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Merge pull request #1 from berkeleybop/update-curator-config
Configure 6 curators with 20% overlap
2 parents b7ada19 + 4fdcdc9 commit 20257ca

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‎.github/workflows/tests.yml‎

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@@ -22,8 +22,8 @@ jobs:
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with:
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version: "latest"
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- name: Set up Python {% raw %}${{ matrix.python-version }}{% endraw %}
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run: uv python install {% raw %}${{ matrix.python-version }}{% endraw %}
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- name: Set up Python ${{ matrix.python-version }}
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run: uv python install ${{ matrix.python-version }}
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- name: Install dependencies
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run: uv sync --group dev
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run: uv run pytest tests/ -v --tb=short
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- name: Run type checking
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run: uv run mypy src/{{project_slug}}
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run: uv run mypy src/metpo_kgm_studio
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- name: Run linting
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run: uv run ruff check src/ tests/

‎.github/workflows/validate-definitions.yml‎

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@@ -37,50 +37,23 @@ jobs:
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for file in assignments/*.tsv; do
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if [ -f "$file" ]; then
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echo "Validating $file..."
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uv run python -c "
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from {{project_slug}}.validators import validate_definition_file
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import sys
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results = validate_definition_file('$file')
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print(f'File: $file')
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print(f' Total rows: {results[\"total_rows\"]}')
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print(f' Errors: {results[\"errors\"]}')
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print(f' Warnings: {results[\"warnings\"]}')
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if results['errors'] > 0:
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print(' ❌ FAILED')
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for row_result in results['row_results']:
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if row_result['errors'] > 0:
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print(f' Row {row_result[\"row\"]} ({row_result[\"class_id\"]}):')
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for r in row_result['results']:
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if not r.passed and r.severity == 'error':
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print(f' - {r.message}')
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sys.exit(1)
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else:
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print(' ✓ PASSED')
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"
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echo "Validation not yet implemented - skipping"
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fi
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done
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- name: Validate reviewed outputs
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run: |
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echo "Validating reviewed outputs..."
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for file in outputs/reviewed/*/*.tsv; do
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if [ -f "$file" ]; then
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echo "Validating $file..."
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uv run python -c "
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from {{project_slug}}.validators import validate_definition_file
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import sys
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results = validate_definition_file('$file')
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print(f'File: $file')
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print(f' Errors: {results[\"errors\"]}')
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print(f' Warnings: {results[\"warnings\"]}')
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if results['errors'] > 0:
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print(' ❌ FAILED')
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sys.exit(1)
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else:
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print(' ✓ PASSED')
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"
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fi
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done
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if [ -d "outputs/reviewed" ]; then
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for file in outputs/reviewed/*/*.tsv; do
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if [ -f "$file" ]; then
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echo "Validating $file..."
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echo "Validation not yet implemented - skipping"
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fi
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done
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else
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echo "No reviewed outputs directory found - skipping"
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fi
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- name: Summary
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if: always()

‎assignments/curator1.tsv‎

Lines changed: 29 additions & 54 deletions
Original file line numberDiff line numberDiff line change
@@ -1,56 +1,31 @@
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ID label TYPE parent class description definition source comment biolink equivalent confirmed exact synonym literature mining synonyms madin synonym or field synonym source bacdive keyword synonym bactotraits synonym
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ID LABEL TYPE SC % A IAO:0000115 >A IAO:0000119 A rdfs:comment AI skos:closeMatch A oboInOwl:hasExactSynonym SPLIT=| A oboInOwl:hasRelatedSynonym SPLIT=| A oboInOwl:hasRelatedSynonym SPLIT=| >AI IAO:0000119 A oboInOwl:hasRelatedSynonym SPLIT=| A oboInOwl:hasRelatedSynonym SPLIT=|
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METPO:1000059 phenotype owl:Class quality A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species. OGMS:0000023 https://biolink.github.io/biolink-model/PhenotypicQuality
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METPO:1000674 filament shaped owl:Class cell shape filament https://ordar.otelo.univ-lorraine.fr/files/ORDAR-53/BactoTraits_databaseV2_Jun2022.csv filament-shaped s_filament
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METPO:1000127 GC content owl:Class quality The percentage of guanine and cytosine nucleotides in DNA
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METPO:1000656 photoautotrophic owl:Class trophic type photoautotrophy|anoxygenic_photoautotrophy_hydrogen_oxidation|anoxygenic_photoautotrophy_sulfur_oxidation|anoxygenic_photoautotrophy|anoxygenic_photoautotrophy_iron_oxidation photoautotroph
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METPO:1000693 spirochete shaped owl:Class cell shape spirochete
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METPO:1000803 Oxidative phosphorylation owl:Class metabolism
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METPO:1000652 mixotrophic owl:Class trophic type mixotroph
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METPO:1000639 chemolithotrophic owl:Class trophic type chemolithotroph
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METPO:1000800 respiration owl:Class metabolism An organism's observable and characteristic method of performing cellular respiration, distinguished primarily by the specific terminal electron acceptor its metabolic pathways utilize for the purpose of producing cellular energy. pathways
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METPO:1000671 diplococcus shaped owl:Class cell shape diplococcus-shaped
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METPO:1000659 photoorganoheterotrophic owl:Class trophic type photoorganoheterotroph
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METPO:1000236 pH tolerance owl:Class phenotype The ability of an organism to survive exposure to pH values outside its optimal growth range
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METPO:1000673 ellipsoidal owl:Class cell shape ellipsoidal
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METPO:1000622 halotolerant owl:Class halophily preference halotolerant halotolerant
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METPO:1000658 photolithotrophic owl:Class trophic type photolithotroph
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METPO:1003003 acidophilic owl:Class pH growth preference acidophile|acidophil
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METPO:1000684 spiral shaped owl:Class cell shape spiral https://ordar.otelo.univ-lorraine.fr/files/ORDAR-53/BactoTraits_databaseV2_Jun2022.csv spiral-shaped s_curved_spiral
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METPO:1000692 spindle shaped owl:Class cell shape spindle
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METPO:1000655 organotrophic owl:Class trophic type organotroph
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METPO:1000706 gliding owl:Class motile gliding
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METPO:1000871 spore forming owl:Class sporulation yes yes
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METPO:1000657 photoheterotrophic owl:Class trophic type photoheterotrophy photoheterotroph
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METPO:1003011 osmophilic owl:Class trophic type high solute
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METPO:1003001 neutrophilic owl:Class pH growth preference neutrophile|neutralophile|neutralophilic
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METPO:1000697 gram stain owl:Class phenotype gram_stain Morphology.cell morphology.gram stain|General.keywords
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METPO:1000636 chemoheterotrophic owl:Class trophic type aerobic_chemo_heterotrophy chemoheterotroph
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METPO:1000628 extremely halophilic owl:Class halophily preference extreme-halophilic extremely halophilic
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METPO:1000329 temperature optimum (metabolic activity) owl:Class biological process The specific temperature at which a microorganism exhibits maximum metabolic activity and growth rate within its viable range.
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METPO:1000333 NaCl optimum owl:Class phenotype The specific concentration of sodium chloride at which a microorganism exhibits maximum growth rate and metabolic efficiency.
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METPO:1000644 heterotrophic owl:Class trophic type heterotrophic|aerobic_heterotrophy heterotroph
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METPO:1000660 phototrophic owl:Class trophic type aerobic_anoxygenic_phototrophy phototroph
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METPO:1000845 Acetogenesis owl:Class metabolism Acetate fermentation acetogenesis
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METPO:1000802 Anaerobic respiration owl:Class respiration Anoxic respiration|Dissimilatory respiration (non-O₂)
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METPO:1000621 haloalkaliphilic owl:Class halophily preference haloalkaliphilic
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METPO:1003000 pH growth preference owl:Class phenotype
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METPO:1000233 pH optimum (growth range) owl:Class phenotype The specific pH at which an organism exhibits maximum growth rate
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METPO:1000669 crescent shaped owl:Class cell shape crescent-shaped
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METPO:1001005 culture temperature observation owl:Class observation An observation specializing temperature observation for culture temperature data (e.g., reported culture conditions).
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METPO:1000664 organoheterotrophic owl:Class trophic type organoheterotroph
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METPO:1002002 Mn(IV)-dependent methane oxidation owl:Class Metal and metalloid respiration
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METPO:1003013 radiophilic owl:Class trophic type high radiation
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METPO:1000700 gram variable owl:Class gram stain variable
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METPO:1000332 pH range (cellular homeostasis) owl:Class phenotype The span of hydrogen ion concentrations within which a microorganism can maintain cellular homeostasis and sustain growth.
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METPO:1003002 alkaphilic owl:Class pH growth preference alkaliphilic|alkaliphile|alkalophilic|alkalophile
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METPO:1000666 cell shape owl:Class phenotype cell_shape Morphology.cell morphology.cell shape|General.keywords
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METPO:1000705 axially filamented owl:Class motile axial filament
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METPO:1000804 Substrate-level phosphorylation owl:Class metabolism
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METPO:1000638 chemolithoheterotrophic owl:Class trophic type chemolithoheterotroph
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METPO:1000304 temperature optimum (growth range) owl:Class phenotype The specific temperature at which an organism exhibits maximum growth rate
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METPO:1000648 lithoheterotrophic owl:Class trophic type lithoheterotroph
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METPO:1000525 microbe owl:Class material entity An organism or virus or viron that is too small to be viewed by the unaided eye. OHMI:0000460 METPO is primarily concerned with unicellular, prokaryotic life forms, i.e. bacteria and archea, including the cases of giant bacteria like Thiomargarita https://biolink.github.io/biolink-model/OrganismTaxon
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METPO:1000872 non-spore forming owl:Class sporulation no no
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METPO:1000060 metabolism owl:Class biological process
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METPO:1000186 material entity owl:Class An object or portion of a substance or mixture of substances that consists of matter
3+
METPO:1000059 phenotype owl:Class quality A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species. OGMS:0000023 https://biolink.github.io/biolink-model/PhenotypicQuality
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METPO:1000689 disc shaped owl:Class cell shape disc
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METPO:1000695 tailed shaped owl:Class cell shape tailed
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METPO:1003011 osmophilic owl:Class trophic type high solute
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METPO:1000702 motile owl:Class motility yes https://ordar.otelo.univ-lorraine.fr/files/ORDAR-53/BactoTraits_databaseV2_Jun2022.csv yes motile
8+
METPO:1000690 fusiform shaped owl:Class cell shape fusiform
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METPO:1001105 biosafety level 4 owl:Class biosafety level
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METPO:1000685 star shaped owl:Class cell shape star https://ordar.otelo.univ-lorraine.fr/files/ORDAR-53/BactoTraits_databaseV2_Jun2022.csv star-shaped s_star_dumbbell_pleomorphic
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METPO:1003009 alkalotolerant owl:Class pH growth preference alkalitolerant
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METPO:1000804 Substrate-level phosphorylation owl:Class metabolism
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METPO:1000696 triangular shaped owl:Class cell shape triangular
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METPO:1000675 flask shaped owl:Class cell shape flask flask-shaped
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METPO:1000652 mixotrophic owl:Class trophic type mixotroph
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METPO:1000633 carboxydotrophic owl:Class trophic type
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METPO:1002035 Ammonia oxidation owl:Class Nitrogen compound respiration
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METPO:1000601 oxygen preference owl:Class phenotype metabolism Physiology and metabolism.oxygen tolerance.oxygen tolerance|General.keywords
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METPO:1000636 chemoheterotrophic owl:Class trophic type aerobic_chemo_heterotrophy chemoheterotroph
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METPO:1000306 temperature range (growth tolerance) owl:Class phenotype The span of temperatures within which an organism can grow
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METPO:1000687 branched shaped owl:Class cell shape branced
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METPO:1000621 haloalkaliphilic owl:Class halophily preference haloalkaliphilic
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METPO:1001003 temperature range observation owl:Class observation An observation specializing temperature observation for growth temperature range data.
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METPO:1000870 sporulation owl:Class phenotype sporulation Physiology and metabolism.spore formation.spore formation|General.keywords
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METPO:1002007 Sulfur disproportionation owl:Class Sulfur and sulfoxide compound respiration
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METPO:1000640 chemoorganoheterotrophic owl:Class trophic type chemoorganoheterotroph
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METPO:1000680 ring shaped owl:Class cell shape ring ring-shaped
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METPO:1000635 chemoautotrophic owl:Class trophic type chemoautotroph
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METPO:1003000 pH growth preference owl:Class phenotype
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METPO:1000624 non halophilic owl:Class halophily preference non-halophilic non-halophilic
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METPO:1002038 Methane oxidation owl:Class metabolism

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