yaml @@ -8,6 +8,8 @@ prefixes: AFO: http://purl.allotrope.org/ontologies/quality# SNOMED: http://snomed.info/id/ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: state_of_matter: @@ -15,7 +17,14 @@ slots: range: StateOfMatterEnum enums: StateOfMatterEnum: + title: State Of Matter description: The physical state or phase of matter + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: SOLID: description: A state of matter where particles are closely packed together with fixed positions @@ -30,7 +39,8 @@ enums: description: An ionized gas with freely moving charged particles meaning: AFO:AFQ_0000115 BOSE_EINSTEIN_CONDENSATE: - description: A state of matter formed at extremely low temperatures where particles occupy the same quantum state + description: A state of matter formed at extremely low temperatures where particles occupy the same quantum + state FERMIONIC_CONDENSATE: description: A superfluid phase formed by fermionic particles at extremely low temperatures SUPERCRITICAL_FLUID: diff --git a/src/valuesets/schema/slot_mixins.yaml b/src/valuesets/schema/slot_mixins.yaml index e8c64fc9..9bcd6f99 100644 --- a/src/valuesets/schema/slot_mixins.yaml +++ b/src/valuesets/schema/slot_mixins.yaml @@ -13,6 +13,8 @@ prefixes: linkml: https://w3id.org/linkml/ # cval: https://w3id.org/linkml-common/ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets default_curi_maps: - semweb_context diff --git a/src/valuesets/schema/social/person_status.yaml b/src/valuesets/schema/social/person_status.yaml index ffbe9e3e..f84a4954 100644 --- a/src/valuesets/schema/social/person_status.yaml +++ b/src/valuesets/schema/social/person_status.yaml @@ -5,6 +5,8 @@ prefixes: # linkml_common: https://w3id.org/linkml-common/ NCIT: http://purl.obolibrary.org/obo/NCIT_ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: person_status: @@ -12,7 +14,14 @@ slots: range: PersonStatusEnum enums: PersonStatusEnum: + title: Person Status description: Vital status of a person (living or deceased) + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ALIVE: description: The person is living diff --git a/src/valuesets/schema/spatial/spatial_qualifiers.yaml b/src/valuesets/schema/spatial/spatial_qualifiers.yaml index 4bdd3c39..44b4acaf 100644 --- a/src/valuesets/schema/spatial/spatial_qualifiers.yaml +++ b/src/valuesets/schema/spatial/spatial_qualifiers.yaml @@ -7,10 +7,13 @@ id: https://w3id.org/linkml/valuesets/spatial/spatial_qualifiers imports: - linkml:types prefixes: + linkml: https://w3id.org/linkml/ valuesets: https://w3id.org/valuesets/ BSPO: http://purl.obolibrary.org/obo/BSPO_ PATO: http://purl.obolibrary.org/obo/PATO_ UBERON: http://purl.obolibrary.org/obo/UBERON_ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: simple_spatial_direction: @@ -36,7 +39,14 @@ slots: range: CellPolarity enums: SimpleSpatialDirection: + title: Simple Spatial Direction description: Basic spatial directional terms for general use + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: LEFT: description: To the left side @@ -79,9 +89,16 @@ enums: annotations: aliases: center, central AnatomicalSide: + title: Anatomical Side description: 'Anatomical sides as defined in the Biological Spatial Ontology (BSPO). An anatomical region bounded by a plane perpendicular to an axis through the middle.' + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: LEFT: title: Left side of a bilaterally symmetric organism @@ -213,7 +230,14 @@ enums: annotations: aliases: middle AnatomicalRegion: + title: Anatomical Region description: Anatomical regions based on spatial position + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ANTERIOR_REGION: title: Region in the anterior portion @@ -276,7 +300,14 @@ enums: - peripheral region meaning: BSPO:0000127 AnatomicalAxis: + title: Anatomical Axis description: Anatomical axes defining spatial organization + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ANTERIOR_POSTERIOR: title: Anterior-posterior axis (head-tail axis) @@ -314,7 +345,14 @@ enums: annotations: context: epithelial cells, plant structures AnatomicalPlane: + title: Anatomical Plane description: Standard anatomical planes for sectioning + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: SAGITTAL: title: Vertical plane dividing body into left and right @@ -359,7 +397,14 @@ enums: annotations: note: angled section SpatialRelationship: + title: Spatial Relationship description: Spatial relationships between anatomical structures + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: ADJACENT_TO: title: Next to or adjoining @@ -430,7 +475,14 @@ enums: annotations: note: requires two reference points CellPolarity: + title: Cell Polarity description: Spatial polarity in cells and tissues + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: APICAL: description: The free surface of an epithelial cell diff --git a/src/valuesets/schema/statistics.yaml b/src/valuesets/schema/statistics.yaml index 52cf99af..ae20debb 100644 --- a/src/valuesets/schema/statistics.yaml +++ b/src/valuesets/schema/statistics.yaml @@ -12,6 +12,8 @@ prefixes: prov: http://www.w3.org/ns/prov# dcterms: http://purl.org/dc/terms/ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: prediction_outcome: @@ -19,6 +21,13 @@ slots: range: PredictionOutcomeType enums: PredictionOutcomeType: + title: Prediction Outcome Type + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: TP: description: True Positive diff --git a/src/valuesets/schema/statistics/prediction_outcomes.yaml b/src/valuesets/schema/statistics/prediction_outcomes.yaml index b5181470..6c215d84 100644 --- a/src/valuesets/schema/statistics/prediction_outcomes.yaml +++ b/src/valuesets/schema/statistics/prediction_outcomes.yaml @@ -3,6 +3,8 @@ id: https://w3id.org/linkml/valuesets/statistics/prediction_outcomes prefixes: # linkml_common: https://w3id.org/linkml-common/ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: outcome_type: @@ -10,7 +12,14 @@ slots: range: OutcomeTypeEnum enums: OutcomeTypeEnum: + title: Outcome Type description: Types of prediction outcomes for classification tasks + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: TP: description: True Positive diff --git a/src/valuesets/schema/stewardship.yaml b/src/valuesets/schema/stewardship.yaml new file mode 100644 index 00000000..8454954a --- /dev/null +++ b/src/valuesets/schema/stewardship.yaml @@ -0,0 +1,248 @@ +name: stewardship +title: Value Set Stewardship Organizations +description: | + Organizations and consortia that steward value sets and terminologies. + + This enum is used with the `stewards`, `publishers`, and `endorsers` slots + defined in the valuesets_meta metamodel to track organizational responsibility + for value set content. + + ## Identifier Guidelines + + - **ROR IDs** (https://ror.org/) are preferred for formal organizations + - For consortia without ROR IDs, use canonical website URLs + - All identifiers should be stable, persistent URIs + +id: https://w3id.org/valuesets/stewardship + +imports: + - linkml:types + +prefixes: + linkml: https://w3id.org/linkml/ + valuesets: https://w3id.org/valuesets/ + ROR: https://ror.org/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ + +default_prefix: valuesets + +slots: + value_set_steward: + description: Organization responsible for stewardship of a value set + range: ValueSetStewardEnum + +enums: + ValueSetStewardEnum: + title: Value Set Steward + description: | + Organizations and consortia that may serve as stewards, publishers, or + endorsers for value sets. Includes standards bodies, bioinformatics + consortia, and data coordination centers. + + Use ROR IDs where available; otherwise use canonical organization URLs. + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ReferenceEnumDefinition + see_also: + - https://ror.org/ + - https://build.fhir.org/metadataresource.html + permissible_values: + # ======================================================================= + # Bioinformatics Consortia (alphabetical) + # ======================================================================= + GA4GH: + title: Global Alliance for Genomics and Health + description: | + International consortium developing standards for responsible sharing + of genomic and health-related data. Develops standards including + Phenopackets, VRS, DRS, and Beacon. + meaning: https://ga4gh.org + aliases: + - Global Alliance for Genomics and Health + annotations: + established: "2013" + headquarters: Multiple host institutions + website: https://ga4gh.org + + GENE_ONTOLOGY_CONSORTIUM: + title: Gene Ontology Consortium + description: | + International consortium developing and maintaining the Gene Ontology, + the world's largest source of information on gene function. Provides + GO annotations and the GO ontology itself. + meaning: https://geneontology.org + aliases: + - GO Consortium + - GOC + annotations: + established: "1998" + website: https://geneontology.org + + GENOMIC_STANDARDS_CONSORTIUM: + title: Genomic Standards Consortium + description: | + Open-membership community developing standards for describing genomes, + metagenomes, and related data. Develops MIxS checklists and related + metadata standards. + meaning: https://gensc.org + aliases: + - GSC + annotations: + established: "2005" + website: https://gensc.org + + MONARCH_INITIATIVE: + title: Monarch Initiative + description: | + International consortium integrating genotype-phenotype data across + species. Develops and maintains ontologies including HPO, Mondo, + and Upheno, and provides data integration services. + meaning: https://monarchinitiative.org + aliases: + - Monarch + annotations: + website: https://monarchinitiative.org + + OBO_FOUNDRY: + title: OBO Foundry + description: | + Collaborative effort to develop interoperable ontologies for the + life sciences. Coordinates ontology development and establishes + principles for ontology best practices. + meaning: https://obofoundry.org + aliases: + - Open Biological and Biomedical Ontologies Foundry + annotations: + established: "2007" + website: https://obofoundry.org + + OHDSI: + title: OHDSI + description: | + Observational Health Data Sciences and Informatics program. + International collaborative developing open-source analytics solutions + for observational health data. Maintains the OMOP Common Data Model. + meaning: https://ohdsi.org + aliases: + - Observational Health Data Sciences and Informatics + annotations: + established: "2014" + website: https://ohdsi.org + coordinating_center: Columbia University + + PHENOPACKETS: + title: Phenopackets + description: | + GA4GH work stream developing standards for sharing disease and + phenotype information. Develops the Phenopacket Schema for + representing clinical and phenotypic data. + meaning: https://phenopackets.org + aliases: + - GA4GH Phenopackets + annotations: + parent_organization: GA4GH + website: https://phenopackets.org + + # ======================================================================= + # Major Research Institutions (with ROR IDs) + # ======================================================================= + EMBL_EBI: + title: European Bioinformatics Institute + description: | + EMBL's European Bioinformatics Institute, a global leader in + bioinformatics services, databases, and tools. Hosts major resources + including UniProt, Ensembl, and the Ontology Lookup Service. + meaning: ROR:02catss52 + aliases: + - EMBL-EBI + - EBI + annotations: + parent_organization: European Molecular Biology Laboratory + website: https://www.ebi.ac.uk/ + location: Hinxton, UK + + NCBI: + title: National Center for Biotechnology Information + description: | + Part of the United States National Library of Medicine. Develops + databases and tools for molecular biology including GenBank, + PubMed, and the NCBI Taxonomy. + meaning: ROR:02meqm098 + aliases: + - National Center for Biotechnology Information + annotations: + parent_organization: National Library of Medicine + website: https://www.ncbi.nlm.nih.gov/ + location: Bethesda, MD, USA + + # ======================================================================= + # Standards Development Organizations (with ROR IDs) + # ======================================================================= + CDISC: + title: CDISC + description: | + Clinical Data Interchange Standards Consortium. Develops global + data standards for clinical research including CDASH, SDTM, + and ADaM. + meaning: https://cdisc.org + aliases: + - Clinical Data Interchange Standards Consortium + annotations: + established: "1997" + website: https://cdisc.org + + HL7: + title: Health Level Seven International + description: | + Standards development organization for healthcare information + exchange. Develops FHIR, CDA, and HL7 v2 messaging standards. + meaning: ROR:029ga8k16 + aliases: + - Health Level Seven + - HL7 International + annotations: + established: "1987" + website: https://www.hl7.org/ + headquarters: Ann Arbor, Michigan + + ISO: + title: International Organization for Standardization + description: | + International standard-setting body for industrial and commercial + standards. Develops standards across many domains including + terminology (ISO 704) and healthcare. + meaning: ROR:004s85t07 + annotations: + established: "1947" + website: https://www.iso.org/ + headquarters: Geneva, Switzerland + + W3C: + title: World Wide Web Consortium + description: | + International standards organization for the World Wide Web. + Develops standards including RDF, OWL, SPARQL, and accessibility + guidelines. + meaning: ROR:0059y1582 + annotations: + established: "1994" + website: https://www.w3.org/ + + # ======================================================================= + # This Repository + # ======================================================================= + VALUESETS_PROJECT: + title: Valuesets Project + description: | + The valuesets repository itself, for value sets that are community + contributions without a specific external steward. Use sparingly; + prefer identifying an appropriate domain consortium. + meaning: https://github.com/linkml/valuesets + aliases: + - LinkML Valuesets + annotations: + website: https://w3id.org/valuesets/ diff --git a/src/valuesets/schema/time/temporal.yaml b/src/valuesets/schema/time/temporal.yaml index b7d0d525..0905f373 100644 --- a/src/valuesets/schema/time/temporal.yaml +++ b/src/valuesets/schema/time/temporal.yaml @@ -5,6 +5,7 @@ id: https://w3id.org/linkml/valuesets/time/temporal imports: - linkml:types prefixes: + linkml: https://w3id.org/linkml/ valuesets: https://w3id.org/valuesets/ TIME: http://www.w3.org/2006/time# greg: http://www.w3.org/ns/time/gregorian# @@ -12,6 +13,8 @@ prefixes: NCIT: http://purl.obolibrary.org/obo/NCIT_ UO: http://purl.obolibrary.org/obo/UO_ ENVO: http://purl.obolibrary.org/obo/ENVO_ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: day_of_week: @@ -43,7 +46,14 @@ slots: range: HistoricalPeriod enums: DayOfWeek: + title: Day Of Week description: Days of the week following ISO 8601 standard (Monday = 1) + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: MONDAY: description: Monday (first day of week in ISO 8601) @@ -109,7 +119,14 @@ enums: iso_number: 7 abbreviation: Sun Month: + title: Month description: Months of the year + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: JANUARY: description: January @@ -232,7 +249,14 @@ enums: abbreviation: Dec days: 31 Quarter: + title: Quarter description: Calendar quarters + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: Q1: description: First quarter (January-March) @@ -251,7 +275,14 @@ enums: annotations: months: Oct-Dec Season: + title: Season description: Seasons of the year (Northern Hemisphere) + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: SPRING: description: Spring season @@ -279,7 +310,14 @@ enums: months: Dec-Feb astronomical_start: ~Dec 21 TimePeriod: + title: Time Period description: Common time periods and intervals + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: HOURLY: description: Every hour @@ -318,7 +356,14 @@ enums: annotations: ucum: 2.a TimeOfDay: + title: Time Of Day description: Common times of day + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: DAWN: description: Dawn (first light) @@ -349,7 +394,14 @@ enums: annotations: typical_time: 00:00 BusinessTimeFrame: + title: Business Time Frame description: Common business and financial time frames + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: REAL_TIME: description: Real-time/instantaneous @@ -400,7 +452,14 @@ enums: annotations: abbreviation: QTD GeologicalEra: + title: Geological Era description: Major geological eras + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: PRECAMBRIAN: description: Precambrian (4.6 billion - 541 million years ago) @@ -411,7 +470,14 @@ enums: CENOZOIC: description: Cenozoic Era (66 million years ago - present) HistoricalPeriod: + title: Historical Period description: Major historical periods + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: PREHISTORIC: description: Before written records diff --git a/src/valuesets/schema/types.yaml b/src/valuesets/schema/types.yaml index 05001112..13ad7327 100644 --- a/src/valuesets/schema/types.yaml +++ b/src/valuesets/schema/types.yaml @@ -8,6 +8,8 @@ prefixes: linkml: https://w3id.org/linkml/ cvs: https://w3id.org/linkml/valuesets/ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets types: CountScalar: diff --git a/src/valuesets/schema/units/measurements.yaml b/src/valuesets/schema/units/measurements.yaml index 83f54413..6828d009 100644 --- a/src/valuesets/schema/units/measurements.yaml +++ b/src/valuesets/schema/units/measurements.yaml @@ -13,6 +13,8 @@ prefixes: QUDT: http://qudt.org/schema/qudt/ SI: http://www.bipm.org/en/si/ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: length_unit: @@ -47,7 +49,14 @@ slots: range: DataSizeUnitEnum enums: LengthUnitEnum: + title: Length Unit description: Units of length/distance measurement + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: METER: title: meter @@ -133,7 +142,14 @@ enums: symbol: nmi conversion_to_meter: '1852' MassUnitEnum: + title: Mass Unit description: Units of mass measurement + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: KILOGRAM: description: Kilogram (SI base unit) @@ -205,7 +221,14 @@ enums: conversion_to_kg: '1.66054e-27' use: molecular mass VolumeUnitEnum: + title: Volume Unit description: Units of volume measurement + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: LITER: description: Liter (SI derived) @@ -306,7 +329,14 @@ enums: symbol: tsp conversion_to_m3: '4.92892e-6' TemperatureUnitEnum: + title: Temperature Unit description: Units of temperature measurement + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: KELVIN: description: Kelvin (SI base unit) @@ -337,7 +367,14 @@ enums: conversion: K * 9/5 absolute: 'true' TimeUnitEnum: + title: Time Unit description: Units of time measurement + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: SECOND: description: Second (SI base unit) @@ -403,7 +440,14 @@ enums: conversion_to_second: '31557600' note: accounts for leap years PressureUnitEnum: + title: Pressure Unit description: Units of pressure measurement + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: PASCAL: description: Pascal (SI derived unit) @@ -461,7 +505,14 @@ enums: conversion_to_pascal: '133.322' use: medical blood pressure ConcentrationUnitEnum: + title: Concentration Unit description: Units of concentration measurement + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: MOLAR: description: Molar (moles per liter) @@ -532,7 +583,14 @@ enums: symbol: ppb conversion_to_fraction: 1e-9 FrequencyUnitEnum: + title: Frequency Unit description: Units of frequency measurement + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: HERTZ: description: Hertz (cycles per second) @@ -569,7 +627,14 @@ enums: conversion_to_hz: '0.0166667' use: heart rate AngleUnitEnum: + title: Angle Unit description: Units of angle measurement + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: RADIAN: description: Radian (SI derived unit) @@ -604,7 +669,14 @@ enums: symbol: turn conversion_to_radian: '6.28319' DataSizeUnitEnum: + title: Data Size Unit description: Units of digital data size + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: BIT: description: Bit (binary digit) diff --git a/src/valuesets/schema/valuesets.yaml b/src/valuesets/schema/valuesets.yaml index dbcba1a0..c04aaaa3 100644 --- a/src/valuesets/schema/valuesets.yaml +++ b/src/valuesets/schema/valuesets.yaml @@ -103,9 +103,11 @@ imports: - lab_automation/thermal_cycling prefixes: valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets classes: - Fake: null + Fake: license: Apache-2.0 see_also: - https://linkml.github.io/valuesets diff --git a/src/valuesets/schema/visual/colors.yaml b/src/valuesets/schema/visual/colors.yaml index 8d941ad6..fef801fd 100644 --- a/src/valuesets/schema/visual/colors.yaml +++ b/src/valuesets/schema/visual/colors.yaml @@ -14,6 +14,8 @@ prefixes: CSS: https://www.w3.org/TR/css-color-3/# PATO: http://purl.obolibrary.org/obo/PATO_ valuesets: https://w3id.org/valuesets/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ default_prefix: valuesets slots: basic_color: @@ -30,7 +32,14 @@ slots: range: ColorSpaceEnum enums: BasicColorEnum: + title: Basic Color description: Basic color names commonly used in everyday language + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: RED: description: Primary red color @@ -106,7 +115,14 @@ enums: annotations: rgb: 255,0,255 WebColorEnum: + title: Web Color description: Standard HTML/CSS named colors (147 colors) + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: INDIAN_RED: description: Indian red @@ -699,7 +715,14 @@ enums: annotations: rgb: 47,79,79 X11ColorEnum: + title: X11 Color description: X11/Unix system colors (extended set) + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: X11_AQUA: description: X11 Aqua @@ -756,7 +779,14 @@ enums: description: X11 Red 4 meaning: HEX:8B0000 ColorSpaceEnum: + title: Color Space description: Color space and model types + status: DRAFT + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition permissible_values: RGB: description: Red Green Blue color model