PyPI - valuesets - Versions diffs - 0.3.1__py3-none-any.whl - Mend

valuesets 0.3.1__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Potentially problematic release.

This version of valuesets might be problematic. Click here for more details.

Files changed (248) hide show

valuesets/__init__.py +7 -0
valuesets/_version.py +8 -0
valuesets/datamodel/valuesets.py +13796 -0
valuesets/datamodel/valuesets_dataclass.py +24503 -0
valuesets/datamodel/valuesets_pydantic.py +13796 -0
valuesets/enums/__init__.py +590 -0
valuesets/enums/academic/__init__.py +1 -0
valuesets/enums/academic/research.py +559 -0
valuesets/enums/analytical_chemistry/__init__.py +1 -0
valuesets/enums/analytical_chemistry/mass_spectrometry.py +198 -0
valuesets/enums/bio/__init__.py +1 -0
valuesets/enums/bio/biological_colors.py +238 -0
valuesets/enums/bio/cell_cycle.py +180 -0
valuesets/enums/bio/currency_chemicals.py +52 -0
valuesets/enums/bio/developmental_stages.py +103 -0
valuesets/enums/bio/genome_features.py +182 -0
valuesets/enums/bio/genomics.py +91 -0
valuesets/enums/bio/go_aspect.py +32 -0
valuesets/enums/bio/go_causality.py +58 -0
valuesets/enums/bio/go_evidence.py +129 -0
valuesets/enums/bio/human_developmental_stages.py +62 -0
valuesets/enums/bio/insdc_geographic_locations.py +591 -0
valuesets/enums/bio/insdc_missing_values.py +49 -0
valuesets/enums/bio/lipid_categories.py +67 -0
valuesets/enums/bio/mouse_developmental_stages.py +62 -0
valuesets/enums/bio/plant_biology.py +86 -0
valuesets/enums/bio/plant_developmental_stages.py +54 -0
valuesets/enums/bio/plant_sex.py +81 -0
valuesets/enums/bio/protein_evidence.py +61 -0
valuesets/enums/bio/proteomics_standards.py +123 -0
valuesets/enums/bio/psi_mi.py +306 -0
valuesets/enums/bio/relationship_to_oxygen.py +37 -0
valuesets/enums/bio/sequence_alphabets.py +449 -0
valuesets/enums/bio/sequence_chemistry.py +357 -0
valuesets/enums/bio/sequencing_platforms.py +302 -0
valuesets/enums/bio/structural_biology.py +320 -0
valuesets/enums/bio/taxonomy.py +238 -0
valuesets/enums/bio/trophic_levels.py +85 -0
valuesets/enums/bio/uniprot_species.py +344 -0
valuesets/enums/bio/viral_genome_types.py +47 -0
valuesets/enums/bioprocessing/__init__.py +1 -0
valuesets/enums/bioprocessing/scale_up.py +249 -0
valuesets/enums/business/__init__.py +1 -0
valuesets/enums/business/human_resources.py +275 -0
valuesets/enums/business/industry_classifications.py +181 -0
valuesets/enums/business/management_operations.py +228 -0
valuesets/enums/business/organizational_structures.py +236 -0
valuesets/enums/business/quality_management.py +181 -0
valuesets/enums/business/supply_chain.py +232 -0
valuesets/enums/chemistry/__init__.py +1 -0
valuesets/enums/chemistry/chemical_entities.py +315 -0
valuesets/enums/chemistry/reaction_directionality.py +65 -0
valuesets/enums/chemistry/reactions.py +256 -0
valuesets/enums/clinical/__init__.py +1 -0
valuesets/enums/clinical/nih_demographics.py +177 -0
valuesets/enums/clinical/phenopackets.py +254 -0
valuesets/enums/common_value_sets.py +8791 -0
valuesets/enums/computing/__init__.py +1 -0
valuesets/enums/computing/file_formats.py +294 -0
valuesets/enums/computing/maturity_levels.py +196 -0
valuesets/enums/computing/mime_types.py +227 -0
valuesets/enums/confidence_levels.py +168 -0
valuesets/enums/contributor.py +30 -0
valuesets/enums/core.py +42 -0
valuesets/enums/data/__init__.py +1 -0
valuesets/enums/data/data_absent_reason.py +53 -0
valuesets/enums/data_science/__init__.py +1 -0
valuesets/enums/data_science/binary_classification.py +87 -0
valuesets/enums/data_science/emotion_classification.py +66 -0
valuesets/enums/data_science/priority_severity.py +73 -0
valuesets/enums/data_science/quality_control.py +46 -0
valuesets/enums/data_science/sentiment_analysis.py +50 -0
valuesets/enums/data_science/text_classification.py +97 -0
valuesets/enums/demographics.py +206 -0
valuesets/enums/ecological_interactions.py +151 -0
valuesets/enums/energy/__init__.py +1 -0
valuesets/enums/energy/energy.py +343 -0
valuesets/enums/energy/fossil_fuels.py +29 -0
valuesets/enums/energy/nuclear/__init__.py +1 -0
valuesets/enums/energy/nuclear/nuclear_facilities.py +195 -0
valuesets/enums/energy/nuclear/nuclear_fuel_cycle.py +96 -0
valuesets/enums/energy/nuclear/nuclear_fuels.py +175 -0
valuesets/enums/energy/nuclear/nuclear_operations.py +191 -0
valuesets/enums/energy/nuclear/nuclear_regulatory.py +188 -0
valuesets/enums/energy/nuclear/nuclear_safety.py +164 -0
valuesets/enums/energy/nuclear/nuclear_waste.py +158 -0
valuesets/enums/energy/nuclear/reactor_types.py +163 -0
valuesets/enums/environmental_health/__init__.py +1 -0
valuesets/enums/environmental_health/exposures.py +265 -0
valuesets/enums/geography/__init__.py +1 -0
valuesets/enums/geography/geographic_codes.py +741 -0
valuesets/enums/health/__init__.py +12 -0
valuesets/enums/health/vaccination.py +98 -0
valuesets/enums/health.py +36 -0
valuesets/enums/health_base.py +36 -0
valuesets/enums/healthcare.py +45 -0
valuesets/enums/industry/__init__.py +1 -0
valuesets/enums/industry/extractive_industry.py +94 -0
valuesets/enums/industry/mining.py +388 -0
valuesets/enums/industry/safety_colors.py +201 -0
valuesets/enums/investigation.py +27 -0
valuesets/enums/materials_science/__init__.py +1 -0
valuesets/enums/materials_science/characterization_methods.py +112 -0
valuesets/enums/materials_science/crystal_structures.py +76 -0
valuesets/enums/materials_science/material_properties.py +119 -0
valuesets/enums/materials_science/material_types.py +104 -0
valuesets/enums/materials_science/pigments_dyes.py +198 -0
valuesets/enums/materials_science/synthesis_methods.py +109 -0
valuesets/enums/medical/__init__.py +1 -0
valuesets/enums/medical/clinical.py +277 -0
valuesets/enums/medical/neuroimaging.py +119 -0
valuesets/enums/mining_processing.py +302 -0
valuesets/enums/physics/__init__.py +1 -0
valuesets/enums/physics/states_of_matter.py +46 -0
valuesets/enums/social/__init__.py +1 -0
valuesets/enums/social/person_status.py +29 -0
valuesets/enums/spatial/__init__.py +1 -0
valuesets/enums/spatial/spatial_qualifiers.py +246 -0
valuesets/enums/statistics/__init__.py +5 -0
valuesets/enums/statistics/prediction_outcomes.py +31 -0
valuesets/enums/statistics.py +31 -0
valuesets/enums/time/__init__.py +1 -0
valuesets/enums/time/temporal.py +254 -0
valuesets/enums/units/__init__.py +1 -0
valuesets/enums/units/measurements.py +310 -0
valuesets/enums/visual/__init__.py +1 -0
valuesets/enums/visual/colors.py +376 -0
valuesets/generators/__init__.py +19 -0
valuesets/generators/auto_slot_injector.py +280 -0
valuesets/generators/enhanced_pydantic_generator.py +100 -0
valuesets/generators/enum_slot_generator.py +201 -0
valuesets/generators/modular_rich_generator.py +353 -0
valuesets/generators/prefix_standardizer.py +198 -0
valuesets/generators/rich_enum.py +127 -0
valuesets/generators/rich_pydantic_generator.py +310 -0
valuesets/generators/smart_slot_syncer.py +428 -0
valuesets/generators/sssom_generator.py +394 -0
valuesets/merged/merged_hierarchy.yaml +21649 -0
valuesets/schema/README.md +3 -0
valuesets/schema/academic/research.yaml +911 -0
valuesets/schema/analytical_chemistry/mass_spectrometry.yaml +206 -0
valuesets/schema/bio/bio_entities.yaml +364 -0
valuesets/schema/bio/biological_colors.yaml +434 -0
valuesets/schema/bio/cell_cycle.yaml +309 -0
valuesets/schema/bio/currency_chemicals.yaml +70 -0
valuesets/schema/bio/developmental_stages.yaml +226 -0
valuesets/schema/bio/genome_features.yaml +342 -0
valuesets/schema/bio/genomics.yaml +101 -0
valuesets/schema/bio/go_aspect.yaml +39 -0
valuesets/schema/bio/go_causality.yaml +119 -0
valuesets/schema/bio/go_evidence.yaml +215 -0
valuesets/schema/bio/insdc_geographic_locations.yaml +911 -0
valuesets/schema/bio/insdc_missing_values.yaml +85 -0
valuesets/schema/bio/lipid_categories.yaml +72 -0
valuesets/schema/bio/plant_biology.yaml +125 -0
valuesets/schema/bio/plant_developmental_stages.yaml +77 -0
valuesets/schema/bio/plant_sex.yaml +108 -0
valuesets/schema/bio/protein_evidence.yaml +63 -0
valuesets/schema/bio/proteomics_standards.yaml +116 -0
valuesets/schema/bio/psi_mi.yaml +400 -0
valuesets/schema/bio/relationship_to_oxygen.yaml +46 -0
valuesets/schema/bio/sequence_alphabets.yaml +1168 -0
valuesets/schema/bio/sequence_chemistry.yaml +477 -0
valuesets/schema/bio/sequencing_platforms.yaml +515 -0
valuesets/schema/bio/structural_biology.yaml +428 -0
valuesets/schema/bio/taxonomy.yaml +453 -0
valuesets/schema/bio/trophic_levels.yaml +118 -0
valuesets/schema/bio/uniprot_species.yaml +1209 -0
valuesets/schema/bio/viral_genome_types.yaml +99 -0
valuesets/schema/bioprocessing/scale_up.yaml +458 -0
valuesets/schema/business/human_resources.yaml +752 -0
valuesets/schema/business/industry_classifications.yaml +448 -0
valuesets/schema/business/management_operations.yaml +602 -0
valuesets/schema/business/organizational_structures.yaml +645 -0
valuesets/schema/business/quality_management.yaml +502 -0
valuesets/schema/business/supply_chain.yaml +688 -0
valuesets/schema/chemistry/chemical_entities.yaml +639 -0
valuesets/schema/chemistry/reaction_directionality.yaml +60 -0
valuesets/schema/chemistry/reactions.yaml +442 -0
valuesets/schema/clinical/nih_demographics.yaml +285 -0
valuesets/schema/clinical/phenopackets.yaml +429 -0
valuesets/schema/computing/file_formats.yaml +631 -0
valuesets/schema/computing/maturity_levels.yaml +229 -0
valuesets/schema/computing/mime_types.yaml +266 -0
valuesets/schema/confidence_levels.yaml +206 -0
valuesets/schema/contributor.yaml +30 -0
valuesets/schema/core.yaml +55 -0
valuesets/schema/data/data_absent_reason.yaml +82 -0
valuesets/schema/data_science/binary_classification.yaml +125 -0
valuesets/schema/data_science/emotion_classification.yaml +109 -0
valuesets/schema/data_science/priority_severity.yaml +122 -0
valuesets/schema/data_science/quality_control.yaml +68 -0
valuesets/schema/data_science/sentiment_analysis.yaml +81 -0
valuesets/schema/data_science/text_classification.yaml +135 -0
valuesets/schema/demographics.yaml +238 -0
valuesets/schema/ecological_interactions.yaml +298 -0
valuesets/schema/energy/energy.yaml +595 -0
valuesets/schema/energy/fossil_fuels.yaml +28 -0
valuesets/schema/energy/nuclear/nuclear_facilities.yaml +463 -0
valuesets/schema/energy/nuclear/nuclear_fuel_cycle.yaml +82 -0
valuesets/schema/energy/nuclear/nuclear_fuels.yaml +421 -0
valuesets/schema/energy/nuclear/nuclear_operations.yaml +480 -0
valuesets/schema/energy/nuclear/nuclear_regulatory.yaml +200 -0
valuesets/schema/energy/nuclear/nuclear_safety.yaml +352 -0
valuesets/schema/energy/nuclear/nuclear_waste.yaml +332 -0
valuesets/schema/energy/nuclear/reactor_types.yaml +394 -0
valuesets/schema/environmental_health/exposures.yaml +355 -0
valuesets/schema/generated_slots.yaml +1828 -0
valuesets/schema/geography/geographic_codes.yaml +1018 -0
valuesets/schema/health/vaccination.yaml +102 -0
valuesets/schema/health.yaml +38 -0
valuesets/schema/healthcare.yaml +53 -0
valuesets/schema/industry/extractive_industry.yaml +89 -0
valuesets/schema/industry/mining.yaml +888 -0
valuesets/schema/industry/safety_colors.yaml +375 -0
valuesets/schema/investigation.yaml +64 -0
valuesets/schema/materials_science/characterization_methods.yaml +193 -0
valuesets/schema/materials_science/crystal_structures.yaml +138 -0
valuesets/schema/materials_science/material_properties.yaml +135 -0
valuesets/schema/materials_science/material_types.yaml +151 -0
valuesets/schema/materials_science/pigments_dyes.yaml +465 -0
valuesets/schema/materials_science/synthesis_methods.yaml +186 -0
valuesets/schema/medical/clinical.yaml +610 -0
valuesets/schema/medical/neuroimaging.yaml +325 -0
valuesets/schema/mining_processing.yaml +295 -0
valuesets/schema/physics/states_of_matter.yaml +46 -0
valuesets/schema/slot_mixins.yaml +143 -0
valuesets/schema/social/person_status.yaml +28 -0
valuesets/schema/spatial/spatial_qualifiers.yaml +466 -0
valuesets/schema/statistics/prediction_outcomes.yaml +26 -0
valuesets/schema/statistics.yaml +34 -0
valuesets/schema/time/temporal.yaml +435 -0
valuesets/schema/types.yaml +15 -0
valuesets/schema/units/measurements.yaml +675 -0
valuesets/schema/valuesets.yaml +100 -0
valuesets/schema/visual/colors.yaml +778 -0
valuesets/utils/__init__.py +6 -0
valuesets/utils/comparison.py +102 -0
valuesets/utils/expand_dynamic_enums.py +414 -0
valuesets/utils/mapping_utils.py +236 -0
valuesets/validators/__init__.py +11 -0
valuesets/validators/enum_evaluator.py +669 -0
valuesets/validators/oak_config.yaml +70 -0
valuesets/validators/validate_with_ols.py +241 -0
valuesets-0.3.1.dist-info/METADATA +395 -0
valuesets-0.3.1.dist-info/RECORD +248 -0
valuesets-0.3.1.dist-info/WHEEL +4 -0
valuesets-0.3.1.dist-info/licenses/LICENSE +201 -0

valuesets/schema/bio/taxonomy.yaml ADDED Viewed

@@ -0,0 +1,453 @@
+name: taxonomy
+title: Taxonomic Classifications
+description: Value sets for taxonomic classifications and model organisms
+id: https://w3id.org/linkml/valuesets/bio/taxonomy
+imports:
+- linkml:types
+prefixes:
+  valuesets: https://w3id.org/valuesets/
+  NCBITaxon: http://purl.obolibrary.org/obo/NCBITaxon_
+  TAXRANK: http://purl.obolibrary.org/obo/TAXRANK_
+default_prefix: valuesets
+slots:
+  organism_taxon:
+    description: The organism taxon classification
+    range: OrganismTaxonEnum
+  common_organism_taxa:
+    description: Common model organisms used in biological research, mapped to NCBI Taxonomy IDs
+    range: CommonOrganismTaxaEnum
+  taxonomic_rank:
+    description: Standard taxonomic ranks used in biological classification
+    range: TaxonomicRank
+  biological_kingdom:
+    description: Major kingdoms/domains of life
+    range: BiologicalKingdom
+enums:
+  OrganismTaxonEnum:
+    reachable_from:
+      source_nodes:
+      - NCBITaxon:1
+      is_direct: false
+      relationship_types:
+      - rdfs:subClassOf
+  CommonOrganismTaxaEnum:
+    description: Common model organisms used in biological research, mapped to NCBI Taxonomy IDs
+    permissible_values:
+      BACTERIA:
+        description: Bacteria domain
+        meaning: NCBITaxon:2
+        instantiates:
+        - taxon:Domain
+      ARCHAEA:
+        description: Archaea domain
+        meaning: NCBITaxon:2157
+      EUKARYOTA:
+        description: Eukaryota domain
+        meaning: NCBITaxon:2759
+      VIRUSES:
+        description: Viruses (not a true domain)
+        meaning: NCBITaxon:10239
+      VERTEBRATA:
+        title: Vertebrata <vertebrates>
+        description: Vertebrates
+        meaning: NCBITaxon:7742
+        is_a: EUKARYOTA
+      MAMMALIA:
+        description: Mammals
+        meaning: NCBITaxon:40674
+        is_a: VERTEBRATA
+      PRIMATES:
+        description: Primates
+        meaning: NCBITaxon:9443
+        is_a: MAMMALIA
+      RODENTIA:
+        description: Rodents
+        meaning: NCBITaxon:9989
+        is_a: MAMMALIA
+      CARNIVORA:
+        description: Carnivores
+        meaning: NCBITaxon:33554
+        is_a: MAMMALIA
+      ARTIODACTYLA:
+        description: Even-toed ungulates
+        meaning: NCBITaxon:91561
+        is_a: MAMMALIA
+      AVES:
+        description: Birds
+        meaning: NCBITaxon:8782
+        is_a: VERTEBRATA
+      ACTINOPTERYGII:
+        description: Ray-finned fishes
+        meaning: NCBITaxon:7898
+        is_a: VERTEBRATA
+      AMPHIBIA:
+        description: Amphibians
+        meaning: NCBITaxon:8292
+        is_a: VERTEBRATA
+      ARTHROPODA:
+        description: Arthropods
+        meaning: NCBITaxon:6656
+        is_a: EUKARYOTA
+      INSECTA:
+        description: Insects
+        meaning: NCBITaxon:50557
+        is_a: ARTHROPODA
+      NEMATODA:
+        description: Roundworms
+        meaning: NCBITaxon:6231
+        is_a: EUKARYOTA
+      FUNGI:
+        description: Fungal kingdom
+        meaning: NCBITaxon:4751
+        is_a: EUKARYOTA
+      ASCOMYCOTA:
+        description: Sac fungi
+        meaning: NCBITaxon:4890
+        is_a: FUNGI
+      VIRIDIPLANTAE:
+        description: Green plants
+        meaning: NCBITaxon:33090
+        is_a: EUKARYOTA
+      MAGNOLIOPHYTA:
+        title: Magnoliopsida
+        description: Flowering plants
+        meaning: NCBITaxon:3398
+        is_a: VIRIDIPLANTAE
+      PROTEOBACTERIA:
+        title: Pseudomonadota
+        description: Proteobacteria
+        meaning: NCBITaxon:1224
+        is_a: BACTERIA
+      GAMMAPROTEOBACTERIA:
+        description: Gamma proteobacteria
+        meaning: NCBITaxon:1236
+        is_a: PROTEOBACTERIA
+      FIRMICUTES:
+        title: Bacillota
+        description: Firmicutes (Gram-positive bacteria)
+        meaning: NCBITaxon:1239
+        is_a: BACTERIA
+      ACTINOBACTERIA:
+        title: Actinomycetota
+        description: Actinobacteria
+        meaning: NCBITaxon:201174
+        is_a: BACTERIA
+      EURYARCHAEOTA:
+        title: Methanobacteriota
+        description: Euryarchaeota
+        meaning: NCBITaxon:28890
+        is_a: ARCHAEA
+      APICOMPLEXA:
+        description: Apicomplexan parasites
+        meaning: NCBITaxon:5794
+        is_a: EUKARYOTA
+      HUMAN:
+        title: Homo sapiens
+        description: Homo sapiens (human)
+        meaning: NCBITaxon:9606
+        is_a: PRIMATES
+      MOUSE:
+        title: Mus musculus
+        description: Mus musculus (house mouse)
+        meaning: NCBITaxon:10090
+        is_a: RODENTIA
+      RAT:
+        title: Rattus norvegicus
+        description: Rattus norvegicus (Norway rat)
+        meaning: NCBITaxon:10116
+        is_a: RODENTIA
+      RHESUS:
+        title: Macaca mulatta
+        description: Macaca mulatta (rhesus macaque)
+        meaning: NCBITaxon:9544
+        is_a: PRIMATES
+      CHIMP:
+        title: Pan troglodytes
+        description: Pan troglodytes (chimpanzee)
+        meaning: NCBITaxon:9598
+        is_a: PRIMATES
+      DOG:
+        title: Canis lupus familiaris
+        description: Canis lupus familiaris (dog)
+        meaning: NCBITaxon:9615
+        is_a: CARNIVORA
+      COW:
+        title: Bos taurus
+        description: Bos taurus (cattle)
+        meaning: NCBITaxon:9913
+        is_a: ARTIODACTYLA
+      PIG:
+        title: Sus scrofa
+        description: Sus scrofa (pig)
+        meaning: NCBITaxon:9823
+        is_a: ARTIODACTYLA
+      CHICKEN:
+        title: Gallus gallus
+        description: Gallus gallus (chicken)
+        meaning: NCBITaxon:9031
+        is_a: AVES
+      ZEBRAFISH:
+        title: Danio rerio
+        description: Danio rerio (zebrafish)
+        meaning: NCBITaxon:7955
+        is_a: ACTINOPTERYGII
+      MEDAKA:
+        title: Oryzias latipes
+        description: Oryzias latipes (Japanese medaka)
+        meaning: NCBITaxon:8090
+        is_a: ACTINOPTERYGII
+      PUFFERFISH:
+        title: Takifugu rubripes
+        description: Takifugu rubripes (torafugu)
+        meaning: NCBITaxon:31033
+        is_a: ACTINOPTERYGII
+      XENOPUS_TROPICALIS:
+        description: Xenopus tropicalis (western clawed frog)
+        meaning: NCBITaxon:8364
+        is_a: AMPHIBIA
+      XENOPUS_LAEVIS:
+        description: Xenopus laevis (African clawed frog)
+        meaning: NCBITaxon:8355
+        is_a: AMPHIBIA
+      DROSOPHILA:
+        title: Drosophila melanogaster
+        description: Drosophila melanogaster (fruit fly)
+        meaning: NCBITaxon:7227
+        is_a: INSECTA
+      C_ELEGANS:
+        title: Caenorhabditis elegans
+        description: Caenorhabditis elegans (roundworm)
+        meaning: NCBITaxon:6239
+        is_a: NEMATODA
+      S_CEREVISIAE:
+        title: Saccharomyces cerevisiae
+        description: Saccharomyces cerevisiae (baker's yeast)
+        meaning: NCBITaxon:4932
+        is_a: ASCOMYCOTA
+      S_CEREVISIAE_S288C:
+        title: Saccharomyces cerevisiae S288C
+        description: Saccharomyces cerevisiae S288C (reference strain)
+        meaning: NCBITaxon:559292
+        is_a: S_CEREVISIAE
+      S_POMBE:
+        title: Schizosaccharomyces pombe
+        description: Schizosaccharomyces pombe (fission yeast)
+        meaning: NCBITaxon:4896
+        is_a: ASCOMYCOTA
+      C_ALBICANS:
+        title: Candida albicans
+        description: Candida albicans (pathogenic yeast)
+        meaning: NCBITaxon:5476
+        is_a: ASCOMYCOTA
+      A_NIDULANS:
+        title: Aspergillus nidulans
+        description: Aspergillus nidulans (filamentous fungus)
+        meaning: NCBITaxon:162425
+        is_a: ASCOMYCOTA
+      N_CRASSA:
+        title: Neurospora crassa
+        description: Neurospora crassa (red bread mold)
+        meaning: NCBITaxon:5141
+        is_a: ASCOMYCOTA
+      ARABIDOPSIS:
+        title: Arabidopsis thaliana
+        description: Arabidopsis thaliana (thale cress)
+        meaning: NCBITaxon:3702
+        is_a: MAGNOLIOPHYTA
+      RICE:
+        title: Oryza sativa
+        description: Oryza sativa (rice)
+        meaning: NCBITaxon:4530
+        is_a: MAGNOLIOPHYTA
+      MAIZE:
+        title: Zea mays
+        description: Zea mays (corn)
+        meaning: NCBITaxon:4577
+        is_a: MAGNOLIOPHYTA
+      TOMATO:
+        title: Solanum lycopersicum
+        description: Solanum lycopersicum (tomato)
+        meaning: NCBITaxon:4081
+        is_a: MAGNOLIOPHYTA
+      TOBACCO:
+        title: Nicotiana tabacum
+        description: Nicotiana tabacum (tobacco)
+        meaning: NCBITaxon:4097
+        is_a: MAGNOLIOPHYTA
+      E_COLI:
+        title: Escherichia coli
+        description: Escherichia coli
+        meaning: NCBITaxon:562
+        is_a: GAMMAPROTEOBACTERIA
+      E_COLI_K12:
+        title: Escherichia coli K-12
+        description: Escherichia coli str. K-12
+        meaning: NCBITaxon:83333
+        is_a: E_COLI
+      B_SUBTILIS:
+        title: Bacillus subtilis
+        description: Bacillus subtilis
+        meaning: NCBITaxon:1423
+        is_a: FIRMICUTES
+      M_TUBERCULOSIS:
+        title: Mycobacterium tuberculosis
+        description: Mycobacterium tuberculosis
+        meaning: NCBITaxon:1773
+        is_a: ACTINOBACTERIA
+      P_AERUGINOSA:
+        title: Pseudomonas aeruginosa
+        description: Pseudomonas aeruginosa
+        meaning: NCBITaxon:287
+        is_a: GAMMAPROTEOBACTERIA
+      S_AUREUS:
+        title: Staphylococcus aureus
+        description: Staphylococcus aureus
+        meaning: NCBITaxon:1280
+        is_a: FIRMICUTES
+      S_PNEUMONIAE:
+        title: Streptococcus pneumoniae
+        description: Streptococcus pneumoniae
+        meaning: NCBITaxon:1313
+        is_a: FIRMICUTES
+      H_PYLORI:
+        title: Helicobacter pylori
+        description: Helicobacter pylori
+        meaning: NCBITaxon:210
+        is_a: PROTEOBACTERIA
+      M_JANNASCHII:
+        title: Methanocaldococcus jannaschii
+        description: Methanocaldococcus jannaschii
+        meaning: NCBITaxon:2190
+        is_a: EURYARCHAEOTA
+      H_SALINARUM:
+        title: Halobacterium salinarum
+        description: Halobacterium salinarum
+        meaning: NCBITaxon:2242
+        is_a: EURYARCHAEOTA
+      P_FALCIPARUM:
+        title: Plasmodium falciparum
+        description: Plasmodium falciparum (malaria parasite)
+        meaning: NCBITaxon:5833
+        is_a: APICOMPLEXA
+      T_GONDII:
+        title: Toxoplasma gondii
+        description: Toxoplasma gondii
+        meaning: NCBITaxon:5811
+        is_a: APICOMPLEXA
+      T_BRUCEI:
+        title: Trypanosoma brucei
+        description: Trypanosoma brucei
+        meaning: NCBITaxon:5691
+        is_a: EUKARYOTA
+      DICTYOSTELIUM:
+        title: Dictyostelium discoideum
+        description: Dictyostelium discoideum (slime mold)
+        meaning: NCBITaxon:44689
+        is_a: EUKARYOTA
+      TETRAHYMENA:
+        title: Tetrahymena thermophila
+        description: Tetrahymena thermophila
+        meaning: NCBITaxon:5911
+        is_a: EUKARYOTA
+      PARAMECIUM:
+        title: Paramecium tetraurelia
+        description: Paramecium tetraurelia
+        meaning: NCBITaxon:5888
+        is_a: EUKARYOTA
+      CHLAMYDOMONAS:
+        title: Chlamydomonas reinhardtii
+        description: Chlamydomonas reinhardtii (green alga)
+        meaning: NCBITaxon:3055
+        is_a: VIRIDIPLANTAE
+      PHAGE_LAMBDA:
+        title: Lambdavirus lambda
+        description: Escherichia phage lambda
+        meaning: NCBITaxon:10710
+        is_a: VIRUSES
+      HIV1:
+        title: Human immunodeficiency virus 1
+        description: Human immunodeficiency virus 1
+        meaning: NCBITaxon:11676
+        is_a: VIRUSES
+      INFLUENZA_A:
+        title: Influenza A virus
+        description: Influenza A virus
+        meaning: NCBITaxon:11320
+        is_a: VIRUSES
+      SARS_COV_2:
+        title: Severe acute respiratory syndrome coronavirus 2
+        description: Severe acute respiratory syndrome coronavirus 2
+        meaning: NCBITaxon:2697049
+        is_a: VIRUSES
+  TaxonomicRank:
+    description: Standard taxonomic ranks used in biological classification
+    permissible_values:
+      DOMAIN:
+        description: Domain (highest rank)
+        meaning: TAXRANK:0000037
+      KINGDOM:
+        description: Kingdom
+        meaning: TAXRANK:0000017
+      PHYLUM:
+        description: Phylum (animals, plants, fungi) or Division (plants)
+        meaning: TAXRANK:0000001
+      CLASS:
+        description: Class
+        meaning: TAXRANK:0000002
+      ORDER:
+        description: Order
+        meaning: TAXRANK:0000003
+      FAMILY:
+        description: Family
+        meaning: TAXRANK:0000004
+      GENUS:
+        description: Genus
+        meaning: TAXRANK:0000005
+      SPECIES:
+        description: Species
+        meaning: TAXRANK:0000006
+      SUBSPECIES:
+        description: Subspecies
+        meaning: TAXRANK:0000023
+      STRAIN:
+        description: Strain (especially for microorganisms)
+        meaning: TAXRANK:0001001
+      VARIETY:
+        title: varietas
+        description: Variety (mainly plants)
+        meaning: TAXRANK:0000016
+      FORM:
+        title: forma
+        description: Form (mainly plants)
+        meaning: TAXRANK:0000026
+      CULTIVAR:
+        description: Cultivar (cultivated variety)
+        meaning: TAXRANK:0000034
+  BiologicalKingdom:
+    description: Major kingdoms/domains of life
+    permissible_values:
+      BACTERIA:
+        description: Bacteria domain
+        meaning: NCBITaxon:2
+      ARCHAEA:
+        description: Archaea domain
+        meaning: NCBITaxon:2157
+      EUKARYOTA:
+        description: Eukaryota domain
+        meaning: NCBITaxon:2759
+      ANIMALIA:
+        title: Metazoa
+        description: Animal kingdom
+        meaning: NCBITaxon:33208
+      PLANTAE:
+        title: Viridiplantae
+        description: Plant kingdom (Viridiplantae)
+        meaning: NCBITaxon:33090
+      FUNGI:
+        description: Fungal kingdom
+        meaning: NCBITaxon:4751
+      PROTISTA:
+        description: Protist kingdom (polyphyletic group)
+      VIRUSES:
+        description: Viruses (not a true kingdom)
+        meaning: NCBITaxon:10239

valuesets/schema/bio/trophic_levels.yaml ADDED Viewed

@@ -0,0 +1,118 @@
+name: trophic_levels
+id: https://w3id.org/linkml/valuesets/bio/trophic_levels
+prefixes:
+  ECOCORE: http://purl.obolibrary.org/obo/ECOCORE_
+  MICRO: http://purl.obolibrary.org/obo/MICRO_
+  BTO: http://purl.obolibrary.org/obo/BTO_
+  mixs: https://genomicsstandardsconsortium.github.io/mixs/
+  valuesets: https://w3id.org/valuesets/
+default_prefix: valuesets
+slots:
+  trophic_level:
+    description: Trophic levels are the feeding position in a food chain
+    range: TrophicLevelEnum
+enums:
+  TrophicLevelEnum:
+    description: Trophic levels are the feeding position in a food chain
+    permissible_values:
+      AUTOTROPH:
+        description: Organism capable of synthesizing its own food from inorganic substances
+        meaning: ECOCORE:00000023
+        title: autotroph
+      CARBOXYDOTROPH:
+        description: Organism that uses carbon monoxide as a source of carbon and energy
+        title: carboxydotroph
+      CHEMOAUTOLITHOTROPH:
+        description: Autotroph that obtains energy from inorganic compounds
+        title: chemoautolithotroph
+      CHEMOAUTOTROPH:
+        description: Organism that obtains energy by oxidizing inorganic compounds
+        meaning: ECOCORE:00000129
+        title: chemoautotroph
+      CHEMOHETEROTROPH:
+        description: Organism that obtains energy from organic compounds
+        meaning: ECOCORE:00000132
+        title: chemoheterotroph
+      CHEMOLITHOAUTOTROPH:
+        description: Organism that uses inorganic compounds as electron donors
+        title: chemolithoautotroph
+      CHEMOLITHOTROPH:
+        description: Organism that obtains energy from oxidation of inorganic compounds
+        title: chemolithotroph
+      CHEMOORGANOHETEROTROPH:
+        description: Organism that uses organic compounds as both carbon and energy source
+        title: chemoorganoheterotroph
+      CHEMOORGANOTROPH:
+        description: Organism that obtains energy from organic compounds
+        meaning: ECOCORE:00000133
+        title: chemoorganotroph
+      CHEMOSYNTHETIC:
+        description: Relating to organisms that produce organic matter through chemosynthesis
+        title: chemosynthetic
+      CHEMOTROPH:
+        description: Organism that obtains energy from chemical compounds
+        title: chemotroph
+      COPIOTROPH:
+        description: Organism that thrives in nutrient-rich environments
+        title: copiotroph
+      DIAZOTROPH:
+        description: Organism capable of fixing atmospheric nitrogen
+        title: diazotroph
+      FACULTATIVE:
+        description: Organism that can switch between different metabolic modes
+        title: facultative
+      HETEROTROPH:
+        description: Organism that obtains carbon from organic compounds
+        meaning: ECOCORE:00000010
+        title: heterotroph
+      LITHOAUTOTROPH:
+        description: Autotroph that uses inorganic compounds as electron donors
+        title: lithoautotroph
+      LITHOHETEROTROPH:
+        description: Heterotroph that uses inorganic compounds as electron donors
+        title: lithoheterotroph
+      LITHOTROPH:
+        description: Organism that uses inorganic substrates as electron donors
+        title: lithotroph
+      METHANOTROPH:
+        description: Organism that uses methane as carbon and energy source
+        title: methanotroph
+      METHYLOTROPH:
+        description: Organism that uses single-carbon compounds
+        title: methylotroph
+      MIXOTROPH:
+        description: Organism that can use both autotrophic and heterotrophic methods
+        title: mixotroph
+      OBLIGATE:
+        description: Organism restricted to a particular metabolic mode
+        title: obligate
+      OLIGOTROPH:
+        description: Organism that thrives in nutrient-poor environments
+        meaning: ECOCORE:00000138
+        title: oligotroph
+      ORGANOHETEROTROPH:
+        description: Organism that uses organic compounds as carbon source
+        title: organoheterotroph
+      ORGANOTROPH:
+        description: Organism that uses organic compounds as electron donors
+        title: organotroph
+      PHOTOAUTOTROPH:
+        description: Organism that uses light energy to synthesize organic compounds
+        meaning: ECOCORE:00000130
+        title: photoautotroph
+      PHOTOHETEROTROPH:
+        description: Organism that uses light for energy but organic compounds for carbon
+        meaning: ECOCORE:00000131
+        title: photoheterotroph
+      PHOTOLITHOAUTOTROPH:
+        description: Photoautotroph that uses inorganic electron donors
+        title: photolithoautotroph
+      PHOTOLITHOTROPH:
+        description: Organism that uses light energy and inorganic electron donors
+        title: photolithotroph
+      PHOTOSYNTHETIC:
+        description: Relating to organisms that produce organic matter through photosynthesis
+        title: photosynthetic
+      PHOTOTROPH:
+        description: Organism that obtains energy from light
+        title: phototroph