From 022e4b3948f33fe9cb1f5605f4f73f46012a2f68 Mon Sep 17 00:00:00 2001 From: dragon-ai-agent Date: Fri, 30 Jan 2026 18:29:22 -0800 Subject: [PATCH 1/3] Fix schema IDs to use https://w3id.org/valuesets Change all schema id: fields from https://w3id.org/linkml/valuesets to https://w3id.org/valuesets to match the registered w3id prefix. Co-Authored-By: Claude Opus 4.5 --- docs/schema/valuesets.yaml | 1310 ++++++++--------- docs/slides/valuesets-slides.pdf | Bin 1269062 -> 1269056 bytes docs/slides/valuesets-slides.pptx | Bin 7438126 -> 7438126 bytes project/jsonschema/valuesets.schema.json | 2 +- src/valuesets/datamodel/valuesets.py | 2 +- src/valuesets/datamodel/valuesets_pydantic.py | 2 +- .../schema/academic/organizations.yaml | 2 +- src/valuesets/schema/academic/research.yaml | 2 +- src/valuesets/schema/bio/bgc_categories.yaml | 2 +- src/valuesets/schema/bio/bio_entities.yaml | 2 +- src/valuesets/schema/bio/biosafety.yaml | 2 +- src/valuesets/schema/bio/cell_cycle.yaml | 2 +- src/valuesets/schema/bio/genome_features.yaml | 2 +- src/valuesets/schema/bio/go_aspect.yaml | 2 +- src/valuesets/schema/bio/go_evidence.yaml | 2 +- .../bio/insdc_geographic_locations.yaml | 2 +- .../schema/bio/insdc_missing_values.yaml | 2 +- src/valuesets/schema/bio/plant_biology.yaml | 2 +- .../bio/plant_experimental_conditions.yaml | 2 +- src/valuesets/schema/bio/plant_sex.yaml | 2 +- .../schema/bio/relationship_to_oxygen.yaml | 2 +- .../schema/bio/sequence_chemistry.yaml | 2 +- .../schema/bio/sequencing_platforms.yaml | 2 +- src/valuesets/schema/bio/taxonomy.yaml | 2 +- src/valuesets/schema/bio/trophic_levels.yaml | 2 +- .../schema/bio/viral_genome_types.yaml | 2 +- .../schema/bioprocessing/scale_up.yaml | 2 +- .../schema/business/human_resources.yaml | 2 +- .../business/industry_classifications.yaml | 2 +- .../business/management_operations.yaml | 2 +- .../business/organizational_structures.yaml | 2 +- .../schema/business/quality_management.yaml | 2 +- .../schema/business/supply_chain.yaml | 2 +- src/valuesets/schema/chemistry/roles.yaml | 2 +- src/valuesets/schema/clinical/genetics.yaml | 2 +- .../schema/clinical/nih_demographics.yaml | 2 +- .../schema/clinical/phenopackets.yaml | 2 +- .../schema/computing/geospatial_formats.yaml | 2 +- .../schema/computing/mime_types.yaml | 2 +- .../data_science/binary_classification.yaml | 2 +- .../data_science/emotion_classification.yaml | 2 +- .../data_science/priority_severity.yaml | 2 +- .../schema/data_science/quality_control.yaml | 2 +- .../data_science/sentiment_analysis.yaml | 2 +- .../data_science/text_classification.yaml | 2 +- src/valuesets/schema/energy/energy.yaml | 2 +- src/valuesets/schema/energy/fossil_fuels.yaml | 2 +- .../energy/nuclear/nuclear_facilities.yaml | 2 +- .../schema/energy/nuclear/nuclear_fuels.yaml | 2 +- .../energy/nuclear/nuclear_operations.yaml | 2 +- .../schema/energy/nuclear/nuclear_safety.yaml | 2 +- .../schema/energy/nuclear/nuclear_waste.yaml | 2 +- .../schema/energy/nuclear/reactor_types.yaml | 2 +- .../schema/energy/renewable/bioenergy.yaml | 2 +- .../schema/energy/renewable/geothermal.yaml | 2 +- .../schema/energy/renewable/hydrogen.yaml | 2 +- .../environmental_health/carcinogenicity.yaml | 2 +- .../schema/environmental_health/gb_edoh.yaml | 2 +- .../environmental_health/radionuclides.yaml | 2 +- .../schema/industry/extractive_industry.yaml | 2 +- src/valuesets/schema/industry/mining.yaml | 2 +- .../schema/lab_automation/devices.yaml | 2 +- .../schema/lab_automation/labware.yaml | 2 +- .../schema/lab_automation/operations.yaml | 2 +- .../schema/lab_automation/protocols.yaml | 2 +- .../schema/lab_automation/standards.yaml | 2 +- .../lab_automation/thermal_cycling.yaml | 2 +- .../characterization_methods.yaml | 2 +- .../materials_science/crystal_structures.yaml | 2 +- .../material_properties.yaml | 2 +- .../materials_science/material_types.yaml | 2 +- .../materials_science/synthesis_methods.yaml | 2 +- .../schema/medical/oncology/icdo.yaml | 2 +- .../diagnosis_categories.yaml | 2 +- .../medical/pediatric_oncology/iccc3.yaml | 2 +- .../staging/neuroblastoma.yaml | 2 +- src/valuesets/schema/physics/radiation.yaml | 2 +- src/valuesets/schema/provenance/evidence.yaml | 2 +- .../schema/publishing/arxiv_categories.yaml | 2 +- .../schema/publishing/osti_record.yaml | 2 +- .../schema/social/person_status.yaml | 2 +- .../schema/spatial/spatial_qualifiers.yaml | 2 +- .../statistics/prediction_outcomes.yaml | 2 +- src/valuesets/schema/time/temporal.yaml | 2 +- src/valuesets/schema/types.yaml | 2 +- src/valuesets/schema/valuesets.yaml | 2 +- 86 files changed, 738 insertions(+), 738 deletions(-) diff --git a/docs/schema/valuesets.yaml b/docs/schema/valuesets.yaml index cf0790d5..5e001866 100644 --- a/docs/schema/valuesets.yaml +++ b/docs/schema/valuesets.yaml @@ -3,7 +3,7 @@ description: A collection of commonly used value sets title: valuesets see_also: - https://linkml.github.io/valuesets -id: https://w3id.org/linkml/valuesets +id: https://w3id.org/valuesets imports: - core - contributor @@ -1323,7 +1323,7 @@ enums: computational analysis, phylogenetic inference, author statements, or electronic annotation. All codes except IEA represent manual curation. title: GO Evidence Code - from_schema: https://w3id.org/linkml/valuesets/bio/go_evidence + from_schema: https://w3id.org/valuesets/bio/go_evidence contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -1840,7 +1840,7 @@ enums: 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 + from_schema: https://w3id.org/valuesets/bio/go_evidence contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -1932,7 +1932,7 @@ enums: instantiates: - valuesets_meta:ValueSetEnumDefinition title: Organism Taxon - from_schema: https://w3id.org/linkml/valuesets/bio/taxonomy + from_schema: https://w3id.org/valuesets/bio/taxonomy contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -1951,7 +1951,7 @@ enums: 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 + from_schema: https://w3id.org/valuesets/bio/taxonomy contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -2384,7 +2384,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Standard taxonomic ranks used in biological classification title: Taxonomic Rank - from_schema: https://w3id.org/linkml/valuesets/bio/taxonomy + from_schema: https://w3id.org/valuesets/bio/taxonomy contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -2451,7 +2451,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Major kingdoms/domains of life title: Biological Kingdom - from_schema: https://w3id.org/linkml/valuesets/bio/taxonomy + from_schema: https://w3id.org/valuesets/bio/taxonomy contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -2497,7 +2497,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/bio/cell_cycle contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -2575,7 +2575,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Stages of mitosis (M phase) title: Mitotic Phase - from_schema: https://w3id.org/linkml/valuesets/bio/cell_cycle + from_schema: https://w3id.org/valuesets/bio/cell_cycle contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -2655,7 +2655,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Cell cycle checkpoints that regulate progression title: Cell Cycle Checkpoint - from_schema: https://w3id.org/linkml/valuesets/bio/cell_cycle + from_schema: https://w3id.org/valuesets/bio/cell_cycle contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -2719,7 +2719,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Phases specific to meiotic cell division title: Meiotic Phase - from_schema: https://w3id.org/linkml/valuesets/bio/cell_cycle + from_schema: https://w3id.org/valuesets/bio/cell_cycle contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -2831,7 +2831,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Types of cell cycle regulatory molecules title: Cell Cycle Regulator - from_schema: https://w3id.org/linkml/valuesets/bio/cell_cycle + from_schema: https://w3id.org/valuesets/bio/cell_cycle contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -2908,7 +2908,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Cell proliferation and growth states title: Cell Proliferation State - from_schema: https://w3id.org/linkml/valuesets/bio/cell_cycle + from_schema: https://w3id.org/valuesets/bio/cell_cycle contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -2977,7 +2977,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/bio/cell_cycle contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -3022,7 +3022,7 @@ enums: Organized hierarchically following the Sequence Ontology structure.' title: Genome Feature Type - from_schema: https://w3id.org/linkml/valuesets/bio/genome_features + from_schema: https://w3id.org/valuesets/bio/genome_features contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -3442,7 +3442,7 @@ enums: including organs, tissues, and body parts' title: Metazoan Anatomical Structure - from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + from_schema: https://w3id.org/valuesets/bio/bio_entities contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -3461,7 +3461,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/bio/bio_entities contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -3480,7 +3480,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/bio/bio_entities contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -3501,7 +3501,7 @@ enums: including native and experimentally modified cells' title: Cell Type - from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + from_schema: https://w3id.org/valuesets/bio/bio_entities contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -3520,7 +3520,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Neuron cell types from the Cell Ontology title: Neuron Type - from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + from_schema: https://w3id.org/valuesets/bio/bio_entities contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -3539,7 +3539,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/bio/bio_entities contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -3558,7 +3558,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Stem cell types and progenitor cells title: Stem Cell - from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + from_schema: https://w3id.org/valuesets/bio/bio_entities contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -3578,7 +3578,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Human diseases from the Mondo Disease Ontology title: Disease - from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + from_schema: https://w3id.org/valuesets/bio/bio_entities contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -3597,7 +3597,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Infectious diseases caused by pathogenic organisms title: Infectious Disease - from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + from_schema: https://w3id.org/valuesets/bio/bio_entities contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -3616,7 +3616,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Neoplastic and cancerous diseases title: Cancer - from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + from_schema: https://w3id.org/valuesets/bio/bio_entities contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -3636,7 +3636,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Hereditary and genetic diseases title: Genetic Disease - from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + from_schema: https://w3id.org/valuesets/bio/bio_entities contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -3656,7 +3656,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Any chemical entity from ChEBI ontology title: Chemical Entity - from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + from_schema: https://w3id.org/valuesets/bio/bio_entities contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -3675,7 +3675,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Pharmaceutical drugs and medications title: Drug - from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + from_schema: https://w3id.org/valuesets/bio/bio_entities contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -3695,7 +3695,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Metabolites and metabolic intermediates title: Metabolite - from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + from_schema: https://w3id.org/valuesets/bio/bio_entities contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -3714,7 +3714,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Proteins and protein complexes title: Protein - from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + from_schema: https://w3id.org/valuesets/bio/bio_entities contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -3733,7 +3733,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Phenotypic abnormalities from Human Phenotype Ontology title: Phenotype - from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + from_schema: https://w3id.org/valuesets/bio/bio_entities contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -3752,7 +3752,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Clinical findings and observations title: Clinical Finding - from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + from_schema: https://w3id.org/valuesets/bio/bio_entities contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -3771,7 +3771,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Biological processes from Gene Ontology title: Biological Process - from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + from_schema: https://w3id.org/valuesets/bio/bio_entities contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -3790,7 +3790,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Metabolic processes and pathways title: Metabolic Process - from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + from_schema: https://w3id.org/valuesets/bio/bio_entities contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -3809,7 +3809,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Molecular functions from Gene Ontology title: Molecular Function - from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + from_schema: https://w3id.org/valuesets/bio/bio_entities contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -3828,7 +3828,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Cellular components and locations from Gene Ontology title: Cellular Component - from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + from_schema: https://w3id.org/valuesets/bio/bio_entities contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -3847,7 +3847,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Sequence features from the Sequence Ontology title: Sequence Feature - from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + from_schema: https://w3id.org/valuesets/bio/bio_entities contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -3866,7 +3866,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Gene-related sequence features title: Gene Feature - from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + from_schema: https://w3id.org/valuesets/bio/bio_entities contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -3885,7 +3885,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Environmental systems and biomes title: Environment - from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + from_schema: https://w3id.org/valuesets/bio/bio_entities contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -3905,7 +3905,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Environmental materials and substances title: Environmental Material - from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + from_schema: https://w3id.org/valuesets/bio/bio_entities contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -3924,7 +3924,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Phenotypic qualities and attributes from PATO title: Quality - from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + from_schema: https://w3id.org/valuesets/bio/bio_entities contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -3943,7 +3943,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Physical qualities like size, shape, color title: Physical Quality - from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + from_schema: https://w3id.org/valuesets/bio/bio_entities contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -5002,7 +5002,7 @@ enums: description: Biosafety levels (BSL) defining containment requirements for biological agents title: Biosafety Level - from_schema: https://w3id.org/linkml/valuesets/bio/biosafety + from_schema: https://w3id.org/valuesets/bio/biosafety contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -5055,7 +5055,7 @@ enums: 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 + from_schema: https://w3id.org/valuesets/bio/insdc_missing_values contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -5189,7 +5189,7 @@ 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 + from_schema: https://w3id.org/valuesets/bio/insdc_geographic_locations contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -6415,7 +6415,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/bio/viral_genome_types contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -6523,7 +6523,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Plant reproductive and sexual system types title: Plant Sex - from_schema: https://w3id.org/linkml/valuesets/bio/plant_sex + from_schema: https://w3id.org/valuesets/bio/plant_sex contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -6653,7 +6653,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/bio/relationship_to_oxygen contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -6704,7 +6704,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/bio/trophic_levels contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -7242,7 +7242,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/time/temporal contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -7353,7 +7353,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Months of the year title: Month - from_schema: https://w3id.org/linkml/valuesets/time/temporal + from_schema: https://w3id.org/valuesets/time/temporal contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -7546,7 +7546,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Calendar quarters title: Quarter - from_schema: https://w3id.org/linkml/valuesets/time/temporal + from_schema: https://w3id.org/valuesets/time/temporal contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -7587,7 +7587,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Seasons of the year (Northern Hemisphere) title: Season - from_schema: https://w3id.org/linkml/valuesets/time/temporal + from_schema: https://w3id.org/valuesets/time/temporal contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -7647,7 +7647,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Common time periods and intervals title: Time Period - from_schema: https://w3id.org/linkml/valuesets/time/temporal + from_schema: https://w3id.org/valuesets/time/temporal contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -7723,7 +7723,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Common times of day title: Time Of Day - from_schema: https://w3id.org/linkml/valuesets/time/temporal + from_schema: https://w3id.org/valuesets/time/temporal contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -7785,7 +7785,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Common business and financial time frames title: Business Time Frame - from_schema: https://w3id.org/linkml/valuesets/time/temporal + from_schema: https://w3id.org/valuesets/time/temporal contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -7881,7 +7881,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Major geological eras title: Geological Era - from_schema: https://w3id.org/linkml/valuesets/time/temporal + from_schema: https://w3id.org/valuesets/time/temporal contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -7906,7 +7906,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Major historical periods title: Historical Period - from_schema: https://w3id.org/linkml/valuesets/time/temporal + from_schema: https://w3id.org/valuesets/time/temporal contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -7949,7 +7949,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Types of academic and research publications title: Publication Type - from_schema: https://w3id.org/linkml/valuesets/academic/research + from_schema: https://w3id.org/valuesets/academic/research contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -8148,7 +8148,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Status of peer review process title: Peer Review Status - from_schema: https://w3id.org/linkml/valuesets/academic/research + from_schema: https://w3id.org/valuesets/academic/research contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -8200,7 +8200,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Academic degrees and qualifications title: Academic Degree - from_schema: https://w3id.org/linkml/valuesets/academic/research + from_schema: https://w3id.org/valuesets/academic/research contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -8456,7 +8456,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Common software and content licenses title: License Type - from_schema: https://w3id.org/linkml/valuesets/academic/research + from_schema: https://w3id.org/valuesets/academic/research contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -8547,7 +8547,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Major research fields and disciplines title: Research Field - from_schema: https://w3id.org/linkml/valuesets/academic/research + from_schema: https://w3id.org/valuesets/academic/research contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -8677,7 +8677,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Types of research funding title: Funding Type - from_schema: https://w3id.org/linkml/valuesets/academic/research + from_schema: https://w3id.org/valuesets/academic/research contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -8722,7 +8722,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Sections of a scientific manuscript or publication title: Manuscript Section - from_schema: https://w3id.org/linkml/valuesets/academic/research + from_schema: https://w3id.org/valuesets/academic/research contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -9086,7 +9086,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Roles in research and authorship title: Research Role - from_schema: https://w3id.org/linkml/valuesets/academic/research + from_schema: https://w3id.org/valuesets/academic/research contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -9187,7 +9187,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Types of open access publishing title: Open Access Type - from_schema: https://w3id.org/linkml/valuesets/academic/research + from_schema: https://w3id.org/valuesets/academic/research contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -9221,7 +9221,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Common citation and reference styles title: Citation Style - from_schema: https://w3id.org/linkml/valuesets/academic/research + from_schema: https://w3id.org/valuesets/academic/research contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -9285,7 +9285,7 @@ enums: 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 + from_schema: https://w3id.org/valuesets/academic/organizations contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -9651,7 +9651,7 @@ enums: 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 + from_schema: https://w3id.org/valuesets/academic/organizations contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -9827,7 +9827,7 @@ enums: comments: - All mapped to ROR (Research Organization Registry) identifiers - Focuses on major funding institutes - from_schema: https://w3id.org/linkml/valuesets/academic/organizations + from_schema: https://w3id.org/valuesets/academic/organizations contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -10039,7 +10039,7 @@ enums: 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 + from_schema: https://w3id.org/valuesets/academic/organizations contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -10128,7 +10128,7 @@ enums: 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 + from_schema: https://w3id.org/valuesets/academic/organizations contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -10219,7 +10219,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Types of energy sources and generation methods title: Energy Source - from_schema: https://w3id.org/linkml/valuesets/energy/energy + from_schema: https://w3id.org/valuesets/energy/energy contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -10569,7 +10569,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Units for measuring energy title: Energy Unit - from_schema: https://w3id.org/linkml/valuesets/energy/energy + from_schema: https://w3id.org/valuesets/energy/energy contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -10805,7 +10805,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Units for measuring power (energy per time) title: Power Unit - from_schema: https://w3id.org/linkml/valuesets/energy/energy + from_schema: https://w3id.org/valuesets/energy/energy contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -10915,7 +10915,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Energy efficiency ratings and standards title: Energy Efficiency Rating - from_schema: https://w3id.org/linkml/valuesets/energy/energy + from_schema: https://w3id.org/valuesets/energy/energy contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -11042,7 +11042,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Building energy efficiency standards and certifications title: Building Energy Standard - from_schema: https://w3id.org/linkml/valuesets/energy/energy + from_schema: https://w3id.org/valuesets/energy/energy contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -11094,7 +11094,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Types of electrical grid systems title: Grid Type - from_schema: https://w3id.org/linkml/valuesets/energy/energy + from_schema: https://w3id.org/valuesets/energy/energy contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -11131,7 +11131,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Types of battery technologies for energy storage title: Battery Type - from_schema: https://w3id.org/linkml/valuesets/energy/energy + from_schema: https://w3id.org/valuesets/energy/energy exact_mappings: - OEO:00000068 - brick:Battery @@ -11258,7 +11258,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Types of photovoltaic cell technologies title: Photovoltaic Cell Type - from_schema: https://w3id.org/linkml/valuesets/energy/energy + from_schema: https://w3id.org/valuesets/energy/energy see_also: - OEO:00000348 contributors: @@ -11457,7 +11457,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Types of photovoltaic system installations title: Photovoltaic System Type - from_schema: https://w3id.org/linkml/valuesets/energy/energy + from_schema: https://w3id.org/valuesets/energy/energy exact_mappings: - OEO:00000324 contributors: @@ -11576,7 +11576,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Types of energy storage systems (categories) title: Energy Storage Type - from_schema: https://w3id.org/linkml/valuesets/energy/energy + from_schema: https://w3id.org/valuesets/energy/energy contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -11696,7 +11696,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Greenhouse gas emission scopes (GHG Protocol) title: Emission Scope - from_schema: https://w3id.org/linkml/valuesets/energy/energy + from_schema: https://w3id.org/valuesets/energy/energy see_also: - OEO:00000147 - OEO:00000020 @@ -11772,7 +11772,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Carbon intensity levels for energy sources title: Carbon Intensity - from_schema: https://w3id.org/linkml/valuesets/energy/energy + from_schema: https://w3id.org/valuesets/energy/energy contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -11827,7 +11827,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Types of electricity markets and pricing title: Electricity Market - from_schema: https://w3id.org/linkml/valuesets/energy/energy + from_schema: https://w3id.org/valuesets/energy/energy contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -11872,7 +11872,7 @@ enums: Applicable to energy facilities, research capabilities, and other infrastructure throughout their lifecycle. title: Capability Status - from_schema: https://w3id.org/linkml/valuesets/energy/energy + from_schema: https://w3id.org/valuesets/energy/energy see_also: - https://www.wikidata.org/wiki/Property:P5817 - https://www.iaea.org/topics/nuclear-power-plant-life-cycle @@ -11958,7 +11958,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/energy/fossil_fuels contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -11986,7 +11986,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/energy/nuclear/reactor_types contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -12297,7 +12297,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Nuclear reactor generational classifications title: Reactor Generation - from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/reactor_types + from_schema: https://w3id.org/valuesets/energy/nuclear/reactor_types contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -12392,7 +12392,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/energy/nuclear/reactor_types contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -12526,7 +12526,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/energy/nuclear/reactor_types contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -12609,7 +12609,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Neutron energy spectrum classifications title: Reactor Neutron Spectrum - from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/reactor_types + from_schema: https://w3id.org/valuesets/energy/nuclear/reactor_types contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -12661,7 +12661,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Nuclear reactor size classifications title: Reactor Size Category - from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/reactor_types + from_schema: https://w3id.org/valuesets/energy/nuclear/reactor_types contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -12735,7 +12735,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_fuels contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -12992,7 +12992,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_fuels contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -13089,7 +13089,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Physical forms of nuclear fuel title: Fuel Form - from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_fuels + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_fuels contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -13199,7 +13199,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Types of fuel assembly configurations title: Fuel Assembly Type - from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_fuels + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_fuels contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -13301,7 +13301,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_fuels contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -13420,7 +13420,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Fissile isotopes used in nuclear fuel title: Fissile Isotope - from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_fuels + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_fuels contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -13510,7 +13510,7 @@ enums: description: IAEA General Safety Requirements radioactive waste classification scheme title: IAEA Waste Classification - from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_waste + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_waste contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -13647,7 +13647,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_waste contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -13746,7 +13746,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_waste contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -13804,7 +13804,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_waste contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -13862,7 +13862,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Methods for radioactive waste disposal title: Waste Disposal Method - from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_waste + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_waste contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -13965,7 +13965,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Sources of radioactive waste generation title: Waste Source - from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_waste + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_waste contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -14090,7 +14090,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Transuranic waste classifications (US system) title: Transuranic Waste Category - from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_waste + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_waste contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -14158,7 +14158,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_safety contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -14319,7 +14319,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Nuclear emergency action levels and classifications title: Emergency Classification - from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_safety + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_safety contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -14417,7 +14417,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_safety contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -14509,7 +14509,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_safety contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -14591,7 +14591,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Fundamental nuclear reactor safety functions title: Reactor Safety Function - from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_safety + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_safety contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -14686,7 +14686,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_safety contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -14770,7 +14770,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_safety contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -14873,7 +14873,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_facilities contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -15156,7 +15156,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_facilities contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -15281,7 +15281,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Types of research reactors title: Research Reactor Type - from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_facilities + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_facilities contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -15392,7 +15392,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_facilities contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -15531,7 +15531,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_facilities contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -15670,7 +15670,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Types of nuclear-powered vessels title: Nuclear Ship Type - from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_facilities + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_facilities contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -15785,7 +15785,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Operational states of nuclear reactors title: Reactor Operating State - from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_operations + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_operations contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -16002,7 +16002,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Types of nuclear facility maintenance activities title: Maintenance Type - from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_operations + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_operations contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -16151,7 +16151,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Nuclear facility licensing stages title: Licensing Stage - from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_operations + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_operations contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -16300,7 +16300,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Nuclear fuel cycle operational activities title: Fuel Cycle Operation - from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_operations + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_operations contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -16498,7 +16498,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_operations contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -16613,7 +16613,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Standard nuclear facility operational procedures title: Operational Procedure - from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_operations + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_operations contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -16763,7 +16763,7 @@ enums: description: Types of geothermal energy systems, including conventional hydrothermal and enhanced/engineered geothermal systems. title: Geothermal System Type - from_schema: https://w3id.org/linkml/valuesets/energy/renewable/geothermal + from_schema: https://w3id.org/valuesets/energy/renewable/geothermal see_also: - https://www.energy.gov/eere/geothermal/enhanced-geothermal-systems - https://gdr.openei.org/ @@ -16852,7 +16852,7 @@ enums: description: Classification of geothermal reservoirs by geological setting and characteristics. title: Geothermal Reservoir Type - from_schema: https://w3id.org/linkml/valuesets/energy/renewable/geothermal + from_schema: https://w3id.org/valuesets/energy/renewable/geothermal contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -16905,7 +16905,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Types of wells used in geothermal energy development and production. title: Geothermal Well Type - from_schema: https://w3id.org/linkml/valuesets/energy/renewable/geothermal + from_schema: https://w3id.org/valuesets/energy/renewable/geothermal contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -16951,7 +16951,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Applications and uses of geothermal energy. title: Geothermal Application - from_schema: https://w3id.org/linkml/valuesets/energy/renewable/geothermal + from_schema: https://w3id.org/valuesets/energy/renewable/geothermal contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -17006,7 +17006,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Classification of geothermal resources by temperature range. title: Geothermal Resource Temperature Classification - from_schema: https://w3id.org/linkml/valuesets/energy/renewable/geothermal + from_schema: https://w3id.org/valuesets/energy/renewable/geothermal contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -17058,7 +17058,7 @@ enums: and carbon intensity. This informal industry taxonomy differentiates hydrogen by its carbon footprint and energy source. title: Hydrogen Type (Color Classification) - from_schema: https://w3id.org/linkml/valuesets/energy/renewable/hydrogen + from_schema: https://w3id.org/valuesets/energy/renewable/hydrogen see_also: - https://www.energy.gov/eere/fuelcells/hydrogen-production - https://www.nationalgrid.com/stories/energy-explained/hydrogen-colour-spectrum @@ -17246,7 +17246,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Methods and processes for producing hydrogen. title: Hydrogen Production Method - from_schema: https://w3id.org/linkml/valuesets/energy/renewable/hydrogen + from_schema: https://w3id.org/valuesets/energy/renewable/hydrogen see_also: - https://www.energy.gov/eere/fuelcells/hydrogen-production contributors: @@ -17418,7 +17418,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Methods for storing hydrogen for later use or transport. title: Hydrogen Storage Method - from_schema: https://w3id.org/linkml/valuesets/energy/renewable/hydrogen + from_schema: https://w3id.org/valuesets/energy/renewable/hydrogen contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -17498,7 +17498,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: End-use applications for hydrogen. title: Hydrogen Application - from_schema: https://w3id.org/linkml/valuesets/energy/renewable/hydrogen + from_schema: https://w3id.org/valuesets/energy/renewable/hydrogen contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -17568,7 +17568,7 @@ enums: Includes dedicated energy crops, agricultural residues, forest residues, and waste streams. title: Biomass Feedstock Type - from_schema: https://w3id.org/linkml/valuesets/energy/renewable/bioenergy + from_schema: https://w3id.org/valuesets/energy/renewable/bioenergy see_also: - https://www.energy.gov/eere/bioenergy/feedstock-technologies - https://www.energy.gov/eere/bioenergy/biomass-resources @@ -17830,7 +17830,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Types of fuels produced from biomass feedstocks. title: Biofuel Type - from_schema: https://w3id.org/linkml/valuesets/energy/renewable/bioenergy + from_schema: https://w3id.org/valuesets/energy/renewable/bioenergy see_also: - https://www.energy.gov/eere/bioenergy/full-text-glossary contributors: @@ -17978,7 +17978,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Classification of biofuels by feedstock source and technology generation. title: Biofuel Generation - from_schema: https://w3id.org/linkml/valuesets/energy/renewable/bioenergy + from_schema: https://w3id.org/valuesets/energy/renewable/bioenergy contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -18047,7 +18047,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Processes for converting biomass feedstocks into biofuels and bioproducts. title: Bioconversion Process - from_schema: https://w3id.org/linkml/valuesets/energy/renewable/bioenergy + from_schema: https://w3id.org/valuesets/energy/renewable/bioenergy contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -18214,7 +18214,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Types of mining operations title: Mining Type - from_schema: https://w3id.org/linkml/valuesets/industry/mining + from_schema: https://w3id.org/valuesets/industry/mining contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -18395,7 +18395,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Categories of minerals and materials title: Mineral Category - from_schema: https://w3id.org/linkml/valuesets/industry/mining + from_schema: https://w3id.org/valuesets/industry/mining contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -18485,7 +18485,7 @@ enums: Based on US Geological Survey and EU critical raw materials lists.' title: Critical Mineral - from_schema: https://w3id.org/linkml/valuesets/industry/mining + from_schema: https://w3id.org/valuesets/industry/mining contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -19175,7 +19175,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Common minerals extracted through mining title: Common Mineral - from_schema: https://w3id.org/linkml/valuesets/industry/mining + from_schema: https://w3id.org/valuesets/industry/mining contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -19414,7 +19414,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Types of mining equipment title: Mining Equipment - from_schema: https://w3id.org/linkml/valuesets/industry/mining + from_schema: https://w3id.org/valuesets/industry/mining contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -19549,7 +19549,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Classification of ore grades title: Ore Grade - from_schema: https://w3id.org/linkml/valuesets/industry/mining + from_schema: https://w3id.org/valuesets/industry/mining contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -19610,7 +19610,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Phases of mining operations title: Mining Phase - from_schema: https://w3id.org/linkml/valuesets/industry/mining + from_schema: https://w3id.org/valuesets/industry/mining contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -19672,7 +19672,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Mining-related hazards and risks title: Mining Hazard - from_schema: https://w3id.org/linkml/valuesets/industry/mining + from_schema: https://w3id.org/valuesets/industry/mining contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -19767,7 +19767,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Environmental impacts of mining title: Environmental Impact - from_schema: https://w3id.org/linkml/valuesets/industry/mining + from_schema: https://w3id.org/valuesets/industry/mining contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -19839,7 +19839,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Types of extractive industry facilities title: Extractive Industry Facility Type - from_schema: https://w3id.org/linkml/valuesets/industry/extractive_industry + from_schema: https://w3id.org/valuesets/industry/extractive_industry contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -19864,7 +19864,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/industry/extractive_industry contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -19910,7 +19910,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/industry/extractive_industry contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -19939,7 +19939,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/industry/extractive_industry contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -19968,7 +19968,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Types of prediction outcomes for classification tasks title: Outcome Type - from_schema: https://w3id.org/linkml/valuesets/statistics/prediction_outcomes + from_schema: https://w3id.org/valuesets/statistics/prediction_outcomes contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -19997,7 +19997,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/social/person_status contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -21322,7 +21322,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Common MIME types for various file formats title: Mime Type - from_schema: https://w3id.org/linkml/valuesets/computing/mime_types + from_schema: https://w3id.org/valuesets/computing/mime_types contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -21595,7 +21595,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Categories of MIME types title: Mime Type Category - from_schema: https://w3id.org/linkml/valuesets/computing/mime_types + from_schema: https://w3id.org/valuesets/computing/mime_types contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -21635,7 +21635,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Character encodings for text content title: Text Charset - from_schema: https://w3id.org/linkml/valuesets/computing/mime_types + from_schema: https://w3id.org/valuesets/computing/mime_types contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -21681,7 +21681,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Compression types used with Content-Encoding title: Compression Type - from_schema: https://w3id.org/linkml/valuesets/computing/mime_types + from_schema: https://w3id.org/valuesets/computing/mime_types contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -24123,7 +24123,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/data_science/sentiment_analysis contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -24162,7 +24162,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/data_science/sentiment_analysis contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -24217,7 +24217,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Generic binary classification labels title: Binary Classification - from_schema: https://w3id.org/linkml/valuesets/data_science/binary_classification + from_schema: https://w3id.org/valuesets/data_science/binary_classification contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -24250,7 +24250,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/data_science/binary_classification contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -24284,7 +24284,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Labels for anomaly detection tasks title: Anomaly Detection - from_schema: https://w3id.org/linkml/valuesets/data_science/binary_classification + from_schema: https://w3id.org/valuesets/data_science/binary_classification contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -24316,7 +24316,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Customer churn prediction labels title: Churn Classification - from_schema: https://w3id.org/linkml/valuesets/data_science/binary_classification + from_schema: https://w3id.org/valuesets/data_science/binary_classification contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -24352,7 +24352,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Fraud detection classification labels title: Fraud Detection - from_schema: https://w3id.org/linkml/valuesets/data_science/binary_classification + from_schema: https://w3id.org/valuesets/data_science/binary_classification contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -24383,7 +24383,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Quality control classification labels title: Quality Control - from_schema: https://w3id.org/linkml/valuesets/data_science/quality_control + from_schema: https://w3id.org/valuesets/data_science/quality_control contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -24416,7 +24416,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Manufacturing defect classification title: Defect Classification - from_schema: https://w3id.org/linkml/valuesets/data_science/quality_control + from_schema: https://w3id.org/valuesets/data_science/quality_control contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -24463,7 +24463,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/data_science/emotion_classification contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -24526,7 +24526,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Extended emotion set including complex emotions title: Extended Emotion - from_schema: https://w3id.org/linkml/valuesets/data_science/emotion_classification + from_schema: https://w3id.org/valuesets/data_science/emotion_classification contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -24592,7 +24592,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/data_science/priority_severity contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -24646,7 +24646,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Severity levels for incident/bug classification title: Severity Level - from_schema: https://w3id.org/linkml/valuesets/data_science/priority_severity + from_schema: https://w3id.org/valuesets/data_science/priority_severity contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -24691,7 +24691,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Confidence levels for predictions and classifications title: Confidence Level - from_schema: https://w3id.org/linkml/valuesets/data_science/priority_severity + from_schema: https://w3id.org/valuesets/data_science/priority_severity contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -24739,7 +24739,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Common news article topic categories title: News Topic Category - from_schema: https://w3id.org/linkml/valuesets/data_science/text_classification + from_schema: https://w3id.org/valuesets/data_science/text_classification contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -24803,7 +24803,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Text toxicity classification labels title: Toxicity Classification - from_schema: https://w3id.org/linkml/valuesets/data_science/text_classification + from_schema: https://w3id.org/valuesets/data_science/text_classification contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -24858,7 +24858,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Common chatbot/NLU intent categories title: Intent Classification - from_schema: https://w3id.org/linkml/valuesets/data_science/text_classification + from_schema: https://w3id.org/valuesets/data_science/text_classification contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -24911,7 +24911,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/spatial/spatial_qualifiers contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -24996,7 +24996,7 @@ enums: 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 + from_schema: https://w3id.org/valuesets/spatial/spatial_qualifiers contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -25191,7 +25191,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Anatomical regions based on spatial position title: Anatomical Region - from_schema: https://w3id.org/linkml/valuesets/spatial/spatial_qualifiers + from_schema: https://w3id.org/valuesets/spatial/spatial_qualifiers contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -25276,7 +25276,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Anatomical axes defining spatial organization title: Anatomical Axis - from_schema: https://w3id.org/linkml/valuesets/spatial/spatial_qualifiers + from_schema: https://w3id.org/valuesets/spatial/spatial_qualifiers contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -25339,7 +25339,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Standard anatomical planes for sectioning title: Anatomical Plane - from_schema: https://w3id.org/linkml/valuesets/spatial/spatial_qualifiers + from_schema: https://w3id.org/valuesets/spatial/spatial_qualifiers contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -25418,7 +25418,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Spatial relationships between anatomical structures title: Spatial Relationship - from_schema: https://w3id.org/linkml/valuesets/spatial/spatial_qualifiers + from_schema: https://w3id.org/valuesets/spatial/spatial_qualifiers contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -25517,7 +25517,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Spatial polarity in cells and tissues title: Cell Polarity - from_schema: https://w3id.org/linkml/valuesets/spatial/spatial_qualifiers + from_schema: https://w3id.org/valuesets/spatial/spatial_qualifiers contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -25583,7 +25583,7 @@ enums: definition_uri: https://w3id.org/valuesets/AnatomicalOrientation description: Directional orientation between anatomical positions based on OME NGFF specification - from_schema: https://w3id.org/linkml/valuesets/spatial/spatial_qualifiers + from_schema: https://w3id.org/valuesets/spatial/spatial_qualifiers permissible_values: LEFT_TO_RIGHT: text: LEFT_TO_RIGHT @@ -25763,7 +25763,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: The seven crystal systems in crystallography title: Crystal System - from_schema: https://w3id.org/linkml/valuesets/materials_science/crystal_structures + from_schema: https://w3id.org/valuesets/materials_science/crystal_structures contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -25827,7 +25827,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/materials_science/crystal_structures contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -25929,7 +25929,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Classification of materials by electrical conductivity title: Electrical Conductivity - from_schema: https://w3id.org/linkml/valuesets/materials_science/material_properties + from_schema: https://w3id.org/valuesets/materials_science/material_properties contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -25968,7 +25968,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Classification of materials by magnetic properties title: Magnetic Property - from_schema: https://w3id.org/linkml/valuesets/materials_science/material_properties + from_schema: https://w3id.org/valuesets/materials_science/material_properties contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -26001,7 +26001,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Optical properties of materials title: Optical Property - from_schema: https://w3id.org/linkml/valuesets/materials_science/material_properties + from_schema: https://w3id.org/valuesets/materials_science/material_properties contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -26044,7 +26044,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Classification by thermal conductivity title: Thermal Conductivity - from_schema: https://w3id.org/linkml/valuesets/materials_science/material_properties + from_schema: https://w3id.org/valuesets/materials_science/material_properties contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -26073,7 +26073,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Mechanical behavior of materials under stress title: Mechanical Behavior - from_schema: https://w3id.org/linkml/valuesets/materials_science/material_properties + from_schema: https://w3id.org/valuesets/materials_science/material_properties contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -26117,7 +26117,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Microscopy techniques for material characterization title: Microscopy Method - from_schema: https://w3id.org/linkml/valuesets/materials_science/characterization_methods + from_schema: https://w3id.org/valuesets/materials_science/characterization_methods contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -26186,7 +26186,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Spectroscopy techniques for material analysis title: Spectroscopy Method - from_schema: https://w3id.org/linkml/valuesets/materials_science/characterization_methods + from_schema: https://w3id.org/valuesets/materials_science/characterization_methods contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -26263,7 +26263,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Thermal analysis techniques title: Thermal Analysis Method - from_schema: https://w3id.org/linkml/valuesets/materials_science/characterization_methods + from_schema: https://w3id.org/valuesets/materials_science/characterization_methods contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -26311,7 +26311,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Mechanical testing methods title: Mechanical Testing Method - from_schema: https://w3id.org/linkml/valuesets/materials_science/characterization_methods + from_schema: https://w3id.org/valuesets/materials_science/characterization_methods contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -26356,7 +26356,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Major classes of materials title: Material Class - from_schema: https://w3id.org/linkml/valuesets/materials_science/material_types + from_schema: https://w3id.org/valuesets/materials_science/material_types contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -26411,7 +26411,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Types of polymer materials title: Polymer Type - from_schema: https://w3id.org/linkml/valuesets/materials_science/material_types + from_schema: https://w3id.org/valuesets/materials_science/material_types contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -26456,7 +26456,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Types of metallic materials title: Metal Type - from_schema: https://w3id.org/linkml/valuesets/materials_science/material_types + from_schema: https://w3id.org/valuesets/materials_science/material_types contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -26499,7 +26499,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Types of composite materials title: Composite Type - from_schema: https://w3id.org/linkml/valuesets/materials_science/material_types + from_schema: https://w3id.org/valuesets/materials_science/material_types contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -26546,7 +26546,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Common material synthesis and processing methods title: Synthesis Method - from_schema: https://w3id.org/linkml/valuesets/materials_science/synthesis_methods + from_schema: https://w3id.org/valuesets/materials_science/synthesis_methods contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -26648,7 +26648,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Methods for growing single crystals title: Crystal Growth Method - from_schema: https://w3id.org/linkml/valuesets/materials_science/synthesis_methods + from_schema: https://w3id.org/valuesets/materials_science/synthesis_methods contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -26715,7 +26715,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: 3D printing and additive manufacturing methods title: Additive Manufacturing - from_schema: https://w3id.org/linkml/valuesets/materials_science/synthesis_methods + from_schema: https://w3id.org/valuesets/materials_science/synthesis_methods contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -31865,7 +31865,7 @@ enums: 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 + from_schema: https://w3id.org/valuesets/bio/sequence_chemistry contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -31938,7 +31938,7 @@ enums: 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 + from_schema: https://w3id.org/valuesets/bio/sequence_chemistry contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -32033,7 +32033,7 @@ enums: rare amino acids, and ambiguity codes' title: IUPAC Amino Acid Codes - from_schema: https://w3id.org/linkml/valuesets/bio/sequence_chemistry + from_schema: https://w3id.org/valuesets/bio/sequence_chemistry contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -32158,7 +32158,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/bio/sequence_chemistry contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -32201,7 +32201,7 @@ enums: Different platforms and software versions use different ASCII offsets.' title: Sequence Quality Score Encodings - from_schema: https://w3id.org/linkml/valuesets/bio/sequence_chemistry + from_schema: https://w3id.org/valuesets/bio/sequence_chemistry contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -32281,7 +32281,7 @@ enums: 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 + from_schema: https://w3id.org/valuesets/bio/sequence_chemistry contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -32534,7 +32534,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/bio/sequence_chemistry contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -32561,7 +32561,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Topological structure of nucleic acid molecules title: Sequence Topology - from_schema: https://w3id.org/linkml/valuesets/bio/sequence_chemistry + from_schema: https://w3id.org/valuesets/bio/sequence_chemistry contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -32588,7 +32588,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/bio/sequence_chemistry contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -32626,7 +32626,7 @@ enums: 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 + from_schema: https://w3id.org/valuesets/bio/sequencing_platforms contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -33051,7 +33051,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/bio/sequencing_platforms contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -33106,7 +33106,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/bio/sequencing_platforms contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -33176,7 +33176,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/bio/sequencing_platforms contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -33259,7 +33259,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/bio/sequencing_platforms contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -33292,7 +33292,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/bio/sequencing_platforms contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -33475,7 +33475,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/bio/sequencing_platforms contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -43975,7 +43975,7 @@ enums: 16607972. Designed for cohort aggregation across federated data resources. Each diagnosis maps to a single dominant category. title: Pediatric Oncology Diagnosis Category - from_schema: https://w3id.org/linkml/valuesets/medical/pediatric_oncology/diagnosis_categories + from_schema: https://w3id.org/valuesets/medical/pediatric_oncology/diagnosis_categories see_also: - https://github.com/CBIIT/ccdi-federation-api/discussions/160 - https://docs.stjude.cloud/cc4k @@ -44395,7 +44395,7 @@ enums: of Childhood Cancer, Third Edition. Based on tumor morphology and primary site with emphasis on morphology. title: ICCC-3 Main Diagnostic Group - from_schema: https://w3id.org/linkml/valuesets/medical/pediatric_oncology/iccc3 + from_schema: https://w3id.org/valuesets/medical/pediatric_oncology/iccc3 see_also: - https://seer.cancer.gov/iccc/ - https://seer.cancer.gov/iccc/iccc3.html @@ -44587,7 +44587,7 @@ enums: Childhood Cancer, Third Edition. These provide more detailed classification within each of the 12 main groups. title: ICCC-3 Diagnostic Subgroup - from_schema: https://w3id.org/linkml/valuesets/medical/pediatric_oncology/iccc3 + from_schema: https://w3id.org/valuesets/medical/pediatric_oncology/iccc3 see_also: - https://seer.cancer.gov/iccc/iccc3.html - https://seer.cancer.gov/iccc/iccc3_ext.html @@ -45151,7 +45151,7 @@ enums: effective for diagnosis years 2024+. Allows staging before any treatment, unlike the surgical INSS system. title: INRGSS Stage - from_schema: https://w3id.org/linkml/valuesets/medical/pediatric_oncology/staging/neuroblastoma + from_schema: https://w3id.org/valuesets/medical/pediatric_oncology/staging/neuroblastoma see_also: - https://staging.seer.cancer.gov/pediatric/input/1.0/neuroblastoma/inrgss/ - https://pmc.ncbi.nlm.nih.gov/articles/PMC2650389/ @@ -45241,7 +45241,7 @@ enums: metastatic spread. This is the legacy system; INRGSS is now preferred for diagnosis years 2024+. title: INSS Stage - from_schema: https://w3id.org/linkml/valuesets/medical/pediatric_oncology/staging/neuroblastoma + from_schema: https://w3id.org/valuesets/medical/pediatric_oncology/staging/neuroblastoma see_also: - https://www.ncbi.nlm.nih.gov/books/NBK65747.5/table/CDR0000062786__725/ - https://www.cancer.org/cancer/types/neuroblastoma/detection-diagnosis-staging/staging.html @@ -45357,7 +45357,7 @@ enums: groups. Combines INRGSS stage with tumor histology, MYCN status, ploidy, and other prognostic factors. title: Neuroblastoma Risk Group - from_schema: https://w3id.org/linkml/valuesets/medical/pediatric_oncology/staging/neuroblastoma + from_schema: https://w3id.org/valuesets/medical/pediatric_oncology/staging/neuroblastoma see_also: - https://pmc.ncbi.nlm.nih.gov/articles/PMC2650388/ contributors: @@ -45418,7 +45418,7 @@ enums: description: Image-defined risk factors (IDRFs) used in INRGSS staging to determine surgical risk. Presence of any IDRF upgrades a tumor from L1 to L2. title: Image-Defined Risk Factor - from_schema: https://w3id.org/linkml/valuesets/medical/pediatric_oncology/staging/neuroblastoma + from_schema: https://w3id.org/valuesets/medical/pediatric_oncology/staging/neuroblastoma see_also: - https://pmc.ncbi.nlm.nih.gov/articles/PMC2650389/ contributors: @@ -45518,7 +45518,7 @@ enums: Respondents may select multiple races.' title: Race OMB1997 - from_schema: https://w3id.org/linkml/valuesets/clinical/nih_demographics + from_schema: https://w3id.org/valuesets/clinical/nih_demographics contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -45620,7 +45620,7 @@ enums: 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 + from_schema: https://w3id.org/valuesets/clinical/nih_demographics contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -45673,7 +45673,7 @@ enums: Required by NIH as a biological variable in research.' title: Biological Sex - from_schema: https://w3id.org/linkml/valuesets/clinical/nih_demographics + from_schema: https://w3id.org/valuesets/clinical/nih_demographics contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -45722,7 +45722,7 @@ enums: 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 + from_schema: https://w3id.org/valuesets/clinical/nih_demographics contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -45830,7 +45830,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/clinical/nih_demographics contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -45860,7 +45860,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/clinical/nih_demographics contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -45912,7 +45912,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/clinical/nih_demographics contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -45995,7 +45995,7 @@ enums: 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 + from_schema: https://w3id.org/valuesets/clinical/phenopackets contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -46137,7 +46137,7 @@ enums: FHIR mapping: AdministrativeGender' title: Phenotypic Sex - from_schema: https://w3id.org/linkml/valuesets/clinical/phenopackets + from_schema: https://w3id.org/valuesets/clinical/phenopackets contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -46183,7 +46183,7 @@ enums: 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 + from_schema: https://w3id.org/valuesets/clinical/phenopackets contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -46256,7 +46256,7 @@ enums: value: https://ga4gh.org description: Laterality/sidedness of a finding or anatomical structure title: Laterality - from_schema: https://w3id.org/linkml/valuesets/clinical/phenopackets + from_schema: https://w3id.org/valuesets/clinical/phenopackets contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -46315,7 +46315,7 @@ enums: 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 + from_schema: https://w3id.org/valuesets/clinical/phenopackets contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -46423,7 +46423,7 @@ enums: 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 + from_schema: https://w3id.org/valuesets/clinical/phenopackets contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -46503,7 +46503,7 @@ enums: value: https://ga4gh.org description: Clinical actionability of a genetic finding for treatment decisions title: Therapeutic Actionability - 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from_schema: https://w3id.org/linkml/valuesets/clinical/phenopackets + from_schema: https://w3id.org/valuesets/clinical/phenopackets contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -46733,7 +46733,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/bioprocessing/scale_up contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -46815,7 +46815,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/bioprocessing/scale_up contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -46927,7 +46927,7 @@ enums: - 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orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -59663,7 +59663,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/lab_automation/devices contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -59775,7 +59775,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/lab_automation/devices contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -59819,7 +59819,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Operations for automated liquid handling in laboratory automation title: Liquid Handling Operation - 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valuesets_meta:ValueSetEnumDefinition description: Types of laboratory containers and labware title: Container Type - from_schema: https://w3id.org/linkml/valuesets/lab_automation/labware + from_schema: https://w3id.org/valuesets/lab_automation/labware contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -60092,7 +60092,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Material composition of laboratory microplates title: Plate Material - from_schema: https://w3id.org/linkml/valuesets/lab_automation/labware + from_schema: https://w3id.org/valuesets/lab_automation/labware contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -60119,7 +60119,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Surface treatment of microplates title: Plate Coating - from_schema: https://w3id.org/linkml/valuesets/lab_automation/labware + from_schema: https://w3id.org/valuesets/lab_automation/labware contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -60152,7 +60152,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/lab_automation/protocols contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -60188,7 +60188,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Types of scheduling algorithms for laboratory automation title: Scheduler Type - from_schema: https://w3id.org/linkml/valuesets/lab_automation/protocols + from_schema: https://w3id.org/valuesets/lab_automation/protocols contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -60226,7 +60226,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Execution states of laboratory protocols title: Protocol State - from_schema: https://w3id.org/linkml/valuesets/lab_automation/protocols + from_schema: https://w3id.org/valuesets/lab_automation/protocols contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -60271,7 +60271,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Modes of protocol execution title: Execution Mode - from_schema: https://w3id.org/linkml/valuesets/lab_automation/protocols + from_schema: https://w3id.org/valuesets/lab_automation/protocols contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -60308,7 +60308,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/lab_automation/protocols contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -60345,7 +60345,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/lab_automation/protocols contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -60398,7 +60398,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Industry standards for laboratory automation systems title: Automation Standard - from_schema: https://w3id.org/linkml/valuesets/lab_automation/standards + from_schema: https://w3id.org/valuesets/lab_automation/standards contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -60488,7 +60488,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Communication protocols for laboratory automation integration title: Communication Protocol - from_schema: https://w3id.org/linkml/valuesets/lab_automation/standards + from_schema: https://w3id.org/valuesets/lab_automation/standards contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -60545,7 +60545,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Standardization specifications for laboratory labware title: Labware Standard - from_schema: https://w3id.org/linkml/valuesets/lab_automation/standards + from_schema: https://w3id.org/valuesets/lab_automation/standards contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -60619,7 +60619,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Integration features for laboratory automation systems title: Integration Feature - from_schema: https://w3id.org/linkml/valuesets/lab_automation/standards + from_schema: https://w3id.org/valuesets/lab_automation/standards contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -60664,7 +60664,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Types of thermal cycling instruments title: Thermal Cycler Type - from_schema: https://w3id.org/linkml/valuesets/lab_automation/thermal_cycling + from_schema: https://w3id.org/valuesets/lab_automation/thermal_cycling contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -60719,7 +60719,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/lab_automation/thermal_cycling contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -60788,7 +60788,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/lab_automation/thermal_cycling contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -60833,7 +60833,7 @@ enums: - 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 + from_schema: https://w3id.org/valuesets/lab_automation/thermal_cycling contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -60874,7 +60874,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Steps in thermal cycling protocols title: Thermal Cycling Step - from_schema: https://w3id.org/linkml/valuesets/lab_automation/thermal_cycling + from_schema: https://w3id.org/valuesets/lab_automation/thermal_cycling contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -60920,7 +60920,7 @@ enums: description: arXiv subject categories for classifying preprints and publications. Categories are organized by major subject groups. title: arXiv Category - from_schema: https://w3id.org/linkml/valuesets/publishing/arxiv_categories + from_schema: https://w3id.org/valuesets/publishing/arxiv_categories contributors: - orcid:0000-0002-6601-2165 - https://github.com/anthropics/claude-code @@ -61937,7 +61937,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Workflow status codes for OSTI record revisions. title: OSTI Workflow Status - from_schema: https://w3id.org/linkml/valuesets/publishing/osti_record + from_schema: https://w3id.org/valuesets/publishing/osti_record see_also: - https://www.osti.gov/elink2api/record-schema contributors: @@ -61966,7 +61966,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Access and distribution limitation codes from OSTI. title: OSTI Access Limitation - from_schema: https://w3id.org/linkml/valuesets/publishing/osti_record + from_schema: https://w3id.org/valuesets/publishing/osti_record see_also: - https://www.osti.gov/elink2api/record-schema contributors: @@ -62015,7 +62015,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Collection type codes used by OSTI for record origin. title: OSTI Collection Type - from_schema: https://w3id.org/linkml/valuesets/publishing/osti_record + from_schema: https://w3id.org/valuesets/publishing/osti_record see_also: - https://www.osti.gov/elink2api/record-schema contributors: @@ -62036,7 +62036,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Sensitivity flags calculated by OSTI for released records. title: OSTI Sensitivity Flag - from_schema: https://w3id.org/linkml/valuesets/publishing/osti_record + from_schema: https://w3id.org/valuesets/publishing/osti_record see_also: - https://www.osti.gov/elink2api/record-schema contributors: @@ -62059,7 +62059,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Identifier types for OSTI organizations. title: OSTI Organization Identifier Type - from_schema: https://w3id.org/linkml/valuesets/publishing/osti_record + from_schema: https://w3id.org/valuesets/publishing/osti_record see_also: - https://www.osti.gov/elink2api/record-schema contributors: @@ -62080,7 +62080,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Product type codes from OSTI record metadata. title: OSTI Product Type - from_schema: https://w3id.org/linkml/valuesets/publishing/osti_record + from_schema: https://w3id.org/valuesets/publishing/osti_record see_also: - https://www.osti.gov/elink2api/record-schema contributors: @@ -62123,7 +62123,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Organization role types used by OSTI. title: OSTI Organization Type - from_schema: https://w3id.org/linkml/valuesets/publishing/osti_record + from_schema: https://w3id.org/valuesets/publishing/osti_record see_also: - https://www.osti.gov/elink2api/record-schema contributors: @@ -62146,7 +62146,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Person role types used by OSTI. title: OSTI Person Type - from_schema: https://w3id.org/linkml/valuesets/publishing/osti_record + from_schema: https://w3id.org/valuesets/publishing/osti_record see_also: - https://www.osti.gov/elink2api/record-schema contributors: @@ -62177,7 +62177,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Contributor role types used by OSTI. title: OSTI Contributor Type - from_schema: https://w3id.org/linkml/valuesets/publishing/osti_record + from_schema: https://w3id.org/valuesets/publishing/osti_record see_also: - https://www.osti.gov/elink2api/record-schema contributors: @@ -62238,7 +62238,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Identifier types for related resources in OSTI. title: OSTI Related Identifier Type - from_schema: https://w3id.org/linkml/valuesets/publishing/osti_record + from_schema: https://w3id.org/valuesets/publishing/osti_record see_also: - https://www.osti.gov/elink2api/record-schema contributors: @@ -62299,7 +62299,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Relationship types between records in OSTI. title: OSTI Relation Type - from_schema: https://w3id.org/linkml/valuesets/publishing/osti_record + from_schema: https://w3id.org/valuesets/publishing/osti_record see_also: - https://www.osti.gov/elink2api/record-schema contributors: @@ -62410,7 +62410,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Identifier type codes from OSTI record metadata. title: OSTI Identifier Type - from_schema: https://w3id.org/linkml/valuesets/publishing/osti_record + from_schema: https://w3id.org/valuesets/publishing/osti_record see_also: - https://www.osti.gov/elink2api/record-schema contributors: @@ -62475,7 +62475,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Geolocation shape types in OSTI record metadata. title: OSTI Geolocation Type - from_schema: https://w3id.org/linkml/valuesets/publishing/osti_record + from_schema: https://w3id.org/valuesets/publishing/osti_record see_also: - https://www.osti.gov/elink2api/record-schema contributors: @@ -62496,7 +62496,7 @@ enums: - valuesets_meta:ValueSetEnumDefinition description: Location indicators for OSTI media files and sets. title: OSTI Media Location Type - from_schema: https://w3id.org/linkml/valuesets/publishing/osti_record + from_schema: https://w3id.org/valuesets/publishing/osti_record see_also: - https://www.osti.gov/elink2api/record-schema contributors: @@ -65289,7 +65289,7 @@ slots: definition_uri: https://w3id.org/valuesets/go_evidence description: Gene Ontology evidence codes mapped to Evidence and Conclusion Ontology (ECO) terms - from_schema: https://w3id.org/linkml/valuesets/bio/go_evidence + from_schema: https://w3id.org/valuesets/bio/go_evidence slot_uri: valuesets:go_evidence range: GOEvidenceCode go_electronic_methods: @@ -65297,14 +65297,14 @@ slots: definition_uri: https://w3id.org/valuesets/go_electronic_methods description: Electronic annotation methods used in Gene Ontology, identified by GO_REF codes - from_schema: https://w3id.org/linkml/valuesets/bio/go_evidence + from_schema: https://w3id.org/valuesets/bio/go_evidence slot_uri: valuesets:go_electronic_methods range: GOElectronicMethods organism_taxon: name: organism_taxon definition_uri: https://w3id.org/valuesets/organism_taxon description: The organism taxon classification - from_schema: https://w3id.org/linkml/valuesets/bio/taxonomy + from_schema: https://w3id.org/valuesets/bio/taxonomy slot_uri: valuesets:organism_taxon range: OrganismTaxonEnum common_organism_taxa: @@ -65312,77 +65312,77 @@ slots: definition_uri: https://w3id.org/valuesets/common_organism_taxa description: Common model organisms used in biological research, mapped to NCBI Taxonomy IDs - from_schema: https://w3id.org/linkml/valuesets/bio/taxonomy + from_schema: https://w3id.org/valuesets/bio/taxonomy slot_uri: valuesets:common_organism_taxa range: CommonOrganismTaxaEnum taxonomic_rank: name: taxonomic_rank definition_uri: https://w3id.org/valuesets/taxonomic_rank description: Standard taxonomic ranks used in biological classification - from_schema: https://w3id.org/linkml/valuesets/bio/taxonomy + from_schema: https://w3id.org/valuesets/bio/taxonomy slot_uri: valuesets:taxonomic_rank range: TaxonomicRank biological_kingdom: name: biological_kingdom definition_uri: https://w3id.org/valuesets/biological_kingdom description: Major kingdoms/domains of life - from_schema: https://w3id.org/linkml/valuesets/bio/taxonomy + from_schema: https://w3id.org/valuesets/bio/taxonomy slot_uri: valuesets:biological_kingdom range: BiologicalKingdom cell_cycle_phase: name: cell_cycle_phase definition_uri: https://w3id.org/valuesets/cell_cycle_phase description: Major phases of the eukaryotic cell cycle - from_schema: https://w3id.org/linkml/valuesets/bio/cell_cycle + from_schema: https://w3id.org/valuesets/bio/cell_cycle slot_uri: valuesets:cell_cycle_phase range: CellCyclePhase mitotic_phase: name: mitotic_phase definition_uri: https://w3id.org/valuesets/mitotic_phase description: Stages of mitosis (M phase) - from_schema: https://w3id.org/linkml/valuesets/bio/cell_cycle + from_schema: https://w3id.org/valuesets/bio/cell_cycle slot_uri: valuesets:mitotic_phase range: MitoticPhase cell_cycle_checkpoint: name: cell_cycle_checkpoint definition_uri: https://w3id.org/valuesets/cell_cycle_checkpoint description: Cell cycle checkpoints that regulate progression - from_schema: https://w3id.org/linkml/valuesets/bio/cell_cycle + from_schema: https://w3id.org/valuesets/bio/cell_cycle slot_uri: valuesets:cell_cycle_checkpoint range: CellCycleCheckpoint meiotic_phase: name: meiotic_phase definition_uri: https://w3id.org/valuesets/meiotic_phase description: Phases specific to meiotic cell division - from_schema: https://w3id.org/linkml/valuesets/bio/cell_cycle + from_schema: https://w3id.org/valuesets/bio/cell_cycle slot_uri: valuesets:meiotic_phase range: MeioticPhase cell_cycle_regulator: name: cell_cycle_regulator definition_uri: https://w3id.org/valuesets/cell_cycle_regulator description: Types of cell cycle regulatory molecules - from_schema: https://w3id.org/linkml/valuesets/bio/cell_cycle + from_schema: https://w3id.org/valuesets/bio/cell_cycle slot_uri: valuesets:cell_cycle_regulator range: CellCycleRegulator cell_proliferation_state: name: cell_proliferation_state definition_uri: https://w3id.org/valuesets/cell_proliferation_state description: Cell proliferation and growth states - from_schema: https://w3id.org/linkml/valuesets/bio/cell_cycle + from_schema: https://w3id.org/valuesets/bio/cell_cycle slot_uri: valuesets:cell_proliferation_state range: CellProliferationState dna_damage_response: name: dna_damage_response definition_uri: https://w3id.org/valuesets/dna_damage_response description: DNA damage response pathways during cell cycle - from_schema: https://w3id.org/linkml/valuesets/bio/cell_cycle + from_schema: https://w3id.org/valuesets/bio/cell_cycle slot_uri: valuesets:dna_damage_response range: DNADamageResponse genome_feature: name: genome_feature definition_uri: https://w3id.org/valuesets/genome_feature description: Genome feature types from SOFA (Sequence Ontology Feature Annotation) - from_schema: https://w3id.org/linkml/valuesets/bio/genome_features + from_schema: https://w3id.org/valuesets/bio/genome_features slot_uri: valuesets:genome_feature range: GenomeFeatureType multivalued: true @@ -65391,21 +65391,21 @@ slots: definition_uri: https://w3id.org/valuesets/metazoan_anatomical_structure description: Any anatomical structure found in metazoan organisms, including organs, tissues, and body parts - from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + from_schema: https://w3id.org/valuesets/bio/bio_entities slot_uri: valuesets:metazoan_anatomical_structure range: MetazoanAnatomicalStructure human_anatomical_structure: name: human_anatomical_structure definition_uri: https://w3id.org/valuesets/human_anatomical_structure description: Anatomical structures specific to humans (Homo sapiens) - from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + from_schema: https://w3id.org/valuesets/bio/bio_entities slot_uri: valuesets:human_anatomical_structure range: HumanAnatomicalStructure plant_anatomical_structure: name: plant_anatomical_structure definition_uri: https://w3id.org/valuesets/plant_anatomical_structure description: Any anatomical structure found in plant organisms - from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + from_schema: https://w3id.org/valuesets/bio/bio_entities slot_uri: valuesets:plant_anatomical_structure range: PlantAnatomicalStructure cell: @@ -65413,133 +65413,133 @@ slots: definition_uri: https://w3id.org/valuesets/cell description: Any cell type from the Cell Ontology (CL), including native and experimentally modified cells - from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + from_schema: https://w3id.org/valuesets/bio/bio_entities slot_uri: valuesets:cell range: CellType neuron: name: neuron definition_uri: https://w3id.org/valuesets/neuron description: Neuron cell types from the Cell Ontology - from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + from_schema: https://w3id.org/valuesets/bio/bio_entities slot_uri: valuesets:neuron range: NeuronType immune_cell: name: immune_cell definition_uri: https://w3id.org/valuesets/immune_cell description: Immune system cell types (leukocytes and their subtypes) - from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + from_schema: https://w3id.org/valuesets/bio/bio_entities slot_uri: valuesets:immune_cell range: ImmuneCell stem_cell: name: stem_cell definition_uri: https://w3id.org/valuesets/stem_cell description: Stem cell types and progenitor cells - from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + from_schema: https://w3id.org/valuesets/bio/bio_entities slot_uri: valuesets:stem_cell range: StemCell disease: name: disease definition_uri: https://w3id.org/valuesets/disease description: Human diseases from the Mondo Disease Ontology - from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + from_schema: https://w3id.org/valuesets/bio/bio_entities slot_uri: valuesets:disease range: Disease infectious_disease: name: infectious_disease definition_uri: https://w3id.org/valuesets/infectious_disease description: Infectious diseases caused by pathogenic organisms - from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + from_schema: https://w3id.org/valuesets/bio/bio_entities slot_uri: valuesets:infectious_disease range: InfectiousDisease cancer: name: cancer definition_uri: https://w3id.org/valuesets/cancer description: Neoplastic and cancerous diseases - from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + from_schema: https://w3id.org/valuesets/bio/bio_entities slot_uri: valuesets:cancer range: Cancer genetic_disease: name: genetic_disease definition_uri: https://w3id.org/valuesets/genetic_disease description: Hereditary and genetic diseases - from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + from_schema: https://w3id.org/valuesets/bio/bio_entities slot_uri: valuesets:genetic_disease range: GeneticDisease chemical_entity: name: chemical_entity definition_uri: https://w3id.org/valuesets/chemical_entity description: Any chemical entity from ChEBI ontology - from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + from_schema: https://w3id.org/valuesets/bio/bio_entities slot_uri: valuesets:chemical_entity range: ChemicalEntity drug: name: drug definition_uri: https://w3id.org/valuesets/drug description: Pharmaceutical drugs and medications - from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + from_schema: https://w3id.org/valuesets/bio/bio_entities slot_uri: valuesets:drug range: Drug metabolite: name: metabolite definition_uri: https://w3id.org/valuesets/metabolite description: Metabolites and metabolic intermediates - from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + from_schema: https://w3id.org/valuesets/bio/bio_entities slot_uri: valuesets:metabolite range: Metabolite protein: name: protein definition_uri: https://w3id.org/valuesets/protein description: Proteins and protein complexes - from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + from_schema: https://w3id.org/valuesets/bio/bio_entities slot_uri: valuesets:protein range: Protein phenotype: name: phenotype definition_uri: https://w3id.org/valuesets/phenotype description: Phenotypic abnormalities from Human Phenotype Ontology - from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + from_schema: https://w3id.org/valuesets/bio/bio_entities slot_uri: valuesets:phenotype range: Phenotype clinical_finding: name: clinical_finding definition_uri: https://w3id.org/valuesets/clinical_finding description: Clinical findings and observations - from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + from_schema: https://w3id.org/valuesets/bio/bio_entities slot_uri: valuesets:clinical_finding range: ClinicalFinding biological_process: name: biological_process definition_uri: https://w3id.org/valuesets/biological_process description: Biological processes from Gene Ontology - from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + from_schema: https://w3id.org/valuesets/bio/bio_entities slot_uri: valuesets:biological_process range: BiologicalProcess metabolic_process: name: metabolic_process definition_uri: https://w3id.org/valuesets/metabolic_process description: Metabolic processes and pathways - from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + from_schema: https://w3id.org/valuesets/bio/bio_entities slot_uri: valuesets:metabolic_process range: MetabolicProcess molecular_function: name: molecular_function definition_uri: https://w3id.org/valuesets/molecular_function description: Molecular functions from Gene Ontology - from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + from_schema: https://w3id.org/valuesets/bio/bio_entities slot_uri: valuesets:molecular_function range: MolecularFunction cellular_component: name: cellular_component definition_uri: https://w3id.org/valuesets/cellular_component description: Cellular components and locations from Gene Ontology - from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + from_schema: https://w3id.org/valuesets/bio/bio_entities slot_uri: valuesets:cellular_component range: CellularComponent sequence_feature: name: sequence_feature definition_uri: https://w3id.org/valuesets/sequence_feature description: Sequence features from the Sequence Ontology - from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + from_schema: https://w3id.org/valuesets/bio/bio_entities slot_uri: valuesets:sequence_feature range: SequenceFeature multivalued: true @@ -65547,7 +65547,7 @@ slots: name: gene_feature definition_uri: https://w3id.org/valuesets/gene_feature description: Gene-related sequence features - from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + from_schema: https://w3id.org/valuesets/bio/bio_entities slot_uri: valuesets:gene_feature range: GeneFeature multivalued: true @@ -65555,28 +65555,28 @@ slots: name: environment definition_uri: https://w3id.org/valuesets/environment description: Environmental systems and biomes - from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + from_schema: https://w3id.org/valuesets/bio/bio_entities slot_uri: valuesets:environment range: Environment environmental_material: name: environmental_material definition_uri: https://w3id.org/valuesets/environmental_material description: Environmental materials and substances - from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + from_schema: https://w3id.org/valuesets/bio/bio_entities slot_uri: valuesets:environmental_material range: EnvironmentalMaterial quality: name: quality definition_uri: https://w3id.org/valuesets/quality description: Phenotypic qualities and attributes from PATO - from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + from_schema: https://w3id.org/valuesets/bio/bio_entities slot_uri: valuesets:quality range: Quality physical_quality: name: physical_quality definition_uri: https://w3id.org/valuesets/physical_quality description: Physical qualities like size, shape, color - from_schema: https://w3id.org/linkml/valuesets/bio/bio_entities + from_schema: https://w3id.org/valuesets/bio/bio_entities slot_uri: valuesets:physical_quality range: PhysicalQuality sample: @@ -65689,7 +65689,7 @@ slots: definition_uri: https://w3id.org/valuesets/biosafety_level description: The biosafety level required for handling biological agents based on potential risk - from_schema: https://w3id.org/linkml/valuesets/bio/biosafety + from_schema: https://w3id.org/valuesets/bio/biosafety slot_uri: valuesets:biosafety_level range: BiosafetyLevelEnum insdc_missing_value: @@ -65697,7 +65697,7 @@ slots: definition_uri: https://w3id.org/valuesets/insdc_missing_value description: INSDC (International Nucleotide Sequence Database Collaboration) controlled vocabulary for missing values in sequence records - from_schema: https://w3id.org/linkml/valuesets/bio/insdc_missing_values + from_schema: https://w3id.org/valuesets/bio/insdc_missing_values slot_uri: valuesets:insdc_missing_value range: InsdcMissingValueEnum insdc_geographic_location: @@ -65705,35 +65705,35 @@ slots: definition_uri: https://w3id.org/valuesets/insdc_geographic_location description: INSDC controlled vocabulary for geographic locations of collected samples - from_schema: https://w3id.org/linkml/valuesets/bio/insdc_geographic_locations + from_schema: https://w3id.org/valuesets/bio/insdc_geographic_locations slot_uri: valuesets:insdc_geographic_location range: InsdcGeographicLocationEnum viral_genome_type: name: viral_genome_type definition_uri: https://w3id.org/valuesets/viral_genome_type description: Types of viral genomes based on Baltimore classification - from_schema: https://w3id.org/linkml/valuesets/bio/viral_genome_types + from_schema: https://w3id.org/valuesets/bio/viral_genome_types slot_uri: valuesets:viral_genome_type range: ViralGenomeTypeEnum plant_sex: name: plant_sex definition_uri: https://w3id.org/valuesets/plant_sex description: Plant reproductive and sexual system types - from_schema: https://w3id.org/linkml/valuesets/bio/plant_sex + from_schema: https://w3id.org/valuesets/bio/plant_sex slot_uri: valuesets:plant_sex range: PlantSexEnum rel_to_oxygen: name: rel_to_oxygen definition_uri: https://w3id.org/valuesets/rel_to_oxygen description: Organism's relationship to oxygen for growth and survival - from_schema: https://w3id.org/linkml/valuesets/bio/relationship_to_oxygen + from_schema: https://w3id.org/valuesets/bio/relationship_to_oxygen slot_uri: valuesets:rel_to_oxygen range: RelToOxygenEnum trophic_level: name: trophic_level definition_uri: https://w3id.org/valuesets/trophic_level description: Trophic levels are the feeding position in a food chain - from_schema: https://w3id.org/linkml/valuesets/bio/trophic_levels + from_schema: https://w3id.org/valuesets/bio/trophic_levels slot_uri: valuesets:trophic_level range: TrophicLevelEnum human_developmental_stage: @@ -65768,644 +65768,644 @@ slots: name: day_of_week definition_uri: https://w3id.org/valuesets/day_of_week description: Days of the week following ISO 8601 standard (Monday = 1) - from_schema: https://w3id.org/linkml/valuesets/time/temporal + from_schema: https://w3id.org/valuesets/time/temporal slot_uri: valuesets:day_of_week range: DayOfWeek month: name: month definition_uri: https://w3id.org/valuesets/month description: Months of the year - from_schema: https://w3id.org/linkml/valuesets/time/temporal + from_schema: https://w3id.org/valuesets/time/temporal slot_uri: valuesets:month range: Month quarter: name: quarter definition_uri: https://w3id.org/valuesets/quarter description: Calendar quarters - from_schema: https://w3id.org/linkml/valuesets/time/temporal + from_schema: https://w3id.org/valuesets/time/temporal slot_uri: valuesets:quarter range: Quarter season: name: season definition_uri: https://w3id.org/valuesets/season description: Seasons of the year (Northern Hemisphere) - from_schema: https://w3id.org/linkml/valuesets/time/temporal + from_schema: https://w3id.org/valuesets/time/temporal slot_uri: valuesets:season range: Season time_period: name: time_period definition_uri: https://w3id.org/valuesets/time_period description: Common time periods and intervals - from_schema: https://w3id.org/linkml/valuesets/time/temporal + from_schema: https://w3id.org/valuesets/time/temporal slot_uri: valuesets:time_period range: TimePeriod time_of_day: name: time_of_day definition_uri: https://w3id.org/valuesets/time_of_day description: Common times of day - from_schema: https://w3id.org/linkml/valuesets/time/temporal + from_schema: https://w3id.org/valuesets/time/temporal slot_uri: valuesets:time_of_day range: TimeOfDay business_time_frame: name: business_time_frame definition_uri: https://w3id.org/valuesets/business_time_frame description: Common business and financial time frames - from_schema: https://w3id.org/linkml/valuesets/time/temporal + from_schema: https://w3id.org/valuesets/time/temporal slot_uri: valuesets:business_time_frame range: BusinessTimeFrame geological_era: name: geological_era definition_uri: https://w3id.org/valuesets/geological_era description: Major geological eras - from_schema: https://w3id.org/linkml/valuesets/time/temporal + from_schema: https://w3id.org/valuesets/time/temporal slot_uri: valuesets:geological_era range: GeologicalEra historical_period: name: historical_period definition_uri: https://w3id.org/valuesets/historical_period description: Major historical periods - from_schema: https://w3id.org/linkml/valuesets/time/temporal + from_schema: https://w3id.org/valuesets/time/temporal slot_uri: valuesets:historical_period range: HistoricalPeriod publication: name: publication definition_uri: https://w3id.org/valuesets/publication description: Types of academic and research publications - from_schema: https://w3id.org/linkml/valuesets/academic/research + from_schema: https://w3id.org/valuesets/academic/research slot_uri: valuesets:publication range: PublicationType peer_review_status: name: peer_review_status definition_uri: https://w3id.org/valuesets/peer_review_status description: Status of peer review process - from_schema: https://w3id.org/linkml/valuesets/academic/research + from_schema: https://w3id.org/valuesets/academic/research slot_uri: valuesets:peer_review_status range: PeerReviewStatus academic_degree: name: academic_degree definition_uri: https://w3id.org/valuesets/academic_degree description: Academic degrees and qualifications - from_schema: https://w3id.org/linkml/valuesets/academic/research + from_schema: https://w3id.org/valuesets/academic/research slot_uri: valuesets:academic_degree range: AcademicDegree license: name: license definition_uri: https://w3id.org/valuesets/license description: Common software and content licenses - from_schema: https://w3id.org/linkml/valuesets/academic/research + from_schema: https://w3id.org/valuesets/academic/research slot_uri: valuesets:license range: LicenseType research_field: name: research_field definition_uri: https://w3id.org/valuesets/research_field description: Major research fields and disciplines - from_schema: https://w3id.org/linkml/valuesets/academic/research + from_schema: https://w3id.org/valuesets/academic/research slot_uri: valuesets:research_field range: ResearchField funding: name: funding definition_uri: https://w3id.org/valuesets/funding description: Types of research funding - from_schema: https://w3id.org/linkml/valuesets/academic/research + from_schema: https://w3id.org/valuesets/academic/research slot_uri: valuesets:funding range: FundingType manuscript_section: name: manuscript_section definition_uri: https://w3id.org/valuesets/manuscript_section description: Sections of a scientific manuscript or publication - from_schema: https://w3id.org/linkml/valuesets/academic/research + from_schema: https://w3id.org/valuesets/academic/research slot_uri: valuesets:manuscript_section range: ManuscriptSection research_role: name: research_role definition_uri: https://w3id.org/valuesets/research_role description: Roles in research and authorship - from_schema: https://w3id.org/linkml/valuesets/academic/research + from_schema: https://w3id.org/valuesets/academic/research slot_uri: valuesets:research_role range: ResearchRole open_access: name: open_access definition_uri: https://w3id.org/valuesets/open_access description: Types of open access publishing - from_schema: https://w3id.org/linkml/valuesets/academic/research + from_schema: https://w3id.org/valuesets/academic/research slot_uri: valuesets:open_access range: OpenAccessType citation_style: name: citation_style definition_uri: https://w3id.org/valuesets/citation_style description: Common citation and reference styles - from_schema: https://w3id.org/linkml/valuesets/academic/research + from_schema: https://w3id.org/valuesets/academic/research slot_uri: valuesets:citation_style range: CitationStyle us_national_laboratory: name: us_national_laboratory definition_uri: https://w3id.org/valuesets/us_national_laboratory description: US Department of Energy National Laboratory - from_schema: https://w3id.org/linkml/valuesets/academic/organizations + from_schema: https://w3id.org/valuesets/academic/organizations slot_uri: valuesets:us_national_laboratory range: USDOENationalLaboratoryEnum us_federal_funding_agency: name: us_federal_funding_agency definition_uri: https://w3id.org/valuesets/us_federal_funding_agency description: US Federal Research Funding Agency - from_schema: https://w3id.org/linkml/valuesets/academic/organizations + from_schema: https://w3id.org/valuesets/academic/organizations slot_uri: valuesets:us_federal_funding_agency range: USFederalFundingAgencyEnum nih_institute_center: name: nih_institute_center definition_uri: https://w3id.org/valuesets/nih_institute_center description: NIH Institute or Center - from_schema: https://w3id.org/linkml/valuesets/academic/organizations + from_schema: https://w3id.org/valuesets/academic/organizations slot_uri: valuesets:nih_institute_center range: NIHInstituteCenterEnum standards_organization: name: standards_organization definition_uri: https://w3id.org/valuesets/standards_organization description: Standards Development Organization - from_schema: https://w3id.org/linkml/valuesets/academic/organizations + from_schema: https://w3id.org/valuesets/academic/organizations slot_uri: valuesets:standards_organization range: StandardsOrganizationEnum un_specialized_agency: name: un_specialized_agency definition_uri: https://w3id.org/valuesets/un_specialized_agency description: United Nations Specialized Agency - from_schema: https://w3id.org/linkml/valuesets/academic/organizations + from_schema: https://w3id.org/valuesets/academic/organizations slot_uri: valuesets:un_specialized_agency range: UNSpecializedAgencyEnum energy_source: name: energy_source definition_uri: https://w3id.org/valuesets/energy_source description: Types of energy sources and generation methods - from_schema: https://w3id.org/linkml/valuesets/energy/energy + from_schema: https://w3id.org/valuesets/energy/energy slot_uri: valuesets:energy_source range: EnergySource energy_unit: name: energy_unit definition_uri: https://w3id.org/valuesets/energy_unit description: Units for measuring energy - from_schema: https://w3id.org/linkml/valuesets/energy/energy + from_schema: https://w3id.org/valuesets/energy/energy slot_uri: valuesets:energy_unit range: EnergyUnit power_unit: name: power_unit definition_uri: https://w3id.org/valuesets/power_unit description: Units for measuring power (energy per time) - from_schema: https://w3id.org/linkml/valuesets/energy/energy + from_schema: https://w3id.org/valuesets/energy/energy slot_uri: valuesets:power_unit range: PowerUnit energy_efficiency_rating: name: energy_efficiency_rating definition_uri: https://w3id.org/valuesets/energy_efficiency_rating description: Energy efficiency ratings and standards - from_schema: https://w3id.org/linkml/valuesets/energy/energy + from_schema: https://w3id.org/valuesets/energy/energy slot_uri: valuesets:energy_efficiency_rating range: EnergyEfficiencyRating building_energy_standard: name: building_energy_standard definition_uri: https://w3id.org/valuesets/building_energy_standard description: Building energy efficiency standards and certifications - from_schema: https://w3id.org/linkml/valuesets/energy/energy + from_schema: https://w3id.org/valuesets/energy/energy slot_uri: valuesets:building_energy_standard range: BuildingEnergyStandard grid: name: grid definition_uri: https://w3id.org/valuesets/grid description: Types of electrical grid systems - from_schema: https://w3id.org/linkml/valuesets/energy/energy + from_schema: https://w3id.org/valuesets/energy/energy slot_uri: valuesets:grid range: GridType energy_storage: name: energy_storage definition_uri: https://w3id.org/valuesets/energy_storage description: Types of energy storage systems - from_schema: https://w3id.org/linkml/valuesets/energy/energy + from_schema: https://w3id.org/valuesets/energy/energy slot_uri: valuesets:energy_storage range: EnergyStorageType battery_type: name: battery_type definition_uri: https://w3id.org/valuesets/battery_type description: Types of battery technologies - from_schema: https://w3id.org/linkml/valuesets/energy/energy + from_schema: https://w3id.org/valuesets/energy/energy slot_uri: valuesets:battery_type range: BatteryType pv_cell_type: name: pv_cell_type definition_uri: https://w3id.org/valuesets/pv_cell_type description: Types of photovoltaic cell technologies - from_schema: https://w3id.org/linkml/valuesets/energy/energy + from_schema: https://w3id.org/valuesets/energy/energy slot_uri: valuesets:pv_cell_type range: PVCellType pv_system_type: name: pv_system_type definition_uri: https://w3id.org/valuesets/pv_system_type description: Types of photovoltaic system installations - from_schema: https://w3id.org/linkml/valuesets/energy/energy + from_schema: https://w3id.org/valuesets/energy/energy slot_uri: valuesets:pv_system_type range: PVSystemType emission_scope: name: emission_scope definition_uri: https://w3id.org/valuesets/emission_scope description: Greenhouse gas emission scopes (GHG Protocol) - from_schema: https://w3id.org/linkml/valuesets/energy/energy + from_schema: https://w3id.org/valuesets/energy/energy slot_uri: valuesets:emission_scope range: EmissionScope carbon_intensity: name: carbon_intensity definition_uri: https://w3id.org/valuesets/carbon_intensity description: Carbon intensity levels for energy sources - from_schema: https://w3id.org/linkml/valuesets/energy/energy + from_schema: https://w3id.org/valuesets/energy/energy slot_uri: valuesets:carbon_intensity range: CarbonIntensity electricity_market: name: electricity_market definition_uri: https://w3id.org/valuesets/electricity_market description: Types of electricity markets and pricing - from_schema: https://w3id.org/linkml/valuesets/energy/energy + from_schema: https://w3id.org/valuesets/energy/energy slot_uri: valuesets:electricity_market range: ElectricityMarket capability_status: name: capability_status definition_uri: https://w3id.org/valuesets/capability_status description: Operational status of a capability or facility - from_schema: https://w3id.org/linkml/valuesets/energy/energy + from_schema: https://w3id.org/valuesets/energy/energy slot_uri: valuesets:capability_status range: CapabilityStatus fossil_fuel_type: name: fossil_fuel_type definition_uri: https://w3id.org/valuesets/fossil_fuel_type description: Types of fossil fuels used for energy generation - from_schema: https://w3id.org/linkml/valuesets/energy/fossil_fuels + from_schema: https://w3id.org/valuesets/energy/fossil_fuels slot_uri: valuesets:fossil_fuel_type range: FossilFuelTypeEnum reactor_type: name: reactor_type definition_uri: https://w3id.org/valuesets/reactor_type description: Nuclear reactor classification by design type - from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/reactor_types + from_schema: https://w3id.org/valuesets/energy/nuclear/reactor_types slot_uri: valuesets:reactor_type range: ReactorTypeEnum reactor_generation: name: reactor_generation definition_uri: https://w3id.org/valuesets/reactor_generation description: Reactor generation classification (I, II, III, III+, IV) - from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/reactor_types + from_schema: https://w3id.org/valuesets/energy/nuclear/reactor_types slot_uri: valuesets:reactor_generation range: ReactorGenerationEnum reactor_coolant: name: reactor_coolant definition_uri: https://w3id.org/valuesets/reactor_coolant description: Primary coolant type used in reactor - from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/reactor_types + from_schema: https://w3id.org/valuesets/energy/nuclear/reactor_types slot_uri: valuesets:reactor_coolant range: ReactorCoolantEnum reactor_moderator: name: reactor_moderator definition_uri: https://w3id.org/valuesets/reactor_moderator description: Neutron moderator type used in reactor - from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/reactor_types + from_schema: https://w3id.org/valuesets/energy/nuclear/reactor_types slot_uri: valuesets:reactor_moderator range: ReactorModeratorEnum reactor_neutron_spectrum: name: reactor_neutron_spectrum definition_uri: https://w3id.org/valuesets/reactor_neutron_spectrum description: Neutron energy spectrum classification - from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/reactor_types + from_schema: https://w3id.org/valuesets/energy/nuclear/reactor_types slot_uri: valuesets:reactor_neutron_spectrum range: ReactorNeutronSpectrumEnum reactor_size_category: name: reactor_size_category definition_uri: https://w3id.org/valuesets/reactor_size_category description: Reactor size classification - from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/reactor_types + from_schema: https://w3id.org/valuesets/energy/nuclear/reactor_types slot_uri: valuesets:reactor_size_category range: ReactorSizeCategoryEnum nuclear_fuel_type: name: nuclear_fuel_type definition_uri: https://w3id.org/valuesets/nuclear_fuel_type description: Type of nuclear fuel material - from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_fuels + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_fuels slot_uri: valuesets:nuclear_fuel_type range: NuclearFuelTypeEnum uranium_enrichment_level: name: uranium_enrichment_level definition_uri: https://w3id.org/valuesets/uranium_enrichment_level description: Uranium-235 enrichment classification - from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_fuels + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_fuels slot_uri: valuesets:uranium_enrichment_level range: UraniumEnrichmentLevelEnum fuel_form: name: fuel_form definition_uri: https://w3id.org/valuesets/fuel_form description: Physical form of nuclear fuel - from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_fuels + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_fuels slot_uri: valuesets:fuel_form range: FuelFormEnum fuel_assembly_type: name: fuel_assembly_type definition_uri: https://w3id.org/valuesets/fuel_assembly_type description: Type of fuel assembly configuration - from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_fuels + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_fuels slot_uri: valuesets:fuel_assembly_type range: FuelAssemblyTypeEnum fuel_cycle_stage: name: fuel_cycle_stage definition_uri: https://w3id.org/valuesets/fuel_cycle_stage description: Stage in the nuclear fuel cycle - from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_fuels + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_fuels slot_uri: valuesets:fuel_cycle_stage range: FuelCycleStageEnum fissile_material: name: fissile_material definition_uri: https://w3id.org/valuesets/fissile_material description: Fissile isotope used in nuclear fuel - from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_fuels + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_fuels slot_uri: valuesets:fissile_material range: FissileIsotopeEnum waste_classification: name: waste_classification definition_uri: https://w3id.org/valuesets/waste_classification description: International radioactive waste classification - from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_waste + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_waste slot_uri: valuesets:waste_classification range: IAEAWasteClassificationEnum nrc_waste_class: name: nrc_waste_class definition_uri: https://w3id.org/valuesets/nrc_waste_class description: US NRC waste classification (10 CFR 61) - from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_waste + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_waste slot_uri: valuesets:nrc_waste_class range: NRCWasteClassEnum waste_heat_generation: name: waste_heat_generation definition_uri: https://w3id.org/valuesets/waste_heat_generation description: Heat generation category of radioactive waste - from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_waste + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_waste slot_uri: valuesets:waste_heat_generation range: WasteHeatGenerationEnum waste_half_life_category: name: waste_half_life_category definition_uri: https://w3id.org/valuesets/waste_half_life_category description: Half-life category for radioactive waste - from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_waste + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_waste slot_uri: valuesets:waste_half_life_category range: WasteHalfLifeCategoryEnum waste_disposal_method: name: waste_disposal_method definition_uri: https://w3id.org/valuesets/waste_disposal_method description: Disposal method for radioactive waste - from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_waste + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_waste slot_uri: valuesets:waste_disposal_method range: WasteDisposalMethodEnum waste_source: name: waste_source definition_uri: https://w3id.org/valuesets/waste_source description: Source of radioactive waste generation - from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_waste + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_waste slot_uri: valuesets:waste_source range: WasteSourceEnum transuranic_category: name: transuranic_category definition_uri: https://w3id.org/valuesets/transuranic_category description: Transuranic waste classification - from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_waste + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_waste slot_uri: valuesets:transuranic_category range: TransuranicWasteCategoryEnum ines_level: name: ines_level definition_uri: https://w3id.org/valuesets/ines_level description: International Nuclear Event Scale level - from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_safety + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_safety slot_uri: valuesets:ines_level range: INESLevelEnum emergency_classification: name: emergency_classification definition_uri: https://w3id.org/valuesets/emergency_classification description: Nuclear emergency action level - from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_safety + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_safety slot_uri: valuesets:emergency_classification range: EmergencyClassificationEnum nuclear_security_category: name: nuclear_security_category definition_uri: https://w3id.org/valuesets/nuclear_security_category description: IAEA nuclear material security category - from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_safety + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_safety slot_uri: valuesets:nuclear_security_category range: NuclearSecurityCategoryEnum safety_system_class: name: safety_system_class definition_uri: https://w3id.org/valuesets/safety_system_class description: Nuclear safety system classification - from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_safety + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_safety slot_uri: valuesets:safety_system_class range: SafetySystemClassEnum reactor_safety_function: name: reactor_safety_function definition_uri: https://w3id.org/valuesets/reactor_safety_function description: Nuclear reactor safety function classification - from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_safety + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_safety slot_uri: valuesets:reactor_safety_function range: ReactorSafetyFunctionEnum defense_in_depth_level: name: defense_in_depth_level definition_uri: https://w3id.org/valuesets/defense_in_depth_level description: Defense in depth barrier level - from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_safety + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_safety slot_uri: valuesets:defense_in_depth_level range: DefenseInDepthLevelEnum radiation_protection_zone: name: radiation_protection_zone definition_uri: https://w3id.org/valuesets/radiation_protection_zone description: Radiation protection zone classification - from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_safety + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_safety slot_uri: valuesets:radiation_protection_zone range: RadiationProtectionZoneEnum nuclear_facility_type: name: nuclear_facility_type definition_uri: https://w3id.org/valuesets/nuclear_facility_type description: Type of nuclear facility - from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_facilities + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_facilities slot_uri: valuesets:nuclear_facility_type range: NuclearFacilityTypeEnum power_plant_status: name: power_plant_status definition_uri: https://w3id.org/valuesets/power_plant_status description: Operational status of nuclear power plant - from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_facilities + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_facilities slot_uri: valuesets:power_plant_status range: PowerPlantStatusEnum research_reactor_type: name: research_reactor_type definition_uri: https://w3id.org/valuesets/research_reactor_type description: Type of research reactor - from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_facilities + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_facilities slot_uri: valuesets:research_reactor_type range: ResearchReactorTypeEnum fuel_cycle_facility_type: name: fuel_cycle_facility_type definition_uri: https://w3id.org/valuesets/fuel_cycle_facility_type description: Type of nuclear fuel cycle facility - from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_facilities + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_facilities slot_uri: valuesets:fuel_cycle_facility_type range: FuelCycleFacilityTypeEnum waste_facility_type: name: waste_facility_type definition_uri: https://w3id.org/valuesets/waste_facility_type description: Type of nuclear waste management facility - from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_facilities + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_facilities slot_uri: valuesets:waste_facility_type range: WasteFacilityTypeEnum nuclear_ship_type: name: nuclear_ship_type definition_uri: https://w3id.org/valuesets/nuclear_ship_type description: Type of nuclear-powered vessel - from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_facilities + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_facilities slot_uri: valuesets:nuclear_ship_type range: NuclearShipTypeEnum reactor_operating_state: name: reactor_operating_state definition_uri: https://w3id.org/valuesets/reactor_operating_state description: Current operational state of nuclear reactor - from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_operations + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_operations slot_uri: valuesets:reactor_operating_state range: ReactorOperatingStateEnum maintenance_type: name: maintenance_type definition_uri: https://w3id.org/valuesets/maintenance_type description: Type of nuclear facility maintenance activity - from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_operations + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_operations slot_uri: valuesets:maintenance_type range: MaintenanceTypeEnum licensing_stage: name: licensing_stage definition_uri: https://w3id.org/valuesets/licensing_stage description: Nuclear facility licensing stage - from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_operations + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_operations slot_uri: valuesets:licensing_stage range: LicensingStageEnum fuel_cycle_operation: name: fuel_cycle_operation definition_uri: https://w3id.org/valuesets/fuel_cycle_operation description: Nuclear fuel cycle operational activity - from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_operations + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_operations slot_uri: valuesets:fuel_cycle_operation range: FuelCycleOperationEnum reactor_control_mode: name: reactor_control_mode definition_uri: https://w3id.org/valuesets/reactor_control_mode description: Reactor control and safety system mode - from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_operations + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_operations slot_uri: valuesets:reactor_control_mode range: ReactorControlModeEnum operational_procedure: name: operational_procedure definition_uri: https://w3id.org/valuesets/operational_procedure description: Standard nuclear operational procedure - from_schema: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_operations + from_schema: https://w3id.org/valuesets/energy/nuclear/nuclear_operations slot_uri: valuesets:operational_procedure range: OperationalProcedureEnum geothermal_system_type: name: geothermal_system_type definition_uri: https://w3id.org/valuesets/geothermal_system_type description: Type of geothermal system - from_schema: https://w3id.org/linkml/valuesets/energy/renewable/geothermal + from_schema: https://w3id.org/valuesets/energy/renewable/geothermal slot_uri: valuesets:geothermal_system_type range: GeothermalSystemType geothermal_reservoir_type: name: geothermal_reservoir_type definition_uri: https://w3id.org/valuesets/geothermal_reservoir_type description: Type of geothermal reservoir - from_schema: https://w3id.org/linkml/valuesets/energy/renewable/geothermal + from_schema: https://w3id.org/valuesets/energy/renewable/geothermal slot_uri: valuesets:geothermal_reservoir_type range: GeothermalReservoirType geothermal_well_type: name: geothermal_well_type definition_uri: https://w3id.org/valuesets/geothermal_well_type description: Type of geothermal well - from_schema: https://w3id.org/linkml/valuesets/energy/renewable/geothermal + from_schema: https://w3id.org/valuesets/energy/renewable/geothermal slot_uri: valuesets:geothermal_well_type range: GeothermalWellType geothermal_application: name: geothermal_application definition_uri: https://w3id.org/valuesets/geothermal_application description: Application of geothermal energy - from_schema: https://w3id.org/linkml/valuesets/energy/renewable/geothermal + from_schema: https://w3id.org/valuesets/energy/renewable/geothermal slot_uri: valuesets:geothermal_application range: GeothermalApplication geothermal_resource_temperature: name: geothermal_resource_temperature definition_uri: https://w3id.org/valuesets/geothermal_resource_temperature description: Temperature classification of geothermal resources - from_schema: https://w3id.org/linkml/valuesets/energy/renewable/geothermal + from_schema: https://w3id.org/valuesets/energy/renewable/geothermal slot_uri: valuesets:geothermal_resource_temperature range: GeothermalResourceTemperature hydrogen_type: name: hydrogen_type definition_uri: https://w3id.org/valuesets/hydrogen_type description: Type of hydrogen classified by production method and carbon intensity - from_schema: https://w3id.org/linkml/valuesets/energy/renewable/hydrogen + from_schema: https://w3id.org/valuesets/energy/renewable/hydrogen slot_uri: valuesets:hydrogen_type range: HydrogenType hydrogen_production_method: name: hydrogen_production_method definition_uri: https://w3id.org/valuesets/hydrogen_production_method description: Method used to produce hydrogen - from_schema: https://w3id.org/linkml/valuesets/energy/renewable/hydrogen + from_schema: https://w3id.org/valuesets/energy/renewable/hydrogen slot_uri: valuesets:hydrogen_production_method range: HydrogenProductionMethod hydrogen_storage_method: name: hydrogen_storage_method definition_uri: https://w3id.org/valuesets/hydrogen_storage_method description: Method used to store hydrogen - from_schema: https://w3id.org/linkml/valuesets/energy/renewable/hydrogen + from_schema: https://w3id.org/valuesets/energy/renewable/hydrogen slot_uri: valuesets:hydrogen_storage_method range: HydrogenStorageMethod hydrogen_application: name: hydrogen_application definition_uri: https://w3id.org/valuesets/hydrogen_application description: Application or end use of hydrogen - from_schema: https://w3id.org/linkml/valuesets/energy/renewable/hydrogen + from_schema: https://w3id.org/valuesets/energy/renewable/hydrogen slot_uri: valuesets:hydrogen_application range: HydrogenApplication biomass_feedstock_type: name: biomass_feedstock_type definition_uri: https://w3id.org/valuesets/biomass_feedstock_type description: Type of biomass feedstock for bioenergy production - from_schema: https://w3id.org/linkml/valuesets/energy/renewable/bioenergy + from_schema: https://w3id.org/valuesets/energy/renewable/bioenergy slot_uri: valuesets:biomass_feedstock_type range: BiomassFeedstockType biofuel_type: name: biofuel_type definition_uri: https://w3id.org/valuesets/biofuel_type description: Type of biofuel product - from_schema: https://w3id.org/linkml/valuesets/energy/renewable/bioenergy + from_schema: https://w3id.org/valuesets/energy/renewable/bioenergy slot_uri: valuesets:biofuel_type range: BiofuelType biofuel_generation: name: biofuel_generation definition_uri: https://w3id.org/valuesets/biofuel_generation description: Generation classification of biofuel - from_schema: https://w3id.org/linkml/valuesets/energy/renewable/bioenergy + from_schema: https://w3id.org/valuesets/energy/renewable/bioenergy slot_uri: valuesets:biofuel_generation range: BiofuelGeneration bioconversion_process: name: bioconversion_process definition_uri: https://w3id.org/valuesets/bioconversion_process description: Process for converting biomass to biofuel - from_schema: https://w3id.org/linkml/valuesets/energy/renewable/bioenergy + from_schema: https://w3id.org/valuesets/energy/renewable/bioenergy slot_uri: valuesets:bioconversion_process range: BioconversionProcess mining: name: mining definition_uri: https://w3id.org/valuesets/mining description: Types of mining operations - from_schema: https://w3id.org/linkml/valuesets/industry/mining + from_schema: https://w3id.org/valuesets/industry/mining slot_uri: valuesets:mining range: MiningType mineral_category: name: mineral_category definition_uri: https://w3id.org/valuesets/mineral_category description: Categories of minerals and materials - from_schema: https://w3id.org/linkml/valuesets/industry/mining + from_schema: https://w3id.org/valuesets/industry/mining slot_uri: valuesets:mineral_category range: MineralCategory critical_mineral: @@ -66413,91 +66413,91 @@ slots: definition_uri: https://w3id.org/valuesets/critical_mineral description: Critical minerals essential for economic and national security, particularly for clean energy, defense, and technology applications - from_schema: https://w3id.org/linkml/valuesets/industry/mining + from_schema: https://w3id.org/valuesets/industry/mining slot_uri: valuesets:critical_mineral range: CriticalMineral common_mineral: name: common_mineral definition_uri: https://w3id.org/valuesets/common_mineral description: Common minerals extracted through mining - from_schema: https://w3id.org/linkml/valuesets/industry/mining + from_schema: https://w3id.org/valuesets/industry/mining slot_uri: valuesets:common_mineral range: CommonMineral mining_equipment: name: mining_equipment definition_uri: https://w3id.org/valuesets/mining_equipment description: Types of mining equipment - from_schema: https://w3id.org/linkml/valuesets/industry/mining + from_schema: https://w3id.org/valuesets/industry/mining slot_uri: valuesets:mining_equipment range: MiningEquipment ore_grade: name: ore_grade definition_uri: https://w3id.org/valuesets/ore_grade description: Classification of ore grades - from_schema: https://w3id.org/linkml/valuesets/industry/mining + from_schema: https://w3id.org/valuesets/industry/mining slot_uri: valuesets:ore_grade range: OreGrade mining_phase: name: mining_phase definition_uri: https://w3id.org/valuesets/mining_phase description: Phases of mining operations - from_schema: https://w3id.org/linkml/valuesets/industry/mining + from_schema: https://w3id.org/valuesets/industry/mining slot_uri: valuesets:mining_phase range: MiningPhase mining_hazard: name: mining_hazard definition_uri: https://w3id.org/valuesets/mining_hazard description: Mining-related hazards and risks - from_schema: https://w3id.org/linkml/valuesets/industry/mining + from_schema: https://w3id.org/valuesets/industry/mining slot_uri: valuesets:mining_hazard range: MiningHazard environmental_impact: name: environmental_impact definition_uri: https://w3id.org/valuesets/environmental_impact description: Environmental impacts of mining - from_schema: https://w3id.org/linkml/valuesets/industry/mining + from_schema: https://w3id.org/valuesets/industry/mining slot_uri: valuesets:environmental_impact range: EnvironmentalImpact extractive_industry_facility_type: name: extractive_industry_facility_type definition_uri: https://w3id.org/valuesets/extractive_industry_facility_type description: Types of extractive industry facilities - from_schema: https://w3id.org/linkml/valuesets/industry/extractive_industry + from_schema: https://w3id.org/valuesets/industry/extractive_industry slot_uri: valuesets:extractive_industry_facility_type range: ExtractiveIndustryFacilityTypeEnum extractive_industry_product_type: name: extractive_industry_product_type definition_uri: https://w3id.org/valuesets/extractive_industry_product_type description: Types of products extracted from extractive industry facilities - from_schema: https://w3id.org/linkml/valuesets/industry/extractive_industry + from_schema: https://w3id.org/valuesets/industry/extractive_industry slot_uri: valuesets:extractive_industry_product_type range: ExtractiveIndustryProductTypeEnum mining_method: name: mining_method definition_uri: https://w3id.org/valuesets/mining_method description: Methods used for extracting minerals from the earth - from_schema: https://w3id.org/linkml/valuesets/industry/extractive_industry + from_schema: https://w3id.org/valuesets/industry/extractive_industry slot_uri: valuesets:mining_method range: MiningMethodEnum well_type: name: well_type definition_uri: https://w3id.org/valuesets/well_type description: Types of wells used for extracting fluid resources - from_schema: https://w3id.org/linkml/valuesets/industry/extractive_industry + from_schema: https://w3id.org/valuesets/industry/extractive_industry slot_uri: valuesets:well_type range: WellTypeEnum outcome_type: name: outcome_type definition_uri: https://w3id.org/valuesets/outcome_type description: Types of prediction outcomes for classification tasks - from_schema: https://w3id.org/linkml/valuesets/statistics/prediction_outcomes + from_schema: https://w3id.org/valuesets/statistics/prediction_outcomes slot_uri: valuesets:outcome_type range: OutcomeTypeEnum person_status: name: person_status definition_uri: https://w3id.org/valuesets/person_status description: Vital status of a person (living or deceased) - from_schema: https://w3id.org/linkml/valuesets/social/person_status + from_schema: https://w3id.org/valuesets/social/person_status slot_uri: valuesets:person_status range: PersonStatusEnum sdoh_domain: @@ -66567,28 +66567,28 @@ slots: name: mime definition_uri: https://w3id.org/valuesets/mime description: Common MIME types for various file formats - from_schema: https://w3id.org/linkml/valuesets/computing/mime_types + from_schema: https://w3id.org/valuesets/computing/mime_types slot_uri: valuesets:mime range: MimeType mime_type_category: name: mime_type_category definition_uri: https://w3id.org/valuesets/mime_type_category description: Categories of MIME types - from_schema: https://w3id.org/linkml/valuesets/computing/mime_types + from_schema: https://w3id.org/valuesets/computing/mime_types slot_uri: valuesets:mime_type_category range: MimeTypeCategory text_charset: name: text_charset definition_uri: https://w3id.org/valuesets/text_charset description: Character encodings for text content - from_schema: https://w3id.org/linkml/valuesets/computing/mime_types + from_schema: https://w3id.org/valuesets/computing/mime_types slot_uri: valuesets:text_charset range: TextCharset compression: name: compression definition_uri: https://w3id.org/valuesets/compression description: Compression types used with Content-Encoding - from_schema: https://w3id.org/linkml/valuesets/computing/mime_types + from_schema: https://w3id.org/valuesets/computing/mime_types slot_uri: valuesets:compression range: CompressionType state_of_matter: @@ -66784,301 +66784,301 @@ slots: name: sentiment_classification definition_uri: https://w3id.org/valuesets/sentiment_classification description: Standard labels for sentiment analysis classification tasks - from_schema: https://w3id.org/linkml/valuesets/data_science/sentiment_analysis + from_schema: https://w3id.org/valuesets/data_science/sentiment_analysis slot_uri: valuesets:sentiment_classification range: SentimentClassificationEnum fine_sentiment_classification: name: fine_sentiment_classification definition_uri: https://w3id.org/valuesets/fine_sentiment_classification description: Fine-grained sentiment analysis labels with intensity levels - from_schema: https://w3id.org/linkml/valuesets/data_science/sentiment_analysis + from_schema: https://w3id.org/valuesets/data_science/sentiment_analysis slot_uri: valuesets:fine_sentiment_classification range: FineSentimentClassificationEnum binary_classification: name: binary_classification definition_uri: https://w3id.org/valuesets/binary_classification description: Generic binary classification labels - from_schema: https://w3id.org/linkml/valuesets/data_science/binary_classification + from_schema: https://w3id.org/valuesets/data_science/binary_classification slot_uri: valuesets:binary_classification range: BinaryClassificationEnum spam_classification: name: spam_classification definition_uri: https://w3id.org/valuesets/spam_classification description: Standard labels for spam/ham email classification - from_schema: https://w3id.org/linkml/valuesets/data_science/binary_classification + from_schema: https://w3id.org/valuesets/data_science/binary_classification slot_uri: valuesets:spam_classification range: SpamClassificationEnum anomaly_detection: name: anomaly_detection definition_uri: https://w3id.org/valuesets/anomaly_detection description: Labels for anomaly detection tasks - from_schema: https://w3id.org/linkml/valuesets/data_science/binary_classification + from_schema: https://w3id.org/valuesets/data_science/binary_classification slot_uri: valuesets:anomaly_detection range: AnomalyDetectionEnum churn_classification: name: churn_classification definition_uri: https://w3id.org/valuesets/churn_classification description: Customer churn prediction labels - from_schema: https://w3id.org/linkml/valuesets/data_science/binary_classification + from_schema: https://w3id.org/valuesets/data_science/binary_classification slot_uri: valuesets:churn_classification range: ChurnClassificationEnum fraud_detection: name: fraud_detection definition_uri: https://w3id.org/valuesets/fraud_detection description: Fraud detection classification labels - from_schema: https://w3id.org/linkml/valuesets/data_science/binary_classification + from_schema: https://w3id.org/valuesets/data_science/binary_classification slot_uri: valuesets:fraud_detection range: FraudDetectionEnum quality_control: name: quality_control definition_uri: https://w3id.org/valuesets/quality_control description: Quality control classification labels - from_schema: https://w3id.org/linkml/valuesets/data_science/quality_control + from_schema: https://w3id.org/valuesets/data_science/quality_control slot_uri: valuesets:quality_control range: QualityControlEnum defect_classification: name: defect_classification definition_uri: https://w3id.org/valuesets/defect_classification description: Manufacturing defect classification - from_schema: https://w3id.org/linkml/valuesets/data_science/quality_control + from_schema: https://w3id.org/valuesets/data_science/quality_control slot_uri: valuesets:defect_classification range: DefectClassificationEnum basic_emotion: name: basic_emotion definition_uri: https://w3id.org/valuesets/basic_emotion description: Ekman's six basic emotions commonly used in emotion recognition - from_schema: https://w3id.org/linkml/valuesets/data_science/emotion_classification + from_schema: https://w3id.org/valuesets/data_science/emotion_classification slot_uri: valuesets:basic_emotion range: BasicEmotionEnum extended_emotion: name: extended_emotion definition_uri: https://w3id.org/valuesets/extended_emotion description: Extended emotion set including complex emotions - from_schema: https://w3id.org/linkml/valuesets/data_science/emotion_classification + from_schema: https://w3id.org/valuesets/data_science/emotion_classification slot_uri: valuesets:extended_emotion range: ExtendedEmotionEnum priority_level: name: priority_level definition_uri: https://w3id.org/valuesets/priority_level description: Standard priority levels for task/issue classification - from_schema: https://w3id.org/linkml/valuesets/data_science/priority_severity + from_schema: https://w3id.org/valuesets/data_science/priority_severity slot_uri: valuesets:priority_level range: PriorityLevelEnum severity_level: name: severity_level definition_uri: https://w3id.org/valuesets/severity_level description: Severity levels for incident/bug classification - from_schema: https://w3id.org/linkml/valuesets/data_science/priority_severity + from_schema: https://w3id.org/valuesets/data_science/priority_severity slot_uri: valuesets:severity_level range: SeverityLevelEnum confidence_level: name: confidence_level definition_uri: https://w3id.org/valuesets/confidence_level description: Confidence levels for predictions and classifications - from_schema: https://w3id.org/linkml/valuesets/data_science/priority_severity + from_schema: https://w3id.org/valuesets/data_science/priority_severity slot_uri: valuesets:confidence_level range: ConfidenceLevelEnum news_topic_category: name: news_topic_category definition_uri: https://w3id.org/valuesets/news_topic_category description: Common news article topic categories - from_schema: https://w3id.org/linkml/valuesets/data_science/text_classification + from_schema: https://w3id.org/valuesets/data_science/text_classification slot_uri: valuesets:news_topic_category range: NewsTopicCategoryEnum toxicity_classification: name: toxicity_classification definition_uri: https://w3id.org/valuesets/toxicity_classification description: Text toxicity classification labels - from_schema: https://w3id.org/linkml/valuesets/data_science/text_classification + from_schema: https://w3id.org/valuesets/data_science/text_classification slot_uri: valuesets:toxicity_classification range: ToxicityClassificationEnum intent_classification: name: intent_classification definition_uri: https://w3id.org/valuesets/intent_classification description: Common chatbot/NLU intent categories - from_schema: https://w3id.org/linkml/valuesets/data_science/text_classification + from_schema: https://w3id.org/valuesets/data_science/text_classification slot_uri: valuesets:intent_classification range: IntentClassificationEnum simple_spatial_direction: name: simple_spatial_direction definition_uri: https://w3id.org/valuesets/simple_spatial_direction description: Basic spatial directional terms for general use - from_schema: https://w3id.org/linkml/valuesets/spatial/spatial_qualifiers + from_schema: https://w3id.org/valuesets/spatial/spatial_qualifiers slot_uri: valuesets:simple_spatial_direction range: SimpleSpatialDirection anatomical_side: name: anatomical_side definition_uri: https://w3id.org/valuesets/anatomical_side description: Anatomical sides as defined in the Biological Spatial Ontology (BSPO) - from_schema: https://w3id.org/linkml/valuesets/spatial/spatial_qualifiers + from_schema: https://w3id.org/valuesets/spatial/spatial_qualifiers slot_uri: valuesets:anatomical_side range: AnatomicalSide anatomical_region: name: anatomical_region definition_uri: https://w3id.org/valuesets/anatomical_region description: Anatomical regions based on spatial position - from_schema: https://w3id.org/linkml/valuesets/spatial/spatial_qualifiers + from_schema: https://w3id.org/valuesets/spatial/spatial_qualifiers slot_uri: valuesets:anatomical_region range: AnatomicalRegion anatomical_axis: name: anatomical_axis definition_uri: https://w3id.org/valuesets/anatomical_axis description: Anatomical axes defining spatial organization - from_schema: https://w3id.org/linkml/valuesets/spatial/spatial_qualifiers + from_schema: https://w3id.org/valuesets/spatial/spatial_qualifiers slot_uri: valuesets:anatomical_axis range: AnatomicalAxis anatomical_plane: name: anatomical_plane definition_uri: https://w3id.org/valuesets/anatomical_plane description: Standard anatomical planes for sectioning - from_schema: https://w3id.org/linkml/valuesets/spatial/spatial_qualifiers + from_schema: https://w3id.org/valuesets/spatial/spatial_qualifiers slot_uri: valuesets:anatomical_plane range: AnatomicalPlane spatial_relationship: name: spatial_relationship definition_uri: https://w3id.org/valuesets/spatial_relationship description: Spatial relationships between anatomical structures - from_schema: https://w3id.org/linkml/valuesets/spatial/spatial_qualifiers + from_schema: https://w3id.org/valuesets/spatial/spatial_qualifiers slot_uri: valuesets:spatial_relationship range: SpatialRelationship cell_polarity: name: cell_polarity definition_uri: https://w3id.org/valuesets/cell_polarity description: Spatial polarity in cells and tissues - from_schema: https://w3id.org/linkml/valuesets/spatial/spatial_qualifiers + from_schema: https://w3id.org/valuesets/spatial/spatial_qualifiers slot_uri: valuesets:cell_polarity range: CellPolarity anatomical_orientation: name: anatomical_orientation definition_uri: https://w3id.org/valuesets/anatomical_orientation description: Directional orientation between anatomical positions - from_schema: https://w3id.org/linkml/valuesets/spatial/spatial_qualifiers + from_schema: https://w3id.org/valuesets/spatial/spatial_qualifiers slot_uri: valuesets:anatomical_orientation range: AnatomicalOrientation crystal_system: name: crystal_system definition_uri: https://w3id.org/valuesets/crystal_system description: The seven crystal systems in crystallography - from_schema: https://w3id.org/linkml/valuesets/materials_science/crystal_structures + from_schema: https://w3id.org/valuesets/materials_science/crystal_structures slot_uri: valuesets:crystal_system range: CrystalSystemEnum bravais_lattice: name: bravais_lattice definition_uri: https://w3id.org/valuesets/bravais_lattice description: The 14 Bravais lattices describing all possible crystal lattices - from_schema: https://w3id.org/linkml/valuesets/materials_science/crystal_structures + from_schema: https://w3id.org/valuesets/materials_science/crystal_structures slot_uri: valuesets:bravais_lattice range: BravaisLatticeEnum electrical_conductivity: name: electrical_conductivity definition_uri: https://w3id.org/valuesets/electrical_conductivity description: Classification of materials by electrical conductivity - from_schema: https://w3id.org/linkml/valuesets/materials_science/material_properties + from_schema: https://w3id.org/valuesets/materials_science/material_properties slot_uri: valuesets:electrical_conductivity range: ElectricalConductivityEnum magnetic_property: name: magnetic_property definition_uri: https://w3id.org/valuesets/magnetic_property description: Classification of materials by magnetic properties - from_schema: https://w3id.org/linkml/valuesets/materials_science/material_properties + from_schema: https://w3id.org/valuesets/materials_science/material_properties slot_uri: valuesets:magnetic_property range: MagneticPropertyEnum optical_property: name: optical_property definition_uri: https://w3id.org/valuesets/optical_property description: Optical properties of materials - from_schema: https://w3id.org/linkml/valuesets/materials_science/material_properties + from_schema: https://w3id.org/valuesets/materials_science/material_properties slot_uri: valuesets:optical_property range: OpticalPropertyEnum thermal_conductivity: name: thermal_conductivity definition_uri: https://w3id.org/valuesets/thermal_conductivity description: Classification by thermal conductivity - from_schema: https://w3id.org/linkml/valuesets/materials_science/material_properties + from_schema: https://w3id.org/valuesets/materials_science/material_properties slot_uri: valuesets:thermal_conductivity range: ThermalConductivityEnum mechanical_behavior: name: mechanical_behavior definition_uri: https://w3id.org/valuesets/mechanical_behavior description: Mechanical behavior of materials under stress - from_schema: https://w3id.org/linkml/valuesets/materials_science/material_properties + from_schema: https://w3id.org/valuesets/materials_science/material_properties slot_uri: valuesets:mechanical_behavior range: MechanicalBehaviorEnum microscopy_method: name: microscopy_method definition_uri: https://w3id.org/valuesets/microscopy_method description: Microscopy techniques for material characterization - from_schema: https://w3id.org/linkml/valuesets/materials_science/characterization_methods + from_schema: https://w3id.org/valuesets/materials_science/characterization_methods slot_uri: valuesets:microscopy_method range: MicroscopyMethodEnum spectroscopy_method: name: spectroscopy_method definition_uri: https://w3id.org/valuesets/spectroscopy_method description: Spectroscopy techniques for material analysis - from_schema: https://w3id.org/linkml/valuesets/materials_science/characterization_methods + from_schema: https://w3id.org/valuesets/materials_science/characterization_methods slot_uri: valuesets:spectroscopy_method range: SpectroscopyMethodEnum thermal_analysis_method: name: thermal_analysis_method definition_uri: https://w3id.org/valuesets/thermal_analysis_method description: Thermal analysis techniques - from_schema: https://w3id.org/linkml/valuesets/materials_science/characterization_methods + from_schema: https://w3id.org/valuesets/materials_science/characterization_methods slot_uri: valuesets:thermal_analysis_method range: ThermalAnalysisMethodEnum mechanical_testing_method: name: mechanical_testing_method definition_uri: https://w3id.org/valuesets/mechanical_testing_method description: Mechanical testing methods - from_schema: https://w3id.org/linkml/valuesets/materials_science/characterization_methods + from_schema: https://w3id.org/valuesets/materials_science/characterization_methods slot_uri: valuesets:mechanical_testing_method range: MechanicalTestingMethodEnum material_class: name: material_class definition_uri: https://w3id.org/valuesets/material_class description: Major classes of materials - from_schema: https://w3id.org/linkml/valuesets/materials_science/material_types + from_schema: https://w3id.org/valuesets/materials_science/material_types slot_uri: valuesets:material_class range: MaterialClassEnum polymer_type: name: polymer_type definition_uri: https://w3id.org/valuesets/polymer_type description: Types of polymer materials - from_schema: https://w3id.org/linkml/valuesets/materials_science/material_types + from_schema: https://w3id.org/valuesets/materials_science/material_types slot_uri: valuesets:polymer_type range: PolymerTypeEnum metal_type: name: metal_type definition_uri: https://w3id.org/valuesets/metal_type description: Types of metallic materials - from_schema: https://w3id.org/linkml/valuesets/materials_science/material_types + from_schema: https://w3id.org/valuesets/materials_science/material_types slot_uri: valuesets:metal_type range: MetalTypeEnum composite_type: name: composite_type definition_uri: https://w3id.org/valuesets/composite_type description: Types of composite materials - from_schema: https://w3id.org/linkml/valuesets/materials_science/material_types + from_schema: https://w3id.org/valuesets/materials_science/material_types slot_uri: valuesets:composite_type range: CompositeTypeEnum synthesis_method: name: synthesis_method definition_uri: https://w3id.org/valuesets/synthesis_method description: Common material synthesis and processing methods - from_schema: https://w3id.org/linkml/valuesets/materials_science/synthesis_methods + from_schema: https://w3id.org/valuesets/materials_science/synthesis_methods slot_uri: valuesets:synthesis_method range: SynthesisMethodEnum crystal_growth_method: name: crystal_growth_method definition_uri: https://w3id.org/valuesets/crystal_growth_method description: Methods for growing single crystals - from_schema: https://w3id.org/linkml/valuesets/materials_science/synthesis_methods + from_schema: https://w3id.org/valuesets/materials_science/synthesis_methods slot_uri: valuesets:crystal_growth_method range: CrystalGrowthMethodEnum additive_manufacturing: name: additive_manufacturing definition_uri: https://w3id.org/valuesets/additive_manufacturing description: 3D printing and additive manufacturing methods - from_schema: https://w3id.org/linkml/valuesets/materials_science/synthesis_methods + from_schema: https://w3id.org/valuesets/materials_science/synthesis_methods slot_uri: valuesets:additive_manufacturing range: AdditiveManufacturingEnum traditional_pigment: @@ -67247,7 +67247,7 @@ slots: definition_uri: https://w3id.org/valuesets/iupac_nucleotide description: Complete IUPAC nucleotide codes including ambiguous bases for DNA/RNA sequences - from_schema: https://w3id.org/linkml/valuesets/bio/sequence_chemistry + from_schema: https://w3id.org/valuesets/bio/sequence_chemistry slot_uri: valuesets:iupac_nucleotide range: IUPACNucleotideCode standard_amino_acid: @@ -67255,7 +67255,7 @@ slots: definition_uri: https://w3id.org/valuesets/standard_amino_acid description: The 20 standard proteinogenic amino acids with IUPAC single-letter codes - from_schema: https://w3id.org/linkml/valuesets/bio/sequence_chemistry + from_schema: https://w3id.org/valuesets/bio/sequence_chemistry slot_uri: valuesets:standard_amino_acid range: StandardAminoAcid iupac_amino_acid: @@ -67263,14 +67263,14 @@ slots: definition_uri: https://w3id.org/valuesets/iupac_amino_acid description: Complete IUPAC amino acid codes including standard amino acids, rare amino acids, and ambiguity codes - from_schema: https://w3id.org/linkml/valuesets/bio/sequence_chemistry + from_schema: https://w3id.org/valuesets/bio/sequence_chemistry slot_uri: valuesets:iupac_amino_acid range: IUPACAminoAcidCode sequence_alphabet: name: sequence_alphabet definition_uri: https://w3id.org/valuesets/sequence_alphabet description: Types of sequence alphabets used in bioinformatics - from_schema: https://w3id.org/linkml/valuesets/bio/sequence_chemistry + from_schema: https://w3id.org/valuesets/bio/sequence_chemistry slot_uri: valuesets:sequence_alphabet range: SequenceAlphabet sequence_quality_encoding: @@ -67278,35 +67278,35 @@ slots: definition_uri: https://w3id.org/valuesets/sequence_quality_encoding description: Quality score encoding standards used in FASTQ files and sequencing data - from_schema: https://w3id.org/linkml/valuesets/bio/sequence_chemistry + from_schema: https://w3id.org/valuesets/bio/sequence_chemistry slot_uri: valuesets:sequence_quality_encoding range: SequenceQualityEncoding genetic_code_table: name: genetic_code_table definition_uri: https://w3id.org/valuesets/genetic_code_table description: NCBI genetic code translation tables for different organisms - from_schema: https://w3id.org/linkml/valuesets/bio/sequence_chemistry + from_schema: https://w3id.org/valuesets/bio/sequence_chemistry slot_uri: valuesets:genetic_code_table range: GeneticCodeTable sequence_strand: name: sequence_strand definition_uri: https://w3id.org/valuesets/sequence_strand description: Strand orientation for nucleic acid sequences - from_schema: https://w3id.org/linkml/valuesets/bio/sequence_chemistry + from_schema: https://w3id.org/valuesets/bio/sequence_chemistry slot_uri: valuesets:sequence_strand range: SequenceStrand sequence_topology: name: sequence_topology definition_uri: https://w3id.org/valuesets/sequence_topology description: Topological structure of nucleic acid molecules - from_schema: https://w3id.org/linkml/valuesets/bio/sequence_chemistry + from_schema: https://w3id.org/valuesets/bio/sequence_chemistry slot_uri: valuesets:sequence_topology range: SequenceTopology sequence_modality: name: sequence_modality definition_uri: https://w3id.org/valuesets/sequence_modality description: Types of sequence data based on experimental method - from_schema: https://w3id.org/linkml/valuesets/bio/sequence_chemistry + from_schema: https://w3id.org/valuesets/bio/sequence_chemistry slot_uri: valuesets:sequence_modality range: SequenceModality sequencing_platform: @@ -67314,49 +67314,49 @@ slots: definition_uri: https://w3id.org/valuesets/sequencing_platform description: Major DNA/RNA sequencing platforms and instruments used in genomics research - from_schema: https://w3id.org/linkml/valuesets/bio/sequencing_platforms + from_schema: https://w3id.org/valuesets/bio/sequencing_platforms slot_uri: valuesets:sequencing_platform range: SequencingPlatform sequencing_chemistry: name: sequencing_chemistry definition_uri: https://w3id.org/valuesets/sequencing_chemistry description: Fundamental chemical methods used for DNA/RNA sequencing - from_schema: https://w3id.org/linkml/valuesets/bio/sequencing_platforms + from_schema: https://w3id.org/valuesets/bio/sequencing_platforms slot_uri: valuesets:sequencing_chemistry range: SequencingChemistry library_preparation: name: library_preparation definition_uri: https://w3id.org/valuesets/library_preparation description: Methods for preparing sequencing libraries from nucleic acid samples - from_schema: https://w3id.org/linkml/valuesets/bio/sequencing_platforms + from_schema: https://w3id.org/valuesets/bio/sequencing_platforms slot_uri: valuesets:library_preparation range: LibraryPreparation sequencing_application: name: sequencing_application definition_uri: https://w3id.org/valuesets/sequencing_application description: Primary applications or assays using DNA/RNA sequencing - from_schema: https://w3id.org/linkml/valuesets/bio/sequencing_platforms + from_schema: https://w3id.org/valuesets/bio/sequencing_platforms slot_uri: valuesets:sequencing_application range: SequencingApplication read: name: read definition_uri: https://w3id.org/valuesets/read description: Configuration of sequencing reads generated by different platforms - from_schema: https://w3id.org/linkml/valuesets/bio/sequencing_platforms + from_schema: https://w3id.org/valuesets/bio/sequencing_platforms slot_uri: valuesets:read range: ReadType sequence_file_format: name: sequence_file_format definition_uri: https://w3id.org/valuesets/sequence_file_format description: Standard file formats used for storing sequence data - from_schema: https://w3id.org/linkml/valuesets/bio/sequencing_platforms + from_schema: https://w3id.org/valuesets/bio/sequencing_platforms slot_uri: valuesets:sequence_file_format range: SequenceFileFormat data_processing_level: name: data_processing_level definition_uri: https://w3id.org/valuesets/data_processing_level description: Levels of processing applied to raw sequencing data - from_schema: https://w3id.org/linkml/valuesets/bio/sequencing_platforms + from_schema: https://w3id.org/valuesets/bio/sequencing_platforms slot_uri: valuesets:data_processing_level range: DataProcessingLevel cds_phase: @@ -67927,7 +67927,7 @@ slots: definition_uri: https://w3id.org/valuesets/race_omb1997 description: Race categories following OMB 1997 standards used by NIH and federal agencies - from_schema: https://w3id.org/linkml/valuesets/clinical/nih_demographics + from_schema: https://w3id.org/valuesets/clinical/nih_demographics slot_uri: valuesets:race_omb1997 range: RaceOMB1997Enum ethnicity_omb1997: @@ -67935,7 +67935,7 @@ slots: definition_uri: https://w3id.org/valuesets/ethnicity_omb1997 description: Ethnicity categories following OMB 1997 standards used by NIH and federal agencies - from_schema: https://w3id.org/linkml/valuesets/clinical/nih_demographics + from_schema: https://w3id.org/valuesets/clinical/nih_demographics slot_uri: valuesets:ethnicity_omb1997 range: EthnicityOMB1997Enum biological_sex: @@ -67943,7 +67943,7 @@ slots: definition_uri: https://w3id.org/valuesets/biological_sex description: Biological sex assigned at birth based on anatomical and physiological traits - from_schema: https://w3id.org/linkml/valuesets/clinical/nih_demographics + from_schema: https://w3id.org/valuesets/clinical/nih_demographics slot_uri: valuesets:biological_sex range: BiologicalSexEnum age_group: @@ -67951,161 +67951,161 @@ slots: definition_uri: https://w3id.org/valuesets/age_group description: Standard age groups used in NIH clinical research, particularly NINDS CDEs - from_schema: https://w3id.org/linkml/valuesets/clinical/nih_demographics + from_schema: https://w3id.org/valuesets/clinical/nih_demographics slot_uri: valuesets:age_group range: AgeGroupEnum participant_vital_status: name: participant_vital_status definition_uri: https://w3id.org/valuesets/participant_vital_status description: Vital status of a research participant in clinical studies - from_schema: https://w3id.org/linkml/valuesets/clinical/nih_demographics + from_schema: https://w3id.org/valuesets/clinical/nih_demographics slot_uri: valuesets:participant_vital_status range: ParticipantVitalStatusEnum recruitment_status: name: recruitment_status definition_uri: https://w3id.org/valuesets/recruitment_status description: Clinical trial or study recruitment status per NIH/ClinicalTrials - from_schema: https://w3id.org/linkml/valuesets/clinical/nih_demographics + from_schema: https://w3id.org/valuesets/clinical/nih_demographics slot_uri: valuesets:recruitment_status range: RecruitmentStatusEnum study_phase: name: study_phase definition_uri: https://w3id.org/valuesets/study_phase description: Clinical trial phases per FDA and NIH definitions - from_schema: https://w3id.org/linkml/valuesets/clinical/nih_demographics + from_schema: https://w3id.org/valuesets/clinical/nih_demographics slot_uri: valuesets:study_phase range: StudyPhaseEnum karyotypic_sex: name: karyotypic_sex definition_uri: https://w3id.org/valuesets/karyotypic_sex description: Karyotypic sex of an individual based on chromosome composition - from_schema: https://w3id.org/linkml/valuesets/clinical/phenopackets + from_schema: https://w3id.org/valuesets/clinical/phenopackets slot_uri: valuesets:karyotypic_sex range: KaryotypicSexEnum phenotypic_sex: name: phenotypic_sex definition_uri: https://w3id.org/valuesets/phenotypic_sex description: Phenotypic sex of an individual based on observable characteristics - from_schema: https://w3id.org/linkml/valuesets/clinical/phenopackets + from_schema: https://w3id.org/valuesets/clinical/phenopackets slot_uri: valuesets:phenotypic_sex range: PhenotypicSexEnum allelic_state: name: allelic_state definition_uri: https://w3id.org/valuesets/allelic_state description: Allelic state/zygosity of a variant or genetic feature - from_schema: https://w3id.org/linkml/valuesets/clinical/phenopackets + from_schema: https://w3id.org/valuesets/clinical/phenopackets slot_uri: valuesets:allelic_state range: AllelicStateEnum laterality: name: laterality definition_uri: https://w3id.org/valuesets/laterality description: Laterality/sidedness of a finding or anatomical structure - from_schema: https://w3id.org/linkml/valuesets/clinical/phenopackets + from_schema: https://w3id.org/valuesets/clinical/phenopackets slot_uri: valuesets:laterality range: LateralityEnum onset_timing: name: onset_timing definition_uri: https://w3id.org/valuesets/onset_timing description: Timing of disease or phenotype onset relative to developmental stages - from_schema: https://w3id.org/linkml/valuesets/clinical/phenopackets + from_schema: https://w3id.org/valuesets/clinical/phenopackets slot_uri: valuesets:onset_timing range: OnsetTimingEnum acmg_pathogenicity: name: acmg_pathogenicity definition_uri: https://w3id.org/valuesets/acmg_pathogenicity description: ACMG/AMP variant pathogenicity classification for clinical genetics - from_schema: https://w3id.org/linkml/valuesets/clinical/phenopackets + from_schema: https://w3id.org/valuesets/clinical/phenopackets slot_uri: valuesets:acmg_pathogenicity range: ACMGPathogenicityEnum therapeutic_actionability: name: therapeutic_actionability definition_uri: https://w3id.org/valuesets/therapeutic_actionability description: Clinical actionability of a genetic finding for treatment decisions - from_schema: https://w3id.org/linkml/valuesets/clinical/phenopackets + from_schema: https://w3id.org/valuesets/clinical/phenopackets slot_uri: valuesets:therapeutic_actionability range: TherapeuticActionabilityEnum interpretation_progress: name: interpretation_progress definition_uri: https://w3id.org/valuesets/interpretation_progress description: Progress status of clinical interpretation or diagnosis - from_schema: https://w3id.org/linkml/valuesets/clinical/phenopackets + from_schema: https://w3id.org/valuesets/clinical/phenopackets slot_uri: valuesets:interpretation_progress range: InterpretationProgressEnum regimen_status: name: regimen_status definition_uri: https://w3id.org/valuesets/regimen_status description: Status of a therapeutic regimen or treatment protocol - from_schema: https://w3id.org/linkml/valuesets/clinical/phenopackets + from_schema: https://w3id.org/valuesets/clinical/phenopackets slot_uri: valuesets:regimen_status range: RegimenStatusEnum drug_response: name: drug_response definition_uri: https://w3id.org/valuesets/drug_response description: Response categories for drug treatment outcomes - from_schema: https://w3id.org/linkml/valuesets/clinical/phenopackets + from_schema: https://w3id.org/valuesets/clinical/phenopackets slot_uri: valuesets:drug_response range: DrugResponseEnum process_scale: name: process_scale definition_uri: https://w3id.org/valuesets/process_scale description: Scale of bioprocessing operations from lab bench to commercial production - from_schema: https://w3id.org/linkml/valuesets/bioprocessing/scale_up + from_schema: https://w3id.org/valuesets/bioprocessing/scale_up slot_uri: valuesets:process_scale range: ProcessScaleEnum bioreactor_type: name: bioreactor_type definition_uri: https://w3id.org/valuesets/bioreactor_type description: Types of bioreactors used in fermentation and cell culture - from_schema: https://w3id.org/linkml/valuesets/bioprocessing/scale_up + from_schema: https://w3id.org/valuesets/bioprocessing/scale_up slot_uri: valuesets:bioreactor_type range: BioreactorTypeEnum fermentation_mode: name: fermentation_mode definition_uri: https://w3id.org/valuesets/fermentation_mode description: Modes of fermentation operation - from_schema: https://w3id.org/linkml/valuesets/bioprocessing/scale_up + from_schema: https://w3id.org/valuesets/bioprocessing/scale_up slot_uri: valuesets:fermentation_mode range: FermentationModeEnum oxygenation_strategy: name: oxygenation_strategy definition_uri: https://w3id.org/valuesets/oxygenation_strategy description: Oxygen supply strategies for fermentation - from_schema: https://w3id.org/linkml/valuesets/bioprocessing/scale_up + from_schema: https://w3id.org/valuesets/bioprocessing/scale_up slot_uri: valuesets:oxygenation_strategy range: OxygenationStrategyEnum agitation_type: name: agitation_type definition_uri: https://w3id.org/valuesets/agitation_type description: Types of agitation/mixing in bioreactors - from_schema: https://w3id.org/linkml/valuesets/bioprocessing/scale_up + from_schema: https://w3id.org/valuesets/bioprocessing/scale_up slot_uri: valuesets:agitation_type range: AgitationTypeEnum downstream_process: name: downstream_process definition_uri: https://w3id.org/valuesets/downstream_process description: Downstream processing unit operations - from_schema: https://w3id.org/linkml/valuesets/bioprocessing/scale_up + from_schema: https://w3id.org/valuesets/bioprocessing/scale_up slot_uri: valuesets:downstream_process range: DownstreamProcessEnum feedstock_type: name: feedstock_type definition_uri: https://w3id.org/valuesets/feedstock_type description: Types of feedstocks for bioprocessing - from_schema: https://w3id.org/linkml/valuesets/bioprocessing/scale_up + from_schema: https://w3id.org/valuesets/bioprocessing/scale_up slot_uri: valuesets:feedstock_type range: FeedstockTypeEnum product_type: name: product_type definition_uri: https://w3id.org/valuesets/product_type description: Types of products from bioprocessing - from_schema: https://w3id.org/linkml/valuesets/bioprocessing/scale_up + from_schema: https://w3id.org/valuesets/bioprocessing/scale_up slot_uri: valuesets:product_type range: ProductTypeEnum sterilization_method: name: sterilization_method definition_uri: https://w3id.org/valuesets/sterilization_method description: Methods for sterilization in bioprocessing - from_schema: https://w3id.org/linkml/valuesets/bioprocessing/scale_up + from_schema: https://w3id.org/valuesets/bioprocessing/scale_up slot_uri: valuesets:sterilization_method range: SterilizationMethodEnum length_unit: @@ -68303,448 +68303,448 @@ slots: name: legal_entity_type definition_uri: https://w3id.org/valuesets/legal_entity_type description: Legal structure of business entity - from_schema: https://w3id.org/linkml/valuesets/business/organizational_structures + from_schema: https://w3id.org/valuesets/business/organizational_structures slot_uri: valuesets:legal_entity_type range: LegalEntityTypeEnum organizational_structure: name: organizational_structure definition_uri: https://w3id.org/valuesets/organizational_structure description: Organizational hierarchy and reporting structure - from_schema: https://w3id.org/linkml/valuesets/business/organizational_structures + from_schema: https://w3id.org/valuesets/business/organizational_structures slot_uri: valuesets:organizational_structure range: OrganizationalStructureEnum management_level: name: management_level definition_uri: https://w3id.org/valuesets/management_level description: Level within organizational hierarchy - from_schema: https://w3id.org/linkml/valuesets/business/organizational_structures + from_schema: https://w3id.org/valuesets/business/organizational_structures slot_uri: valuesets:management_level range: ManagementLevelEnum corporate_governance_role: name: corporate_governance_role definition_uri: https://w3id.org/valuesets/corporate_governance_role description: Role in corporate governance structure - from_schema: https://w3id.org/linkml/valuesets/business/organizational_structures + from_schema: https://w3id.org/valuesets/business/organizational_structures slot_uri: valuesets:corporate_governance_role range: CorporateGovernanceRoleEnum business_ownership_type: name: business_ownership_type definition_uri: https://w3id.org/valuesets/business_ownership_type description: Type of business ownership structure - from_schema: https://w3id.org/linkml/valuesets/business/organizational_structures + from_schema: https://w3id.org/valuesets/business/organizational_structures slot_uri: valuesets:business_ownership_type range: BusinessOwnershipTypeEnum business_size_classification: name: business_size_classification definition_uri: https://w3id.org/valuesets/business_size_classification description: Size classification of business entity - from_schema: https://w3id.org/linkml/valuesets/business/organizational_structures + from_schema: https://w3id.org/valuesets/business/organizational_structures slot_uri: valuesets:business_size_classification range: BusinessSizeClassificationEnum business_lifecycle_stage: name: business_lifecycle_stage definition_uri: https://w3id.org/valuesets/business_lifecycle_stage description: Stage in business development lifecycle - from_schema: https://w3id.org/linkml/valuesets/business/organizational_structures + from_schema: https://w3id.org/valuesets/business/organizational_structures slot_uri: valuesets:business_lifecycle_stage range: BusinessLifecycleStageEnum naics_sector: name: naics_sector definition_uri: https://w3id.org/valuesets/naics_sector description: NAICS two-digit sector classification - from_schema: https://w3id.org/linkml/valuesets/business/industry_classifications + from_schema: https://w3id.org/valuesets/business/industry_classifications slot_uri: valuesets:naics_sector range: NAICSSectorEnum economic_sector: name: economic_sector definition_uri: https://w3id.org/valuesets/economic_sector description: Broad economic sector classification - from_schema: https://w3id.org/linkml/valuesets/business/industry_classifications + from_schema: https://w3id.org/valuesets/business/industry_classifications slot_uri: valuesets:economic_sector range: EconomicSectorEnum business_activity_type: name: business_activity_type definition_uri: https://w3id.org/valuesets/business_activity_type description: Type of primary business activity - from_schema: https://w3id.org/linkml/valuesets/business/industry_classifications + from_schema: https://w3id.org/valuesets/business/industry_classifications slot_uri: valuesets:business_activity_type range: BusinessActivityTypeEnum industry_maturity: name: industry_maturity definition_uri: https://w3id.org/valuesets/industry_maturity description: Industry lifecycle and maturity stage - from_schema: https://w3id.org/linkml/valuesets/business/industry_classifications + from_schema: https://w3id.org/valuesets/business/industry_classifications slot_uri: valuesets:industry_maturity range: IndustryMaturityEnum market_structure: name: market_structure definition_uri: https://w3id.org/valuesets/market_structure description: Competitive structure of industry market - from_schema: https://w3id.org/linkml/valuesets/business/industry_classifications + from_schema: https://w3id.org/valuesets/business/industry_classifications slot_uri: valuesets:market_structure range: MarketStructureEnum industry_regulation_level: name: industry_regulation_level definition_uri: https://w3id.org/valuesets/industry_regulation_level description: Level of government regulation in industry - from_schema: https://w3id.org/linkml/valuesets/business/industry_classifications + from_schema: https://w3id.org/valuesets/business/industry_classifications slot_uri: valuesets:industry_regulation_level range: IndustryRegulationLevelEnum management_methodology: name: management_methodology definition_uri: https://w3id.org/valuesets/management_methodology description: Management approach or methodology - from_schema: https://w3id.org/linkml/valuesets/business/management_operations + from_schema: https://w3id.org/valuesets/business/management_operations slot_uri: valuesets:management_methodology range: ManagementMethodologyEnum strategic_framework: name: strategic_framework definition_uri: https://w3id.org/valuesets/strategic_framework description: Strategic planning and analysis framework - from_schema: https://w3id.org/linkml/valuesets/business/management_operations + from_schema: https://w3id.org/valuesets/business/management_operations slot_uri: valuesets:strategic_framework range: StrategicFrameworkEnum operational_model: name: operational_model definition_uri: https://w3id.org/valuesets/operational_model description: Business operational model or approach - from_schema: https://w3id.org/linkml/valuesets/business/management_operations + from_schema: https://w3id.org/valuesets/business/management_operations slot_uri: valuesets:operational_model range: OperationalModelEnum performance_measurement: name: performance_measurement definition_uri: https://w3id.org/valuesets/performance_measurement description: Performance measurement system or approach - from_schema: https://w3id.org/linkml/valuesets/business/management_operations + from_schema: https://w3id.org/valuesets/business/management_operations slot_uri: valuesets:performance_measurement range: PerformanceMeasurementEnum decision_making_style: name: decision_making_style definition_uri: https://w3id.org/valuesets/decision_making_style description: Decision-making approach or style - from_schema: https://w3id.org/linkml/valuesets/business/management_operations + from_schema: https://w3id.org/valuesets/business/management_operations slot_uri: valuesets:decision_making_style range: DecisionMakingStyleEnum leadership_style: name: leadership_style definition_uri: https://w3id.org/valuesets/leadership_style description: Leadership approach or style - from_schema: https://w3id.org/linkml/valuesets/business/management_operations + from_schema: https://w3id.org/valuesets/business/management_operations slot_uri: valuesets:leadership_style range: LeadershipStyleEnum business_process_type: name: business_process_type definition_uri: https://w3id.org/valuesets/business_process_type description: Type of business process - from_schema: https://w3id.org/linkml/valuesets/business/management_operations + from_schema: https://w3id.org/valuesets/business/management_operations slot_uri: valuesets:business_process_type range: BusinessProcessTypeEnum quality_standard: name: quality_standard definition_uri: https://w3id.org/valuesets/quality_standard description: Quality management standard or framework - from_schema: https://w3id.org/linkml/valuesets/business/quality_management + from_schema: https://w3id.org/valuesets/business/quality_management slot_uri: valuesets:quality_standard range: QualityStandardEnum quality_methodology: name: quality_methodology definition_uri: https://w3id.org/valuesets/quality_methodology description: Quality improvement methodology - from_schema: https://w3id.org/linkml/valuesets/business/quality_management + from_schema: https://w3id.org/valuesets/business/quality_management slot_uri: valuesets:quality_methodology range: QualityMethodologyEnum quality_control_technique: name: quality_control_technique definition_uri: https://w3id.org/valuesets/quality_control_technique description: Quality control technique or tool - from_schema: https://w3id.org/linkml/valuesets/business/quality_management + from_schema: https://w3id.org/valuesets/business/quality_management slot_uri: valuesets:quality_control_technique range: QualityControlTechniqueEnum quality_assurance_level: name: quality_assurance_level definition_uri: https://w3id.org/valuesets/quality_assurance_level description: Level of quality assurance implementation - from_schema: https://w3id.org/linkml/valuesets/business/quality_management + from_schema: https://w3id.org/valuesets/business/quality_management slot_uri: valuesets:quality_assurance_level range: QualityAssuranceLevelEnum process_improvement_approach: name: process_improvement_approach definition_uri: https://w3id.org/valuesets/process_improvement_approach description: Process improvement methodology - from_schema: https://w3id.org/linkml/valuesets/business/quality_management + from_schema: https://w3id.org/valuesets/business/quality_management slot_uri: valuesets:process_improvement_approach range: ProcessImprovementApproachEnum quality_maturity_level: name: quality_maturity_level definition_uri: https://w3id.org/valuesets/quality_maturity_level description: Organizational quality maturity level - from_schema: https://w3id.org/linkml/valuesets/business/quality_management + from_schema: https://w3id.org/valuesets/business/quality_management slot_uri: valuesets:quality_maturity_level range: QualityMaturityLevelEnum procurement_type: name: procurement_type definition_uri: https://w3id.org/valuesets/procurement_type description: Type of procurement activity or approach - from_schema: https://w3id.org/linkml/valuesets/business/supply_chain + from_schema: https://w3id.org/valuesets/business/supply_chain slot_uri: valuesets:procurement_type range: ProcurementTypeEnum vendor_category: name: vendor_category definition_uri: https://w3id.org/valuesets/vendor_category description: Vendor classification category - from_schema: https://w3id.org/linkml/valuesets/business/supply_chain + from_schema: https://w3id.org/valuesets/business/supply_chain slot_uri: valuesets:vendor_category range: VendorCategoryEnum supply_chain_strategy: name: supply_chain_strategy definition_uri: https://w3id.org/valuesets/supply_chain_strategy description: Supply chain strategic approach - from_schema: https://w3id.org/linkml/valuesets/business/supply_chain + from_schema: https://w3id.org/valuesets/business/supply_chain slot_uri: valuesets:supply_chain_strategy range: SupplyChainStrategyEnum logistics_operation: name: logistics_operation definition_uri: https://w3id.org/valuesets/logistics_operation description: Type of logistics operation - from_schema: https://w3id.org/linkml/valuesets/business/supply_chain + from_schema: https://w3id.org/valuesets/business/supply_chain slot_uri: valuesets:logistics_operation range: LogisticsOperationEnum sourcing_strategy: name: sourcing_strategy definition_uri: https://w3id.org/valuesets/sourcing_strategy description: Sourcing strategy approach - from_schema: https://w3id.org/linkml/valuesets/business/supply_chain + from_schema: https://w3id.org/valuesets/business/supply_chain slot_uri: valuesets:sourcing_strategy range: SourcingStrategyEnum supplier_relationship_type: name: supplier_relationship_type definition_uri: https://w3id.org/valuesets/supplier_relationship_type description: Type of supplier relationship management - from_schema: https://w3id.org/linkml/valuesets/business/supply_chain + from_schema: https://w3id.org/valuesets/business/supply_chain slot_uri: valuesets:supplier_relationship_type range: SupplierRelationshipTypeEnum inventory_management_approach: name: inventory_management_approach definition_uri: https://w3id.org/valuesets/inventory_management_approach description: Inventory management methodology - from_schema: https://w3id.org/linkml/valuesets/business/supply_chain + from_schema: https://w3id.org/valuesets/business/supply_chain slot_uri: valuesets:inventory_management_approach range: InventoryManagementApproachEnum employment_type: name: employment_type definition_uri: https://w3id.org/valuesets/employment_type description: Type of employment arrangement - from_schema: https://w3id.org/linkml/valuesets/business/human_resources + from_schema: https://w3id.org/valuesets/business/human_resources slot_uri: valuesets:employment_type range: EmploymentTypeEnum job_level: name: job_level definition_uri: https://w3id.org/valuesets/job_level description: Organizational job level or seniority - from_schema: https://w3id.org/linkml/valuesets/business/human_resources + from_schema: https://w3id.org/valuesets/business/human_resources slot_uri: valuesets:job_level range: JobLevelEnum hr_function: name: hr_function definition_uri: https://w3id.org/valuesets/hr_function description: Human resources functional area - from_schema: https://w3id.org/linkml/valuesets/business/human_resources + from_schema: https://w3id.org/valuesets/business/human_resources slot_uri: valuesets:hr_function range: HRFunctionEnum compensation_type: name: compensation_type definition_uri: https://w3id.org/valuesets/compensation_type description: Type of employee compensation - from_schema: https://w3id.org/linkml/valuesets/business/human_resources + from_schema: https://w3id.org/valuesets/business/human_resources slot_uri: valuesets:compensation_type range: CompensationTypeEnum performance_rating: name: performance_rating definition_uri: https://w3id.org/valuesets/performance_rating description: Employee performance evaluation rating - from_schema: https://w3id.org/linkml/valuesets/business/human_resources + from_schema: https://w3id.org/valuesets/business/human_resources slot_uri: valuesets:performance_rating range: PerformanceRatingEnum recruitment_source: name: recruitment_source definition_uri: https://w3id.org/valuesets/recruitment_source description: Source of candidate recruitment - from_schema: https://w3id.org/linkml/valuesets/business/human_resources + from_schema: https://w3id.org/valuesets/business/human_resources slot_uri: valuesets:recruitment_source range: RecruitmentSourceEnum training_type: name: training_type definition_uri: https://w3id.org/valuesets/training_type description: Type of employee training or development - from_schema: https://w3id.org/linkml/valuesets/business/human_resources + from_schema: https://w3id.org/valuesets/business/human_resources slot_uri: valuesets:training_type range: TrainingTypeEnum employee_status: name: employee_status definition_uri: https://w3id.org/valuesets/employee_status description: Current employment status - from_schema: https://w3id.org/linkml/valuesets/business/human_resources + from_schema: https://w3id.org/valuesets/business/human_resources slot_uri: valuesets:employee_status range: EmployeeStatusEnum work_arrangement: name: work_arrangement definition_uri: https://w3id.org/valuesets/work_arrangement description: Work location and arrangement type - from_schema: https://w3id.org/linkml/valuesets/business/human_resources + from_schema: https://w3id.org/valuesets/business/human_resources slot_uri: valuesets:work_arrangement range: WorkArrangementEnum benefits_category: name: benefits_category definition_uri: https://w3id.org/valuesets/benefits_category description: Category of employee benefits - from_schema: https://w3id.org/linkml/valuesets/business/human_resources + from_schema: https://w3id.org/valuesets/business/human_resources slot_uri: valuesets:benefits_category range: BenefitsCategoryEnum laboratory_device_type: name: laboratory_device_type definition_uri: https://w3id.org/valuesets/laboratory_device_type description: Type of automated laboratory equipment or device - from_schema: https://w3id.org/linkml/valuesets/lab_automation/devices + from_schema: https://w3id.org/valuesets/lab_automation/devices slot_uri: valuesets:laboratory_device_type range: LaboratoryDeviceTypeEnum robotic_arm_type: name: robotic_arm_type definition_uri: https://w3id.org/valuesets/robotic_arm_type description: Type of robotic arm used in laboratory automation - from_schema: https://w3id.org/linkml/valuesets/lab_automation/devices + from_schema: https://w3id.org/valuesets/lab_automation/devices slot_uri: valuesets:robotic_arm_type range: RoboticArmTypeEnum liquid_handling_operation: name: liquid_handling_operation definition_uri: https://w3id.org/valuesets/liquid_handling_operation description: Type of liquid handling operation in automated laboratory workflows - from_schema: https://w3id.org/linkml/valuesets/lab_automation/operations + from_schema: https://w3id.org/valuesets/lab_automation/operations slot_uri: valuesets:liquid_handling_operation range: LiquidHandlingOperationEnum sample_processing_operation: name: sample_processing_operation definition_uri: https://w3id.org/valuesets/sample_processing_operation description: Type of sample processing operation - from_schema: https://w3id.org/linkml/valuesets/lab_automation/operations + from_schema: https://w3id.org/valuesets/lab_automation/operations slot_uri: valuesets:sample_processing_operation range: SampleProcessingOperationEnum microplate_format: name: microplate_format definition_uri: https://w3id.org/valuesets/microplate_format description: Standard microplate well configuration - from_schema: https://w3id.org/linkml/valuesets/lab_automation/labware + from_schema: https://w3id.org/valuesets/lab_automation/labware slot_uri: valuesets:microplate_format range: MicroplateFormatEnum container_type: name: container_type definition_uri: https://w3id.org/valuesets/container_type description: Type of laboratory container - from_schema: https://w3id.org/linkml/valuesets/lab_automation/labware + from_schema: https://w3id.org/valuesets/lab_automation/labware slot_uri: valuesets:container_type range: ContainerTypeEnum plate_material: name: plate_material definition_uri: https://w3id.org/valuesets/plate_material description: Material composition of laboratory plates - from_schema: https://w3id.org/linkml/valuesets/lab_automation/labware + from_schema: https://w3id.org/valuesets/lab_automation/labware slot_uri: valuesets:plate_material range: PlateMaterialEnum plate_coating: name: plate_coating definition_uri: https://w3id.org/valuesets/plate_coating description: Surface treatment of laboratory plates - from_schema: https://w3id.org/linkml/valuesets/lab_automation/labware + from_schema: https://w3id.org/valuesets/lab_automation/labware slot_uri: valuesets:plate_coating range: PlateCoatingEnum workflow_orchestration_type: name: workflow_orchestration_type definition_uri: https://w3id.org/valuesets/workflow_orchestration_type description: Type of workflow orchestration approach - from_schema: https://w3id.org/linkml/valuesets/lab_automation/protocols + from_schema: https://w3id.org/valuesets/lab_automation/protocols slot_uri: valuesets:workflow_orchestration_type range: WorkflowOrchestrationTypeEnum scheduler_type: name: scheduler_type definition_uri: https://w3id.org/valuesets/scheduler_type description: Type of scheduling algorithm for laboratory automation - from_schema: https://w3id.org/linkml/valuesets/lab_automation/protocols + from_schema: https://w3id.org/valuesets/lab_automation/protocols slot_uri: valuesets:scheduler_type range: SchedulerTypeEnum protocol_state: name: protocol_state definition_uri: https://w3id.org/valuesets/protocol_state description: Execution state of a laboratory protocol - from_schema: https://w3id.org/linkml/valuesets/lab_automation/protocols + from_schema: https://w3id.org/valuesets/lab_automation/protocols slot_uri: valuesets:protocol_state range: ProtocolStateEnum execution_mode: name: execution_mode definition_uri: https://w3id.org/valuesets/execution_mode description: Mode of protocol execution - from_schema: https://w3id.org/linkml/valuesets/lab_automation/protocols + from_schema: https://w3id.org/valuesets/lab_automation/protocols slot_uri: valuesets:execution_mode range: ExecutionModeEnum automation_standard: name: automation_standard definition_uri: https://w3id.org/valuesets/automation_standard description: Industry standard for laboratory automation - from_schema: https://w3id.org/linkml/valuesets/lab_automation/standards + from_schema: https://w3id.org/valuesets/lab_automation/standards slot_uri: valuesets:automation_standard range: AutomationStandardEnum communication_protocol: name: communication_protocol definition_uri: https://w3id.org/valuesets/communication_protocol description: Communication protocol for laboratory device integration - from_schema: https://w3id.org/linkml/valuesets/lab_automation/standards + from_schema: https://w3id.org/valuesets/lab_automation/standards slot_uri: valuesets:communication_protocol range: CommunicationProtocolEnum labware_standard: name: labware_standard definition_uri: https://w3id.org/valuesets/labware_standard description: Standardization specification for laboratory labware - from_schema: https://w3id.org/linkml/valuesets/lab_automation/standards + from_schema: https://w3id.org/valuesets/lab_automation/standards slot_uri: valuesets:labware_standard range: LabwareStandardEnum thermal_cycler_type: name: thermal_cycler_type definition_uri: https://w3id.org/valuesets/thermal_cycler_type description: Type of thermal cycling instrument - from_schema: https://w3id.org/linkml/valuesets/lab_automation/thermal_cycling + from_schema: https://w3id.org/valuesets/lab_automation/thermal_cycling slot_uri: valuesets:thermal_cycler_type range: ThermalCyclerTypeEnum pcr_operation_type: name: pcr_operation_type definition_uri: https://w3id.org/valuesets/pcr_operation_type description: Type of PCR operation - from_schema: https://w3id.org/linkml/valuesets/lab_automation/thermal_cycling + from_schema: https://w3id.org/valuesets/lab_automation/thermal_cycling slot_uri: valuesets:pcr_operation_type range: PCROperationTypeEnum detection_mode: name: detection_mode definition_uri: https://w3id.org/valuesets/detection_mode description: Detection mode for real-time PCR - from_schema: https://w3id.org/linkml/valuesets/lab_automation/thermal_cycling + from_schema: https://w3id.org/valuesets/lab_automation/thermal_cycling slot_uri: valuesets:detection_mode range: DetectionModeEnum arxiv_category: name: arxiv_category definition_uri: https://w3id.org/valuesets/arxiv_category description: arXiv subject category for a preprint or publication - from_schema: https://w3id.org/linkml/valuesets/publishing/arxiv_categories + from_schema: https://w3id.org/valuesets/publishing/arxiv_categories slot_uri: valuesets:arxiv_category range: ArxivCategory arxiv_primary_category: name: arxiv_primary_category definition_uri: https://w3id.org/valuesets/arxiv_primary_category description: Primary arXiv subject category - from_schema: https://w3id.org/linkml/valuesets/publishing/arxiv_categories + from_schema: https://w3id.org/valuesets/publishing/arxiv_categories slot_uri: valuesets:arxiv_primary_category range: ArxivCategory arxiv_secondary_categories: name: arxiv_secondary_categories definition_uri: https://w3id.org/valuesets/arxiv_secondary_categories description: Secondary/cross-list arXiv subject categories - from_schema: https://w3id.org/linkml/valuesets/publishing/arxiv_categories + from_schema: https://w3id.org/valuesets/publishing/arxiv_categories slot_uri: valuesets:arxiv_secondary_categories range: ArxivCategory multivalued: true @@ -68752,98 +68752,98 @@ slots: name: osti_workflow_status definition_uri: https://w3id.org/valuesets/osti_workflow_status description: OSTI workflow status code for a record revision - from_schema: https://w3id.org/linkml/valuesets/publishing/osti_record + from_schema: https://w3id.org/valuesets/publishing/osti_record slot_uri: valuesets:osti_workflow_status range: OstiWorkflowStatus osti_access_limitation: name: osti_access_limitation definition_uri: https://w3id.org/valuesets/osti_access_limitation description: Access/distribution limitation code for a record - from_schema: https://w3id.org/linkml/valuesets/publishing/osti_record + from_schema: https://w3id.org/valuesets/publishing/osti_record slot_uri: valuesets:osti_access_limitation range: OstiAccessLimitation osti_collection_type: name: osti_collection_type definition_uri: https://w3id.org/valuesets/osti_collection_type description: OSTI collection type for the record origin - from_schema: https://w3id.org/linkml/valuesets/publishing/osti_record + from_schema: https://w3id.org/valuesets/publishing/osti_record slot_uri: valuesets:osti_collection_type range: OstiCollectionType osti_sensitivity_flag: name: osti_sensitivity_flag definition_uri: https://w3id.org/valuesets/osti_sensitivity_flag description: OSTI sensitivity flag for released records - from_schema: https://w3id.org/linkml/valuesets/publishing/osti_record + from_schema: https://w3id.org/valuesets/publishing/osti_record slot_uri: valuesets:osti_sensitivity_flag range: OstiSensitivityFlag osti_organization_identifier_type: name: osti_organization_identifier_type definition_uri: https://w3id.org/valuesets/osti_organization_identifier_type description: Identifier type for OSTI organizations - from_schema: https://w3id.org/linkml/valuesets/publishing/osti_record + from_schema: https://w3id.org/valuesets/publishing/osti_record slot_uri: valuesets:osti_organization_identifier_type range: OstiOrganizationIdentifierType osti_product_type: name: osti_product_type definition_uri: https://w3id.org/valuesets/osti_product_type description: OSTI product type code - from_schema: https://w3id.org/linkml/valuesets/publishing/osti_record + from_schema: https://w3id.org/valuesets/publishing/osti_record slot_uri: valuesets:osti_product_type range: OstiProductType osti_organization_type: name: osti_organization_type definition_uri: https://w3id.org/valuesets/osti_organization_type description: OSTI organization role type - from_schema: https://w3id.org/linkml/valuesets/publishing/osti_record + from_schema: https://w3id.org/valuesets/publishing/osti_record slot_uri: valuesets:osti_organization_type range: OstiOrganizationType osti_person_type: name: osti_person_type definition_uri: https://w3id.org/valuesets/osti_person_type description: OSTI person role type - from_schema: https://w3id.org/linkml/valuesets/publishing/osti_record + from_schema: https://w3id.org/valuesets/publishing/osti_record slot_uri: valuesets:osti_person_type range: OstiPersonType osti_contributor_type: name: osti_contributor_type definition_uri: https://w3id.org/valuesets/osti_contributor_type description: OSTI contributor role type - from_schema: https://w3id.org/linkml/valuesets/publishing/osti_record + from_schema: https://w3id.org/valuesets/publishing/osti_record slot_uri: valuesets:osti_contributor_type range: OstiContributorType osti_related_identifier_type: name: osti_related_identifier_type definition_uri: https://w3id.org/valuesets/osti_related_identifier_type description: Identifier type for related resources in OSTI - from_schema: https://w3id.org/linkml/valuesets/publishing/osti_record + from_schema: https://w3id.org/valuesets/publishing/osti_record slot_uri: valuesets:osti_related_identifier_type range: OstiRelatedIdentifierType osti_relation_type: name: osti_relation_type definition_uri: https://w3id.org/valuesets/osti_relation_type description: Relationship type between records in OSTI - from_schema: https://w3id.org/linkml/valuesets/publishing/osti_record + from_schema: https://w3id.org/valuesets/publishing/osti_record slot_uri: valuesets:osti_relation_type range: OstiRelationType osti_identifier_type: name: osti_identifier_type definition_uri: https://w3id.org/valuesets/osti_identifier_type description: Identifier type for OSTI identifiers - from_schema: https://w3id.org/linkml/valuesets/publishing/osti_record + from_schema: https://w3id.org/valuesets/publishing/osti_record slot_uri: valuesets:osti_identifier_type range: OstiIdentifierType osti_geolocation_type: name: osti_geolocation_type definition_uri: https://w3id.org/valuesets/osti_geolocation_type description: Geolocation shape type used by OSTI - from_schema: https://w3id.org/linkml/valuesets/publishing/osti_record + from_schema: https://w3id.org/valuesets/publishing/osti_record slot_uri: valuesets:osti_geolocation_type range: OstiGeolocationType osti_media_location_type: name: osti_media_location_type definition_uri: https://w3id.org/valuesets/osti_media_location_type description: Media location indicator for OSTI files and media sets - from_schema: https://w3id.org/linkml/valuesets/publishing/osti_record + from_schema: https://w3id.org/valuesets/publishing/osti_record slot_uri: valuesets:osti_media_location_type range: OstiMediaLocationType preservation_event_type: @@ -68941,11 +68941,11 @@ classes: Fake: name: Fake definition_uri: https://w3id.org/valuesets/Fake - from_schema: https://w3id.org/linkml/valuesets + from_schema: https://w3id.org/valuesets class_uri: valuesets:Fake metamodel_version: 1.7.0 source_file: valuesets.yaml -source_file_date: '2025-12-22T18:22:13' -source_file_size: 3479 -generation_date: '2026-01-28T07:53:41' +source_file_date: '2026-01-30T18:18:29' +source_file_size: 3472 +generation_date: '2026-01-30T18:19:30' diff --git a/docs/slides/valuesets-slides.pdf b/docs/slides/valuesets-slides.pdf index 0d740395e3381b8c73d26d2d6b051330a7d95b44..2108f67a14571e89bfa37f78157858b29e4f27ee 100644 GIT binary patch delta 6793 zcmcJQXHe5?yY2x679b)`q(-Hw2rRlpigb_?q_=<|MS_S@0)+B+NdR@xk=`K?LJJ58 zgc6V@MS4JbQ3xdTUJPv4K4;!}&;D>`_MEfln)%)BntSH{@XXVNGi=2fzCltWX^@wY zmyxtcIwU>v4*7teVYfBILu{2DT=_+Yooe?(s@Vn509O{Hp4mxiPe#fIICcu;H7oZ;0{B^oE+!u znfY&uM4<&+pq(hn>W~Re+MdOjrqAbyl&|r_Mk3}4M40#Q$+_!$nI^*b)#cm~8b075 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'https://w3id.org/valuesets', 'name': 'valuesets', 'title': 'valuesets'}) class RelativeTimeEnum(RichEnum): """ diff --git a/src/valuesets/datamodel/valuesets_pydantic.py b/src/valuesets/datamodel/valuesets_pydantic.py index bd82dd4e..620606f8 100644 --- a/src/valuesets/datamodel/valuesets_pydantic.py +++ b/src/valuesets/datamodel/valuesets_pydantic.py @@ -52,7 +52,7 @@ def __contains__(self, key: str) -> bool: return key in self.root -linkml_meta = LinkMLMeta({'default_prefix': 'valuesets', 'description': 'A collection of commonly used value sets', 'id': 'https://w3id.org/linkml/valuesets', 'name': 'valuesets', 'title': 'valuesets'}) +linkml_meta = LinkMLMeta({'default_prefix': 'valuesets', 'description': 'A collection of commonly used value sets', 'id': 'https://w3id.org/valuesets', 'name': 'valuesets', 'title': 'valuesets'}) class RelativeTimeEnum(RichEnum): """ diff --git a/src/valuesets/schema/academic/organizations.yaml b/src/valuesets/schema/academic/organizations.yaml index 6a1b2847..4bb79f4a 100644 --- a/src/valuesets/schema/academic/organizations.yaml +++ b/src/valuesets/schema/academic/organizations.yaml @@ -14,7 +14,7 @@ description: | - ROR API: https://api.ror.org/organizations ROR IDs should be used in the `meaning` field with the full URL format (e.g., https://ror.org/05gvnxz63). -id: https://w3id.org/linkml/valuesets/academic/organizations +id: https://w3id.org/valuesets/academic/organizations imports: - linkml:types prefixes: diff --git a/src/valuesets/schema/academic/research.yaml b/src/valuesets/schema/academic/research.yaml index 54071487..8f093dc8 100644 --- a/src/valuesets/schema/academic/research.yaml +++ b/src/valuesets/schema/academic/research.yaml @@ -1,7 +1,7 @@ name: research title: Academic and Research Value Sets description: Value sets for academic publishing, research, and scholarly communication -id: https://w3id.org/linkml/valuesets/academic/research +id: https://w3id.org/valuesets/academic/research imports: - linkml:types prefixes: diff --git a/src/valuesets/schema/bio/bgc_categories.yaml b/src/valuesets/schema/bio/bgc_categories.yaml index 133cf661..6be559ac 100644 --- a/src/valuesets/schema/bio/bgc_categories.yaml +++ b/src/valuesets/schema/bio/bgc_categories.yaml @@ -7,7 +7,7 @@ description: 'Value sets for biosynthetic gene cluster (BGC) categories used in BGCs. Based on the MIBiG (Minimum Information about a Biosynthetic Gene cluster) standard.' -id: https://w3id.org/linkml/valuesets/bio/bgc_categories +id: https://w3id.org/valuesets/bio/bgc_categories imports: - linkml:types prefixes: diff --git a/src/valuesets/schema/bio/bio_entities.yaml b/src/valuesets/schema/bio/bio_entities.yaml index d0c780b0..db249bf0 100644 --- a/src/valuesets/schema/bio/bio_entities.yaml +++ b/src/valuesets/schema/bio/bio_entities.yaml @@ -5,7 +5,7 @@ description: 'Dynamic enumerations for biological entities including anatomical cell types, diseases, and chemical entities. These enums are populated dynamically from ontologies.' -id: https://w3id.org/linkml/valuesets/bio/bio_entities +id: https://w3id.org/valuesets/bio/bio_entities imports: - linkml:types prefixes: diff --git a/src/valuesets/schema/bio/biosafety.yaml b/src/valuesets/schema/bio/biosafety.yaml index 963156d9..3e9a13eb 100644 --- a/src/valuesets/schema/bio/biosafety.yaml +++ b/src/valuesets/schema/bio/biosafety.yaml @@ -1,5 +1,5 @@ name: biosafety -id: https://w3id.org/linkml/valuesets/bio/biosafety +id: https://w3id.org/valuesets/bio/biosafety prefixes: SNOMED: http://snomed.info/id/ METPO: https://w3id.org/metpo/ diff --git a/src/valuesets/schema/bio/cell_cycle.yaml b/src/valuesets/schema/bio/cell_cycle.yaml index b8bdcd74..0f0b0410 100644 --- a/src/valuesets/schema/bio/cell_cycle.yaml +++ b/src/valuesets/schema/bio/cell_cycle.yaml @@ -1,7 +1,7 @@ name: cell_cycle title: Cell Cycle Value Sets description: Value sets for cell cycle phases, checkpoints, and related concepts -id: https://w3id.org/linkml/valuesets/bio/cell_cycle +id: https://w3id.org/valuesets/bio/cell_cycle imports: - linkml:types prefixes: diff --git a/src/valuesets/schema/bio/genome_features.yaml b/src/valuesets/schema/bio/genome_features.yaml index 26fbb567..1296e33a 100644 --- a/src/valuesets/schema/bio/genome_features.yaml +++ b/src/valuesets/schema/bio/genome_features.yaml @@ -5,7 +5,7 @@ description: 'Genome feature types from SOFA (Sequence Ontology Feature Annotati the subset of SO used in GFF3 files for genome annotation. Organized hierarchically following the Sequence Ontology structure.' -id: https://w3id.org/linkml/valuesets/bio/genome_features +id: https://w3id.org/valuesets/bio/genome_features imports: - linkml:types prefixes: diff --git a/src/valuesets/schema/bio/go_aspect.yaml b/src/valuesets/schema/bio/go_aspect.yaml index 5ba3d302..3843240f 100644 --- a/src/valuesets/schema/bio/go_aspect.yaml +++ b/src/valuesets/schema/bio/go_aspect.yaml @@ -1,7 +1,7 @@ name: go_aspect title: Gene Ontology Aspects description: The three main aspects of Gene Ontology - Molecular Function, Biological Process, and Cellular Component -id: https://w3id.org/linkml/valuesets/bio/go_aspect +id: https://w3id.org/valuesets/bio/go_aspect imports: - linkml:types prefixes: diff --git a/src/valuesets/schema/bio/go_evidence.yaml b/src/valuesets/schema/bio/go_evidence.yaml index 329e6095..9823f245 100644 --- a/src/valuesets/schema/bio/go_evidence.yaml +++ b/src/valuesets/schema/bio/go_evidence.yaml @@ -1,7 +1,7 @@ name: go_evidence title: Gene Ontology Evidence Codes description: Value sets for Gene Ontology evidence codes and electronic annotation methods -id: https://w3id.org/linkml/valuesets/bio/go_evidence +id: https://w3id.org/valuesets/bio/go_evidence imports: - linkml:types prefixes: diff --git a/src/valuesets/schema/bio/insdc_geographic_locations.yaml b/src/valuesets/schema/bio/insdc_geographic_locations.yaml index f21943aa..2509c814 100644 --- a/src/valuesets/schema/bio/insdc_geographic_locations.yaml +++ b/src/valuesets/schema/bio/insdc_geographic_locations.yaml @@ -7,7 +7,7 @@ description: 'INSDC controlled vocabulary for geographic locations used in seque Countries are mapped to ISO 3166-1 alpha-2 codes using Library of Congress URIs. Source: https://www.insdc.org/submitting-standards/geo_loc_name-qualifier-vocabulary/' -id: https://w3id.org/linkml/valuesets/bio/insdc_geographic_locations +id: https://w3id.org/valuesets/bio/insdc_geographic_locations prefixes: # linkml_common: https://w3id.org/valuesets/ insdc: https://www.insdc.org/controlled-vocabulary/geographic-location/ diff --git a/src/valuesets/schema/bio/insdc_missing_values.yaml b/src/valuesets/schema/bio/insdc_missing_values.yaml index 5bc57d18..cdd4410a 100644 --- a/src/valuesets/schema/bio/insdc_missing_values.yaml +++ b/src/valuesets/schema/bio/insdc_missing_values.yaml @@ -1,5 +1,5 @@ name: insdc_missing_values -id: https://w3id.org/linkml/valuesets/bio/insdc_missing_values +id: https://w3id.org/valuesets/bio/insdc_missing_values prefixes: NCIT: http://purl.obolibrary.org/obo/NCIT_ OBI: http://purl.obolibrary.org/obo/OBI_ diff --git a/src/valuesets/schema/bio/plant_biology.yaml b/src/valuesets/schema/bio/plant_biology.yaml index 5d50ea30..afc7975d 100644 --- a/src/valuesets/schema/bio/plant_biology.yaml +++ b/src/valuesets/schema/bio/plant_biology.yaml @@ -3,7 +3,7 @@ title: Plant Biology Value Sets description: 'Value sets related to plant biology, including reproductive systems, breeding systems, and other plant-specific characteristics.' -id: https://w3id.org/linkml/valuesets/bio/plant_biology +id: https://w3id.org/valuesets/bio/plant_biology imports: - linkml:types prefixes: diff --git a/src/valuesets/schema/bio/plant_experimental_conditions.yaml b/src/valuesets/schema/bio/plant_experimental_conditions.yaml index b03a3027..e053d457 100644 --- a/src/valuesets/schema/bio/plant_experimental_conditions.yaml +++ b/src/valuesets/schema/bio/plant_experimental_conditions.yaml @@ -3,7 +3,7 @@ title: Plant Experimental Conditions Value Sets description: >- Value sets based on the Plant Experimental Conditions Ontology (PECO), including plant exposures and study conditions. -id: https://w3id.org/linkml/valuesets/bio/plant_experimental_conditions +id: https://w3id.org/valuesets/bio/plant_experimental_conditions imports: - linkml:types prefixes: diff --git a/src/valuesets/schema/bio/plant_sex.yaml b/src/valuesets/schema/bio/plant_sex.yaml index cb9715e5..d98a99ab 100644 --- a/src/valuesets/schema/bio/plant_sex.yaml +++ b/src/valuesets/schema/bio/plant_sex.yaml @@ -1,5 +1,5 @@ name: plant_sex -id: https://w3id.org/linkml/valuesets/bio/plant_sex +id: https://w3id.org/valuesets/bio/plant_sex prefixes: PATO: http://purl.obolibrary.org/obo/PATO_ ECOCORE: http://purl.obolibrary.org/obo/ECOCORE_ diff --git a/src/valuesets/schema/bio/relationship_to_oxygen.yaml b/src/valuesets/schema/bio/relationship_to_oxygen.yaml index 33313f8f..fec4c460 100644 --- a/src/valuesets/schema/bio/relationship_to_oxygen.yaml +++ b/src/valuesets/schema/bio/relationship_to_oxygen.yaml @@ -1,5 +1,5 @@ name: relationship_to_oxygen -id: https://w3id.org/linkml/valuesets/bio/relationship_to_oxygen +id: https://w3id.org/valuesets/bio/relationship_to_oxygen prefixes: ECOCORE: http://purl.obolibrary.org/obo/ECOCORE_ OMP: http://purl.obolibrary.org/obo/OMP_ diff --git a/src/valuesets/schema/bio/sequence_chemistry.yaml b/src/valuesets/schema/bio/sequence_chemistry.yaml index f5e4be8d..f55cdfee 100644 --- a/src/valuesets/schema/bio/sequence_chemistry.yaml +++ b/src/valuesets/schema/bio/sequence_chemistry.yaml @@ -3,7 +3,7 @@ title: Sequence Chemistry Value Sets description: 'Value sets for nucleic acid and protein sequence chemistry, including standard and extended alphabets, quality encodings, and molecular representations' -id: https://w3id.org/linkml/valuesets/bio/sequence_chemistry +id: https://w3id.org/valuesets/bio/sequence_chemistry imports: - linkml:types prefixes: diff --git a/src/valuesets/schema/bio/sequencing_platforms.yaml b/src/valuesets/schema/bio/sequencing_platforms.yaml index 81a72bdb..fc10174e 100644 --- a/src/valuesets/schema/bio/sequencing_platforms.yaml +++ b/src/valuesets/schema/bio/sequencing_platforms.yaml @@ -1,7 +1,7 @@ name: sequencing_platforms title: Sequencing Platform Value Sets description: Value sets for DNA/RNA sequencing platforms, technologies, and methodologies -id: https://w3id.org/linkml/valuesets/bio/sequencing_platforms +id: https://w3id.org/valuesets/bio/sequencing_platforms imports: - linkml:types prefixes: diff --git a/src/valuesets/schema/bio/taxonomy.yaml b/src/valuesets/schema/bio/taxonomy.yaml index f96abc77..1c9c47b4 100644 --- a/src/valuesets/schema/bio/taxonomy.yaml +++ b/src/valuesets/schema/bio/taxonomy.yaml @@ -1,7 +1,7 @@ name: taxonomy title: Taxonomic Classifications description: Value sets for taxonomic classifications and model organisms -id: https://w3id.org/linkml/valuesets/bio/taxonomy +id: https://w3id.org/valuesets/bio/taxonomy imports: - linkml:types prefixes: diff --git a/src/valuesets/schema/bio/trophic_levels.yaml b/src/valuesets/schema/bio/trophic_levels.yaml index 9c2a31d6..1c73f93d 100644 --- a/src/valuesets/schema/bio/trophic_levels.yaml +++ b/src/valuesets/schema/bio/trophic_levels.yaml @@ -1,5 +1,5 @@ name: trophic_levels -id: https://w3id.org/linkml/valuesets/bio/trophic_levels +id: https://w3id.org/valuesets/bio/trophic_levels prefixes: ECOCORE: http://purl.obolibrary.org/obo/ECOCORE_ MICRO: http://purl.obolibrary.org/obo/MICRO_ diff --git a/src/valuesets/schema/bio/viral_genome_types.yaml b/src/valuesets/schema/bio/viral_genome_types.yaml index 4abb2ae7..ebb0a7f5 100644 --- a/src/valuesets/schema/bio/viral_genome_types.yaml +++ b/src/valuesets/schema/bio/viral_genome_types.yaml @@ -1,5 +1,5 @@ name: viral_genome_types -id: https://w3id.org/linkml/valuesets/bio/viral_genome_types +id: https://w3id.org/valuesets/bio/viral_genome_types prefixes: NCIT: http://purl.obolibrary.org/obo/NCIT_ CHEBI: http://purl.obolibrary.org/obo/CHEBI_ diff --git a/src/valuesets/schema/bioprocessing/scale_up.yaml b/src/valuesets/schema/bioprocessing/scale_up.yaml index e5287870..c54b1949 100644 --- a/src/valuesets/schema/bioprocessing/scale_up.yaml +++ b/src/valuesets/schema/bioprocessing/scale_up.yaml @@ -3,7 +3,7 @@ title: Bioprocessing Scale-up Value Sets description: 'Value sets for bioprocessing scale-up facilities, fermentation, and biomanufacturing operations like those at ABPDU (Advanced Biofuels and Bioproducts Process Development Unit)' -id: https://w3id.org/linkml/valuesets/bioprocessing/scale_up +id: https://w3id.org/valuesets/bioprocessing/scale_up imports: - linkml:types prefixes: diff --git a/src/valuesets/schema/business/human_resources.yaml b/src/valuesets/schema/business/human_resources.yaml index 8d06e078..b1a446c3 100644 --- a/src/valuesets/schema/business/human_resources.yaml +++ b/src/valuesets/schema/business/human_resources.yaml @@ -2,7 +2,7 @@ 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.' -id: https://w3id.org/linkml/valuesets/business/human_resources +id: https://w3id.org/valuesets/business/human_resources imports: - linkml:types prefixes: diff --git a/src/valuesets/schema/business/industry_classifications.yaml b/src/valuesets/schema/business/industry_classifications.yaml index c67f90b5..3a2abb50 100644 --- a/src/valuesets/schema/business/industry_classifications.yaml +++ b/src/valuesets/schema/business/industry_classifications.yaml @@ -2,7 +2,7 @@ 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.' -id: https://w3id.org/linkml/valuesets/business/industry_classifications +id: https://w3id.org/valuesets/business/industry_classifications imports: - linkml:types prefixes: diff --git a/src/valuesets/schema/business/management_operations.yaml b/src/valuesets/schema/business/management_operations.yaml index c28fbdb3..8d4f369b 100644 --- a/src/valuesets/schema/business/management_operations.yaml +++ b/src/valuesets/schema/business/management_operations.yaml @@ -2,7 +2,7 @@ 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.' -id: https://w3id.org/linkml/valuesets/business/management_operations +id: https://w3id.org/valuesets/business/management_operations imports: - linkml:types prefixes: diff --git a/src/valuesets/schema/business/organizational_structures.yaml b/src/valuesets/schema/business/organizational_structures.yaml index a07c1bb4..a2dacf62 100644 --- a/src/valuesets/schema/business/organizational_structures.yaml +++ b/src/valuesets/schema/business/organizational_structures.yaml @@ -3,7 +3,7 @@ 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.' -id: https://w3id.org/linkml/valuesets/business/organizational_structures +id: https://w3id.org/valuesets/business/organizational_structures imports: - linkml:types prefixes: diff --git a/src/valuesets/schema/business/quality_management.yaml b/src/valuesets/schema/business/quality_management.yaml index 12ef9716..feac5ed6 100644 --- a/src/valuesets/schema/business/quality_management.yaml +++ b/src/valuesets/schema/business/quality_management.yaml @@ -2,7 +2,7 @@ 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.' -id: https://w3id.org/linkml/valuesets/business/quality_management +id: https://w3id.org/valuesets/business/quality_management imports: - linkml:types prefixes: diff --git a/src/valuesets/schema/business/supply_chain.yaml b/src/valuesets/schema/business/supply_chain.yaml index 8d2503ee..01e19ca6 100644 --- a/src/valuesets/schema/business/supply_chain.yaml +++ b/src/valuesets/schema/business/supply_chain.yaml @@ -2,7 +2,7 @@ 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.' -id: https://w3id.org/linkml/valuesets/business/supply_chain +id: https://w3id.org/valuesets/business/supply_chain imports: - linkml:types prefixes: diff --git a/src/valuesets/schema/chemistry/roles.yaml b/src/valuesets/schema/chemistry/roles.yaml index 4cd0717b..d08b963d 100644 --- a/src/valuesets/schema/chemistry/roles.yaml +++ b/src/valuesets/schema/chemistry/roles.yaml @@ -3,7 +3,7 @@ title: Chemical and Biological Roles description: >- Value sets for chemical and biological roles that molecular entities can play, based on the ChEBI ontology role hierarchy. -id: https://w3id.org/linkml/valuesets/chemistry/roles +id: https://w3id.org/valuesets/chemistry/roles imports: - linkml:types prefixes: diff --git a/src/valuesets/schema/clinical/genetics.yaml b/src/valuesets/schema/clinical/genetics.yaml index 8cf373d3..5aa122e0 100644 --- a/src/valuesets/schema/clinical/genetics.yaml +++ b/src/valuesets/schema/clinical/genetics.yaml @@ -1,7 +1,7 @@ name: genetics title: Clinical Genetics Value Sets description: Value sets for clinical genetics including modes of inheritance -id: https://w3id.org/linkml/valuesets/clinical/genetics +id: https://w3id.org/valuesets/clinical/genetics imports: - linkml:types prefixes: diff --git a/src/valuesets/schema/clinical/nih_demographics.yaml b/src/valuesets/schema/clinical/nih_demographics.yaml index f87b4711..4c9d5127 100644 --- a/src/valuesets/schema/clinical/nih_demographics.yaml +++ b/src/valuesets/schema/clinical/nih_demographics.yaml @@ -3,7 +3,7 @@ title: NIH Demographics and Common Data Elements description: 'Standard value sets for NIH Common Data Elements (CDEs) including demographics, race, ethnicity, sex, and other clinical variables following NIH and OMB standards' -id: https://w3id.org/linkml/valuesets/clinical/nih_demographics +id: https://w3id.org/valuesets/clinical/nih_demographics imports: - linkml:types prefixes: diff --git a/src/valuesets/schema/clinical/phenopackets.yaml b/src/valuesets/schema/clinical/phenopackets.yaml index deeb6a0b..5d6e24a2 100644 --- a/src/valuesets/schema/clinical/phenopackets.yaml +++ b/src/valuesets/schema/clinical/phenopackets.yaml @@ -1,7 +1,7 @@ name: phenopackets title: Phenopackets Clinical Value Sets description: Value sets derived from GA4GH Phenopackets Schema for clinical genomics and phenotyping -id: https://w3id.org/linkml/valuesets/clinical/phenopackets +id: https://w3id.org/valuesets/clinical/phenopackets imports: - linkml:types prefixes: diff --git a/src/valuesets/schema/computing/geospatial_formats.yaml b/src/valuesets/schema/computing/geospatial_formats.yaml index 6343f90d..22f46f45 100644 --- a/src/valuesets/schema/computing/geospatial_formats.yaml +++ b/src/valuesets/schema/computing/geospatial_formats.yaml @@ -4,7 +4,7 @@ description: >- File formats commonly used for geospatial and environmental data, including raster formats, vector formats, and scientific data formats with spatial extensions. -id: https://w3id.org/linkml/valuesets/computing/geospatial_formats +id: https://w3id.org/valuesets/computing/geospatial_formats imports: - linkml:types prefixes: diff --git a/src/valuesets/schema/computing/mime_types.yaml b/src/valuesets/schema/computing/mime_types.yaml index 7df7bab3..6480b330 100644 --- a/src/valuesets/schema/computing/mime_types.yaml +++ b/src/valuesets/schema/computing/mime_types.yaml @@ -2,7 +2,7 @@ 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. -id: https://w3id.org/linkml/valuesets/computing/mime_types +id: https://w3id.org/valuesets/computing/mime_types imports: - linkml:types prefixes: diff --git a/src/valuesets/schema/data_science/binary_classification.yaml b/src/valuesets/schema/data_science/binary_classification.yaml index efb5663f..7dcaff3a 100644 --- a/src/valuesets/schema/data_science/binary_classification.yaml +++ b/src/valuesets/schema/data_science/binary_classification.yaml @@ -1,5 +1,5 @@ name: binary_classification -id: https://w3id.org/linkml/valuesets/data_science/binary_classification +id: https://w3id.org/valuesets/data_science/binary_classification prefixes: # linkml_common: https://w3id.org/linkml-common/ STATO: http://purl.obolibrary.org/obo/STATO_ diff --git a/src/valuesets/schema/data_science/emotion_classification.yaml b/src/valuesets/schema/data_science/emotion_classification.yaml index f779501a..98dfc753 100644 --- a/src/valuesets/schema/data_science/emotion_classification.yaml +++ b/src/valuesets/schema/data_science/emotion_classification.yaml @@ -1,5 +1,5 @@ name: emotion_classification -id: https://w3id.org/linkml/valuesets/data_science/emotion_classification +id: https://w3id.org/valuesets/data_science/emotion_classification prefixes: # linkml_common: https://w3id.org/linkml-common/ MFOEM: http://purl.obolibrary.org/obo/MFOEM_ diff --git a/src/valuesets/schema/data_science/priority_severity.yaml b/src/valuesets/schema/data_science/priority_severity.yaml index 49e8b043..7e555dbd 100644 --- a/src/valuesets/schema/data_science/priority_severity.yaml +++ b/src/valuesets/schema/data_science/priority_severity.yaml @@ -1,5 +1,5 @@ name: priority_severity -id: https://w3id.org/linkml/valuesets/data_science/priority_severity +id: https://w3id.org/valuesets/data_science/priority_severity prefixes: # linkml_common: https://w3id.org/linkml-common/ NCIT: http://purl.obolibrary.org/obo/NCIT_ diff --git a/src/valuesets/schema/data_science/quality_control.yaml b/src/valuesets/schema/data_science/quality_control.yaml index e7c4660f..dd6de330 100644 --- a/src/valuesets/schema/data_science/quality_control.yaml +++ b/src/valuesets/schema/data_science/quality_control.yaml @@ -1,5 +1,5 @@ name: quality_control -id: https://w3id.org/linkml/valuesets/data_science/quality_control +id: https://w3id.org/valuesets/data_science/quality_control prefixes: # linkml_common: https://w3id.org/linkml-common/ NCIT: http://purl.obolibrary.org/obo/NCIT_ diff --git a/src/valuesets/schema/data_science/sentiment_analysis.yaml b/src/valuesets/schema/data_science/sentiment_analysis.yaml index 85b5948f..8c88132d 100644 --- a/src/valuesets/schema/data_science/sentiment_analysis.yaml +++ b/src/valuesets/schema/data_science/sentiment_analysis.yaml @@ -1,5 +1,5 @@ name: sentiment_analysis -id: https://w3id.org/linkml/valuesets/data_science/sentiment_analysis +id: https://w3id.org/valuesets/data_science/sentiment_analysis prefixes: # linkml_common: https://w3id.org/linkml-common/ NCIT: http://purl.obolibrary.org/obo/NCIT_ diff --git a/src/valuesets/schema/data_science/text_classification.yaml b/src/valuesets/schema/data_science/text_classification.yaml index 21d5dd00..6152391a 100644 --- a/src/valuesets/schema/data_science/text_classification.yaml +++ b/src/valuesets/schema/data_science/text_classification.yaml @@ -1,5 +1,5 @@ name: text_classification -id: https://w3id.org/linkml/valuesets/data_science/text_classification +id: https://w3id.org/valuesets/data_science/text_classification prefixes: # linkml_common: https://w3id.org/linkml-common/ NCIT: http://purl.obolibrary.org/obo/NCIT_ diff --git a/src/valuesets/schema/energy/energy.yaml b/src/valuesets/schema/energy/energy.yaml index 660f5981..21582a4a 100644 --- a/src/valuesets/schema/energy/energy.yaml +++ b/src/valuesets/schema/energy/energy.yaml @@ -1,7 +1,7 @@ name: energy title: Energy and Power Value Sets description: Value sets for energy sources, units, consumption, and related concepts -id: https://w3id.org/linkml/valuesets/energy/energy +id: https://w3id.org/valuesets/energy/energy imports: - linkml:types prefixes: diff --git a/src/valuesets/schema/energy/fossil_fuels.yaml b/src/valuesets/schema/energy/fossil_fuels.yaml index 08c2a978..3c61b0d4 100644 --- a/src/valuesets/schema/energy/fossil_fuels.yaml +++ b/src/valuesets/schema/energy/fossil_fuels.yaml @@ -1,5 +1,5 @@ name: fossil_fuels -id: https://w3id.org/linkml/valuesets/energy/fossil_fuels +id: https://w3id.org/valuesets/energy/fossil_fuels prefixes: # linkml_common: https://w3id.org/linkml-common/ ENVO: http://purl.obolibrary.org/obo/ENVO_ diff --git a/src/valuesets/schema/energy/nuclear/nuclear_facilities.yaml b/src/valuesets/schema/energy/nuclear/nuclear_facilities.yaml index 094edb94..37f0b112 100644 --- a/src/valuesets/schema/energy/nuclear/nuclear_facilities.yaml +++ b/src/valuesets/schema/energy/nuclear/nuclear_facilities.yaml @@ -2,7 +2,7 @@ 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.' -id: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_facilities +id: https://w3id.org/valuesets/energy/nuclear/nuclear_facilities imports: - linkml:types prefixes: diff --git a/src/valuesets/schema/energy/nuclear/nuclear_fuels.yaml b/src/valuesets/schema/energy/nuclear/nuclear_fuels.yaml index 37814055..65d91f7d 100644 --- a/src/valuesets/schema/energy/nuclear/nuclear_fuels.yaml +++ b/src/valuesets/schema/energy/nuclear/nuclear_fuels.yaml @@ -2,7 +2,7 @@ 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.' -id: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_fuels +id: https://w3id.org/valuesets/energy/nuclear/nuclear_fuels imports: - linkml:types prefixes: diff --git a/src/valuesets/schema/energy/nuclear/nuclear_operations.yaml b/src/valuesets/schema/energy/nuclear/nuclear_operations.yaml index 36d3f67a..7201ed07 100644 --- a/src/valuesets/schema/energy/nuclear/nuclear_operations.yaml +++ b/src/valuesets/schema/energy/nuclear/nuclear_operations.yaml @@ -2,7 +2,7 @@ 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.' -id: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_operations +id: https://w3id.org/valuesets/energy/nuclear/nuclear_operations imports: - linkml:types prefixes: diff --git a/src/valuesets/schema/energy/nuclear/nuclear_safety.yaml b/src/valuesets/schema/energy/nuclear/nuclear_safety.yaml index 42df935c..2ddce07d 100644 --- a/src/valuesets/schema/energy/nuclear/nuclear_safety.yaml +++ b/src/valuesets/schema/energy/nuclear/nuclear_safety.yaml @@ -2,7 +2,7 @@ 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.' -id: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_safety +id: https://w3id.org/valuesets/energy/nuclear/nuclear_safety imports: - linkml:types prefixes: diff --git a/src/valuesets/schema/energy/nuclear/nuclear_waste.yaml b/src/valuesets/schema/energy/nuclear/nuclear_waste.yaml index fc657871..82f225c8 100644 --- a/src/valuesets/schema/energy/nuclear/nuclear_waste.yaml +++ b/src/valuesets/schema/energy/nuclear/nuclear_waste.yaml @@ -2,7 +2,7 @@ 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.' -id: https://w3id.org/linkml/valuesets/energy/nuclear/nuclear_waste +id: https://w3id.org/valuesets/energy/nuclear/nuclear_waste imports: - linkml:types prefixes: diff --git a/src/valuesets/schema/energy/nuclear/reactor_types.yaml b/src/valuesets/schema/energy/nuclear/reactor_types.yaml index 7b288f72..2b9224dc 100644 --- a/src/valuesets/schema/energy/nuclear/reactor_types.yaml +++ b/src/valuesets/schema/energy/nuclear/reactor_types.yaml @@ -2,7 +2,7 @@ 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.' -id: https://w3id.org/linkml/valuesets/energy/nuclear/reactor_types +id: https://w3id.org/valuesets/energy/nuclear/reactor_types imports: - linkml:types prefixes: diff --git a/src/valuesets/schema/energy/renewable/bioenergy.yaml b/src/valuesets/schema/energy/renewable/bioenergy.yaml index cc70d7dd..88aacdcd 100644 --- a/src/valuesets/schema/energy/renewable/bioenergy.yaml +++ b/src/valuesets/schema/energy/renewable/bioenergy.yaml @@ -3,7 +3,7 @@ title: Bioenergy and Biofuels Value Sets description: >- Value sets for bioenergy feedstocks, biofuels, and conversion processes. Based on DOE Bioenergy Technologies Office terminology and glossary. -id: https://w3id.org/linkml/valuesets/energy/renewable/bioenergy +id: https://w3id.org/valuesets/energy/renewable/bioenergy imports: - linkml:types prefixes: diff --git a/src/valuesets/schema/energy/renewable/geothermal.yaml b/src/valuesets/schema/energy/renewable/geothermal.yaml index e5b047b5..7aa1c858 100644 --- a/src/valuesets/schema/energy/renewable/geothermal.yaml +++ b/src/valuesets/schema/energy/renewable/geothermal.yaml @@ -3,7 +3,7 @@ title: Geothermal Energy Value Sets description: >- Value sets for geothermal energy systems, reservoir types, well types, and technologies. Based on DOE Geothermal Technologies Office terminology and the Geothermal Data Repository standards. -id: https://w3id.org/linkml/valuesets/energy/renewable/geothermal +id: https://w3id.org/valuesets/energy/renewable/geothermal imports: - linkml:types prefixes: diff --git a/src/valuesets/schema/energy/renewable/hydrogen.yaml b/src/valuesets/schema/energy/renewable/hydrogen.yaml index 1806f528..39d6cfff 100644 --- a/src/valuesets/schema/energy/renewable/hydrogen.yaml +++ b/src/valuesets/schema/energy/renewable/hydrogen.yaml @@ -4,7 +4,7 @@ description: >- Value sets for hydrogen production, storage, and utilization. Includes the color-coded hydrogen classification system used by industry. Based on DOE Hydrogen and Fuel Cell Technologies Office terminology. -id: https://w3id.org/linkml/valuesets/energy/renewable/hydrogen +id: https://w3id.org/valuesets/energy/renewable/hydrogen imports: - linkml:types prefixes: diff --git a/src/valuesets/schema/environmental_health/carcinogenicity.yaml b/src/valuesets/schema/environmental_health/carcinogenicity.yaml index 8ddde0c8..c3e52c45 100644 --- a/src/valuesets/schema/environmental_health/carcinogenicity.yaml +++ b/src/valuesets/schema/environmental_health/carcinogenicity.yaml @@ -4,7 +4,7 @@ description: >- Standard carcinogenicity classifications from IARC (International Agency for Research on Cancer), EPA IRIS (Integrated Risk Information System), and NTP (National Toxicology Program). -id: https://w3id.org/linkml/valuesets/environmental_health/carcinogenicity +id: https://w3id.org/valuesets/environmental_health/carcinogenicity imports: - linkml:types prefixes: diff --git a/src/valuesets/schema/environmental_health/gb_edoh.yaml b/src/valuesets/schema/environmental_health/gb_edoh.yaml index 67b23323..51b84632 100644 --- a/src/valuesets/schema/environmental_health/gb_edoh.yaml +++ b/src/valuesets/schema/environmental_health/gb_edoh.yaml @@ -5,7 +5,7 @@ description: >- program for standardizing geospatial-based environmental determinants of health (GB-EDoH) data and metadata. These value sets support OMOP integration and environmental epidemiology studies. -id: https://w3id.org/linkml/valuesets/environmental_health/gb_edoh +id: https://w3id.org/valuesets/environmental_health/gb_edoh imports: - linkml:types prefixes: diff --git a/src/valuesets/schema/environmental_health/radionuclides.yaml b/src/valuesets/schema/environmental_health/radionuclides.yaml index c9f0fe33..421e5dc5 100644 --- a/src/valuesets/schema/environmental_health/radionuclides.yaml +++ b/src/valuesets/schema/environmental_health/radionuclides.yaml @@ -3,7 +3,7 @@ title: Radionuclide Value Sets description: >- Radioactive elements and isotopes of environmental and health concern, commonly measured in environmental monitoring and exposure assessment. -id: https://w3id.org/linkml/valuesets/environmental_health/radionuclides +id: https://w3id.org/valuesets/environmental_health/radionuclides imports: - linkml:types prefixes: diff --git a/src/valuesets/schema/industry/extractive_industry.yaml b/src/valuesets/schema/industry/extractive_industry.yaml index 67c3e3fe..c4718593 100644 --- a/src/valuesets/schema/industry/extractive_industry.yaml +++ b/src/valuesets/schema/industry/extractive_industry.yaml @@ -1,5 +1,5 @@ name: extractive_industry -id: https://w3id.org/linkml/valuesets/industry/extractive_industry +id: https://w3id.org/valuesets/industry/extractive_industry prefixes: # linkml_common: https://w3id.org/linkml-common/ valuesets: https://w3id.org/valuesets/ diff --git a/src/valuesets/schema/industry/mining.yaml b/src/valuesets/schema/industry/mining.yaml index a9f0a1c1..2547b3f5 100644 --- a/src/valuesets/schema/industry/mining.yaml +++ b/src/valuesets/schema/industry/mining.yaml @@ -1,7 +1,7 @@ name: mining title: Mining and Extractive Industry Value Sets description: Value sets for mining operations, minerals, extraction methods, and related concepts -id: https://w3id.org/linkml/valuesets/industry/mining +id: https://w3id.org/valuesets/industry/mining imports: - linkml:types prefixes: diff --git a/src/valuesets/schema/lab_automation/devices.yaml b/src/valuesets/schema/lab_automation/devices.yaml index 755739fe..d7b3ab84 100644 --- a/src/valuesets/schema/lab_automation/devices.yaml +++ b/src/valuesets/schema/lab_automation/devices.yaml @@ -1,5 +1,5 @@ name: lab_automation_devices -id: https://w3id.org/linkml/valuesets/lab_automation/devices +id: https://w3id.org/valuesets/lab_automation/devices prefixes: OBI: http://purl.obolibrary.org/obo/OBI_ SNOMED: http://snomed.info/id/ diff --git a/src/valuesets/schema/lab_automation/labware.yaml b/src/valuesets/schema/lab_automation/labware.yaml index 9afc1e6d..56ea772c 100644 --- a/src/valuesets/schema/lab_automation/labware.yaml +++ b/src/valuesets/schema/lab_automation/labware.yaml @@ -1,5 +1,5 @@ name: lab_automation_labware -id: https://w3id.org/linkml/valuesets/lab_automation/labware +id: https://w3id.org/valuesets/lab_automation/labware prefixes: NCIT: http://purl.obolibrary.org/obo/NCIT_ BAO: http://www.bioassayontology.org/bao#BAO_ diff --git a/src/valuesets/schema/lab_automation/operations.yaml b/src/valuesets/schema/lab_automation/operations.yaml index cf11b1b4..274656d3 100644 --- a/src/valuesets/schema/lab_automation/operations.yaml +++ b/src/valuesets/schema/lab_automation/operations.yaml @@ -1,5 +1,5 @@ name: lab_automation_operations -id: https://w3id.org/linkml/valuesets/lab_automation/operations +id: https://w3id.org/valuesets/lab_automation/operations prefixes: EFO: http://www.ebi.ac.uk/efo/EFO_ MMO: http://purl.obolibrary.org/obo/MMO_ diff --git a/src/valuesets/schema/lab_automation/protocols.yaml b/src/valuesets/schema/lab_automation/protocols.yaml index d17c11ec..8271f9c5 100644 --- a/src/valuesets/schema/lab_automation/protocols.yaml +++ b/src/valuesets/schema/lab_automation/protocols.yaml @@ -1,5 +1,5 @@ name: lab_automation_protocols -id: https://w3id.org/linkml/valuesets/lab_automation/protocols +id: https://w3id.org/valuesets/lab_automation/protocols prefixes: valuesets: https://w3id.org/valuesets/ orcid: https://orcid.org/ diff --git a/src/valuesets/schema/lab_automation/standards.yaml b/src/valuesets/schema/lab_automation/standards.yaml index 7ea17695..611491b6 100644 --- a/src/valuesets/schema/lab_automation/standards.yaml +++ b/src/valuesets/schema/lab_automation/standards.yaml @@ -1,5 +1,5 @@ name: lab_automation_standards -id: https://w3id.org/linkml/valuesets/lab_automation/standards +id: https://w3id.org/valuesets/lab_automation/standards prefixes: valuesets: https://w3id.org/valuesets/ orcid: https://orcid.org/ diff --git a/src/valuesets/schema/lab_automation/thermal_cycling.yaml b/src/valuesets/schema/lab_automation/thermal_cycling.yaml index dea8a929..934f4b95 100644 --- a/src/valuesets/schema/lab_automation/thermal_cycling.yaml +++ b/src/valuesets/schema/lab_automation/thermal_cycling.yaml @@ -1,5 +1,5 @@ name: lab_automation_thermal_cycling -id: https://w3id.org/linkml/valuesets/lab_automation/thermal_cycling +id: https://w3id.org/valuesets/lab_automation/thermal_cycling prefixes: OBI: http://purl.obolibrary.org/obo/OBI_ NCIT: http://purl.obolibrary.org/obo/NCIT_ diff --git a/src/valuesets/schema/materials_science/characterization_methods.yaml b/src/valuesets/schema/materials_science/characterization_methods.yaml index 81467346..891536e3 100644 --- a/src/valuesets/schema/materials_science/characterization_methods.yaml +++ b/src/valuesets/schema/materials_science/characterization_methods.yaml @@ -1,5 +1,5 @@ name: characterization_methods -id: https://w3id.org/linkml/valuesets/materials_science/characterization_methods +id: https://w3id.org/valuesets/materials_science/characterization_methods prefixes: OBI: http://purl.obolibrary.org/obo/OBI_ CHMO: http://purl.obolibrary.org/obo/CHMO_ diff --git a/src/valuesets/schema/materials_science/crystal_structures.yaml b/src/valuesets/schema/materials_science/crystal_structures.yaml index 754277da..d5a7446d 100644 --- a/src/valuesets/schema/materials_science/crystal_structures.yaml +++ b/src/valuesets/schema/materials_science/crystal_structures.yaml @@ -1,5 +1,5 @@ name: crystal_structures -id: https://w3id.org/linkml/valuesets/materials_science/crystal_structures +id: https://w3id.org/valuesets/materials_science/crystal_structures prefixes: CHEBI: http://purl.obolibrary.org/obo/CHEBI_ EMMO: http://emmo.info/emmo# diff --git a/src/valuesets/schema/materials_science/material_properties.yaml b/src/valuesets/schema/materials_science/material_properties.yaml index 1b157863..e38e2e7c 100644 --- a/src/valuesets/schema/materials_science/material_properties.yaml +++ b/src/valuesets/schema/materials_science/material_properties.yaml @@ -1,5 +1,5 @@ name: material_properties -id: https://w3id.org/linkml/valuesets/materials_science/material_properties +id: https://w3id.org/valuesets/materials_science/material_properties prefixes: CHEBI: http://purl.obolibrary.org/obo/CHEBI_ NCIT: http://purl.obolibrary.org/obo/NCIT_ diff --git a/src/valuesets/schema/materials_science/material_types.yaml b/src/valuesets/schema/materials_science/material_types.yaml index 32d95e78..f4726b5c 100644 --- a/src/valuesets/schema/materials_science/material_types.yaml +++ b/src/valuesets/schema/materials_science/material_types.yaml @@ -1,5 +1,5 @@ name: material_types -id: https://w3id.org/linkml/valuesets/materials_science/material_types +id: https://w3id.org/valuesets/materials_science/material_types prefixes: CHEBI: http://purl.obolibrary.org/obo/CHEBI_ ENVO: http://purl.obolibrary.org/obo/ENVO_ diff --git a/src/valuesets/schema/materials_science/synthesis_methods.yaml b/src/valuesets/schema/materials_science/synthesis_methods.yaml index 635eadd1..63ab69df 100644 --- a/src/valuesets/schema/materials_science/synthesis_methods.yaml +++ b/src/valuesets/schema/materials_science/synthesis_methods.yaml @@ -1,5 +1,5 @@ name: synthesis_methods -id: https://w3id.org/linkml/valuesets/materials_science/synthesis_methods +id: https://w3id.org/valuesets/materials_science/synthesis_methods prefixes: OBI: http://purl.obolibrary.org/obo/OBI_ CHMO: http://purl.obolibrary.org/obo/CHMO_ diff --git a/src/valuesets/schema/medical/oncology/icdo.yaml b/src/valuesets/schema/medical/oncology/icdo.yaml index 49c6f485..f8b8c9a4 100644 --- a/src/valuesets/schema/medical/oncology/icdo.yaml +++ b/src/valuesets/schema/medical/oncology/icdo.yaml @@ -4,7 +4,7 @@ description: >- Value sets based on the International Classification of Diseases for Oncology (ICD-O) bi-axial classification system. ICD-O uses two independent axes: topography (anatomic site) and morphology (histological type and behavior). -id: https://w3id.org/linkml/valuesets/medical/oncology/icdo +id: https://w3id.org/valuesets/medical/oncology/icdo imports: - linkml:types prefixes: diff --git a/src/valuesets/schema/medical/pediatric_oncology/diagnosis_categories.yaml b/src/valuesets/schema/medical/pediatric_oncology/diagnosis_categories.yaml index f1a5b89d..0d872209 100644 --- a/src/valuesets/schema/medical/pediatric_oncology/diagnosis_categories.yaml +++ b/src/valuesets/schema/medical/pediatric_oncology/diagnosis_categories.yaml @@ -6,7 +6,7 @@ description: >- developed through consensus by St. Jude, CBTN, Treehouse, and NCI to enable cohort aggregation across federated pediatric cancer data resources. Categories are aligned with WHO CNS5, WHO-HAEM5, and WHO Pediatric Blue Book. -id: https://w3id.org/linkml/valuesets/medical/pediatric_oncology/diagnosis_categories +id: https://w3id.org/valuesets/medical/pediatric_oncology/diagnosis_categories imports: - linkml:types prefixes: diff --git a/src/valuesets/schema/medical/pediatric_oncology/iccc3.yaml b/src/valuesets/schema/medical/pediatric_oncology/iccc3.yaml index 8f9b125b..d5bf664e 100644 --- a/src/valuesets/schema/medical/pediatric_oncology/iccc3.yaml +++ b/src/valuesets/schema/medical/pediatric_oncology/iccc3.yaml @@ -6,7 +6,7 @@ description: >- cancers, emphasizing tumor morphology rather than primary site (as used for adult cancers). ICCC-3 classifies tumors coded according to ICD-O-3 into 12 main groups and 47 subgroups. -id: https://w3id.org/linkml/valuesets/medical/pediatric_oncology/iccc3 +id: https://w3id.org/valuesets/medical/pediatric_oncology/iccc3 imports: - linkml:types prefixes: diff --git a/src/valuesets/schema/medical/pediatric_oncology/staging/neuroblastoma.yaml b/src/valuesets/schema/medical/pediatric_oncology/staging/neuroblastoma.yaml index 49d0a05d..98140360 100644 --- a/src/valuesets/schema/medical/pediatric_oncology/staging/neuroblastoma.yaml +++ b/src/valuesets/schema/medical/pediatric_oncology/staging/neuroblastoma.yaml @@ -6,7 +6,7 @@ description: >- System (INSS). INRGSS is the current standard (effective 2024+) based on imaging and image-defined risk factors. INSS is the legacy surgical staging system still used for historical data. -id: https://w3id.org/linkml/valuesets/medical/pediatric_oncology/staging/neuroblastoma +id: https://w3id.org/valuesets/medical/pediatric_oncology/staging/neuroblastoma imports: - linkml:types prefixes: diff --git a/src/valuesets/schema/physics/radiation.yaml b/src/valuesets/schema/physics/radiation.yaml index 179cd8e0..16cd410e 100644 --- a/src/valuesets/schema/physics/radiation.yaml +++ b/src/valuesets/schema/physics/radiation.yaml @@ -3,7 +3,7 @@ title: Radiation Types Value Sets description: >- Value sets for radiation types based on the Environment Ontology (ENVO), including electromagnetic radiation, ionizing radiation, and acoustic radiation. -id: https://w3id.org/linkml/valuesets/physics/radiation +id: https://w3id.org/valuesets/physics/radiation imports: - linkml:types prefixes: diff --git a/src/valuesets/schema/provenance/evidence.yaml b/src/valuesets/schema/provenance/evidence.yaml index 7a5029d4..ed1b4682 100644 --- a/src/valuesets/schema/provenance/evidence.yaml +++ b/src/valuesets/schema/provenance/evidence.yaml @@ -3,7 +3,7 @@ title: Evidence and Provenance Value Sets description: >- Value sets for evidence types and provenance information, based on the Evidence and Conclusion Ontology (ECO). -id: https://w3id.org/linkml/valuesets/provenance/evidence +id: https://w3id.org/valuesets/provenance/evidence imports: - linkml:types prefixes: diff --git a/src/valuesets/schema/publishing/arxiv_categories.yaml b/src/valuesets/schema/publishing/arxiv_categories.yaml index bc717faf..3f4ed5bd 100644 --- a/src/valuesets/schema/publishing/arxiv_categories.yaml +++ b/src/valuesets/schema/publishing/arxiv_categories.yaml @@ -3,7 +3,7 @@ title: arXiv Subject Categories description: >- Value sets for arXiv preprint subject categories and taxonomy. Based on the official arXiv category taxonomy. -id: https://w3id.org/linkml/valuesets/publishing/arxiv_categories +id: https://w3id.org/valuesets/publishing/arxiv_categories imports: - linkml:types prefixes: diff --git a/src/valuesets/schema/publishing/osti_record.yaml b/src/valuesets/schema/publishing/osti_record.yaml index eb275a05..c6c64dff 100644 --- a/src/valuesets/schema/publishing/osti_record.yaml +++ b/src/valuesets/schema/publishing/osti_record.yaml @@ -3,7 +3,7 @@ title: OSTI Record Metadata Value Sets description: | Value sets derived from the OSTI E-Link 2 record schema for bibliographic and submission metadata. -id: https://w3id.org/linkml/valuesets/publishing/osti_record +id: https://w3id.org/valuesets/publishing/osti_record imports: - linkml:types prefixes: diff --git a/src/valuesets/schema/social/person_status.yaml b/src/valuesets/schema/social/person_status.yaml index f84a4954..64631c67 100644 --- a/src/valuesets/schema/social/person_status.yaml +++ b/src/valuesets/schema/social/person_status.yaml @@ -1,5 +1,5 @@ name: person_status -id: https://w3id.org/linkml/valuesets/social/person_status +id: https://w3id.org/valuesets/social/person_status prefixes: PATO: http://purl.obolibrary.org/obo/PATO_ # linkml_common: https://w3id.org/linkml-common/ diff --git a/src/valuesets/schema/spatial/spatial_qualifiers.yaml b/src/valuesets/schema/spatial/spatial_qualifiers.yaml index f35327a9..4dc7772d 100644 --- a/src/valuesets/schema/spatial/spatial_qualifiers.yaml +++ b/src/valuesets/schema/spatial/spatial_qualifiers.yaml @@ -3,7 +3,7 @@ title: Spatial Qualifier Value Sets description: 'Value sets for spatial qualifiers, directions, and anatomical positions, including both simple directional terms and biological spatial terminology' -id: https://w3id.org/linkml/valuesets/spatial/spatial_qualifiers +id: https://w3id.org/valuesets/spatial/spatial_qualifiers imports: - linkml:types prefixes: diff --git a/src/valuesets/schema/statistics/prediction_outcomes.yaml b/src/valuesets/schema/statistics/prediction_outcomes.yaml index 6c215d84..30282347 100644 --- a/src/valuesets/schema/statistics/prediction_outcomes.yaml +++ b/src/valuesets/schema/statistics/prediction_outcomes.yaml @@ -1,5 +1,5 @@ name: prediction_outcomes -id: https://w3id.org/linkml/valuesets/statistics/prediction_outcomes +id: https://w3id.org/valuesets/statistics/prediction_outcomes prefixes: # linkml_common: https://w3id.org/linkml-common/ valuesets: https://w3id.org/valuesets/ diff --git a/src/valuesets/schema/time/temporal.yaml b/src/valuesets/schema/time/temporal.yaml index 0495da10..7dcae6a8 100644 --- a/src/valuesets/schema/time/temporal.yaml +++ b/src/valuesets/schema/time/temporal.yaml @@ -1,7 +1,7 @@ name: temporal title: Temporal and Time-Related Value Sets description: Value sets for temporal concepts including days, months, time periods, and durations -id: https://w3id.org/linkml/valuesets/time/temporal +id: https://w3id.org/valuesets/time/temporal imports: - linkml:types prefixes: diff --git a/src/valuesets/schema/types.yaml b/src/valuesets/schema/types.yaml index 56a2c5a8..30f0b399 100644 --- a/src/valuesets/schema/types.yaml +++ b/src/valuesets/schema/types.yaml @@ -1,7 +1,7 @@ name: types title: Common Type Definitions description: Common type definitions for value sets -id: https://w3id.org/linkml/valuesets/types +id: https://w3id.org/valuesets/types imports: - linkml:types prefixes: diff --git a/src/valuesets/schema/valuesets.yaml b/src/valuesets/schema/valuesets.yaml index 4b85314e..05f3776e 100644 --- a/src/valuesets/schema/valuesets.yaml +++ b/src/valuesets/schema/valuesets.yaml @@ -1,7 +1,7 @@ name: valuesets title: valuesets description: A collection of commonly used value sets -id: https://w3id.org/linkml/valuesets +id: https://w3id.org/valuesets imports: - core - contributor From b76603ab8a288cf80723e3ae3bfd426d4ae771ea Mon Sep 17 00:00:00 2001 From: dragon-ai-agent Date: Fri, 30 Jan 2026 18:40:05 -0800 Subject: [PATCH 2/3] Fix remaining URL references to use https://w3id.org/valuesets - Update merged_hierarchy.yaml id and valuesets prefix - Update merge_enums_hierarchy.py script with correct URLs - Update sssom_generator.py with correct mapping_set_id - Update docs and test files Co-Authored-By: Claude Opus 4.5 --- docs/manuscript/manuscript.md | 2 +- docs/schema/valuesets.yaml | 2 +- docs/slides/valuesets-slides.pdf | Bin 1269056 -> 1269056 bytes docs/slides/valuesets-slides.pptx | Bin 7438126 -> 7438126 bytes scripts/merge_enums_hierarchy.py | 4 +- .../datamodel/valuesets_dataclass.py | 916 +++++++++++++++++- src/valuesets/generators/sssom_generator.py | 2 +- src/valuesets/merged/merged_hierarchy.yaml | 4 +- test_mappings.sssom.tsv | 2 +- 9 files changed, 922 insertions(+), 10 deletions(-) diff --git a/docs/manuscript/manuscript.md b/docs/manuscript/manuscript.md index 9a57b05f..63aa5f20 100644 --- a/docs/manuscript/manuscript.md +++ b/docs/manuscript/manuscript.md @@ -98,7 +98,7 @@ CVS schemas are authored in YAML following LinkML syntax. Each schema file defin ```yaml name: schema_name -id: https://w3id.org/linkml/valuesets/domain/schema_name +id: https://w3id.org/valuesets/domain/schema_name prefixes: ontology_prefix: http://purl.obolibrary.org/obo/ONTOLOGY_ diff --git a/docs/schema/valuesets.yaml b/docs/schema/valuesets.yaml index 5e001866..d9d7f5a3 100644 --- a/docs/schema/valuesets.yaml +++ b/docs/schema/valuesets.yaml @@ -68947,5 +68947,5 @@ metamodel_version: 1.7.0 source_file: valuesets.yaml source_file_date: '2026-01-30T18:18:29' source_file_size: 3472 -generation_date: '2026-01-30T18:19:30' +generation_date: '2026-01-30T18:35:49' diff --git a/docs/slides/valuesets-slides.pdf b/docs/slides/valuesets-slides.pdf index 2108f67a14571e89bfa37f78157858b29e4f27ee..2b0424e49b3ec259fe2b51b055add6b4615b03c3 100644 GIT binary patch delta 4324 zcmZwGRaDdsy9IE%>m?M1Qc6m?!vSfeq@|R0Na^NJ4BbO_4bolG-6=D)f=I)FQqpjI z&&4_CTkG8X)?WMBw@+`odT+aW5ELDX0mX!3L9wAYP+TY;6dy_eC4>?|iJ>G=QYabp 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zAnTfhviNYyWkr``3qBQpt_H4#a^!lcSDFSb_^BMZo`3k{GY~s_4RDpNL9u*r<@eRM z1{3hPm5X(*fcuK7kP_Li%;5@9_MZxA1zX3gh4q28upV10Eoc5^>%i8dy@uBFHSm|C zJ&RU Dict[str, Any]: # Initialize the merged schema merged_schema = { - 'id': 'https://w3id.org/linkml/valuesets/merged', + 'id': 'https://w3id.org/valuesets/merged', 'name': 'valuesets_merged_hierarchy', 'title': 'Merged Value Sets with Hierarchical Structure', 'description': 'All value sets merged into a single hierarchical structure with is_a relationships', 'license': 'MIT', 'prefixes': { 'linkml': 'https://w3id.org/linkml/', - 'valuesets': 'https://w3id.org/linkml/valuesets/', + 'valuesets': 'https://w3id.org/valuesets/', }, 'default_prefix': 'valuesets', 'imports': ['linkml:types'], diff --git a/src/valuesets/datamodel/valuesets_dataclass.py b/src/valuesets/datamodel/valuesets_dataclass.py index 45c8c1bb..02d280d2 100644 --- a/src/valuesets/datamodel/valuesets_dataclass.py +++ b/src/valuesets/datamodel/valuesets_dataclass.py @@ -1,8 +1,8 @@ # Auto generated from valuesets.yaml by pythongen.py version: 0.0.1 -# Generation date: 2025-12-22T07:10:11 +# Generation date: 2026-01-30T18:34:51 # Schema: valuesets # -# id: https://w3id.org/linkml/valuesets +# id: https://w3id.org/valuesets # description: A collection of commonly used value sets # license: Apache-2.0 @@ -9850,6 +9850,890 @@ class PersonStatusEnum(EnumDefinitionImpl): description="Vital status of a person (living or deceased)", ) +class GravitySdohDomainEnum(EnumDefinitionImpl): + """ + Social Determinants of Health domains as defined by the Gravity Project. These domains represent key areas of + social need that impact health outcomes. + """ + FOOD_INSECURITY = PermissibleValue( + text="FOOD_INSECURITY", + description="Limited or uncertain availability of nutritionally adequate and safe foods", + meaning=NCIT["C171542"]) + HOUSING_INSTABILITY = PermissibleValue( + text="HOUSING_INSTABILITY", + description="Challenges with housing including trouble paying rent or frequent moves", + meaning=SNOMED["1156191002"]) + HOMELESSNESS = PermissibleValue( + text="HOMELESSNESS", + description="The condition of lacking stable, safe, and adequate housing", + meaning=SNOMED["32911000"]) + INADEQUATE_HOUSING = PermissibleValue( + text="INADEQUATE_HOUSING", + description="Housing that does not meet basic standards for safety and habitability", + meaning=SNOMED["105531004"]) + TRANSPORTATION_INSECURITY = PermissibleValue( + text="TRANSPORTATION_INSECURITY", + description="Lack of reliable, safe, and affordable transportation") + FINANCIAL_INSECURITY = PermissibleValue( + text="FINANCIAL_INSECURITY", + description="Inability to meet basic financial needs and obligations") + MATERIAL_HARDSHIP = PermissibleValue( + text="MATERIAL_HARDSHIP", + description="Difficulty affording basic necessities such as food, housing, and utilities") + EMPLOYMENT_STATUS = PermissibleValue( + text="EMPLOYMENT_STATUS", + description="Current employment situation and stability", + meaning=NCIT["C179143"]) + EDUCATIONAL_ATTAINMENT = PermissibleValue( + text="EDUCATIONAL_ATTAINMENT", + description="Highest level of education completed", + meaning=EFO["0011015"]) + VETERAN_STATUS = PermissibleValue( + text="VETERAN_STATUS", + description="Military veteran status and related needs") + STRESS = PermissibleValue( + text="STRESS", + description="Psychological stress affecting health and wellbeing", + meaning=NCIT["C35041"]) + SOCIAL_CONNECTION = PermissibleValue( + text="SOCIAL_CONNECTION", + description="Quality and quantity of social relationships and support networks") + INTIMATE_PARTNER_VIOLENCE = PermissibleValue( + text="INTIMATE_PARTNER_VIOLENCE", + description="Abuse occurring between people in a close relationship", + meaning=MESH["D000066511"]) + ELDER_ABUSE = PermissibleValue( + text="ELDER_ABUSE", + description="Abuse, neglect, or exploitation of older adults", + meaning=MESH["D004552"]) + HEALTH_LITERACY = PermissibleValue( + text="HEALTH_LITERACY", + description="Ability to obtain, process, and understand health information", + meaning=MESH["D057220"]) + MEDICAL_COST_BURDEN = PermissibleValue( + text="MEDICAL_COST_BURDEN", + description="Financial strain from healthcare costs") + HEALTH_INSURANCE_COVERAGE_STATUS = PermissibleValue( + text="HEALTH_INSURANCE_COVERAGE_STATUS", + description="Status of health insurance coverage", + meaning=NCIT["C157356"]) + DIGITAL_LITERACY = PermissibleValue( + text="DIGITAL_LITERACY", + description="Ability to use digital technology and access digital resources") + DIGITAL_ACCESS = PermissibleValue( + text="DIGITAL_ACCESS", + description="Access to internet and digital devices") + UTILITY_INSECURITY = PermissibleValue( + text="UTILITY_INSECURITY", + description="Difficulty paying for utilities such as electricity, gas, or water") + + _defn = EnumDefinition( + name="GravitySdohDomainEnum", + description="""Social Determinants of Health domains as defined by the Gravity Project. These domains represent key areas of social need that impact health outcomes.""", + ) + +class EducationalAttainmentEnum(EnumDefinitionImpl): + """ + Levels of educational attainment for survey and demographic purposes. Based on standard US educational categories. + """ + EIGHTH_GRADE_OR_LESS = PermissibleValue( + text="EIGHTH_GRADE_OR_LESS", + description="Completed 8th grade or less") + HIGH_SCHOOL_NO_DIPLOMA = PermissibleValue( + text="HIGH_SCHOOL_NO_DIPLOMA", + description="Some high school but no diploma", + meaning=NCIT["C76123"]) + HIGH_SCHOOL_GRADUATE_GED = PermissibleValue( + text="HIGH_SCHOOL_GRADUATE_GED", + description="High school graduate or GED equivalent", + meaning=NCIT["C67136"]) + SOME_COLLEGE_NO_DEGREE = PermissibleValue( + text="SOME_COLLEGE_NO_DEGREE", + description="Some college or technical school but no degree") + ASSOCIATE_DEGREE = PermissibleValue( + text="ASSOCIATE_DEGREE", + description="Associate degree (2-year college)", + meaning=NCIT["C71344"]) + BACHELORS_DEGREE = PermissibleValue( + text="BACHELORS_DEGREE", + description="Bachelor's degree (4-year college)", + meaning=NCIT["C71345"]) + MASTERS_DEGREE = PermissibleValue( + text="MASTERS_DEGREE", + description="Master's degree", + meaning=NCIT["C39452"]) + DOCTORAL_DEGREE = PermissibleValue( + text="DOCTORAL_DEGREE", + description="Doctoral or professional degree (PhD, MD, JD, etc.)", + meaning=NCIT["C39387"]) + + _defn = EnumDefinition( + name="EducationalAttainmentEnum", + description="""Levels of educational attainment for survey and demographic purposes. Based on standard US educational categories.""", + ) + +class SpecimenPreparationMethodEnum(EnumDefinitionImpl): + """ + Methods for preparing and preserving biological specimens for analysis. Sourced from NF-OSI metadata dictionary + and Human Cell Atlas standards. + """ + FFPE = PermissibleValue( + text="FFPE", + description="Formalin-fixed, paraffin-embedded tissue preservation", + meaning=NCIT["C143028"]) + FORMALIN_FIXED = PermissibleValue( + text="FORMALIN_FIXED", + description="Tissue fixed with formalin without paraffin embedding") + CRYOPRESERVED = PermissibleValue( + text="CRYOPRESERVED", + description="Specimen preserved by freezing with cryoprotectant", + meaning=NCIT["C16475"]) + VIABLY_FROZEN = PermissibleValue( + text="VIABLY_FROZEN", + description="Specimen frozen while maintaining cell viability") + FLASH_FROZEN = PermissibleValue( + text="FLASH_FROZEN", + description="Rapid freezing to preserve molecular integrity") + FRESH_COLLECTED = PermissibleValue( + text="FRESH_COLLECTED", + description="Freshly collected specimen without preservation") + OCT_EMBEDDED = PermissibleValue( + text="OCT_EMBEDDED", + description="Tissue embedded in optimal cutting temperature compound") + RNALATER = PermissibleValue( + text="RNALATER", + description="Storage in reagent that stabilizes and protects cellular RNA") + ETHANOL_PRESERVED = PermissibleValue( + text="ETHANOL_PRESERVED", + description="Specimen preserved in ethanol") + METHANOL_FIXED = PermissibleValue( + text="METHANOL_FIXED", + description="Specimen fixed with methanol") + ACETONE_FIXED = PermissibleValue( + text="ACETONE_FIXED", + description="Specimen fixed with acetone") + PAXgene_FIXED = PermissibleValue( + text="PAXgene_FIXED", + description="Tissue fixed using PAXgene tissue system") + DRIED = PermissibleValue( + text="DRIED", + description="Air-dried or desiccated specimen") + LYOPHILIZED = PermissibleValue( + text="LYOPHILIZED", + description="Freeze-dried specimen", + meaning=NCIT["C28150"]) + + _defn = EnumDefinition( + name="SpecimenPreparationMethodEnum", + description="""Methods for preparing and preserving biological specimens for analysis. Sourced from NF-OSI metadata dictionary and Human Cell Atlas standards.""", + ) + +class TissuePreservationEnum(EnumDefinitionImpl): + """ + Broader categorization of tissue preservation approaches + """ + FROZEN = PermissibleValue( + text="FROZEN", + description="Tissue preserved by freezing", + meaning=NCIT["C70717"]) + FIXED = PermissibleValue( + text="FIXED", + description="Tissue preserved by chemical fixation", + meaning=NCIT["C25219"]) + FRESH = PermissibleValue( + text="FRESH", + description="Fresh unfixed tissue") + EMBEDDED = PermissibleValue( + text="EMBEDDED", + description="Tissue embedded in medium (paraffin, OCT, etc.)") + + _defn = EnumDefinition( + name="TissuePreservationEnum", + description="Broader categorization of tissue preservation approaches", + ) + +class SpecimenCollectionMethodEnum(EnumDefinitionImpl): + """ + Methods for collecting biological specimens + """ + BIOPSY = PermissibleValue( + text="BIOPSY", + description="Tissue sample obtained by biopsy", + meaning=NCIT["C15189"]) + SURGICAL_RESECTION = PermissibleValue( + text="SURGICAL_RESECTION", + description="Tissue obtained during surgical resection", + meaning=NCIT["C15329"]) + AUTOPSY = PermissibleValue( + text="AUTOPSY", + description="Specimen obtained at autopsy", + meaning=NCIT["C25153"]) + FINE_NEEDLE_ASPIRATE = PermissibleValue( + text="FINE_NEEDLE_ASPIRATE", + description="Sample obtained by fine needle aspiration", + meaning=NCIT["C15361"]) + CORE_NEEDLE_BIOPSY = PermissibleValue( + text="CORE_NEEDLE_BIOPSY", + description="Sample obtained by core needle biopsy", + meaning=NCIT["C15190"]) + PUNCH_BIOPSY = PermissibleValue( + text="PUNCH_BIOPSY", + description="Sample obtained by punch biopsy") + SWAB = PermissibleValue( + text="SWAB", + description="Sample collected by swabbing") + VENIPUNCTURE = PermissibleValue( + text="VENIPUNCTURE", + description="Blood sample obtained by venipuncture", + meaning=NCIT["C28221"]) + LUMBAR_PUNCTURE = PermissibleValue( + text="LUMBAR_PUNCTURE", + description="CSF sample obtained by lumbar puncture", + meaning=NCIT["C15327"]) + LAVAGE = PermissibleValue( + text="LAVAGE", + description="Sample obtained by lavage (washing)") + + _defn = EnumDefinition( + name="SpecimenCollectionMethodEnum", + description="Methods for collecting biological specimens", + ) + +class SpecimenTypeEnum(EnumDefinitionImpl): + """ + Types of biological specimens used in research + """ + TISSUE = PermissibleValue( + text="TISSUE", + description="Solid tissue specimen", + meaning=NCIT["C12801"]) + BLOOD = PermissibleValue( + text="BLOOD", + description="Whole blood specimen", + meaning=NCIT["C12434"]) + PLASMA = PermissibleValue( + text="PLASMA", + description="Blood plasma specimen", + meaning=NCIT["C13356"]) + SERUM = PermissibleValue( + text="SERUM", + description="Blood serum specimen", + meaning=NCIT["C13325"]) + BUFFY_COAT = PermissibleValue( + text="BUFFY_COAT", + description="Leukocyte-enriched blood fraction", + meaning=NCIT["C84507"]) + URINE = PermissibleValue( + text="URINE", + description="Urine specimen", + meaning=NCIT["C13283"]) + SALIVA = PermissibleValue( + text="SALIVA", + description="Saliva specimen", + meaning=NCIT["C13275"]) + STOOL = PermissibleValue( + text="STOOL", + description="Stool/fecal specimen", + meaning=NCIT["C13234"]) + CSF = PermissibleValue( + text="CSF", + description="Cerebrospinal fluid specimen", + meaning=NCIT["C12692"]) + SWEAT = PermissibleValue( + text="SWEAT", + description="Sweat specimen") + MUCUS = PermissibleValue( + text="MUCUS", + description="Mucus specimen") + BONE_MARROW = PermissibleValue( + text="BONE_MARROW", + description="Bone marrow specimen", + meaning=NCIT["C12431"]) + PRIMARY_TUMOR = PermissibleValue( + text="PRIMARY_TUMOR", + description="Primary tumor tissue specimen", + meaning=NCIT["C8509"]) + METASTATIC_TUMOR = PermissibleValue( + text="METASTATIC_TUMOR", + description="Metastatic tumor tissue specimen", + meaning=NCIT["C3261"]) + TUMOR_ADJACENT_NORMAL = PermissibleValue( + text="TUMOR_ADJACENT_NORMAL", + description="Normal tissue adjacent to tumor", + meaning=NCIT["C164032"]) + ORGANOID = PermissibleValue( + text="ORGANOID", + description="Organoid specimen", + meaning=NCIT["C172259"]) + SPHEROID = PermissibleValue( + text="SPHEROID", + description="Cell spheroid specimen") + MICROTISSUE = PermissibleValue( + text="MICROTISSUE", + description="Engineered microtissue specimen") + PDX_TISSUE = PermissibleValue( + text="PDX_TISSUE", + description="Patient-derived xenograft tissue", + meaning=NCIT["C122936"]) + CDX_TISSUE = PermissibleValue( + text="CDX_TISSUE", + description="Cell line-derived xenograft tissue") + + _defn = EnumDefinition( + name="SpecimenTypeEnum", + description="Types of biological specimens used in research", + ) + +class AnalyteTypeEnum(EnumDefinitionImpl): + """ + Types of analytes that can be extracted from biological specimens for molecular analysis. + """ + DNA = PermissibleValue( + text="DNA", + description="Deoxyribonucleic acid", + meaning=NCIT["C198567"]) + RNA = PermissibleValue( + text="RNA", + description="Ribonucleic acid", + meaning=NCIT["C198568"]) + TOTAL_RNA = PermissibleValue( + text="TOTAL_RNA", + description="Total RNA including all RNA species") + FFPE_DNA = PermissibleValue( + text="FFPE_DNA", + description="DNA extracted from formalin-fixed paraffin-embedded tissue") + FFPE_RNA = PermissibleValue( + text="FFPE_RNA", + description="RNA extracted from formalin-fixed paraffin-embedded tissue") + cfDNA = PermissibleValue( + text="cfDNA", + description="Cell-free DNA found in blood plasma", + meaning=NCIT["C128274"]) + PROTEIN = PermissibleValue( + text="PROTEIN", + description="Protein analyte", + meaning=NCIT["C17021"]) + NUCLEI_RNA = PermissibleValue( + text="NUCLEI_RNA", + description="RNA isolated from cell nuclei") + REPLI_G_DNA = PermissibleValue( + text="REPLI_G_DNA", + description="Whole genome amplified DNA using Repli-G technology") + REPLI_G_X_DNA = PermissibleValue( + text="REPLI_G_X_DNA", + description="Whole genome amplified DNA using Repli-G X technology") + REPLI_G_POOLED_DNA = PermissibleValue( + text="REPLI_G_POOLED_DNA", + description="Pooled whole genome amplified DNA using Repli-G") + GENOMEPLEX_DNA = PermissibleValue( + text="GENOMEPLEX_DNA", + description="Whole genome amplified DNA using GenomePlex technology") + EBV_IMMORTALIZED = PermissibleValue( + text="EBV_IMMORTALIZED", + description="DNA/cells from EBV immortalized cell lines") + + _defn = EnumDefinition( + name="AnalyteTypeEnum", + description="Types of analytes that can be extracted from biological specimens for molecular analysis.", + ) + +class SourceMaterialTypeEnum(EnumDefinitionImpl): + """ + Types of source materials from which specimens are derived, particularly relevant for cancer and tissue banking + research. + """ + PRIMARY_TUMOR = PermissibleValue( + text="PRIMARY_TUMOR", + description="Primary tumor tissue", + meaning=NCIT["C8509"]) + METASTATIC = PermissibleValue( + text="METASTATIC", + description="Metastatic tumor tissue", + meaning=NCIT["C3261"]) + RECURRENT_TUMOR = PermissibleValue( + text="RECURRENT_TUMOR", + description="Recurrent tumor tissue", + meaning=NCIT["C4798"]) + BLOOD_DERIVED_NORMAL = PermissibleValue( + text="BLOOD_DERIVED_NORMAL", + description="Normal cells derived from blood") + BLOOD_DERIVED_CANCER_PERIPHERAL_BLOOD = PermissibleValue( + text="BLOOD_DERIVED_CANCER_PERIPHERAL_BLOOD", + description="Cancer cells from peripheral blood") + BLOOD_DERIVED_CANCER_BONE_MARROW = PermissibleValue( + text="BLOOD_DERIVED_CANCER_BONE_MARROW", + description="Cancer cells from bone marrow") + BONE_MARROW_NORMAL = PermissibleValue( + text="BONE_MARROW_NORMAL", + description="Normal bone marrow cells") + SOLID_TISSUE_NORMAL = PermissibleValue( + text="SOLID_TISSUE_NORMAL", + description="Normal solid tissue") + BUCCAL_CELL_NORMAL = PermissibleValue( + text="BUCCAL_CELL_NORMAL", + description="Normal buccal (cheek) cells") + NORMAL_ADJACENT_TISSUE = PermissibleValue( + text="NORMAL_ADJACENT_TISSUE", + description="Normal tissue adjacent to tumor", + meaning=NCIT["C164032"]) + CELL_LINES = PermissibleValue( + text="CELL_LINES", + description="Established cell lines", + meaning=NCIT["C16403"]) + PRIMARY_XENOGRAFT_TISSUE = PermissibleValue( + text="PRIMARY_XENOGRAFT_TISSUE", + description="Tissue from primary xenograft") + XENOGRAFT_TISSUE = PermissibleValue( + text="XENOGRAFT_TISSUE", + description="Tissue derived from xenograft models") + NEXT_GENERATION_CANCER_MODEL = PermissibleValue( + text="NEXT_GENERATION_CANCER_MODEL", + description="Tissue from next-generation cancer models") + PLEURAL_EFFUSION = PermissibleValue( + text="PLEURAL_EFFUSION", + description="Fluid from pleural effusion", + meaning=NCIT["C3331"]) + SALIVA = PermissibleValue( + text="SALIVA", + description="Saliva specimen", + meaning=NCIT["C13275"]) + GRANULOCYTES = PermissibleValue( + text="GRANULOCYTES", + description="Granulocyte cells", + meaning=NCIT["C12530"]) + EBV_IMMORTALIZED_NORMAL = PermissibleValue( + text="EBV_IMMORTALIZED_NORMAL", + description="EBV immortalized normal cells") + CONTROL_ANALYTE = PermissibleValue( + text="CONTROL_ANALYTE", + description="Control analyte material") + FFPE_SCROLLS = PermissibleValue( + text="FFPE_SCROLLS", + description="FFPE tissue scrolls") + FFPE_RECURRENT = PermissibleValue( + text="FFPE_RECURRENT", + description="FFPE tissue from recurrent tumor") + NOT_REPORTED = PermissibleValue( + text="NOT_REPORTED", + description="Source material type not reported") + UNKNOWN = PermissibleValue( + text="UNKNOWN", + description="Unknown source material type", + meaning=NCIT["C17998"]) + + _defn = EnumDefinition( + name="SourceMaterialTypeEnum", + description="""Types of source materials from which specimens are derived, particularly relevant for cancer and tissue banking research.""", + ) + +class SpecimenCreationActivityTypeEnum(EnumDefinitionImpl): + """ + High-level types of activities through which specimens are generated, either by collection from source or + derivation from existing specimens. + """ + COLLECTION_FROM_SOURCE = PermissibleValue( + text="COLLECTION_FROM_SOURCE", + description="Activity that collects an initial sample directly from a subject or source", + meaning=OBI["0000659"]) + DERIVATION_FROM_SPECIMEN = PermissibleValue( + text="DERIVATION_FROM_SPECIMEN", + description="Activity that derives a new specimen from an existing one", + meaning=OBI["0000094"]) + + _defn = EnumDefinition( + name="SpecimenCreationActivityTypeEnum", + description="""High-level types of activities through which specimens are generated, either by collection from source or derivation from existing specimens.""", + ) + +class SpecimenProcessingActivityTypeEnum(EnumDefinitionImpl): + """ + High-level types of specimen processing activities + """ + FIXATION = PermissibleValue( + text="FIXATION", + description="Chemical preservation to maintain structural and molecular features", + meaning=NCIT["C25219"]) + FREEZING = PermissibleValue( + text="FREEZING", + description="Processing activity that freezes a specimen", + meaning=NCIT["C70717"]) + MOUNTING = PermissibleValue( + text="MOUNTING", + description="Securing a specimen in place for examination") + PRESERVATION = PermissibleValue( + text="PRESERVATION", + description="Processing activity that preserves a specimen for storage") + + _defn = EnumDefinition( + name="SpecimenProcessingActivityTypeEnum", + description="High-level types of specimen processing activities", + ) + +class SpecimenQualityObservationTypeEnum(EnumDefinitionImpl): + """ + Types of measurements that reflect specimen quality or suitability for use + """ + A260_A280_RATIO = PermissibleValue( + text="A260_A280_RATIO", + description="Ratio of absorbance at 260nm to 280nm wavelength for nucleic acid purity") + RIBOSOMAL_RNA_28S_16S_RATIO = PermissibleValue( + text="RIBOSOMAL_RNA_28S_16S_RATIO", + description="Ratio of 28S to 16S ribosomal RNA for RNA integrity") + + _defn = EnumDefinition( + name="SpecimenQualityObservationTypeEnum", + description="Types of measurements that reflect specimen quality or suitability for use", + ) + +class SpecimenQualityObservationMethodEnum(EnumDefinitionImpl): + """ + Methods used for determining specimen quality + """ + UV_SPEC = PermissibleValue( + text="UV_SPEC", + description="UV-Vis spectrophotometry measuring absorbance across UV and visible ranges", + meaning=NCIT["C116701"]) + PICO_GREEN = PermissibleValue( + text="PICO_GREEN", + description="Fluorescent dye assay for quantifying double-stranded DNA") + + _defn = EnumDefinition( + name="SpecimenQualityObservationMethodEnum", + description="Methods used for determining specimen quality", + ) + +class SpecimenQuantityObservationTypeEnum(EnumDefinitionImpl): + """ + Types of quantity measurements for specimens + """ + WEIGHT = PermissibleValue( + text="WEIGHT", + description="Current weight of the specimen", + meaning=NCIT["C25208"]) + VOLUME = PermissibleValue( + text="VOLUME", + description="Current volume of the specimen", + meaning=NCIT["C25335"]) + CONCENTRATION = PermissibleValue( + text="CONCENTRATION", + description="Concentration of extracted analyte in specimen", + meaning=NCIT["C41185"]) + + _defn = EnumDefinition( + name="SpecimenQuantityObservationTypeEnum", + description="Types of quantity measurements for specimens", + ) + +class SectionLocationEnum(EnumDefinitionImpl): + """ + Location in a parent specimen from which a section was excised + """ + TOP = PermissibleValue( + text="TOP", + description="The top portion of a specimen per orientation criteria") + BOTTOM = PermissibleValue( + text="BOTTOM", + description="The bottom portion of a specimen per orientation criteria") + UNKNOWN = PermissibleValue( + text="UNKNOWN", + description="Unknown location on a specimen", + meaning=NCIT["C17998"]) + + _defn = EnumDefinition( + name="SectionLocationEnum", + description="Location in a parent specimen from which a section was excised", + ) + +class ConditionProvenanceEnum(EnumDefinitionImpl): + """ + Sources of condition/diagnosis records indicating how the condition was documented or determined. + """ + EHR_BILLING_DIAGNOSIS = PermissibleValue( + text="EHR_BILLING_DIAGNOSIS", + description="Diagnosis recorded for billing purposes in EHR") + EHR_CHIEF_COMPLAINT = PermissibleValue( + text="EHR_CHIEF_COMPLAINT", + description="Condition documented as chief complaint in EHR") + EHR_ENCOUNTER_DIAGNOSIS = PermissibleValue( + text="EHR_ENCOUNTER_DIAGNOSIS", + description="Diagnosis recorded during healthcare encounter") + EHR_EPISODE_ENTRY = PermissibleValue( + text="EHR_EPISODE_ENTRY", + description="Condition recorded as part of care episode") + EHR_PROBLEM_LIST_ENTRY = PermissibleValue( + text="EHR_PROBLEM_LIST_ENTRY", + description="Condition on patient problem list in EHR") + FIRST_POSITION_CONDITION = PermissibleValue( + text="FIRST_POSITION_CONDITION", + description="Primary diagnosis in first position on claim") + NLP_DERIVED = PermissibleValue( + text="NLP_DERIVED", + description="Condition derived through natural language processing") + OBSERVATION_RECORDED_FROM_EHR = PermissibleValue( + text="OBSERVATION_RECORDED_FROM_EHR", + description="Condition recorded as observation in EHR") + PATIENT_SELF_REPORTED_CONDITION = PermissibleValue( + text="PATIENT_SELF_REPORTED_CONDITION", + description="Condition reported by the patient") + PRIMARY_CONDITION = PermissibleValue( + text="PRIMARY_CONDITION", + description="Primary condition for an encounter or episode") + REFERRAL_RECORD = PermissibleValue( + text="REFERRAL_RECORD", + description="Condition documented in referral record") + SECONDARY_CONDITION = PermissibleValue( + text="SECONDARY_CONDITION", + description="Secondary or comorbid condition") + TUMOR_REGISTRY = PermissibleValue( + text="TUMOR_REGISTRY", + description="Condition from tumor registry") + WORKING_DIAGNOSIS = PermissibleValue( + text="WORKING_DIAGNOSIS", + description="Preliminary or working diagnosis") + CLINICAL_DIAGNOSIS = PermissibleValue( + text="CLINICAL_DIAGNOSIS", + description="Clinically confirmed diagnosis") + + _defn = EnumDefinition( + name="ConditionProvenanceEnum", + description="Sources of condition/diagnosis records indicating how the condition was documented or determined.", + ) + +class VisitProvenanceEnum(EnumDefinitionImpl): + """ + Sources of healthcare visit/encounter records indicating the origin of the visit documentation. + """ + CASE_REPORT_FORM = PermissibleValue( + text="CASE_REPORT_FORM", + description="Visit from clinical trial case report form") + CLAIM = PermissibleValue( + text="CLAIM", + description="Visit derived from insurance claim") + EHR = PermissibleValue( + text="EHR", + description="Visit from electronic health record") + EHR_ENCOUNTER_RECORD = PermissibleValue( + text="EHR_ENCOUNTER_RECORD", + description="Visit from EHR encounter documentation") + EHR_ADMISSION_NOTE = PermissibleValue( + text="EHR_ADMISSION_NOTE", + description="Visit from EHR admission note") + EHR_DISCHARGE_RECORD = PermissibleValue( + text="EHR_DISCHARGE_RECORD", + description="Visit from EHR discharge documentation") + EHR_EMERGENCY_ROOM_NOTE = PermissibleValue( + text="EHR_EMERGENCY_ROOM_NOTE", + description="Visit from EHR emergency room note") + EHR_INPATIENT_NOTE = PermissibleValue( + text="EHR_INPATIENT_NOTE", + description="Visit from EHR inpatient note") + EHR_OUTPATIENT_NOTE = PermissibleValue( + text="EHR_OUTPATIENT_NOTE", + description="Visit from EHR outpatient note") + INPATIENT_CLAIM = PermissibleValue( + text="INPATIENT_CLAIM", + description="Visit from inpatient insurance claim") + OUTPATIENT_CLAIM = PermissibleValue( + text="OUTPATIENT_CLAIM", + description="Visit from outpatient insurance claim") + FACILITY_CLAIM = PermissibleValue( + text="FACILITY_CLAIM", + description="Visit from facility insurance claim") + PROFESSIONAL_CLAIM = PermissibleValue( + text="PROFESSIONAL_CLAIM", + description="Visit from professional services claim") + PHARMACY_CLAIM = PermissibleValue( + text="PHARMACY_CLAIM", + description="Visit from pharmacy claim") + LAB = PermissibleValue( + text="LAB", + description="Visit from laboratory record") + REGISTRY = PermissibleValue( + text="REGISTRY", + description="Visit from disease or patient registry") + SURVEY = PermissibleValue( + text="SURVEY", + description="Visit from patient survey") + PATIENT_SELF_REPORT = PermissibleValue( + text="PATIENT_SELF_REPORT", + description="Visit reported by patient") + NLP = PermissibleValue( + text="NLP", + description="Visit derived through natural language processing") + HEALTH_INFORMATION_EXCHANGE_RECORD = PermissibleValue( + text="HEALTH_INFORMATION_EXCHANGE_RECORD", + description="Visit from health information exchange") + + _defn = EnumDefinition( + name="VisitProvenanceEnum", + description="Sources of healthcare visit/encounter records indicating the origin of the visit documentation.", + ) + +class DrugExposureProvenanceEnum(EnumDefinitionImpl): + """ + Sources of drug exposure records indicating how the medication information was documented. + """ + RANDOMIZED_DRUG = PermissibleValue( + text="RANDOMIZED_DRUG", + description="Drug from clinical trial randomization") + PATIENT_SELF_REPORTED_MEDICATION = PermissibleValue( + text="PATIENT_SELF_REPORTED_MEDICATION", + description="Medication reported by patient") + NLP_DERIVED = PermissibleValue( + text="NLP_DERIVED", + description="Drug exposure derived through NLP") + PRESCRIPTION_DISPENSED_IN_PHARMACY = PermissibleValue( + text="PRESCRIPTION_DISPENSED_IN_PHARMACY", + description="Prescription dispensed at pharmacy") + PHYSICIAN_ADMINISTERED_DRUG_FROM_EHR_ORDER = PermissibleValue( + text="PHYSICIAN_ADMINISTERED_DRUG_FROM_EHR_ORDER", + description="Drug administered by physician from EHR order") + DISPENSED_IN_OUTPATIENT_OFFICE = PermissibleValue( + text="DISPENSED_IN_OUTPATIENT_OFFICE", + description="Drug dispensed in outpatient office") + PRESCRIPTION_DISPENSED_THROUGH_MAIL_ORDER = PermissibleValue( + text="PRESCRIPTION_DISPENSED_THROUGH_MAIL_ORDER", + description="Prescription dispensed via mail order") + PRESCRIPTION_WRITTEN = PermissibleValue( + text="PRESCRIPTION_WRITTEN", + description="Prescription written by provider") + MEDICATION_LIST_ENTRY = PermissibleValue( + text="MEDICATION_LIST_ENTRY", + description="Drug from medication list") + PHYSICIAN_ADMINISTERED_DRUG_AS_PROCEDURE = PermissibleValue( + text="PHYSICIAN_ADMINISTERED_DRUG_AS_PROCEDURE", + description="Drug administered as procedure") + INPATIENT_ADMINISTRATION = PermissibleValue( + text="INPATIENT_ADMINISTRATION", + description="Drug administered during inpatient stay") + + _defn = EnumDefinition( + name="DrugExposureProvenanceEnum", + description="Sources of drug exposure records indicating how the medication information was documented.", + ) + +class StatusEnum(EnumDefinitionImpl): + """ + Values indicating whether a condition or observation is present, absent, or of unknown status. + """ + PRESENT = PermissibleValue( + text="PRESENT", + description="Was present in the patient at observation time") + ABSENT = PermissibleValue( + text="ABSENT", + description="Was absent in the patient at observation time") + UNKNOWN = PermissibleValue( + text="UNKNOWN", + description="Status was unknown at observation time") + + _defn = EnumDefinition( + name="StatusEnum", + description="Values indicating whether a condition or observation is present, absent, or of unknown status.", + ) + +class HistoricalStatusEnum(EnumDefinitionImpl): + """ + Extended status values including historical presence of conditions or observations. + """ + PRESENT = PermissibleValue( + text="PRESENT", + description="Currently present in the patient") + ABSENT = PermissibleValue( + text="ABSENT", + description="Currently absent in the patient") + UNKNOWN = PermissibleValue( + text="UNKNOWN", + description="Current status is unknown") + HISTORICAL = PermissibleValue( + text="HISTORICAL", + description="Was present in the patient historically but not currently") + + _defn = EnumDefinition( + name="HistoricalStatusEnum", + description="Extended status values including historical presence of conditions or observations.", + ) + +class ResearchProjectTypeEnum(EnumDefinitionImpl): + """ + Types of research projects and studies + """ + CONSORTIUM = PermissibleValue( + text="CONSORTIUM", + description="Multi-institutional research consortium") + STUDY = PermissibleValue( + text="STUDY", + description="Individual research study") + + _defn = EnumDefinition( + name="ResearchProjectTypeEnum", + description="Types of research projects and studies", + ) + +class DataUsePermissionEnum(EnumDefinitionImpl): + """ + Primary data use permissions from the GA4GH Data Use Ontology (DUO) indicating what research purposes data can be + used for. + """ + GRU = PermissibleValue( + text="GRU", + description="""General research use - allowed for any research purpose including health/medical/biomedical, fundamental biology, population origins, statistical methods development, and social-sciences research.""", + meaning=DUO["0000042"]) + HMB = PermissibleValue( + text="HMB", + description="""Health/medical/biomedical research only - does not include study of population origins or ancestry.""", + meaning=DUO["0000006"]) + DS = PermissibleValue( + text="DS", + description="""Disease-specific research - use allowed only for research related to specified disease(s). Should be coupled with disease ontology term.""", + meaning=DUO["0000007"]) + NO_RESTRICTION = PermissibleValue( + text="NO_RESTRICTION", + description="No restriction on use of the data.", + meaning=DUO["0000004"]) + + _defn = EnumDefinition( + name="DataUsePermissionEnum", + description="""Primary data use permissions from the GA4GH Data Use Ontology (DUO) indicating what research purposes data can be used for.""", + ) + +class DataUseModifierEnum(EnumDefinitionImpl): + """ + Additional conditions and modifiers for data use from the GA4GH Data Use Ontology (DUO). + """ + NPUNCU = PermissibleValue( + text="NPUNCU", + description="Not-for-profit use only - use limited to not-for-profit organizations and non-commercial use.", + meaning=DUO["0000018"]) + NPO = PermissibleValue( + text="NPO", + description="Use limited to not-for-profit organizations only.", + meaning=DUO["0000045"]) + NCU = PermissibleValue( + text="NCU", + description="""Non-commercial use only - data can be used by commercial organizations for research but not commercial purposes.""", + meaning=DUO["0000046"]) + IRB = PermissibleValue( + text="IRB", + description="Ethics approval required - requestor must provide documentation of local IRB/ERB approval.", + meaning=DUO["0000021"]) + NRES = PermissibleValue( + text="NRES", + description="No restriction on data use.", + meaning=DUO["0000004"]) + NMDS = PermissibleValue( + text="NMDS", + description="No general methods research - does not allow methods development.", + meaning=DUO["0000015"]) + RS = PermissibleValue( + text="RS", + description="Research-specific restrictions apply.", + meaning=DUO["0000012"]) + + _defn = EnumDefinition( + name="DataUseModifierEnum", + description="Additional conditions and modifiers for data use from the GA4GH Data Use Ontology (DUO).", + ) + class MimeType(EnumDefinitionImpl): """ Common MIME types for various file formats @@ -31309,6 +32193,33 @@ class slots: slots.person_status = Slot(uri=VALUESETS.person_status, name="person_status", curie=VALUESETS.curie('person_status'), model_uri=VALUESETS.person_status, domain=None, range=Optional[Union[str, "PersonStatusEnum"]]) +slots.sdoh_domain = Slot(uri=VALUESETS.sdoh_domain, name="sdoh_domain", curie=VALUESETS.curie('sdoh_domain'), + model_uri=VALUESETS.sdoh_domain, domain=None, range=Optional[Union[str, "GravitySdohDomainEnum"]]) + +slots.educational_attainment = Slot(uri=VALUESETS.educational_attainment, name="educational_attainment", curie=VALUESETS.curie('educational_attainment'), + model_uri=VALUESETS.educational_attainment, domain=None, range=Optional[Union[str, "EducationalAttainmentEnum"]]) + +slots.specimen_preparation_method = Slot(uri=VALUESETS.specimen_preparation_method, name="specimen_preparation_method", curie=VALUESETS.curie('specimen_preparation_method'), + model_uri=VALUESETS.specimen_preparation_method, domain=None, range=Optional[Union[str, "SpecimenPreparationMethodEnum"]]) + +slots.tissue_preservation = Slot(uri=VALUESETS.tissue_preservation, name="tissue_preservation", curie=VALUESETS.curie('tissue_preservation'), + model_uri=VALUESETS.tissue_preservation, domain=None, range=Optional[Union[str, "TissuePreservationEnum"]]) + +slots.condition_provenance = Slot(uri=VALUESETS.condition_provenance, name="condition_provenance", curie=VALUESETS.curie('condition_provenance'), + model_uri=VALUESETS.condition_provenance, domain=None, range=Optional[Union[str, "ConditionProvenanceEnum"]]) + +slots.visit_provenance = Slot(uri=VALUESETS.visit_provenance, name="visit_provenance", curie=VALUESETS.curie('visit_provenance'), + model_uri=VALUESETS.visit_provenance, domain=None, range=Optional[Union[str, "VisitProvenanceEnum"]]) + +slots.drug_provenance = Slot(uri=VALUESETS.drug_provenance, name="drug_provenance", curie=VALUESETS.curie('drug_provenance'), + model_uri=VALUESETS.drug_provenance, domain=None, range=Optional[Union[str, "DrugExposureProvenanceEnum"]]) + +slots.data_use_permission = Slot(uri=VALUESETS.data_use_permission, name="data_use_permission", curie=VALUESETS.curie('data_use_permission'), + model_uri=VALUESETS.data_use_permission, domain=None, range=Optional[Union[str, "DataUsePermissionEnum"]]) + +slots.data_use_modifier = Slot(uri=VALUESETS.data_use_modifier, name="data_use_modifier", curie=VALUESETS.curie('data_use_modifier'), + model_uri=VALUESETS.data_use_modifier, domain=None, range=Optional[Union[str, "DataUseModifierEnum"]]) + slots.mime = Slot(uri=VALUESETS.mime, name="mime", curie=VALUESETS.curie('mime'), model_uri=VALUESETS.mime, domain=None, range=Optional[Union[str, "MimeType"]]) @@ -32310,3 +33221,4 @@ class slots: slots.data_service_type = Slot(uri=VALUESETS.data_service_type, name="data_service_type", curie=VALUESETS.curie('data_service_type'), model_uri=VALUESETS.data_service_type, domain=None, range=Optional[Union[str, "DataServiceType"]]) + diff --git a/src/valuesets/generators/sssom_generator.py b/src/valuesets/generators/sssom_generator.py index e5517f96..15b4b4e2 100644 --- a/src/valuesets/generators/sssom_generator.py +++ b/src/valuesets/generators/sssom_generator.py @@ -257,7 +257,7 @@ def write_sssom_tsv(self, mappings: List[Dict[str, Any]], output_path: Path, # Prepare metadata meta = metadata or {} - meta.setdefault("mapping_set_id", f"https://w3id.org/linkml/valuesets/mappings") + meta.setdefault("mapping_set_id", f"https://w3id.org/valuesets/mappings") meta.setdefault("mapping_set_version", datetime.now().strftime("%Y-%m-%d")) meta.setdefault("license", "https://creativecommons.org/publicdomain/zero/1.0/") meta.setdefault("creator_id", "https://github.com/linkml/linkml-valuesets") diff --git a/src/valuesets/merged/merged_hierarchy.yaml b/src/valuesets/merged/merged_hierarchy.yaml index 77906301..145a9379 100644 --- a/src/valuesets/merged/merged_hierarchy.yaml +++ b/src/valuesets/merged/merged_hierarchy.yaml @@ -1,11 +1,11 @@ -id: https://w3id.org/linkml/valuesets/merged +id: https://w3id.org/valuesets/merged name: valuesets_merged_hierarchy title: Merged Value Sets with Hierarchical Structure description: All value sets merged into a single hierarchical structure with is_a relationships license: MIT prefixes: linkml: https://w3id.org/linkml/ - valuesets: https://w3id.org/linkml/valuesets/ + valuesets: https://w3id.org/valuesets/ DCMITYPE: http://purl.org/dc/dcmitype/ FABIO: http://purl.org/spar/fabio/ SPDX: https://spdx.org/licenses/ diff --git a/test_mappings.sssom.tsv b/test_mappings.sssom.tsv index 7cd1b29f..cee22096 100644 --- a/test_mappings.sssom.tsv +++ b/test_mappings.sssom.tsv @@ -6,7 +6,7 @@ # sssom: "https://w3id.org/sssom/" # dcterms: "http://purl.org/dc/terms/" # -#mapping_set_id: https://w3id.org/linkml/valuesets/mappings +#mapping_set_id: https://w3id.org/valuesets/mappings #mapping_set_version: 2025-09-15 #license: https://creativecommons.org/publicdomain/zero/1.0/ #creator_id: https://github.com/linkml/linkml-valuesets From 91141ba6e468f7e28cfc0ca9fd1ae1ca9af96d3a Mon Sep 17 00:00:00 2001 From: dragon-ai-agent Date: Fri, 30 Jan 2026 18:49:37 -0800 Subject: [PATCH 3/3] Fix ExtractableTargetElement enum - Remove inconsistent REE_ prefix, use standard element symbols - Add human-readable titles (e.g., "Lanthanum" not "REE_LA") - Add proper descriptions with context about element uses - Add CHEBI ontology mappings for all elements - Add aliases matching CHEBI labels for validation Co-Authored-By: Claude Opus 4.5 --- src/valuesets/schema/mining_processing.yaml | 172 +++++++++++++------- 1 file changed, 115 insertions(+), 57 deletions(-) diff --git a/src/valuesets/schema/mining_processing.yaml b/src/valuesets/schema/mining_processing.yaml index 6e31f6b5..0984b0b0 100644 --- a/src/valuesets/schema/mining_processing.yaml +++ b/src/valuesets/schema/mining_processing.yaml @@ -158,10 +158,11 @@ 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. - - ' + title: Extractable Target Elements + description: >- + Target elements for extraction in mining operations, including rare earth elements (REE), + critical minerals, and battery metals. These elements are strategically important for + clean energy technologies, electronics, and defense applications. status: DRAFT contributors: - orcid:0000-0002-6601-2165 @@ -169,63 +170,120 @@ enums: instantiates: - valuesets_meta:ValueSetEnumDefinition permissible_values: - REE_LA: - title: REE_LA - description: Lanthanum - REE_CE: - title: REE_CE - description: Cerium - REE_PR: - title: REE_PR - description: Praseodymium - REE_ND: - title: REE_ND - description: Neodymium - REE_PM: - title: REE_PM - description: Promethium - REE_SM: - title: REE_SM - description: Samarium - REE_EU: - title: REE_EU - description: Europium - REE_GD: - title: REE_GD - description: Gadolinium - REE_TB: - title: REE_TB - description: Terbium - REE_DY: - title: REE_DY - description: Dysprosium - REE_HO: - title: REE_HO - description: Holmium - REE_ER: - title: REE_ER - description: Erbium - REE_TM: - title: REE_TM - description: Thulium - REE_YB: - title: REE_YB - description: Ytterbium - REE_LU: - title: REE_LU - description: Lutetium + LA: + title: Lanthanum + aliases: + - lanthanum atom + description: Light rare earth element (atomic number 57) used in catalysts, optics, and battery electrodes + meaning: CHEBI:33336 + CE: + title: Cerium + aliases: + - cerium + description: Light rare earth element (atomic number 58) used in catalytic converters, glass polishing, and metallurgy + meaning: CHEBI:33369 + PR: + title: Praseodymium + aliases: + - praseodymium atom + description: Light rare earth element (atomic number 59) used in magnets, lasers, and aircraft engines + meaning: CHEBI:49828 + ND: + title: Neodymium + aliases: + - neodymium atom + description: Light rare earth element (atomic number 60) essential for high-strength permanent magnets in wind turbines and EVs + meaning: CHEBI:33372 + PM: + title: Promethium + aliases: + - promethium atom + description: Radioactive rare earth element (atomic number 61) used in nuclear batteries and luminous paint + meaning: CHEBI:33373 + SM: + title: Samarium + aliases: + - samarium atom + description: Light rare earth element (atomic number 62) used in samarium-cobalt magnets and cancer treatment + meaning: CHEBI:33374 + EU: + title: Europium + aliases: + - europium atom + description: Rare earth element (atomic number 63) used in phosphors for displays and fluorescent lighting + meaning: CHEBI:32999 + GD: + title: Gadolinium + aliases: + - gadolinium atom + description: Heavy rare earth element (atomic number 64) used in MRI contrast agents and nuclear reactor control rods + meaning: CHEBI:33375 + TB: + title: Terbium + aliases: + - terbium atom + description: Heavy rare earth element (atomic number 65) used in solid-state devices and green phosphors + meaning: CHEBI:33376 + DY: + title: Dysprosium + aliases: + - dysprosium atom + description: Heavy rare earth element (atomic number 66) critical for high-temperature permanent magnets + meaning: CHEBI:33377 + HO: + title: Holmium + aliases: + - holmium atom + description: Heavy rare earth element (atomic number 67) used in lasers and magnetic flux concentrators + meaning: CHEBI:49648 + ER: + title: Erbium + aliases: + - erbium + description: Heavy rare earth element (atomic number 68) used in fiber optic amplifiers and lasers + meaning: CHEBI:33379 + TM: + title: Thulium + aliases: + - thulium atom + description: Heavy rare earth element (atomic number 69) used in portable X-ray devices and lasers + meaning: CHEBI:33380 + YB: + title: Ytterbium + aliases: + - ytterbium + description: Heavy rare earth element (atomic number 70) used in metallurgy, lasers, and atomic clocks + meaning: CHEBI:33381 + LU: + title: Lutetium + aliases: + - lutetium atom + description: Heavy rare earth element (atomic number 71) used in PET scan detectors and cancer treatment + meaning: CHEBI:33382 SC: - title: SC - description: Scandium + title: Scandium + aliases: + - scandium atom + description: Transition metal (atomic number 21) used in aluminum alloys for aerospace and sports equipment + meaning: CHEBI:33330 CO: - title: CO - description: Cobalt + title: Cobalt + aliases: + - cobalt atom + description: Transition metal (atomic number 27) essential for lithium-ion battery cathodes and superalloys + meaning: CHEBI:27638 NI: - title: NI - description: Nickel + title: Nickel + aliases: + - nickel atom + description: Transition metal (atomic number 28) used in stainless steel, batteries, and electroplating + meaning: CHEBI:28112 LI: - title: LI - description: Lithium + title: Lithium + aliases: + - lithium atom + description: Alkali metal (atomic number 3) essential for lithium-ion batteries and energy storage systems + meaning: CHEBI:30145 SensorWhileDrillingFeature: title: Sensor While Drilling Feature description: 'Measurement while drilling (MWD) and logging while drilling (LWD) features for orebody ML and geosteering