Merge pull request #32 from linkml/additional-metadata

Add comprehensive enum metadata and stewardship framework

Author: cmungall

.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:

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
+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

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

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)