From d46a0cb7f839ef170fd47942537d58cab6254354 Mon Sep 17 00:00:00 2001 From: dragon-ai-agent Date: Tue, 9 Dec 2025 18:39:16 -0800 Subject: [PATCH 1/3] Add environmental health, oncology, and EDoH value sets MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit New schema files for environmental health and medical domains: Environmental Health: - gb_edoh.yaml: GB-EDoH value sets for NIH HEW Data Accelerator - ExtremeWeatherEventEnum (19 values): heat waves, wildfires, floods, etc. - ExposureAgentCategoryEnum (17 values): air pollutants, radionuclides, etc. - TemporalAggregationEnum (18 values): daily mean, annual mean, etc. - SpatialResolutionEnum (18 values): census tract, grid cells, etc. - carcinogenicity.yaml: IARC, EPA IRIS, NTP classification groups - radionuclides.yaml: Radioactive elements with CHEBI/NCIT mappings Medical/Oncology: - icdo.yaml: ICD-O bi-axial classification system - TumorTopography: anatomic sites (C00-C80) - TumorMorphology: histological types - TumorBehavior: benign/in situ/malignant codes - TumorGrade: differentiation grades I-IV Other additions: - geospatial_formats.yaml: GeoTIFF, NetCDF, Shapefile, GeoJSON, etc. - genetics.yaml: Mode of inheritance from HP ontology - roles.yaml: Dynamic ChemicalRole/BiologicalRole from CHEBI - evidence.yaml: Dynamic EvidenceType from ECO ontology All schemas validated with `just validate-schema`. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 --- src/valuesets/schema/chemistry/roles.yaml | 66 ++ src/valuesets/schema/clinical/genetics.yaml | 134 ++++ .../schema/computing/geospatial_formats.yaml | 268 ++++++++ .../environmental_health/carcinogenicity.yaml | 223 ++++++ .../schema/environmental_health/gb_edoh.yaml | 649 ++++++++++++++++++ .../environmental_health/radionuclides.yaml | 248 +++++++ .../schema/medical/oncology/icdo.yaml | 555 +++++++++++++++ src/valuesets/schema/provenance/evidence.yaml | 42 ++ 8 files changed, 2185 insertions(+) create mode 100644 src/valuesets/schema/chemistry/roles.yaml create mode 100644 src/valuesets/schema/clinical/genetics.yaml create mode 100644 src/valuesets/schema/computing/geospatial_formats.yaml create mode 100644 src/valuesets/schema/environmental_health/carcinogenicity.yaml create mode 100644 src/valuesets/schema/environmental_health/gb_edoh.yaml create mode 100644 src/valuesets/schema/environmental_health/radionuclides.yaml create mode 100644 src/valuesets/schema/medical/oncology/icdo.yaml create mode 100644 src/valuesets/schema/provenance/evidence.yaml diff --git a/src/valuesets/schema/chemistry/roles.yaml b/src/valuesets/schema/chemistry/roles.yaml new file mode 100644 index 00000000..4cd0717b --- /dev/null +++ b/src/valuesets/schema/chemistry/roles.yaml @@ -0,0 +1,66 @@ +name: roles +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 +imports: +- linkml:types +prefixes: + linkml: https://w3id.org/linkml/ + valuesets: https://w3id.org/valuesets/ + CHEBI: http://purl.obolibrary.org/obo/CHEBI_ + rdfs: http://www.w3.org/2000/01/rdf-schema# + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ +default_prefix: valuesets +slots: + chemical_role: + description: A role played by a molecular entity within a chemical context + range: ChemicalRole + biological_role: + description: A role played by a molecular entity within a biological context + range: BiologicalRole +enums: + ChemicalRole: + title: Chemical Role + description: >- + Roles played by molecular entities within a chemical context, dynamically + populated from ChEBI. Includes roles such as catalyst, reagent, solvent, + indicator, buffer, and other chemical functions. + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + stewards: https://www.ebi.ac.uk/chebi + publishers: https://www.ebi.ac.uk/chebi + reachable_from: + source_nodes: + - CHEBI:51086 + is_direct: false + relationship_types: + - rdfs:subClassOf + BiologicalRole: + title: Biological Role + description: >- + Roles played by molecular entities within a biological context, dynamically + populated from ChEBI. Includes biochemical roles, pharmacological roles, + physiological roles, and other biological functions. + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + stewards: https://www.ebi.ac.uk/chebi + publishers: https://www.ebi.ac.uk/chebi + reachable_from: + source_nodes: + - CHEBI:24432 + is_direct: false + relationship_types: + - rdfs:subClassOf diff --git a/src/valuesets/schema/clinical/genetics.yaml b/src/valuesets/schema/clinical/genetics.yaml new file mode 100644 index 00000000..8cf373d3 --- /dev/null +++ b/src/valuesets/schema/clinical/genetics.yaml @@ -0,0 +1,134 @@ +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 +imports: +- linkml:types +prefixes: + linkml: https://w3id.org/linkml/ + valuesets: https://w3id.org/valuesets/ + HP: http://purl.obolibrary.org/obo/HP_ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ +default_prefix: valuesets +slots: + mode_of_inheritance: + description: The mode of inheritance for a genetic condition + range: ModeOfInheritance +enums: + ModeOfInheritance: + title: Mode of Inheritance + description: >- + Patterns of genetic inheritance describing how traits or disorders are passed + between generations. Based on HP:0000005 (Mode of inheritance). + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + stewards: https://hpo.jax.org + publishers: https://hpo.jax.org + permissible_values: + AUTOSOMAL_DOMINANT: + title: Autosomal dominant inheritance + description: >- + A mode of inheritance that is observed for traits related to a gene + encoded on one of the autosomes in which a trait manifests in heterozygotes. + meaning: HP:0000006 + AUTOSOMAL_RECESSIVE: + title: Autosomal recessive inheritance + description: >- + A mode of inheritance that is observed for traits related to a gene + encoded on one of the autosomes in which a trait manifests in individuals + with two pathogenic alleles. + meaning: HP:0000007 + X_LINKED: + title: X-linked inheritance + description: >- + A mode of inheritance that is observed for traits related to a gene + encoded on the X chromosome. + meaning: HP:0001417 + X_LINKED_DOMINANT: + title: X-linked dominant inheritance + description: >- + A mode of inheritance that is observed for dominant traits related to + a gene encoded on the X chromosome. + meaning: HP:0001423 + is_a: X_LINKED + X_LINKED_RECESSIVE: + title: X-linked recessive inheritance + description: >- + A mode of inheritance that is observed for recessive traits related to + a gene encoded on the X chromosome. + meaning: HP:0001419 + is_a: X_LINKED + Y_LINKED: + title: Y-linked inheritance + description: >- + A mode of inheritance that is observed for traits related to a gene + encoded on the Y chromosome. + meaning: HP:0001450 + MITOCHONDRIAL: + title: Mitochondrial inheritance + description: >- + A mode of inheritance that is observed for traits related to a gene + encoded on the mitochondrial genome. Maternally inherited. + meaning: HP:0001427 + MENDELIAN: + title: Mendelian inheritance + description: >- + A mode of inheritance of diseases whose pathophysiology can be traced + back to deleterious variants in a single gene. + meaning: HP:0034345 + NON_MENDELIAN: + title: Non-Mendelian inheritance + description: >- + A mode of inheritance that depends on genetic determinants in more than one gene. + meaning: HP:0001426 + DIGENIC: + title: Digenic inheritance + description: >- + A type of multifactorial inheritance governed by the simultaneous action + of two gene loci. + meaning: HP:0010984 + is_a: NON_MENDELIAN + OLIGOGENIC: + title: Oligogenic inheritance + description: >- + A type of multifactorial inheritance governed by the simultaneous action + of a few gene loci (typically three). + meaning: HP:0010983 + is_a: NON_MENDELIAN + POLYGENIC: + title: Polygenic inheritance + description: >- + A mode of inheritance that depends on a mixture of major and minor genetic + determinants possibly together with environmental factors. + meaning: HP:0010982 + is_a: NON_MENDELIAN + SEMIDOMINANT: + title: Semidominant inheritance + description: >- + A mode of inheritance for traits that can manifest in both monoallelic + and biallelic states, with similar or differing phenotype severity. + meaning: HP:0032113 + PSEUDOAUTOSOMAL: + title: Pseudoautosomal inheritance + description: >- + A pattern of inheritance observed for alleles in the X-Y identical regions, + resembling autosomal inheritance. + meaning: HP:0034339 + PSEUDOAUTOSOMAL_DOMINANT: + title: Pseudoautosomal dominant inheritance + description: >- + A type of pseudoautosomal inheritance that is dominant. + meaning: HP:0034340 + is_a: PSEUDOAUTOSOMAL + PSEUDOAUTOSOMAL_RECESSIVE: + title: Pseudoautosomal recessive inheritance + description: >- + A type of pseudoautosomal inheritance that is recessive. + meaning: HP:0034341 + is_a: PSEUDOAUTOSOMAL diff --git a/src/valuesets/schema/computing/geospatial_formats.yaml b/src/valuesets/schema/computing/geospatial_formats.yaml new file mode 100644 index 00000000..6343f90d --- /dev/null +++ b/src/valuesets/schema/computing/geospatial_formats.yaml @@ -0,0 +1,268 @@ +name: geospatial_formats +title: Geospatial Data Format Value Sets +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 +imports: +- linkml:types +prefixes: + linkml: https://w3id.org/linkml/ + valuesets: https://w3id.org/valuesets/ + EDAM: http://edamontology.org/ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ +default_prefix: valuesets +slots: + geospatial_raster_format: + description: Raster/gridded geospatial data formats + range: GeospatialRasterFormat + geospatial_vector_format: + description: Vector geospatial data formats + range: GeospatialVectorFormat +enums: + GeospatialRasterFormat: + title: Geospatial Raster Format + description: >- + File formats for raster (gridded) geospatial data including satellite imagery, + digital elevation models, and environmental model outputs. + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + GEOTIFF: + title: GeoTIFF + description: >- + TIFF image format with embedded georeferencing information. Standard + format for satellite imagery and raster GIS data. + annotations: + extension: .tif, .tiff + mime_type: image/tiff + georeferencing: embedded + organization: OGC + COG: + title: Cloud Optimized GeoTIFF + description: >- + GeoTIFF optimized for cloud storage with internal tiling and overviews + for efficient partial reads over HTTP. + annotations: + extension: .tif + mime_type: image/tiff + georeferencing: embedded + features: cloud-optimized, COG + NETCDF: + title: NetCDF + description: >- + Network Common Data Form. Self-describing array-oriented scientific data + format widely used for climate and environmental data. + meaning: EDAM:format_3650 + annotations: + extension: .nc, .nc4 + mime_type: application/x-netcdf + organization: Unidata + conventions: CF (Climate and Forecast) + HDF5: + title: HDF5 + description: >- + Hierarchical Data Format version 5. High-performance format for large + scientific datasets including satellite data. + meaning: EDAM:format_3590 + annotations: + extension: .h5, .hdf5, .he5 + mime_type: application/x-hdf + organization: HDF Group + HDF_EOS: + title: HDF-EOS + description: >- + HDF format extended for NASA Earth Observing System data. Used for + MODIS, ASTER, and other NASA satellite products. + annotations: + extension: .hdf + organization: NASA + variants: HDF-EOS2, HDF-EOS5 + GRIB: + title: GRIB + description: >- + GRIdded Binary format. Standard WMO format for meteorological data + exchange. + annotations: + extension: .grib, .grb, .grib2 + organization: WMO + versions: GRIB1, GRIB2 + JPEG2000: + title: JPEG 2000 + description: >- + Wavelet-based image compression format with georeferencing capability. + Used for satellite imagery distribution. + annotations: + extension: .jp2, .j2k + mime_type: image/jp2 + features: lossy/lossless compression + MRF: + title: Meta Raster Format + description: >- + NASA format optimized for cloud storage and fast random access to + large imagery datasets. + annotations: + extension: .mrf + organization: NASA + features: cloud-optimized + ZARR: + title: Zarr + description: >- + Chunked, compressed, N-dimensional array format designed for cloud + storage. Growing adoption for climate data. + annotations: + extension: .zarr (directory) + features: cloud-native, chunked + python: zarr library + ENVI: + title: ENVI + description: >- + Format used by ENVI remote sensing software. Binary raster with + separate header file. + annotations: + extension: .dat, .bsq, .bil, .bip + header: .hdr + ERDAS_IMAGINE: + title: ERDAS IMAGINE + description: >- + Proprietary format for ERDAS IMAGINE software. Commonly used for + satellite imagery processing. + annotations: + extension: .img + organization: Hexagon Geospatial + ASCII_GRID: + title: Esri ASCII Grid + description: >- + Simple text-based raster format. Header followed by space-delimited + cell values. + annotations: + extension: .asc + format: text + organization: Esri + GeospatialVectorFormat: + title: Geospatial Vector Format + description: >- + File formats for vector (point, line, polygon) geospatial data including + geographic boundaries, infrastructure, and sampling locations. + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + SHAPEFILE: + title: Esri Shapefile + description: >- + Widely used vector format consisting of multiple files (.shp, .shx, .dbf). + De facto standard despite limitations. + annotations: + extension: .shp (+ .shx, .dbf, .prj) + organization: Esri + limitations: 2GB size limit, 10-char field names + GEOJSON: + title: GeoJSON + description: >- + JSON-based format for encoding geographic data structures. Web-friendly + and human-readable. + annotations: + extension: .geojson, .json + mime_type: application/geo+json + organization: IETF (RFC 7946) + crs: WGS84 only + GEOPACKAGE: + title: GeoPackage + description: >- + OGC standard SQLite-based format for vector and raster data. Modern + replacement for Shapefile. + annotations: + extension: .gpkg + organization: OGC + features: single file, no size limit, transactions + KML: + title: KML + description: >- + Keyhole Markup Language. XML-based format for Google Earth and other + applications. + annotations: + extension: .kml + mime_type: application/vnd.google-earth.kml+xml + organization: OGC (originally Google) + KMZ: + title: KMZ + description: >- + Compressed KML file (ZIP archive containing KML and supporting files). + annotations: + extension: .kmz + mime_type: application/vnd.google-earth.kmz + compression: ZIP + GML: + title: GML + description: >- + Geography Markup Language. OGC XML-based format for geographic features. + annotations: + extension: .gml + mime_type: application/gml+xml + organization: OGC + TOPOJSON: + title: TopoJSON + description: >- + Extension of GeoJSON that encodes topology. Smaller file sizes through + shared arc representation. + annotations: + extension: .topojson, .json + features: topology encoding, smaller files + FLATGEOBUF: + title: FlatGeobuf + description: >- + Binary format optimized for fast streaming and random access. Cloud-native + alternative to Shapefile. + annotations: + extension: .fgb + features: streaming, spatial index + GEOPARQUET: + title: GeoParquet + description: >- + Apache Parquet with geospatial extensions. Columnar format optimized + for analytics on large vector datasets. + annotations: + extension: .parquet + features: columnar, cloud-optimized + GEODATABASE: + title: Esri File Geodatabase + description: >- + Esri proprietary format for storing multiple feature classes and tables + in a folder structure. + annotations: + extension: .gdb (folder) + organization: Esri + features: multiple layers, domains, relationships + GPKG_VECTOR: + title: GeoPackage (Vector) + description: >- + Vector data stored in GeoPackage format. Can coexist with raster data + in same file. + annotations: + extension: .gpkg + organization: OGC + WKT: + title: Well-Known Text + description: >- + Text markup language for representing vector geometry objects. + annotations: + format: text + organization: OGC + use: geometry representation + WKB: + title: Well-Known Binary + description: >- + Binary equivalent of WKT for efficient storage and transfer. + annotations: + format: binary + organization: OGC diff --git a/src/valuesets/schema/environmental_health/carcinogenicity.yaml b/src/valuesets/schema/environmental_health/carcinogenicity.yaml new file mode 100644 index 00000000..8ddde0c8 --- /dev/null +++ b/src/valuesets/schema/environmental_health/carcinogenicity.yaml @@ -0,0 +1,223 @@ +name: carcinogenicity +title: Carcinogenicity Classification Value Sets +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 +imports: +- linkml:types +prefixes: + linkml: https://w3id.org/linkml/ + valuesets: https://w3id.org/valuesets/ + NCIT: http://purl.obolibrary.org/obo/NCIT_ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ +default_prefix: valuesets +slots: + iarc_classification: + description: IARC carcinogenicity classification + range: IARCCarcinogenicityGroup + epa_iris_classification: + description: EPA IRIS carcinogenicity classification + range: EPAIRISCarcinogenicityGroup + ntp_classification: + description: NTP carcinogenicity classification + range: NTPCarcinogenicityGroup +enums: + IARCCarcinogenicityGroup: + title: IARC Carcinogenicity Group + description: >- + International Agency for Research on Cancer (IARC) classification groups + for carcinogenic hazard to humans. IARC evaluates the strength of evidence + that an agent can cause cancer in humans. + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + stewards: https://www.iarc.who.int + publishers: https://www.iarc.who.int + source: https://monographs.iarc.who.int/agents-classified-by-the-iarc/ + permissible_values: + GROUP_1: + title: Carcinogenic to humans + description: >- + Sufficient evidence of carcinogenicity in humans. The agent is + carcinogenic to humans. + annotations: + evidence_level: sufficient in humans + examples: asbestos, benzene, tobacco smoking, ionizing radiation + GROUP_2A: + title: Probably carcinogenic to humans + description: >- + Limited evidence of carcinogenicity in humans and sufficient evidence + in experimental animals. The agent is probably carcinogenic to humans. + annotations: + evidence_level: limited in humans, sufficient in animals + examples: red meat, night shift work, glyphosate + GROUP_2B: + title: Possibly carcinogenic to humans + description: >- + Limited evidence of carcinogenicity in humans and less than sufficient + evidence in experimental animals. The agent is possibly carcinogenic + to humans. + annotations: + evidence_level: limited in humans or animals + examples: coffee, pickled vegetables, gasoline engine exhaust + GROUP_3: + title: Not classifiable as to carcinogenicity + description: >- + Inadequate evidence of carcinogenicity in humans and inadequate or + limited evidence in experimental animals. The agent is not classifiable + as to its carcinogenicity to humans. + annotations: + evidence_level: inadequate + examples: caffeine, cholesterol, saccharin + EPAIRISCarcinogenicityGroup: + title: EPA IRIS Carcinogenicity Group + description: >- + U.S. Environmental Protection Agency Integrated Risk Information System + (IRIS) weight-of-evidence descriptors for carcinogenicity. These classifications + characterize the extent to which available data support the hypothesis that + an agent causes cancer in humans. + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + stewards: https://www.epa.gov + publishers: https://www.epa.gov/iris + source: https://www.epa.gov/iris + permissible_values: + CARCINOGENIC_TO_HUMANS: + title: Carcinogenic to Humans + description: >- + Strong evidence of human carcinogenicity. This descriptor is appropriate + when there is convincing epidemiologic evidence of a causal association + between human exposure and cancer. + annotations: + legacy_group: A + evidence: convincing epidemiologic evidence + LIKELY_CARCINOGENIC: + title: Likely to Be Carcinogenic to Humans + description: >- + Evidence is adequate to demonstrate carcinogenic potential to humans but + does not reach the weight of evidence for Carcinogenic to Humans. + annotations: + legacy_group: B1/B2 + evidence: adequate evidence + SUGGESTIVE_EVIDENCE: + title: Suggestive Evidence of Carcinogenic Potential + description: >- + Evidence is suggestive of carcinogenicity but not sufficient to assess + human carcinogenic potential. + annotations: + legacy_group: C + evidence: suggestive but not sufficient + INADEQUATE_INFORMATION: + title: Inadequate Information to Assess Carcinogenic Potential + description: >- + Available data are inadequate for an assessment of human carcinogenic + potential. + annotations: + legacy_group: D + evidence: inadequate data + NOT_LIKELY_CARCINOGENIC: + title: Not Likely to Be Carcinogenic to Humans + description: >- + Available data are considered robust for deciding that there is no basis + for human hazard concern. + annotations: + legacy_group: E + evidence: robust evidence of no hazard + GROUP_A: + title: Group A - Human Carcinogen (Legacy) + description: >- + Legacy EPA classification. Sufficient evidence from epidemiologic studies + to support a causal association between exposure and cancer. + annotations: + status: legacy + superseded_by: CARCINOGENIC_TO_HUMANS + GROUP_B1: + title: Group B1 - Probable Human Carcinogen (Legacy) + description: >- + Legacy EPA classification. Limited evidence of carcinogenicity from + epidemiologic studies. + annotations: + status: legacy + superseded_by: LIKELY_CARCINOGENIC + GROUP_B2: + title: Group B2 - Probable Human Carcinogen (Legacy) + description: >- + Legacy EPA classification. Sufficient evidence from animal studies and + inadequate evidence from epidemiologic studies. + annotations: + status: legacy + superseded_by: LIKELY_CARCINOGENIC + GROUP_C: + title: Group C - Possible Human Carcinogen (Legacy) + description: >- + Legacy EPA classification. Limited evidence of carcinogenicity in animals + in the absence of human data. + annotations: + status: legacy + superseded_by: SUGGESTIVE_EVIDENCE + GROUP_D: + title: Group D - Not Classifiable (Legacy) + description: >- + Legacy EPA classification. Inadequate human and animal evidence of + carcinogenicity or no data available. + annotations: + status: legacy + superseded_by: INADEQUATE_INFORMATION + GROUP_E: + title: Group E - Evidence of Non-Carcinogenicity (Legacy) + description: >- + Legacy EPA classification. No evidence of carcinogenicity in at least + two adequate animal tests or in adequate epidemiologic and animal studies. + annotations: + status: legacy + superseded_by: NOT_LIKELY_CARCINOGENIC + NTPCarcinogenicityGroup: + title: NTP Carcinogenicity Group + description: >- + U.S. National Toxicology Program (NTP) Report on Carcinogens classifications. + The NTP identifies and discusses agents, substances, mixtures, or exposure + circumstances that may pose a carcinogenic hazard to human health. + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + stewards: https://ntp.niehs.nih.gov + publishers: https://ntp.niehs.nih.gov + source: https://ntp.niehs.nih.gov/go/roc + permissible_values: + KNOWN_CARCINOGEN: + title: Known To Be Human Carcinogen + description: >- + There is sufficient evidence of carcinogenicity from studies in humans, + which indicates a causal relationship between exposure to the agent and + human cancer. + annotations: + abbreviation: K + evidence: sufficient human evidence + examples: arsenic, asbestos, benzene, vinyl chloride + RAHC: + title: Reasonably Anticipated To Be Human Carcinogen + description: >- + There is limited evidence of carcinogenicity from studies in humans, which + indicates that causal interpretation is credible but alternative explanations + cannot be ruled out, OR there is sufficient evidence of carcinogenicity + from studies in experimental animals. + annotations: + abbreviation: RAHC + evidence: limited human or sufficient animal evidence + examples: lead compounds, styrene, trichloroethylene diff --git a/src/valuesets/schema/environmental_health/gb_edoh.yaml b/src/valuesets/schema/environmental_health/gb_edoh.yaml new file mode 100644 index 00000000..67b23323 --- /dev/null +++ b/src/valuesets/schema/environmental_health/gb_edoh.yaml @@ -0,0 +1,649 @@ +name: gb_edoh +title: Geospatial-Based Environmental Determinants of Health Value Sets +description: >- + Value sets supporting the NIH/NIEHS Health and Extreme Weather (HEW) Data Accelerator + 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 +imports: +- linkml:types +prefixes: + linkml: https://w3id.org/linkml/ + valuesets: https://w3id.org/valuesets/ + ENVO: http://purl.obolibrary.org/obo/ENVO_ + NCIT: http://purl.obolibrary.org/obo/NCIT_ + CHEBI: http://purl.obolibrary.org/obo/CHEBI_ + ExO: http://purl.obolibrary.org/obo/ExO_ + ECTO: http://purl.obolibrary.org/obo/ECTO_ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ +default_prefix: valuesets +slots: + extreme_weather_event: + description: Type of extreme weather event + range: ExtremeWeatherEventEnum + exposure_agent_category: + description: Category of environmental exposure agent + range: ExposureAgentCategoryEnum + temporal_aggregation: + description: Method used to aggregate exposure data over time + range: TemporalAggregationEnum + spatial_resolution: + description: Spatial resolution or geographic unit of exposure estimate + range: SpatialResolutionEnum +enums: + ExtremeWeatherEventEnum: + title: Extreme Weather Event + description: >- + Types of extreme weather events relevant to health outcomes and environmental + epidemiology. Used for characterizing weather-related health impacts in the + NIH Health and Extreme Weather (HEW) program. + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + program: NIH HEW Data Accelerator + use_case: GB-EDoH classification + permissible_values: + HEAT_WAVE: + title: Heat wave + description: >- + Prolonged period of excessively hot weather relative to the expected + conditions for a given area. Associated with increased mortality, heat + stroke, and cardiovascular events. + annotations: + health_impacts: heat stroke, cardiovascular events, mortality + nws_threshold: 2+ days of heat index >= 105F + COLD_WAVE: + title: Cold wave + description: >- + Prolonged period of excessively cold weather relative to the expected + conditions for a given area. Associated with hypothermia and cardiovascular + events. + annotations: + health_impacts: hypothermia, cardiovascular events, frostbite + WILDFIRE: + title: wildfire + description: >- + Uncontrolled fire in vegetated areas producing smoke containing particulate + matter and hazardous air pollutants. Major source of PM2.5 exposure. + meaning: ENVO:01000787 + annotations: + health_impacts: respiratory illness, cardiovascular events, mental health + exposure_agent: PM2.5, CO, VOCs + FOREST_FIRE: + title: forest fire + description: >- + Wildfire occurring primarily in forested areas, producing dense smoke + plumes that can travel long distances. + meaning: ENVO:01000791 + is_a: WILDFIRE + TROPICAL_STORM: + title: tropical storm + description: >- + Atmospheric storm originating over tropical waters with organized + circulation and sustained winds 39-73 mph. Precursor to hurricanes. + meaning: ENVO:01001296 + annotations: + health_impacts: injuries, drowning, displacement, mental health + HURRICANE: + title: Hurricane/Typhoon/Cyclone + description: >- + Intense tropical cyclone with sustained winds of 74 mph or greater. + Called hurricane (Atlantic/E. Pacific), typhoon (W. Pacific), or cyclone + (Indian Ocean). + annotations: + saffir_simpson: Category 1-5 + health_impacts: traumatic injuries, drowning, displacement, infectious disease + related: ENVO:01001297 + TORNADO: + title: tornado + description: >- + Violently rotating column of air extending from a thunderstorm to the + ground. Characterized by extreme winds and path of destruction. + meaning: ENVO:01001482 + annotations: + ef_scale: EF0-EF5 + health_impacts: traumatic injuries, death, mental health + FLOOD: + title: flood + description: >- + Unusual accumulation of water above ground caused by high tide, heavy + rain, melting snow, or dam failure. + meaning: ENVO:01000710 + annotations: + health_impacts: drowning, waterborne disease, injuries, displacement + RIVERINE_FLOOD: + title: riverine flood + description: >- + Flood occurring when river flow exceeds channel capacity, typically + developing over hours to days. + meaning: ENVO:01000712 + is_a: FLOOD + COASTAL_FLOOD: + title: coastal flood + description: >- + Flood caused by storm surge, high tides, or sea level rise affecting + coastal areas. + meaning: ENVO:01000711 + is_a: FLOOD + FLASH_FLOOD: + title: flash flood + description: >- + Rapid flooding of low-lying areas within 6 hours of heavy rainfall or + dam failure. Particularly dangerous due to sudden onset. + meaning: ENVO:01000713 + is_a: FLOOD + DROUGHT: + title: drought + description: >- + Extended period of deficient precipitation resulting in water shortage. + Affects water quality, food security, and mental health. + meaning: ENVO:1000745 + annotations: + health_impacts: water quality, food insecurity, mental health + indices: PDSI, SPI, USDM + BLIZZARD: + title: blizzard + description: >- + Severe snowstorm with sustained winds >= 35 mph and reduced visibility + for 3+ hours. Creates dangerous travel conditions and cold exposure risk. + meaning: ENVO:01000903 + annotations: + health_impacts: hypothermia, injuries, carbon monoxide poisoning + WINTER_STORM: + title: Winter storm + description: >- + Storm producing significant snow, ice, or sleet. Includes ice storms, + nor'easters, and lake-effect snow events. + annotations: + health_impacts: injuries, hypothermia, carbon monoxide poisoning + SEVERE_THUNDERSTORM: + title: convective storm + description: >- + Thunderstorm producing hail >= 1 inch, wind gusts >= 58 mph, or a + tornado. Source of lightning, flash flooding, and wind damage. + meaning: ENVO:01001294 + annotations: + health_impacts: lightning injuries, wind injuries, flash flooding + DUST_STORM: + title: Dust storm + description: >- + Meteorological event with strong winds lifting large amounts of sand + and dust into the atmosphere. Reduces visibility and air quality. + annotations: + health_impacts: respiratory illness, traffic accidents + related: haboob, sandstorm + EXTREME_PRECIPITATION: + title: Extreme precipitation + description: >- + Precipitation event exceeding historical norms for intensity or duration. + Often precedes flooding events. + annotations: + health_impacts: flooding, infrastructure damage + STORM_SURGE: + title: storm surge + description: >- + Abnormal rise in sea level during a storm, caused by wind pushing water + toward shore. Major cause of hurricane-related deaths. + meaning: ENVO:01000714 + annotations: + health_impacts: drowning, injuries + LANDSLIDE: + title: Landslide + description: >- + Mass movement of rock, debris, or earth down a slope. Often triggered + by extreme precipitation or earthquakes. + annotations: + health_impacts: traumatic injuries, burial, displacement + AIR_QUALITY_EVENT: + title: Air quality event + description: >- + Period of degraded air quality due to pollution accumulation, typically + during temperature inversions or stagnant air conditions. + annotations: + health_impacts: respiratory illness, cardiovascular events + indices: AQI, PM2.5, ozone + + ExposureAgentCategoryEnum: + title: Exposure Agent Category + description: >- + Categories of environmental exposure agents for GB-EDoH classification. + Used to categorize the type of environmental factor being measured and + modeled in geospatial exposure assessments. + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + program: NIH HEW Data Accelerator + use_case: GB-EDoH metadata + permissible_values: + CRITERIA_AIR_POLLUTANT: + title: Criteria air pollutant + description: >- + EPA-regulated criteria air pollutants under the Clean Air Act: PM2.5, + PM10, O3, NO2, SO2, CO, and Pb. + annotations: + examples: PM2.5, PM10, O3, NO2, SO2, CO, Pb + regulatory: EPA NAAQS + HAZARDOUS_AIR_POLLUTANT: + title: Hazardous air pollutant + description: >- + EPA-designated hazardous air pollutants (HAPs) known to cause cancer + or other serious health effects. + annotations: + examples: benzene, formaldehyde, acetaldehyde + regulatory: EPA HAPs list (187 pollutants) + WILDFIRE_SMOKE: + title: Wildfire smoke + description: >- + Smoke from wildfires containing PM2.5, CO, VOCs, and other combustion + products. Distinct from anthropogenic air pollution. + annotations: + components: PM2.5, CO, VOCs, PAHs + WATER_CONTAMINANT: + title: Water contaminant + description: >- + Chemical, biological, or physical contaminants in drinking water or + recreational water bodies. + annotations: + examples: lead, arsenic, nitrates, PFAS, pathogens + SOIL_CONTAMINANT: + title: Soil contaminant + description: >- + Chemical contaminants in soil that may affect health through direct + contact, ingestion, or vapor intrusion. + annotations: + examples: lead, arsenic, petroleum, pesticides + RADIONUCLIDE: + title: Radionuclide + description: >- + Naturally occurring or anthropogenic radioactive materials in the + environment, including radon gas. + annotations: + examples: radon-222, uranium, radium + EXTREME_HEAT: + title: Extreme heat + description: >- + Ambient heat exposure characterized by temperature, heat index, or + other thermal comfort metrics. + annotations: + metrics: temperature, heat index, WBGT, apparent temperature + EXTREME_COLD: + title: Extreme cold + description: >- + Ambient cold exposure characterized by temperature or wind chill. + annotations: + metrics: temperature, wind chill + UV_RADIATION: + title: UV radiation + description: >- + Solar ultraviolet radiation exposure, particularly UVB relevant to + skin cancer and vitamin D synthesis. + annotations: + metrics: UV index, erythemal UV dose + NOISE: + title: Environmental noise + description: >- + Ambient noise from traffic, airports, industry, and other sources. + Associated with cardiovascular and mental health effects. + annotations: + metrics: Lden, Lnight, LAeq + LIGHT_POLLUTION: + title: Light pollution + description: >- + Artificial light at night from urban and industrial sources. Associated + with circadian disruption. + annotations: + metrics: radiance, sky brightness + ALLERGEN: + title: Aeroallergen + description: >- + Airborne allergens including pollen, mold spores, and other biological + particles triggering allergic responses. + annotations: + examples: tree pollen, grass pollen, ragweed, mold spores + VECTOR_HABITAT: + title: Vector habitat suitability + description: >- + Environmental conditions favoring disease vector populations (mosquitoes, + ticks) based on climate and land use. + annotations: + vectors: Aedes mosquitoes, Ixodes ticks + diseases: dengue, Zika, Lyme disease + GREEN_SPACE: + title: Green space + description: >- + Access to and amount of vegetated areas including parks, forests, and + urban greenery. Associated with mental and physical health benefits. + annotations: + metrics: NDVI, park access, tree canopy cover + BLUE_SPACE: + title: Blue space + description: >- + Access to and proximity to water bodies including lakes, rivers, and + coastal areas. + annotations: + metrics: distance to water, water body area + BUILT_ENVIRONMENT: + title: Built environment + description: >- + Characteristics of the human-made environment including walkability, + food access, and housing quality. + annotations: + metrics: walkability score, food desert index, housing age + SOCIOECONOMIC_DEPRIVATION: + title: Socioeconomic deprivation + description: >- + Area-level measures of socioeconomic disadvantage that modify or + mediate environmental health effects. + annotations: + indices: ADI, NDI, SVI + + TemporalAggregationEnum: + title: Temporal Aggregation Method + description: >- + Methods used to aggregate environmental exposure data over time. Critical + metadata for GB-EDoH to ensure comparability across studies and integration + with health outcome data. + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + program: NIH HEW Data Accelerator + use_case: GB-EDoH temporal metadata + permissible_values: + INSTANTANEOUS: + title: Instantaneous + description: >- + Single point-in-time measurement without temporal aggregation. + annotations: + example: hourly sensor reading + HOURLY_MEAN: + title: Hourly mean + description: >- + Arithmetic mean of measurements within a 1-hour window. + annotations: + window: 1 hour + DAILY_MEAN: + title: Daily mean (24-hour average) + description: >- + Arithmetic mean of measurements over a 24-hour period. Standard for + many EPA air quality standards. + annotations: + window: 24 hours + regulatory: EPA PM2.5 24-hour standard + DAILY_MAX: + title: Daily maximum + description: >- + Maximum value recorded during a 24-hour period. + annotations: + window: 24 hours + DAILY_MIN: + title: Daily minimum + description: >- + Minimum value recorded during a 24-hour period. + annotations: + window: 24 hours + DAILY_MAX_8HR: + title: Daily maximum 8-hour average + description: >- + Maximum of rolling 8-hour averages within a day. Standard metric for + ozone exposure assessment. + annotations: + window: 8-hour rolling within 24 hours + regulatory: EPA ozone standard + WEEKLY_MEAN: + title: Weekly mean + description: >- + Arithmetic mean of daily values over a 7-day period. + annotations: + window: 7 days + MONTHLY_MEAN: + title: Monthly mean + description: >- + Arithmetic mean of daily values over a calendar month. + annotations: + window: calendar month + QUARTERLY_MEAN: + title: Quarterly mean + description: >- + Arithmetic mean of daily values over a 3-month period. + annotations: + window: 3 months + ANNUAL_MEAN: + title: Annual mean + description: >- + Arithmetic mean of daily values over a calendar year. Standard for + EPA PM2.5 annual standard. + annotations: + window: calendar year + regulatory: EPA PM2.5 annual standard + CUMULATIVE: + title: Cumulative + description: >- + Sum of exposure values over a defined period, representing total dose. + annotations: + example: cumulative UV dose, total precipitation + DAYS_ABOVE_THRESHOLD: + title: Days above threshold + description: >- + Count of days exceeding a specified threshold value within a period. + annotations: + example: days with AQI > 100 + PERCENTILE: + title: Percentile + description: >- + Specified percentile of distribution (e.g., 98th percentile of daily + values). Captures extreme exposure events. + annotations: + example: 98th percentile of daily PM2.5 + MOVING_AVERAGE: + title: Moving average + description: >- + Rolling average over a specified window (e.g., 7-day moving average). + Smooths short-term variability. + annotations: + example: 7-day rolling average + TRIMESTER_MEAN: + title: Trimester mean + description: >- + Mean exposure during a pregnancy trimester. Used in birth outcomes + research. + annotations: + window: ~13 weeks + use_case: perinatal epidemiology + HEATING_SEASON_MEAN: + title: Heating season mean + description: >- + Mean during heating season (typically Oct-Mar in Northern Hemisphere). + Relevant for indoor air quality. + annotations: + window: heating season + COOLING_SEASON_MEAN: + title: Cooling season mean + description: >- + Mean during cooling season (typically May-Sep in Northern Hemisphere). + Relevant for heat exposure and ozone. + annotations: + window: cooling season + + SpatialResolutionEnum: + title: Spatial Resolution + description: >- + Geographic units and spatial resolutions used for GB-EDoH exposure estimates. + Critical metadata for understanding exposure misclassification and supporting + OMOP geocoding requirements. + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + program: NIH HEW Data Accelerator + use_case: GB-EDoH spatial metadata + permissible_values: + POINT_LOCATION: + title: Point location (lat/lon) + description: >- + Exact geographic coordinates. Highest spatial precision but may require + privacy protection measures. + annotations: + precision: exact coordinates + privacy: requires protection + ADDRESS_GEOCODED: + title: Geocoded address + description: >- + Address geocoded to rooftop or parcel level. Standard for linking + patient data to environmental exposures. + annotations: + precision: parcel level + use_case: patient-level exposure + CENSUS_BLOCK: + title: Census block + description: >- + US Census block, the smallest geographic unit. Typically contains + 600-3000 people. + annotations: + typical_population: 600-3000 + country: US + CENSUS_BLOCK_GROUP: + title: Census block group + description: >- + US Census block group, a cluster of blocks. Standard unit for many + socioeconomic and environmental datasets. + annotations: + typical_population: 600-3000 + country: US + CENSUS_TRACT: + title: Census tract + description: >- + US Census tract, designed to be relatively homogeneous in population + characteristics. Common for health research. + annotations: + typical_population: 2500-8000 + country: US + ZIP_CODE: + title: ZIP code + description: >- + US Postal Service ZIP code. Common in administrative health data but + boundaries change and may cross jurisdictions. + annotations: + typical_population: varies widely + country: US + limitations: unstable boundaries + ZCTA: + title: ZIP Code Tabulation Area + description: >- + Census Bureau generalization of ZIP codes with stable boundaries. + Preferred over ZIP codes for research. + annotations: + country: US + advantage: stable boundaries + COUNTY: + title: County/Parish + description: >- + County or parish level. Used for many public health surveillance + systems and vital statistics. + annotations: + country: US + use_case: vital statistics, surveillance + STATE: + title: State/Territory + description: >- + State or territory level. Coarsest common administrative unit. + annotations: + country: US + GRID_1KM: + title: 1 km grid cell + description: >- + 1 kilometer resolution grid. Common for satellite-derived and modeled + air quality data. + annotations: + resolution: 1 km + example: EPA downscaler output + GRID_4KM: + title: 4 km grid cell + description: >- + 4 kilometer resolution grid. Common for weather and some air quality + models. + annotations: + resolution: 4 km + example: HRRR weather model + GRID_12KM: + title: 12 km grid cell + description: >- + 12 kilometer resolution grid. Standard CMAQ model output resolution. + annotations: + resolution: 12 km + example: EPA CMAQ output + GRID_36KM: + title: 36 km grid cell + description: >- + 36 kilometer resolution grid. Coarse model output. + annotations: + resolution: 36 km + HUC8: + title: HUC-8 watershed + description: >- + 8-digit Hydrologic Unit Code watershed. Medium-sized watershed for + water quality assessment. + annotations: + typical_area: 700 sq mi + use_case: water quality + HUC12: + title: HUC-12 subwatershed + description: >- + 12-digit Hydrologic Unit Code subwatershed. Finest watershed unit. + annotations: + typical_area: 40 sq mi + use_case: local water quality + AIRSHED: + title: Airshed + description: >- + Geographic area defined by air pollution transport patterns. May cross + administrative boundaries. + annotations: + example: South Coast Air Basin + BUFFER_500M: + title: 500 meter buffer + description: >- + Circular buffer of 500 meters around a point. Common for traffic-related + air pollution exposure. + annotations: + radius: 500 m + use_case: TRAP exposure + BUFFER_1KM: + title: 1 kilometer buffer + description: >- + Circular buffer of 1 kilometer around a point. + annotations: + radius: 1 km + BUFFER_5KM: + title: 5 kilometer buffer + description: >- + Circular buffer of 5 kilometers around a point. + annotations: + radius: 5 km + CUSTOM_POLYGON: + title: Custom polygon + description: >- + User-defined geographic area. Requires specification of boundary source. + annotations: + example: school district, hospital service area +license: MIT +see_also: +- https://linkml.github.io/valuesets +- https://www.niehs.nih.gov/research/programs/geh +- https://ohdsi.github.io/CommonDataModel/ diff --git a/src/valuesets/schema/environmental_health/radionuclides.yaml b/src/valuesets/schema/environmental_health/radionuclides.yaml new file mode 100644 index 00000000..4e979ae0 --- /dev/null +++ b/src/valuesets/schema/environmental_health/radionuclides.yaml @@ -0,0 +1,248 @@ +name: radionuclides +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 +imports: +- linkml:types +prefixes: + linkml: https://w3id.org/linkml/ + valuesets: https://w3id.org/valuesets/ + CHEBI: http://purl.obolibrary.org/obo/CHEBI_ + NCIT: http://purl.obolibrary.org/obo/NCIT_ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ +default_prefix: valuesets +slots: + radionuclide: + description: Radioactive elements and isotopes of environmental concern + range: RadionuclideEnum + naturally_occurring_radionuclide: + description: Naturally occurring radioactive materials (NORM) + range: NORMEnum +enums: + RadionuclideEnum: + title: Radionuclide + description: >- + Radioactive elements and isotopes commonly measured in environmental + health studies, including naturally occurring radioactive materials (NORM) + and anthropogenic radionuclides. + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + permissible_values: + RADON_222: + title: radon-222 atom + description: >- + Radioactive noble gas produced by decay of radium-226. Major contributor + to natural background radiation and indoor air quality concern. + meaning: CHEBI:33492 + annotations: + symbol: Rn-222 + half_life: 3.82 days + decay_mode: alpha + parent: Ra-226 + health_concern: lung cancer risk from inhalation + URANIUM_238: + title: Uranium-238 + description: >- + Most abundant uranium isotope, primordial radionuclide. Parent of the + uranium decay series. + annotations: + symbol: U-238 + half_life: 4.47 billion years + decay_mode: alpha + abundance: 99.3% + URANIUM_235: + title: Uranium-235 + description: >- + Fissile uranium isotope used in nuclear reactors and weapons. + annotations: + symbol: U-235 + half_life: 704 million years + decay_mode: alpha + abundance: 0.7% + THORIUM_232: + title: Thorium-232 + description: >- + Primordial radionuclide, parent of the thorium decay series. Found in + soil, rocks, and building materials. + annotations: + symbol: Th-232 + half_life: 14 billion years + decay_mode: alpha + RADIUM_226: + title: Radium-226 + description: >- + Radioactive alkaline earth metal in the uranium decay series. Historically + significant in medicine and industry. + meaning: CHEBI:80504 + annotations: + symbol: Ra-226 + half_life: 1600 years + decay_mode: alpha + daughter: Rn-222 + RADIUM_228: + title: Radium-228 + description: >- + Radioactive isotope in the thorium decay series. + meaning: CHEBI:80505 + annotations: + symbol: Ra-228 + half_life: 5.75 years + decay_mode: beta + POTASSIUM_40: + title: Potassium-40 + description: >- + Primordial radionuclide, naturally occurring in all potassium. Major + contributor to internal dose from dietary intake. + annotations: + symbol: K-40 + half_life: 1.25 billion years + decay_mode: beta, electron capture + abundance: 0.012% of natural potassium + CESIUM_137: + title: Cesium Cs 137 + description: >- + Anthropogenic radionuclide from nuclear fission. Environmental contaminant + from nuclear weapons testing and accidents. + meaning: NCIT:C68812 + annotations: + symbol: Cs-137 + half_life: 30.17 years + decay_mode: beta + source: nuclear fission + STRONTIUM_90: + title: Strontium Sr-90 + description: >- + Anthropogenic radionuclide from nuclear fission. Bone-seeking due to + chemical similarity to calcium. + meaning: NCIT:C29776 + annotations: + symbol: Sr-90 + half_life: 28.8 years + decay_mode: beta + health_concern: bone cancer, leukemia + IODINE_131: + title: Iodine I-131 + description: >- + Radioactive iodine isotope from nuclear fission. Concentrates in thyroid + gland. Used medically and released in nuclear accidents. + meaning: NCIT:C1639 + annotations: + symbol: I-131 + half_life: 8.02 days + decay_mode: beta + health_concern: thyroid cancer + PLUTONIUM_239: + title: Plutonium-239 + description: >- + Transuranic element produced in nuclear reactors. Highly toxic alpha + emitter with very long half-life. + meaning: NCIT:C29774 + annotations: + symbol: Pu-239 + half_life: 24100 years + decay_mode: alpha + source: nuclear reactors + AMERICIUM_241: + title: Americium-241 + description: >- + Transuranic element, alpha emitter. Used in smoke detectors. + annotations: + symbol: Am-241 + half_life: 432 years + decay_mode: alpha + use: smoke detectors + TRITIUM: + title: tritium atom + description: >- + Radioactive hydrogen isotope. Produced naturally and in nuclear reactors. + Weak beta emitter. + meaning: CHEBI:29238 + annotations: + symbol: H-3 + half_life: 12.3 years + decay_mode: beta (weak) + CARBON_14: + title: Carbon C-14 + description: >- + Cosmogenic radionuclide used in radiocarbon dating. Produced by cosmic + ray interactions in atmosphere. + meaning: NCIT:C1638 + annotations: + symbol: C-14 + half_life: 5730 years + decay_mode: beta + use: radiocarbon dating + LEAD_210: + title: Lead-210 + description: >- + Radioactive lead isotope in uranium decay series. Used as environmental + tracer for sedimentation dating. + annotations: + symbol: Pb-210 + half_life: 22.3 years + decay_mode: beta + use: sediment dating + POLONIUM_210: + title: Polonium-210 + description: >- + Highly radioactive alpha emitter in uranium decay series. Found in + tobacco smoke. + annotations: + symbol: Po-210 + half_life: 138 days + decay_mode: alpha + health_concern: lung cancer from tobacco + NORMEnum: + title: Naturally Occurring Radioactive Material + description: >- + Naturally occurring radioactive materials (NORM) found in the environment. + These are primordial radionuclides and their decay products. + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + acronym: NORM + permissible_values: + URANIUM_SERIES: + title: Uranium-238 decay series + description: >- + The uranium decay series starting from U-238 and ending with stable Pb-206. + Includes Ra-226, Rn-222, Po-210, and other isotopes. + annotations: + parent: U-238 + end_product: Pb-206 + key_members: Ra-226, Rn-222, Po-210, Pb-210 + THORIUM_SERIES: + title: Thorium-232 decay series + description: >- + The thorium decay series starting from Th-232 and ending with stable Pb-208. + Includes Ra-228, Rn-220 (thoron), and other isotopes. + annotations: + parent: Th-232 + end_product: Pb-208 + key_members: Ra-228, Rn-220, Pb-212 + ACTINIUM_SERIES: + title: Actinium (Uranium-235) decay series + description: >- + The actinium decay series starting from U-235 and ending with stable Pb-207. + annotations: + parent: U-235 + end_product: Pb-207 + POTASSIUM_40_PRIMORDIAL: + title: Potassium-40 + description: >- + Primordial radionuclide present in all potassium-bearing minerals and + biological tissues. + annotations: + type: primordial + ubiquity: present in all potassium diff --git a/src/valuesets/schema/medical/oncology/icdo.yaml b/src/valuesets/schema/medical/oncology/icdo.yaml new file mode 100644 index 00000000..747a5260 --- /dev/null +++ b/src/valuesets/schema/medical/oncology/icdo.yaml @@ -0,0 +1,555 @@ +name: icdo +title: ICD-O Cancer Classification Value Sets +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 +imports: +- linkml:types +prefixes: + linkml: https://w3id.org/linkml/ + valuesets: https://w3id.org/valuesets/ + NCIT: http://purl.obolibrary.org/obo/NCIT_ + UBERON: http://purl.obolibrary.org/obo/UBERON_ + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ +default_prefix: valuesets +slots: + tumor_topography: + description: Anatomic site of tumor (ICD-O topography axis) + range: TumorTopography + tumor_morphology: + description: Histological type of tumor (ICD-O morphology axis) + range: TumorMorphology + tumor_behavior: + description: Biological behavior of tumor (ICD-O behavior code) + range: TumorBehavior + tumor_grade: + description: Histological grade/differentiation of tumor + range: TumorGrade +enums: + TumorTopography: + title: Tumor Topography + description: >- + Major anatomic sites for tumor classification based on ICD-O topography + codes (C00-C80). These represent primary sites where neoplasms occur. + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + source: ICD-O-3 + axis: topography + permissible_values: + LIP_ORAL_CAVITY_PHARYNX: + title: Lip, oral cavity, and pharynx + description: Malignant neoplasms of lip, oral cavity and pharynx (C00-C14) + annotations: + icdo_range: C00-C14 + DIGESTIVE_ORGANS: + title: Digestive organs + description: Malignant neoplasms of digestive organs (C15-C26) + annotations: + icdo_range: C15-C26 + ESOPHAGUS: + title: Esophagus + description: Malignant neoplasm of esophagus (C15) + annotations: + icdo_code: C15 + uberon: UBERON:0001043 + is_a: DIGESTIVE_ORGANS + STOMACH: + title: Stomach + description: Malignant neoplasm of stomach (C16) + annotations: + icdo_code: C16 + uberon: UBERON:0000945 + is_a: DIGESTIVE_ORGANS + COLON: + title: Colon + description: Malignant neoplasm of colon (C18) + annotations: + icdo_code: C18 + uberon: UBERON:0001155 + is_a: DIGESTIVE_ORGANS + RECTUM: + title: Rectum + description: Malignant neoplasm of rectum (C20) + annotations: + icdo_code: C20 + uberon: UBERON:0001052 + is_a: DIGESTIVE_ORGANS + LIVER: + title: Liver + description: Malignant neoplasm of liver and intrahepatic bile ducts (C22) + annotations: + icdo_code: C22 + uberon: UBERON:0002107 + is_a: DIGESTIVE_ORGANS + PANCREAS: + title: Pancreas + description: Malignant neoplasm of pancreas (C25) + annotations: + icdo_code: C25 + uberon: UBERON:0001264 + is_a: DIGESTIVE_ORGANS + RESPIRATORY_INTRATHORACIC: + title: Respiratory and intrathoracic organs + description: Malignant neoplasms of respiratory and intrathoracic organs (C30-C39) + annotations: + icdo_range: C30-C39 + LUNG: + title: Lung + description: Malignant neoplasm of bronchus and lung (C34) + annotations: + icdo_code: C34 + uberon: UBERON:0002048 + is_a: RESPIRATORY_INTRATHORACIC + BONE_ARTICULAR_CARTILAGE: + title: Bone and articular cartilage + description: Malignant neoplasms of bone and articular cartilage (C40-C41) + annotations: + icdo_range: C40-C41 + SKIN: + title: Skin + description: Melanoma and other malignant neoplasms of skin (C43-C44) + annotations: + icdo_range: C43-C44 + uberon: UBERON:0002097 + SOFT_TISSUE: + title: Mesothelial and soft tissue + description: Malignant neoplasms of mesothelial and soft tissues (C45-C49) + annotations: + icdo_range: C45-C49 + BREAST: + title: Breast + description: Malignant neoplasm of breast (C50) + annotations: + icdo_code: C50 + uberon: UBERON:0000310 + FEMALE_GENITAL: + title: Female genital organs + description: Malignant neoplasms of female genital organs (C51-C58) + annotations: + icdo_range: C51-C58 + CERVIX_UTERI: + title: Cervix uteri + description: Malignant neoplasm of cervix uteri (C53) + annotations: + icdo_code: C53 + is_a: FEMALE_GENITAL + OVARY: + title: Ovary + description: Malignant neoplasm of ovary (C56) + annotations: + icdo_code: C56 + uberon: UBERON:0000992 + is_a: FEMALE_GENITAL + MALE_GENITAL: + title: Male genital organs + description: Malignant neoplasms of male genital organs (C60-C63) + annotations: + icdo_range: C60-C63 + PROSTATE: + title: Prostate + description: Malignant neoplasm of prostate (C61) + annotations: + icdo_code: C61 + uberon: UBERON:0002367 + is_a: MALE_GENITAL + TESTIS: + title: Testis + description: Malignant neoplasm of testis (C62) + annotations: + icdo_code: C62 + uberon: UBERON:0000473 + is_a: MALE_GENITAL + URINARY_TRACT: + title: Urinary tract + description: Malignant neoplasms of urinary tract (C64-C68) + annotations: + icdo_range: C64-C68 + KIDNEY: + title: Kidney + description: Malignant neoplasm of kidney (C64) + annotations: + icdo_code: C64 + uberon: UBERON:0002113 + is_a: URINARY_TRACT + BLADDER: + title: Bladder + description: Malignant neoplasm of bladder (C67) + annotations: + icdo_code: C67 + uberon: UBERON:0001255 + is_a: URINARY_TRACT + EYE_BRAIN_CNS: + title: Eye, brain, and CNS + description: Malignant neoplasms of eye, brain and other parts of CNS (C69-C72) + annotations: + icdo_range: C69-C72 + BRAIN: + title: Brain + description: Malignant neoplasm of brain (C71) + annotations: + icdo_code: C71 + uberon: UBERON:0000955 + is_a: EYE_BRAIN_CNS + THYROID_ENDOCRINE: + title: Thyroid and other endocrine glands + description: Malignant neoplasms of thyroid and other endocrine glands (C73-C75) + annotations: + icdo_range: C73-C75 + THYROID: + title: Thyroid gland + description: Malignant neoplasm of thyroid gland (C73) + annotations: + icdo_code: C73 + uberon: UBERON:0002046 + is_a: THYROID_ENDOCRINE + LYMPH_NODES: + title: Lymph nodes + description: Malignant neoplasms of lymph nodes (C77) + annotations: + icdo_code: C77 + UNKNOWN_PRIMARY: + title: Unknown primary site + description: Malignant neoplasm of unknown primary site (C80) + annotations: + icdo_code: C80 + TumorMorphology: + title: Tumor Morphology + description: >- + Major histological types for tumor classification based on ICD-O morphology + codes. These represent the cell type and histological pattern of neoplasms. + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + source: ICD-O-3 + axis: morphology + permissible_values: + CARCINOMA_NOS: + title: Carcinoma + description: >- + Malignant epithelial neoplasm, not otherwise specified. General term + for cancers arising from epithelial cells. + meaning: NCIT:C2916 + annotations: + icdo_code: 8010 + ADENOCARCINOMA_NOS: + title: Adenocarcinoma + description: >- + Malignant glandular epithelial neoplasm. Cancer arising from glandular + epithelium. + meaning: NCIT:C2852 + annotations: + icdo_code: 8140 + is_a: CARCINOMA_NOS + SQUAMOUS_CELL_CARCINOMA: + title: Squamous Cell Carcinoma + description: >- + Malignant neoplasm arising from squamous epithelium. Common in skin, + lung, esophagus, and cervix. + meaning: NCIT:C2929 + annotations: + icdo_code: 8070 + is_a: CARCINOMA_NOS + TRANSITIONAL_CELL_CARCINOMA: + title: Transitional Cell Carcinoma + description: >- + Malignant neoplasm arising from transitional epithelium (urothelium). + Most common in bladder and urinary tract. + meaning: NCIT:C2930 + annotations: + icdo_code: 8120 + is_a: CARCINOMA_NOS + SMALL_CELL_CARCINOMA: + title: Small Cell Neuroendocrine Carcinoma + description: >- + Highly malignant neuroendocrine carcinoma with small cells. Most common + in lung. + meaning: NCIT:C3915 + annotations: + icdo_code: 8041 + is_a: CARCINOMA_NOS + LARGE_CELL_CARCINOMA: + title: Large cell carcinoma + description: Undifferentiated carcinoma with large cells. + annotations: + icdo_code: 8012 + is_a: CARCINOMA_NOS + SARCOMA_NOS: + title: Sarcoma + description: >- + Malignant mesenchymal neoplasm, not otherwise specified. Cancers arising + from connective tissue, bone, cartilage, fat, muscle, or blood vessels. + meaning: NCIT:C9118 + annotations: + icdo_code: 8800 + OSTEOSARCOMA: + title: Osteosarcoma + description: Malignant bone-forming tumor. Most common primary malignant bone tumor. + meaning: NCIT:C9145 + annotations: + icdo_code: 9180 + is_a: SARCOMA_NOS + CHONDROSARCOMA: + title: Chondrosarcoma + description: Malignant cartilage-forming tumor. + meaning: NCIT:C2946 + annotations: + icdo_code: 9220 + is_a: SARCOMA_NOS + LIPOSARCOMA: + title: Liposarcoma + description: Malignant tumor arising from adipose tissue. + meaning: NCIT:C3194 + annotations: + icdo_code: 8850 + is_a: SARCOMA_NOS + LEIOMYOSARCOMA: + title: Leiomyosarcoma + description: Malignant tumor arising from smooth muscle. + meaning: NCIT:C3158 + annotations: + icdo_code: 8890 + is_a: SARCOMA_NOS + RHABDOMYOSARCOMA: + title: Rhabdomyosarcoma + description: Malignant tumor arising from skeletal muscle. + meaning: NCIT:C3359 + annotations: + icdo_code: 8900 + is_a: SARCOMA_NOS + LYMPHOMA_NOS: + title: Lymphoma + description: >- + Malignant neoplasm of lymphoid tissue, not otherwise specified. Includes + Hodgkin and non-Hodgkin lymphomas. + meaning: NCIT:C3208 + annotations: + icdo_code: 9590 + HODGKIN_LYMPHOMA: + title: Hodgkin Lymphoma + description: >- + Lymphoma characterized by presence of Reed-Sternberg cells and specific + histological patterns. + meaning: NCIT:C9357 + annotations: + icdo_code: 9650 + is_a: LYMPHOMA_NOS + NON_HODGKIN_LYMPHOMA: + title: Non-Hodgkin Lymphoma + description: >- + All lymphomas other than Hodgkin lymphoma. Includes B-cell and T-cell + lymphomas. + meaning: NCIT:C3211 + annotations: + icdo_codes: 9591, 9670-9729 + is_a: LYMPHOMA_NOS + DIFFUSE_LARGE_B_CELL_LYMPHOMA: + title: Diffuse large B-cell lymphoma + description: Most common type of non-Hodgkin lymphoma. + meaning: NCIT:C8851 + annotations: + icdo_code: 9680 + is_a: NON_HODGKIN_LYMPHOMA + LEUKEMIA_NOS: + title: Leukemia + description: >- + Malignant neoplasm of blood-forming tissues, not otherwise specified. + meaning: NCIT:C3161 + annotations: + icdo_code: 9800 + ACUTE_LYMPHOBLASTIC_LEUKEMIA: + title: Acute lymphoblastic leukemia + description: Acute leukemia of lymphoid precursor cells. + meaning: NCIT:C3167 + annotations: + icdo_code: 9811 + is_a: LEUKEMIA_NOS + ACUTE_MYELOID_LEUKEMIA: + title: Acute myeloid leukemia + description: Acute leukemia of myeloid precursor cells. + meaning: NCIT:C3171 + annotations: + icdo_code: 9861 + is_a: LEUKEMIA_NOS + CHRONIC_LYMPHOCYTIC_LEUKEMIA: + title: Chronic lymphocytic leukemia + description: Chronic leukemia of mature B lymphocytes. + meaning: NCIT:C3163 + annotations: + icdo_code: 9823 + is_a: LEUKEMIA_NOS + CHRONIC_MYELOID_LEUKEMIA: + title: Chronic myeloid leukemia + description: Chronic leukemia characterized by BCR-ABL1 fusion gene. + annotations: + icdo_code: 9875 + is_a: LEUKEMIA_NOS + MELANOMA: + title: Melanoma + description: Malignant neoplasm arising from melanocytes. + meaning: NCIT:C3224 + annotations: + icdo_code: 8720 + MESOTHELIOMA: + title: Mesothelioma + description: >- + Malignant tumor arising from mesothelial cells lining pleura, peritoneum, + or pericardium. Strongly associated with asbestos exposure. + meaning: NCIT:C3234 + annotations: + icdo_code: 9050 + GERM_CELL_TUMOR: + title: Germ cell tumor + description: Tumor arising from germ cells. Includes seminoma, teratoma, etc. + meaning: NCIT:C3708 + annotations: + icdo_codes: 9060-9110 + NEUROENDOCRINE_TUMOR: + title: Neuroendocrine tumor + description: Tumor arising from neuroendocrine cells. + annotations: + icdo_codes: 8240-8249 + TumorBehavior: + title: Tumor Behavior + description: >- + Biological behavior codes used in ICD-O morphology (5th digit). Indicates + whether a neoplasm is benign, uncertain, in situ, or malignant. + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + source: ICD-O-3 + permissible_values: + BENIGN: + title: Benign Neoplasm + description: >- + Non-cancerous neoplasm that does not invade surrounding tissue or + metastasize. + meaning: NCIT:C3677 + annotations: + icdo_behavior: /0 + UNCERTAIN_BORDERLINE: + title: Uncertain whether benign or malignant + description: >- + Neoplasm with borderline malignancy or uncertain behavior. May recur + but typically does not metastasize. + annotations: + icdo_behavior: /1 + IN_SITU: + title: Carcinoma In Situ + description: >- + Malignant cells confined to epithelium without invasion through basement + membrane. Pre-invasive cancer. + meaning: NCIT:C2917 + annotations: + icdo_behavior: /2 + MALIGNANT_PRIMARY: + title: Malignant, primary site + description: >- + Invasive malignant neoplasm at primary site. Cancer that has invaded + through basement membrane. + annotations: + icdo_behavior: /3 + MALIGNANT_METASTATIC: + title: Malignant, metastatic site + description: >- + Malignant neoplasm that has spread from primary site to secondary + (metastatic) site. + annotations: + icdo_behavior: /6 + MALIGNANT_UNCERTAIN_PRIMARY_METASTATIC: + title: Malignant, uncertain whether primary or metastatic + description: >- + Malignant neoplasm where it is uncertain if this is the primary site + or a metastatic site. + annotations: + icdo_behavior: /9 + TumorGrade: + title: Tumor Grade + description: >- + Histological grade/differentiation codes used in ICD-O (6th digit). Indicates + how abnormal the tumor cells appear compared to normal cells. + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + source: ICD-O-3 + permissible_values: + GRADE_1: + title: Grade I - Well differentiated + description: >- + Tumor cells closely resemble normal cells. Typically slow-growing with + better prognosis. + annotations: + icdo_grade: 1 + differentiation: well differentiated + GRADE_2: + title: Grade II - Moderately differentiated + description: >- + Tumor cells show moderate resemblance to normal cells. Intermediate + behavior. + annotations: + icdo_grade: 2 + differentiation: moderately differentiated + GRADE_3: + title: Grade III - Poorly differentiated + description: >- + Tumor cells show little resemblance to normal cells. More aggressive + with poorer prognosis. + annotations: + icdo_grade: 3 + differentiation: poorly differentiated + GRADE_4: + title: Grade IV - Undifferentiated/Anaplastic + description: >- + Tumor cells bear no resemblance to normal cells. Most aggressive with + poorest prognosis. + annotations: + icdo_grade: 4 + differentiation: undifferentiated, anaplastic + GRADE_NOT_DETERMINED: + title: Grade not determined + description: Histological grade has not been assessed or is not applicable. + annotations: + icdo_grade: 9 + T_CELL: + title: T-cell + description: Lymphoma/leukemia of T-cell origin. + annotations: + icdo_grade: 5 + use: lymphomas/leukemias + B_CELL: + title: B-cell + description: Lymphoma/leukemia of B-cell origin. + annotations: + icdo_grade: 6 + use: lymphomas/leukemias + NULL_CELL: + title: Null cell (non-T, non-B) + description: Lymphoma/leukemia of neither T-cell nor B-cell origin. + annotations: + icdo_grade: 7 + use: lymphomas/leukemias + NK_CELL: + title: NK cell + description: Lymphoma/leukemia of natural killer cell origin. + annotations: + icdo_grade: 8 + use: lymphomas/leukemias diff --git a/src/valuesets/schema/provenance/evidence.yaml b/src/valuesets/schema/provenance/evidence.yaml new file mode 100644 index 00000000..7a5029d4 --- /dev/null +++ b/src/valuesets/schema/provenance/evidence.yaml @@ -0,0 +1,42 @@ +name: evidence +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 +imports: +- linkml:types +prefixes: + linkml: https://w3id.org/linkml/ + valuesets: https://w3id.org/valuesets/ + ECO: http://purl.obolibrary.org/obo/ECO_ + rdfs: http://www.w3.org/2000/01/rdf-schema# + orcid: https://orcid.org/ + valuesets_meta: https://w3id.org/valuesets/meta/ +default_prefix: valuesets +slots: + evidence_type: + description: The type of evidence supporting an assertion + range: EvidenceType +enums: + EvidenceType: + title: Evidence Type + description: >- + Types of evidence used to support assertions, dynamically populated from + the Evidence and Conclusion Ontology (ECO). Includes experimental evidence, + computational evidence, author statements, and other evidence types. + status: STANDARD + contributors: + - orcid:0000-0002-6601-2165 + - https://github.com/anthropics/claude-code + instantiates: + - valuesets_meta:ValueSetEnumDefinition + annotations: + stewards: https://evidenceontology.org + publishers: https://evidenceontology.org + reachable_from: + source_nodes: + - ECO:0000000 + is_direct: false + relationship_types: + - rdfs:subClassOf From e21fcdf662d14c94bdd8ee70d6fb4cf5cb2a103b Mon Sep 17 00:00:00 2001 From: Chris Mungall Date: Tue, 9 Dec 2025 18:51:57 -0800 Subject: [PATCH 2/3] Update src/valuesets/schema/medical/oncology/icdo.yaml Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --- src/valuesets/schema/medical/oncology/icdo.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/src/valuesets/schema/medical/oncology/icdo.yaml b/src/valuesets/schema/medical/oncology/icdo.yaml index 747a5260..49c6f485 100644 --- a/src/valuesets/schema/medical/oncology/icdo.yaml +++ b/src/valuesets/schema/medical/oncology/icdo.yaml @@ -392,6 +392,7 @@ enums: CHRONIC_MYELOID_LEUKEMIA: title: Chronic myeloid leukemia description: Chronic leukemia characterized by BCR-ABL1 fusion gene. + meaning: NCIT:C3174 annotations: icdo_code: 9875 is_a: LEUKEMIA_NOS From 64cbb3ca8ff8582533e50de71174b87c4de2d95f Mon Sep 17 00:00:00 2001 From: dragon-ai-agent Date: Tue, 9 Dec 2025 18:59:30 -0800 Subject: [PATCH 3/3] Add CHEBI isotope-specific mappings to radionuclides MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Updated radionuclides.yaml to prefer CHEBI isotope-specific terms over NCIT: - CESIUM_137: NCIT:C68812 → CHEBI:196959 (caesium-137) - CARBON_14: NCIT:C1638 → CHEBI:36927 (carbon-14 atom) - POLONIUM_210: Added meaning CHEBI:37340 (polonium-210 atom) Titles updated to match CHEBI labels for validation. Related: https://github.com/chemkg/chemrof/issues/49 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 --- .../schema/environmental_health/radionuclides.yaml | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/src/valuesets/schema/environmental_health/radionuclides.yaml b/src/valuesets/schema/environmental_health/radionuclides.yaml index 4e979ae0..c9f0fe33 100644 --- a/src/valuesets/schema/environmental_health/radionuclides.yaml +++ b/src/valuesets/schema/environmental_health/radionuclides.yaml @@ -106,11 +106,11 @@ enums: decay_mode: beta, electron capture abundance: 0.012% of natural potassium CESIUM_137: - title: Cesium Cs 137 + title: caesium-137 description: >- Anthropogenic radionuclide from nuclear fission. Environmental contaminant from nuclear weapons testing and accidents. - meaning: NCIT:C68812 + meaning: CHEBI:196959 annotations: symbol: Cs-137 half_life: 30.17 years @@ -169,11 +169,11 @@ enums: half_life: 12.3 years decay_mode: beta (weak) CARBON_14: - title: Carbon C-14 + title: carbon-14 atom description: >- Cosmogenic radionuclide used in radiocarbon dating. Produced by cosmic ray interactions in atmosphere. - meaning: NCIT:C1638 + meaning: CHEBI:36927 annotations: symbol: C-14 half_life: 5730 years @@ -190,10 +190,11 @@ enums: decay_mode: beta use: sediment dating POLONIUM_210: - title: Polonium-210 + title: polonium-210 atom description: >- Highly radioactive alpha emitter in uranium decay series. Found in tobacco smoke. + meaning: CHEBI:37340 annotations: symbol: Po-210 half_life: 138 days