name: als_kg description: Comprehensive ontology model for the ALS Knowledge Graph (ALS-KG). Uses a local default namespace for ALS-specific classes and slots, explicit Biolink/ontology URIs only for externally defined concepts and predicates, direct object properties for canonical KG edges, and optional evidence-bearing association classes for provenance-rich statements. title: ALS Knowledge Graph Ontology Model comments: - Reactome pathways are modeled as Pathway entities using Reactome stable identifiers; KEGG pathway prefixes and KEGG-specific mappings are intentionally omitted. - 'URI policy: ALS-KG-specific classes and slots use the schema default_prefix (alskb) and do not need explicit class_uri/slot_uri declarations. Use class_uri/slot_uri only when a term is intended to be equivalent to an external model term; use exact_mappings or close_mappings when alignment is useful but not identical.' id: https://cair2015.github.io/als-kg version: 2.1.2 imports: - linkml:types license: MIT prefixes: linkml: prefix_prefix: linkml prefix_reference: https://w3id.org/linkml/ alskb: prefix_prefix: alskb prefix_reference: https://cair2015.github.io/als-kg/elements/ biolink: prefix_prefix: biolink prefix_reference: https://w3id.org/biolink/vocab/ owl: prefix_prefix: owl prefix_reference: http://www.w3.org/2002/07/owl# rdf: prefix_prefix: rdf prefix_reference: http://www.w3.org/1999/02/22-rdf-syntax-ns# rdfs: prefix_prefix: rdfs prefix_reference: http://www.w3.org/2000/01/rdf-schema# obo: prefix_prefix: obo prefix_reference: http://purl.obolibrary.org/obo/ MONDO: prefix_prefix: MONDO prefix_reference: http://purl.obolibrary.org/obo/MONDO_ HP: prefix_prefix: HP prefix_reference: http://purl.obolibrary.org/obo/HP_ UBERON: prefix_prefix: UBERON prefix_reference: http://purl.obolibrary.org/obo/UBERON_ NCBIGene: prefix_prefix: NCBIGene prefix_reference: https://www.ncbi.nlm.nih.gov/gene/ UniProtKB: prefix_prefix: UniProtKB prefix_reference: https://www.uniprot.org/uniprot/ ClinVar: prefix_prefix: ClinVar prefix_reference: https://www.ncbi.nlm.nih.gov/clinvar/variation/ DrugBank: prefix_prefix: DrugBank prefix_reference: https://www.drugbank.ca/drugs/ GO: prefix_prefix: GO prefix_reference: http://purl.obolibrary.org/obo/GO_ Reactome: prefix_prefix: Reactome prefix_reference: https://identifiers.org/reactome/ CTD: prefix_prefix: CTD prefix_reference: http://ctdbase.org/detail.go?type=chem&acc= xsd: prefix_prefix: xsd prefix_reference: http://www.w3.org/2001/XMLSchema# schema: prefix_prefix: schema prefix_reference: http://schema.org/ dcterms: prefix_prefix: dcterms prefix_reference: http://purl.org/dc/terms/ IAO: prefix_prefix: IAO prefix_reference: http://purl.obolibrary.org/obo/IAO_ RO: prefix_prefix: RO prefix_reference: http://purl.obolibrary.org/obo/RO_ BFO: prefix_prefix: BFO prefix_reference: http://purl.obolibrary.org/obo/BFO_ ECO: prefix_prefix: ECO prefix_reference: http://purl.obolibrary.org/obo/ECO_ SIO: prefix_prefix: SIO prefix_reference: http://semanticscience.org/resource/ oboInOwl: prefix_prefix: oboInOwl prefix_reference: http://www.geneontology.org/formats/oboInOwl# HGNC: prefix_prefix: HGNC prefix_reference: https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/ ENSEMBL: prefix_prefix: ENSEMBL prefix_reference: https://identifiers.org/ensembl/ dbSNP: prefix_prefix: dbSNP prefix_reference: https://www.ncbi.nlm.nih.gov/snp/ ChEMBL: prefix_prefix: ChEMBL prefix_reference: https://www.ebi.ac.uk/chembl/compound_report_card/ MeSH: prefix_prefix: MeSH prefix_reference: https://id.nlm.nih.gov/mesh/ OMIM: prefix_prefix: OMIM prefix_reference: https://omim.org/entry/ ORPHANET: prefix_prefix: ORPHANET prefix_reference: http://www.orpha.net/ORDO/Orphanet_ UMLS: prefix_prefix: UMLS prefix_reference: https://uts.nlm.nih.gov/uts/umls/concept/ ICD10CM: prefix_prefix: ICD10CM prefix_reference: https://icd.codes/icd10cm/ CAS: prefix_prefix: CAS prefix_reference: https://commonchemistry.cas.org/detail?cas_rn= DOI: prefix_prefix: DOI prefix_reference: https://doi.org/ PMID: prefix_prefix: PMID prefix_reference: https://pubmed.ncbi.nlm.nih.gov/ default_prefix: alskb default_range: string types: MondoIdentifier: name: MondoIdentifier definition_uri: https://cair2015.github.io/als-kg/elements/MondoIdentifier description: MONDO disease ontology identifier (e.g. MONDO:0007743) from_schema: https://cair2015.github.io/als-kg typeof: string base: str uri: xsd:string pattern: ^MONDO:\d{7}$ HpoIdentifier: name: HpoIdentifier definition_uri: https://cair2015.github.io/als-kg/elements/HpoIdentifier description: HPO phenotype term identifier (e.g. HP:0007354) from_schema: https://cair2015.github.io/als-kg typeof: string base: str uri: xsd:string pattern: ^HP:\d{7}$ UberonIdentifier: name: UberonIdentifier definition_uri: https://cair2015.github.io/als-kg/elements/UberonIdentifier description: UBERON anatomy ontology identifier from_schema: https://cair2015.github.io/als-kg typeof: string base: str uri: xsd:string pattern: ^UBERON:\d+$ NcbiGeneIdentifier: name: NcbiGeneIdentifier definition_uri: https://cair2015.github.io/als-kg/elements/NcbiGeneIdentifier description: NCBI Entrez Gene numeric ID from_schema: https://cair2015.github.io/als-kg typeof: string base: str uri: xsd:string pattern: ^\d+$ UniprotIdentifier: name: UniprotIdentifier definition_uri: https://cair2015.github.io/als-kg/elements/UniprotIdentifier description: UniProt accession identifier from_schema: https://cair2015.github.io/als-kg typeof: string base: str uri: xsd:string pattern: ^[A-Z0-9]{6}$ ClinvarIdentifier: name: ClinvarIdentifier definition_uri: https://cair2015.github.io/als-kg/elements/ClinvarIdentifier description: ClinVar variation numeric ID from_schema: https://cair2015.github.io/als-kg typeof: string base: str uri: xsd:string pattern: ^\d+$ DrugBankIdentifier: name: DrugBankIdentifier definition_uri: https://cair2015.github.io/als-kg/elements/DrugBankIdentifier description: DrugBank primary identifier (e.g. DB00533) from_schema: https://cair2015.github.io/als-kg typeof: string base: str uri: xsd:string pattern: ^DB\d{5}$ GoIdentifier: name: GoIdentifier definition_uri: https://cair2015.github.io/als-kg/elements/GoIdentifier description: Gene Ontology term identifier (e.g. GO:0006810) from_schema: https://cair2015.github.io/als-kg typeof: string base: str uri: xsd:string pattern: ^GO:\d{7}$ ReactomeIdentifier: name: ReactomeIdentifier definition_uri: https://cair2015.github.io/als-kg/elements/ReactomeIdentifier description: Reactome stable pathway identifier as a CURIE (e.g. Reactome:R-HSA-5673001) from_schema: https://cair2015.github.io/als-kg typeof: string base: str uri: xsd:string pattern: ^Reactome:R-HSA-\d+(\.\d+)?$ CtdIdentifier: name: CtdIdentifier definition_uri: https://cair2015.github.io/als-kg/elements/CtdIdentifier description: CTD chemical/stressor identifier from_schema: https://cair2015.github.io/als-kg typeof: string base: str uri: xsd:string string: name: string definition_uri: https://w3id.org/linkml/String description: A character string notes: - In RDF serializations, a slot with range of string is treated as a literal or type xsd:string. If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "string". from_schema: https://w3id.org/linkml/types imported_from: linkml:types exact_mappings: - schema:Text base: str uri: xsd:string integer: name: integer definition_uri: https://w3id.org/linkml/Integer description: An integer notes: - If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "integer". from_schema: https://w3id.org/linkml/types imported_from: linkml:types exact_mappings: - schema:Integer base: int uri: xsd:integer boolean: name: boolean definition_uri: https://w3id.org/linkml/Boolean description: A binary (true or false) value notes: - If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "boolean". from_schema: https://w3id.org/linkml/types imported_from: linkml:types exact_mappings: - schema:Boolean base: Bool uri: xsd:boolean repr: bool float: name: float definition_uri: https://w3id.org/linkml/Float description: A real number that conforms to the xsd:float specification notes: - If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "float". from_schema: https://w3id.org/linkml/types imported_from: linkml:types exact_mappings: - schema:Float base: float uri: xsd:float double: name: double definition_uri: https://w3id.org/linkml/Double description: A real number that conforms to the xsd:double specification notes: - If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "double". from_schema: https://w3id.org/linkml/types imported_from: linkml:types close_mappings: - schema:Float base: float uri: xsd:double decimal: name: decimal definition_uri: https://w3id.org/linkml/Decimal description: A real number with arbitrary precision that conforms to the xsd:decimal specification notes: - If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "decimal". from_schema: https://w3id.org/linkml/types imported_from: linkml:types broad_mappings: - schema:Number base: Decimal uri: xsd:decimal time: name: time definition_uri: https://w3id.org/linkml/Time description: A time object represents a (local) time of day, independent of any particular day notes: - URI is dateTime because OWL reasoners do not work with straight date or time - If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "time". from_schema: https://w3id.org/linkml/types imported_from: linkml:types exact_mappings: - schema:Time base: XSDTime uri: xsd:time repr: str date: name: date definition_uri: https://w3id.org/linkml/Date description: a date (year, month and day) in an idealized calendar notes: - URI is dateTime because OWL reasoners don't work with straight date or time - If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "date". from_schema: https://w3id.org/linkml/types imported_from: linkml:types exact_mappings: - schema:Date base: XSDDate uri: xsd:date repr: str datetime: name: datetime definition_uri: https://w3id.org/linkml/Datetime description: The combination of a date and time notes: - If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "datetime". from_schema: https://w3id.org/linkml/types imported_from: linkml:types exact_mappings: - schema:DateTime base: XSDDateTime uri: xsd:dateTime repr: str date_or_datetime: name: date_or_datetime definition_uri: https://w3id.org/linkml/DateOrDatetime description: Either a date or a datetime notes: - If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "date_or_datetime". from_schema: https://w3id.org/linkml/types imported_from: linkml:types base: str uri: linkml:DateOrDatetime repr: str uriorcurie: name: uriorcurie definition_uri: https://w3id.org/linkml/Uriorcurie description: a URI or a CURIE notes: - If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "uriorcurie". from_schema: https://w3id.org/linkml/types imported_from: linkml:types base: URIorCURIE uri: xsd:anyURI repr: str curie: name: curie definition_uri: https://w3id.org/linkml/Curie conforms_to: https://www.w3.org/TR/curie/ description: a compact URI notes: - If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "curie". comments: - in RDF serializations this MUST be expanded to a URI - in non-RDF serializations MAY be serialized as the compact representation from_schema: https://w3id.org/linkml/types imported_from: linkml:types base: Curie uri: xsd:string repr: str uri: name: uri definition_uri: https://w3id.org/linkml/Uri conforms_to: https://www.ietf.org/rfc/rfc3987.txt description: a complete URI notes: - If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "uri". comments: - in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node from_schema: https://w3id.org/linkml/types imported_from: linkml:types close_mappings: - schema:URL base: URI uri: xsd:anyURI repr: str ncname: name: ncname definition_uri: https://w3id.org/linkml/Ncname description: Prefix part of CURIE notes: - If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "ncname". from_schema: https://w3id.org/linkml/types imported_from: linkml:types base: NCName uri: xsd:string repr: str objectidentifier: name: objectidentifier definition_uri: https://w3id.org/linkml/Objectidentifier description: A URI or CURIE that represents an object in the model. notes: - If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "objectidentifier". comments: - Used for inheritance and type checking from_schema: https://w3id.org/linkml/types imported_from: linkml:types base: ElementIdentifier uri: shex:iri repr: str nodeidentifier: name: nodeidentifier definition_uri: https://w3id.org/linkml/Nodeidentifier description: A URI, CURIE or BNODE that represents a node in a model. notes: - If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "nodeidentifier". from_schema: https://w3id.org/linkml/types imported_from: linkml:types base: NodeIdentifier uri: shex:nonLiteral repr: str jsonpointer: name: jsonpointer definition_uri: https://w3id.org/linkml/Jsonpointer conforms_to: https://datatracker.ietf.org/doc/html/rfc6901 description: A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. notes: - If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "jsonpointer". from_schema: https://w3id.org/linkml/types imported_from: linkml:types base: str uri: xsd:string repr: str jsonpath: name: jsonpath definition_uri: https://w3id.org/linkml/Jsonpath conforms_to: https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html description: A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. notes: - If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "jsonpath". from_schema: https://w3id.org/linkml/types imported_from: linkml:types base: str uri: xsd:string repr: str sparqlpath: name: sparqlpath definition_uri: https://w3id.org/linkml/Sparqlpath conforms_to: https://www.w3.org/TR/sparql11-query/#propertypaths description: A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. notes: - If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "sparqlpath". from_schema: https://w3id.org/linkml/types imported_from: linkml:types base: str uri: xsd:string repr: str enums: DiseaseTypeEnum: name: DiseaseTypeEnum definition_uri: https://cair2015.github.io/als-kg/elements/DiseaseTypeEnum from_schema: https://cair2015.github.io/als-kg permissible_values: sporadic: text: sporadic description: Occurs without family history familial: text: familial description: Inherited pattern of occurrence syndromic: text: syndromic description: Part of larger syndrome OnsetTypeEnum: name: OnsetTypeEnum definition_uri: https://cair2015.github.io/als-kg/elements/OnsetTypeEnum from_schema: https://cair2015.github.io/als-kg permissible_values: bulbar: text: bulbar description: Facial/tongue muscles affected first limb: text: limb description: Arm or leg muscles affected first respiratory: text: respiratory description: Breathing muscles affected first generalized: text: generalized description: Multiple sites affected simultaneously unknown: text: unknown description: Onset location unknown GeneTypeEnum: name: GeneTypeEnum definition_uri: https://cair2015.github.io/als-kg/elements/GeneTypeEnum from_schema: https://cair2015.github.io/als-kg permissible_values: protein_coding: text: protein_coding lncRNA: text: lncRNA miRNA: text: miRNA pseudogene: text: pseudogene other: text: other VariantTypeEnum: name: VariantTypeEnum definition_uri: https://cair2015.github.io/als-kg/elements/VariantTypeEnum from_schema: https://cair2015.github.io/als-kg permissible_values: SNV: text: SNV description: Single nucleotide variant indel: text: indel description: Insertion or deletion repeat_expansion: text: repeat_expansion description: Trinucleotide repeat expansion CNV: text: CNV description: Copy number variation structural: text: structural description: Structural variant (inversion, translocation) RelationshipTypeEnum: name: RelationshipTypeEnum definition_uri: https://cair2015.github.io/als-kg/elements/RelationshipTypeEnum description: Standard relationship types following RDF/OWL semantics from_schema: https://cair2015.github.io/als-kg permissible_values: is_a: text: is_a description: Subclass relationship (taxonomic) part_of: text: part_of description: Mereological (compositional) relationship proper_part_of: text: proper_part_of description: Strict part-of (excludes identity) participates_in: text: participates_in description: Agent participates in process has_participant: text: has_participant description: Process has participant regulates: text: regulates description: Regulatory relationship (direction unspecified) positively_regulates: text: positively_regulates description: Upregulation/activation negatively_regulates: text: negatively_regulates description: Downregulation/inhibition associated_with: text: associated_with description: Statistical/empirical association affects: text: affects description: Causal or functional modification EvidenceTypeEnum: name: EvidenceTypeEnum definition_uri: https://cair2015.github.io/als-kg/elements/EvidenceTypeEnum from_schema: https://cair2015.github.io/als-kg permissible_values: curated: text: curated description: Manually curated from literature experimental: text: experimental description: Derived from wet-lab experiments computational: text: computational description: Result of computational analysis inferred: text: inferred description: Inferred from other statements predicted: text: predicted description: Machine learning prediction text_mined: text: text_mined description: Extracted via natural language processing slots: id: name: id definition_uri: https://cair2015.github.io/als-kg/elements/id description: Unique identifier (IRI or URI) from_schema: https://cair2015.github.io/als-kg mappings: - schema:identifier slot_uri: schema:identifier identifier: true range: uriorcurie required: true label: name: label definition_uri: https://cair2015.github.io/als-kg/elements/label description: Human-readable label for the entity from_schema: https://cair2015.github.io/als-kg mappings: - rdfs:label slot_uri: rdfs:label range: string required: true definition: name: definition definition_uri: https://cair2015.github.io/als-kg/elements/definition description: Textual definition following OBO definition format from_schema: https://cair2015.github.io/als-kg mappings: - IAO:0000115 slot_uri: IAO:0000115 range: string synonym: name: synonym definition_uri: https://cair2015.github.io/als-kg/elements/synonym description: Alternative names or labels from_schema: https://cair2015.github.io/als-kg mappings: - oboInOwl:hasRelatedSynonym slot_uri: oboInOwl:hasRelatedSynonym range: string multivalued: true xref: name: xref definition_uri: https://cair2015.github.io/als-kg/elements/xref description: 'Cross-reference to equivalent entity in another ontology. Format: ONTOLOGY_PREFIX:identifier (e.g. OMIM:104300, Reactome:R-HSA-5673001, GO:0006810)' from_schema: https://cair2015.github.io/als-kg mappings: - oboInOwl:hasDbXref slot_uri: oboInOwl:hasDbXref range: string multivalued: true comment: name: comment definition_uri: https://cair2015.github.io/als-kg/elements/comment description: Informal comment or note on entity from_schema: https://cair2015.github.io/als-kg mappings: - rdfs:comment slot_uri: rdfs:comment range: string is_obsolete: name: is_obsolete definition_uri: https://cair2015.github.io/als-kg/elements/is_obsolete description: Whether this entity is deprecated/obsolete from_schema: https://cair2015.github.io/als-kg mappings: - owl:deprecated slot_uri: owl:deprecated ifabsent: 'false' range: boolean subject: name: subject definition_uri: https://cair2015.github.io/als-kg/elements/subject description: Subject of the relationship (resource IRI) from_schema: https://cair2015.github.io/als-kg mappings: - rdf:subject slot_uri: rdf:subject range: string required: true predicate: name: predicate definition_uri: https://cair2015.github.io/als-kg/elements/predicate description: Predicate / property type IRI from_schema: https://cair2015.github.io/als-kg mappings: - rdf:predicate slot_uri: rdf:predicate range: uriorcurie required: true object: name: object definition_uri: https://cair2015.github.io/als-kg/elements/object description: Object of the relationship (resource IRI) from_schema: https://cair2015.github.io/als-kg mappings: - rdf:object slot_uri: rdf:object range: string required: true has_anatomy: name: has_anatomy definition_uri: https://cair2015.github.io/als-kg/elements/has_anatomy description: Referenced anatomy entity in an association record. from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:has_anatomy range: Anatomy has_disease: name: has_disease definition_uri: https://cair2015.github.io/als-kg/elements/has_disease description: Referenced disease entity in an association record. from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:has_disease range: Disease has_drug: name: has_drug definition_uri: https://cair2015.github.io/als-kg/elements/has_drug description: Referenced drug entity in an association record. from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:has_drug range: Drug has_gene: name: has_gene definition_uri: https://cair2015.github.io/als-kg/elements/has_gene description: Referenced gene entity in an association record. from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:has_gene range: Gene has_phenotype: name: has_phenotype definition_uri: https://cair2015.github.io/als-kg/elements/has_phenotype description: Referenced phenotype entity in an association record. from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:has_phenotype range: Phenotype has_protein: name: has_protein definition_uri: https://cair2015.github.io/als-kg/elements/has_protein description: Referenced protein entity in an association record. from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:has_protein range: Protein has_pathway: name: has_pathway definition_uri: https://cair2015.github.io/als-kg/elements/has_pathway description: Referenced Reactome pathway entity in an association record. from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:has_pathway range: Pathway has_variant: name: has_variant definition_uri: https://cair2015.github.io/als-kg/elements/has_variant description: Referenced variant entity in an association record. from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:has_variant range: Variant disease_manifests_as_phenotype: name: disease_manifests_as_phenotype definition_uri: https://cair2015.github.io/als-kg/elements/disease_manifests_as_phenotype description: Disease has or presents with a phenotype or clinical feature. from_schema: https://cair2015.github.io/als-kg mappings: - biolink:has_phenotype domain: Disease slot_uri: biolink:has_phenotype owner: disease_manifests_as_phenotype range: Phenotype multivalued: true disease_affects_anatomy: name: disease_affects_anatomy definition_uri: https://cair2015.github.io/als-kg/elements/disease_affects_anatomy description: Disease affects, involves, or primarily manifests in an anatomical structure. from_schema: https://cair2015.github.io/als-kg close_mappings: - biolink:affects domain: Disease slot_uri: alskb:disease_affects_anatomy owner: disease_affects_anatomy range: Anatomy multivalued: true gene_associated_with_disease: name: gene_associated_with_disease definition_uri: https://cair2015.github.io/als-kg/elements/gene_associated_with_disease description: Gene has causal, risk, modifier, protective, or correlative association with disease. from_schema: https://cair2015.github.io/als-kg mappings: - biolink:gene_associated_with_condition domain: Gene slot_uri: biolink:gene_associated_with_condition owner: gene_associated_with_disease range: Disease multivalued: true variant_associated_with_disease: name: variant_associated_with_disease definition_uri: https://cair2015.github.io/als-kg/elements/variant_associated_with_disease description: Sequence variant has causal, risk, modifier, protective, or correlative association with disease. from_schema: https://cair2015.github.io/als-kg mappings: - biolink:variant_associated_with_condition domain: Variant slot_uri: biolink:variant_associated_with_condition owner: variant_associated_with_disease range: Disease multivalued: true variant_affects_protein: name: variant_affects_protein definition_uri: https://cair2015.github.io/als-kg/elements/variant_affects_protein description: Sequence variant changes or is predicted to affect a protein product. from_schema: https://cair2015.github.io/als-kg close_mappings: - biolink:affects domain: Variant slot_uri: alskb:variant_affects_protein owner: variant_affects_protein range: Protein multivalued: true gene_encodes_protein: name: gene_encodes_protein definition_uri: https://cair2015.github.io/als-kg/elements/gene_encodes_protein description: Gene encodes a protein product. from_schema: https://cair2015.github.io/als-kg mappings: - RO:0002205 domain: Gene slot_uri: RO:0002205 owner: gene_encodes_protein range: Protein multivalued: true protein_interacts_with_protein: name: protein_interacts_with_protein definition_uri: https://cair2015.github.io/als-kg/elements/protein_interacts_with_protein description: Protein physically or functionally interacts with another protein. from_schema: https://cair2015.github.io/als-kg mappings: - biolink:interacts_with domain: Protein slot_uri: biolink:interacts_with owner: protein_interacts_with_protein range: Protein multivalued: true protein_participates_in_pathway: name: protein_participates_in_pathway definition_uri: https://cair2015.github.io/als-kg/elements/protein_participates_in_pathway description: Protein participates in or is annotated to a Reactome pathway. from_schema: https://cair2015.github.io/als-kg mappings: - biolink:participates_in domain: Protein slot_uri: biolink:participates_in owner: protein_participates_in_pathway range: Pathway multivalued: true drug_targets_molecular_entity: name: drug_targets_molecular_entity definition_uri: https://cair2015.github.io/als-kg/elements/drug_targets_molecular_entity description: Drug, biologic, ASO, or other therapeutic agent targets a gene or protein. from_schema: https://cair2015.github.io/als-kg mappings: - biolink:targets domain: Drug slot_uri: biolink:targets owner: drug_targets_molecular_entity range: MolecularEntity multivalued: true inlined: true inlined_as_list: true drug_treats_or_modulates_disease: name: drug_treats_or_modulates_disease definition_uri: https://cair2015.github.io/als-kg/elements/drug_treats_or_modulates_disease description: Drug treats, modifies, palliates, or is being investigated for a disease. from_schema: https://cair2015.github.io/als-kg close_mappings: - biolink:treats domain: Drug slot_uri: alskb:drug_treats_or_modulates_disease owner: drug_treats_or_modulates_disease range: Disease multivalued: true exposure_associated_with_disease: name: exposure_associated_with_disease definition_uri: https://cair2015.github.io/als-kg/elements/exposure_associated_with_disease description: Environmental exposure or stressor is associated with disease risk or progression. from_schema: https://cair2015.github.io/als-kg close_mappings: - biolink:associated_with domain: ExposureOrStressor slot_uri: alskb:exposure_associated_with_disease owner: exposure_associated_with_disease range: Disease multivalued: true transcription_factor_regulates_gene: name: transcription_factor_regulates_gene definition_uri: https://cair2015.github.io/als-kg/elements/transcription_factor_regulates_gene description: Transcription factor regulates the expression of a target gene. from_schema: https://cair2015.github.io/als-kg mappings: - biolink:regulates domain: TranscriptionFactor slot_uri: biolink:regulates owner: transcription_factor_regulates_gene range: Gene multivalued: true gene_expressed_in_anatomy: name: gene_expressed_in_anatomy definition_uri: https://cair2015.github.io/als-kg/elements/gene_expressed_in_anatomy description: Gene is expressed in an anatomical structure, tissue, or cell-type context. from_schema: https://cair2015.github.io/als-kg mappings: - biolink:expressed_in domain: Gene slot_uri: biolink:expressed_in owner: gene_expressed_in_anatomy range: Anatomy multivalued: true disease_related_to_disease: name: disease_related_to_disease definition_uri: https://cair2015.github.io/als-kg/elements/disease_related_to_disease description: Disease is related to another disease by comorbidity, shared etiology, similar mechanism, or phenotypic similarity. from_schema: https://cair2015.github.io/als-kg mappings: - biolink:related_to domain: Disease slot_uri: biolink:related_to owner: disease_related_to_disease range: Disease multivalued: true gene_participates_in_process: name: gene_participates_in_process definition_uri: https://cair2015.github.io/als-kg/elements/gene_participates_in_process description: Gene or gene product participates in a biological process. from_schema: https://cair2015.github.io/als-kg mappings: - biolink:participates_in domain: Gene slot_uri: biolink:participates_in owner: gene_participates_in_process range: BiologicalProcess multivalued: true gene_has_molecular_function: name: gene_has_molecular_function definition_uri: https://cair2015.github.io/als-kg/elements/gene_has_molecular_function description: Gene or gene product has a molecular activity or function. from_schema: https://cair2015.github.io/als-kg mappings: - RO:0000085 domain: Gene slot_uri: RO:0000085 owner: gene_has_molecular_function range: MolecularFunction multivalued: true protein_localized_to_cellular_component: name: protein_localized_to_cellular_component definition_uri: https://cair2015.github.io/als-kg/elements/protein_localized_to_cellular_component description: Protein localizes to or is active in a cellular component. from_schema: https://cair2015.github.io/als-kg mappings: - biolink:located_in domain: Protein slot_uri: biolink:located_in owner: protein_localized_to_cellular_component range: CellularComponent multivalued: true source: name: source definition_uri: https://cair2015.github.io/als-kg/elements/source description: Data source name from_schema: https://cair2015.github.io/als-kg mappings: - dcterms:source slot_uri: dcterms:source range: string source_version: name: source_version definition_uri: https://cair2015.github.io/als-kg/elements/source_version description: Source version or release date from_schema: https://cair2015.github.io/als-kg mappings: - dcterms:hasVersion slot_uri: dcterms:hasVersion range: string source_url: name: source_url definition_uri: https://cair2015.github.io/als-kg/elements/source_url description: URL to source resource from_schema: https://cair2015.github.io/als-kg mappings: - schema:url slot_uri: schema:url range: uriorcurie confidence: name: confidence definition_uri: https://cair2015.github.io/als-kg/elements/confidence description: Confidence or quality score (0.0-1.0) from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:confidence range: float minimum_value: 0.0 maximum_value: 1.0 evidence_type: name: evidence_type definition_uri: https://cair2015.github.io/als-kg/elements/evidence_type description: Type of supporting evidence from_schema: https://cair2015.github.io/als-kg mappings: - ECO:0000000 slot_uri: ECO:0000000 range: EvidenceTypeEnum evidence_source: name: evidence_source definition_uri: https://cair2015.github.io/als-kg/elements/evidence_source description: Specific study/publication supporting the statement from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:evidence_source range: string ingest_date: name: ingest_date definition_uri: https://cair2015.github.io/als-kg/elements/ingest_date description: Date of ETL ingest from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:ingest_date range: date last_updated: name: last_updated definition_uri: https://cair2015.github.io/als-kg/elements/last_updated description: Last modification date from_schema: https://cair2015.github.io/als-kg mappings: - dcterms:modified slot_uri: dcterms:modified range: date namedEntity__id: name: namedEntity__id description: Persistent unique identifier (IRI) from_schema: https://cair2015.github.io/als-kg mappings: - schema:identifier slot_uri: schema:identifier alias: id owner: NamedEntity domain_of: - NamedEntity range: string required: true namedEntity__label: name: namedEntity__label description: Preferred human-readable label from_schema: https://cair2015.github.io/als-kg mappings: - rdfs:label slot_uri: rdfs:label alias: label owner: NamedEntity domain_of: - NamedEntity range: string required: true namedEntity__definition: name: namedEntity__definition description: Formal textual definition from_schema: https://cair2015.github.io/als-kg mappings: - IAO:0000115 slot_uri: IAO:0000115 alias: definition owner: NamedEntity domain_of: - NamedEntity range: string namedEntity__synonym: name: namedEntity__synonym description: Alternative names from_schema: https://cair2015.github.io/als-kg mappings: - oboInOwl:hasRelatedSynonym slot_uri: oboInOwl:hasRelatedSynonym alias: synonym owner: NamedEntity domain_of: - NamedEntity range: string namedEntity__xref: name: namedEntity__xref description: Cross-references to external ontologies from_schema: https://cair2015.github.io/als-kg mappings: - oboInOwl:hasDbXref slot_uri: oboInOwl:hasDbXref alias: xref owner: NamedEntity domain_of: - NamedEntity range: string namedEntity__comment: name: namedEntity__comment description: Informal notes or comments from_schema: https://cair2015.github.io/als-kg mappings: - rdfs:comment slot_uri: rdfs:comment alias: comment owner: NamedEntity domain_of: - NamedEntity range: string namedEntity__is_obsolete: name: namedEntity__is_obsolete description: Deprecation flag from_schema: https://cair2015.github.io/als-kg mappings: - owl:deprecated slot_uri: owl:deprecated ifabsent: 'false' alias: is_obsolete owner: NamedEntity domain_of: - NamedEntity range: string namedEntity__source: name: namedEntity__source description: Original source/database from_schema: https://cair2015.github.io/als-kg mappings: - dcterms:source slot_uri: dcterms:source alias: source owner: NamedEntity domain_of: - NamedEntity range: string namedEntity__last_updated: name: namedEntity__last_updated description: Last modification timestamp from_schema: https://cair2015.github.io/als-kg mappings: - dcterms:modified slot_uri: dcterms:modified alias: last_updated owner: NamedEntity domain_of: - NamedEntity range: string ontologyClass__source_version: name: ontologyClass__source_version description: Source database/ontology version from_schema: https://cair2015.github.io/als-kg mappings: - dcterms:hasVersion slot_uri: dcterms:hasVersion alias: source_version owner: OntologyClass domain_of: - OntologyClass range: string ontologyClass__ingest_date: name: ontologyClass__ingest_date description: When entity was imported into ALS-KG from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:ingest_date alias: ingest_date owner: OntologyClass domain_of: - OntologyClass range: string relationship__subject: name: relationship__subject description: Subject resource IRI from_schema: https://cair2015.github.io/als-kg mappings: - rdf:subject slot_uri: rdf:subject alias: subject owner: Relationship domain_of: - Relationship range: string required: true relationship__predicate: name: relationship__predicate description: Relationship type IRI from_schema: https://cair2015.github.io/als-kg mappings: - rdf:predicate slot_uri: rdf:predicate alias: predicate owner: Relationship domain_of: - Relationship range: string required: true relationship__object: name: relationship__object description: Object resource IRI from_schema: https://cair2015.github.io/als-kg mappings: - rdf:object slot_uri: rdf:object alias: object owner: Relationship domain_of: - Relationship range: string required: true relationship__source: name: relationship__source description: Data source for this relationship from_schema: https://cair2015.github.io/als-kg mappings: - dcterms:source slot_uri: dcterms:source alias: source owner: Relationship domain_of: - Relationship range: string relationship__confidence: name: relationship__confidence description: Confidence score (0-1) from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:confidence alias: confidence owner: Relationship domain_of: - Relationship range: string relationship__evidence_type: name: relationship__evidence_type description: Type of evidence supporting relationship from_schema: https://cair2015.github.io/als-kg mappings: - ECO:0000000 slot_uri: ECO:0000000 alias: evidence_type owner: Relationship domain_of: - Relationship range: string relationship__evidence_source: name: relationship__evidence_source description: Citation or study ID from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:evidence_source alias: evidence_source owner: Relationship domain_of: - Relationship range: string relationship__ingest_date: name: relationship__ingest_date description: Ingest date from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:ingest_date alias: ingest_date owner: Relationship domain_of: - Relationship range: string diseaseOrPhenotype__mondo_id: name: diseaseOrPhenotype__mondo_id description: MONDO cross-reference from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:mondo_id alias: mondo_id owner: DiseaseOrPhenotype domain_of: - DiseaseOrPhenotype range: MondoIdentifier diseaseOrPhenotype__hpo_id: name: diseaseOrPhenotype__hpo_id description: HPO cross-reference from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:hpo_id alias: hpo_id owner: DiseaseOrPhenotype domain_of: - DiseaseOrPhenotype range: HpoIdentifier disease__mondo_id: name: disease__mondo_id from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:mondo_id identifier: true alias: mondo_id owner: Disease domain_of: - Disease range: MondoIdentifier required: true disease__name: name: disease__name description: Disease name (preferred from MONDO) from_schema: https://cair2015.github.io/als-kg mappings: - schema:name slot_uri: schema:name alias: name owner: Disease domain_of: - Disease range: string disease__disease_type: name: disease__disease_type from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:disease_type alias: disease_type owner: Disease domain_of: - Disease range: DiseaseTypeEnum disease__onset_type: name: disease__onset_type from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:onset_type alias: onset_type owner: Disease domain_of: - Disease range: OnsetTypeEnum disease__umls_cui: name: disease__umls_cui description: UMLS Concept Unique Identifier from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:umls_cui alias: umls_cui owner: Disease domain_of: - Disease range: string disease__omim_id: name: disease__omim_id description: OMIM (Online Mendelian Inheritance in Man) ID from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:omim_id alias: omim_id owner: Disease domain_of: - Disease range: string disease__orphanet_id: name: disease__orphanet_id description: Orphanet rare disease identifier from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:orphanet_id alias: orphanet_id owner: Disease domain_of: - Disease range: string disease__icd10_code: name: disease__icd10_code description: ICD-10-CM code for billing/clinical use from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:icd10_code alias: icd10_code owner: Disease domain_of: - Disease range: string phenotype__hpo_id: name: phenotype__hpo_id from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:hpo_id identifier: true alias: hpo_id owner: Phenotype domain_of: - Phenotype range: HpoIdentifier required: true phenotype__frequency: name: phenotype__frequency description: Frequency of phenotype in affected individuals (e.g. Frequent 75-99%) from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:frequency alias: frequency owner: Phenotype domain_of: - Phenotype range: string phenotype__severity: name: phenotype__severity description: Severity scale from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:severity alias: severity owner: Phenotype domain_of: - Phenotype range: string anatomy__uberon_id: name: anatomy__uberon_id from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:uberon_id identifier: true alias: uberon_id owner: Anatomy domain_of: - Anatomy range: UberonIdentifier required: true anatomy__bto_id: name: anatomy__bto_id description: Brenda Tissue Ontology ID from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:bto_id alias: bto_id owner: Anatomy domain_of: - Anatomy range: string anatomy__mesh_id: name: anatomy__mesh_id description: MeSH cross-reference from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:mesh_id alias: mesh_id owner: Anatomy domain_of: - Anatomy range: string anatomy__anatomical_system: name: anatomy__anatomical_system description: Anatomical system classification from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:anatomical_system alias: anatomical_system owner: Anatomy domain_of: - Anatomy range: string gene__ncbi_gene_id: name: gene__ncbi_gene_id from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:ncbi_gene_id identifier: true alias: ncbi_gene_id owner: Gene domain_of: - Gene range: NcbiGeneIdentifier required: true gene__hgnc_symbol: name: gene__hgnc_symbol description: Official HGNC gene symbol from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:hgnc_symbol alias: hgnc_symbol owner: Gene domain_of: - Gene range: string gene__ensembl_id: name: gene__ensembl_id description: Ensembl gene identifier from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:ensembl_id alias: ensembl_id owner: Gene domain_of: - Gene range: string gene__chromosome: name: gene__chromosome description: Cytogenetic location (e.g. 21q22.11 for SOD1) from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:chromosome alias: chromosome owner: Gene domain_of: - Gene range: string gene__genomic_pos_start: name: gene__genomic_pos_start description: GRCh38 start coordinate (1-based) from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:genomic_pos_start alias: genomic_pos_start owner: Gene domain_of: - Gene range: integer gene__genomic_pos_end: name: gene__genomic_pos_end description: GRCh38 end coordinate from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:genomic_pos_end alias: genomic_pos_end owner: Gene domain_of: - Gene range: integer gene__als_risk_tier: name: gene__als_risk_tier description: Evidence tier for ALS association (ALSoD classification) - definitive, strong, moderate, or candidate from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:als_risk_tier alias: als_risk_tier owner: Gene domain_of: - Gene range: string transcriptionFactor__tf_family: name: transcriptionFactor__tf_family description: Structural family (C2H2-ZF, bHLH, Homeodomain, etc.) from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:tf_family alias: tf_family owner: TranscriptionFactor domain_of: - TranscriptionFactor range: string transcriptionFactor__dorothea_confidence: name: transcriptionFactor__dorothea_confidence description: DoRothEA confidence level (A=high, D=low) from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:dorothea_confidence alias: dorothea_confidence owner: TranscriptionFactor domain_of: - TranscriptionFactor range: string protein__uniprot_id: name: protein__uniprot_id from_schema: https://cair2015.github.io/als-kg mappings: - 'UniProtKB:' slot_uri: 'UniProtKB:' identifier: true alias: uniprot_id owner: Protein domain_of: - Protein range: UniprotIdentifier required: true protein__protein_name: name: protein__protein_name description: Protein name (UniProt recommended name) from_schema: https://cair2015.github.io/als-kg mappings: - schema:name slot_uri: schema:name alias: protein_name owner: Protein domain_of: - Protein range: string protein__hgnc_symbol: name: protein__hgnc_symbol description: Gene name (cross-reference to Gene entity) from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:hgnc_symbol alias: hgnc_symbol owner: Protein domain_of: - Protein range: string protein__molecular_weight_kda: name: protein__molecular_weight_kda description: Molecular weight in kDa from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:molecular_weight_kda alias: molecular_weight_kda owner: Protein domain_of: - Protein range: float protein__protein_family: name: protein__protein_family description: Protein family classification (Pfam) from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:protein_family alias: protein_family owner: Protein domain_of: - Protein range: string protein__subcellular_location: name: protein__subcellular_location description: Cellular compartment(s) where protein is localized (e.g. mitochondrion, nucleus, axon) from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:subcellular_location alias: subcellular_location owner: Protein domain_of: - Protein range: string multivalued: true protein__aggregation_prone: name: protein__aggregation_prone description: Known to form aggregates (TDP-43, SOD1, FUS) from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:aggregation_prone alias: aggregation_prone owner: Protein domain_of: - Protein range: boolean protein__has_prion_like_domain: name: protein__has_prion_like_domain description: Contains intrinsically disordered prion-like region from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:has_prion_like_domain alias: has_prion_like_domain owner: Protein domain_of: - Protein range: boolean variant__clinvar_id: name: variant__clinvar_id from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:clinvar_id identifier: true alias: clinvar_id owner: Variant domain_of: - Variant range: ClinvarIdentifier required: true variant__rsid: name: variant__rsid description: dbSNP reference SNP ID from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:rsid alias: rsid owner: Variant domain_of: - Variant range: string variant__hgvs_c: name: variant__hgvs_c description: HGVS coding sequence notation (e.g. c.10A>G) from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:hgvs_c alias: hgvs_c owner: Variant domain_of: - Variant range: string variant__hgvs_p: name: variant__hgvs_p description: HGVS protein notation (e.g. p.Ala4Val) from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:hgvs_p alias: hgvs_p owner: Variant domain_of: - Variant range: string variant__variant_type: name: variant__variant_type from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:variant_type alias: variant_type owner: Variant domain_of: - Variant range: VariantTypeEnum variant__clinical_significance: name: variant__clinical_significance description: ClinVar clinical interpretation from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:clinical_significance alias: clinical_significance owner: Variant domain_of: - Variant range: string variant__als_class: name: variant__als_class description: ALS-specific classification (causal, risk, modifier, protective) from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:als_class alias: als_class owner: Variant domain_of: - Variant range: string variant__maf: name: variant__maf description: Minor allele frequency in gnomAD non-neuro cohort from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:maf alias: maf owner: Variant domain_of: - Variant range: float minimum_value: 0.0 maximum_value: 1.0 drug__drugbank_id: name: drug__drugbank_id from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:drugbank_id identifier: true alias: drugbank_id owner: Drug domain_of: - Drug range: DrugBankIdentifier required: true drug__drug_name: name: drug__drug_name description: Preferred drug name from_schema: https://cair2015.github.io/als-kg mappings: - schema:name slot_uri: schema:name alias: drug_name owner: Drug domain_of: - Drug range: string drug__chembl_id: name: drug__chembl_id description: ChEMBL compound ID from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:chembl_id alias: chembl_id owner: Drug domain_of: - Drug range: string drug__inchi_key: name: drug__inchi_key description: Standard InChIKey hash from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:inchi_key alias: inchi_key owner: Drug domain_of: - Drug range: string drug__smiles: name: drug__smiles description: Canonical SMILES string from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:smiles alias: smiles owner: Drug domain_of: - Drug range: string drug__drug_type: name: drug__drug_type description: Categorization (small molecule, biologic, ASO, cell therapy, gene therapy) from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:drug_type alias: drug_type owner: Drug domain_of: - Drug range: string drug__als_approved: name: drug__als_approved description: FDA approval status for ALS treatment from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:als_approved alias: als_approved owner: Drug domain_of: - Drug range: boolean drug__trial_status: name: drug__trial_status description: Highest clinical trial phase reached from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:trial_status alias: trial_status owner: Drug domain_of: - Drug range: string drug__mechanism: name: drug__mechanism description: Known mechanism of action from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:mechanism alias: mechanism owner: Drug domain_of: - Drug range: string drug__indication: name: drug__indication description: Clinical indication from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:indication alias: indication owner: Drug domain_of: - Drug range: string exposureOrStressor__ctd_id: name: exposureOrStressor__ctd_id from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:ctd_id identifier: true alias: ctd_id owner: ExposureOrStressor domain_of: - ExposureOrStressor range: CtdIdentifier required: true exposureOrStressor__exposure_name: name: exposureOrStressor__exposure_name description: Standard name of exposure/stressor from_schema: https://cair2015.github.io/als-kg mappings: - schema:name slot_uri: schema:name alias: exposure_name owner: ExposureOrStressor domain_of: - ExposureOrStressor range: string exposureOrStressor__exposure_type: name: exposureOrStressor__exposure_type description: Category (chemical, metal, pesticide, radiation, biological, other) from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:exposure_type alias: exposure_type owner: ExposureOrStressor domain_of: - ExposureOrStressor range: string exposureOrStressor__mesh_id: name: exposureOrStressor__mesh_id description: MeSH ID for exposure agent from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:mesh_id alias: mesh_id owner: ExposureOrStressor domain_of: - ExposureOrStressor range: string exposureOrStressor__cas_number: name: exposureOrStressor__cas_number description: CAS Registry number from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:cas_number alias: cas_number owner: ExposureOrStressor domain_of: - ExposureOrStressor range: string exposureOrStressor__als_relevance: name: exposureOrStressor__als_relevance description: Flagged as ALS-relevant in literature from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:als_relevance alias: als_relevance owner: ExposureOrStressor domain_of: - ExposureOrStressor range: boolean biologicalProcess__go_id: name: biologicalProcess__go_id from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:go_id identifier: true alias: go_id owner: BiologicalProcess domain_of: - BiologicalProcess range: GoIdentifier required: true biologicalProcess__process_name: name: biologicalProcess__process_name description: Standard process name from GO from_schema: https://cair2015.github.io/als-kg mappings: - schema:name slot_uri: schema:name alias: process_name owner: BiologicalProcess domain_of: - BiologicalProcess range: string biologicalProcess__go_definition: name: biologicalProcess__go_definition description: GO textual definition from_schema: https://cair2015.github.io/als-kg mappings: - IAO:0000115 slot_uri: IAO:0000115 alias: go_definition owner: BiologicalProcess domain_of: - BiologicalProcess range: string molecularFunction__go_id: name: molecularFunction__go_id from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:go_id identifier: true alias: go_id owner: MolecularFunction domain_of: - MolecularFunction range: GoIdentifier required: true molecularFunction__function_name: name: molecularFunction__function_name description: Molecular function name from GO from_schema: https://cair2015.github.io/als-kg mappings: - schema:name slot_uri: schema:name alias: function_name owner: MolecularFunction domain_of: - MolecularFunction range: string molecularFunction__go_definition: name: molecularFunction__go_definition description: GO textual definition from_schema: https://cair2015.github.io/als-kg mappings: - IAO:0000115 slot_uri: IAO:0000115 alias: go_definition owner: MolecularFunction domain_of: - MolecularFunction range: string cellularComponent__go_id: name: cellularComponent__go_id from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:go_id identifier: true alias: go_id owner: CellularComponent domain_of: - CellularComponent range: GoIdentifier required: true cellularComponent__component_name: name: cellularComponent__component_name description: Cellular component name from GO from_schema: https://cair2015.github.io/als-kg mappings: - schema:name slot_uri: schema:name alias: component_name owner: CellularComponent domain_of: - CellularComponent range: string cellularComponent__go_definition: name: cellularComponent__go_definition description: GO textual definition from_schema: https://cair2015.github.io/als-kg mappings: - IAO:0000115 slot_uri: IAO:0000115 alias: go_definition owner: CellularComponent domain_of: - CellularComponent range: string pathway__reactome_id: name: pathway__reactome_id from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:reactome_id identifier: true alias: reactome_id owner: Pathway domain_of: - Pathway range: ReactomeIdentifier required: true pathway__pathway_name: name: pathway__pathway_name description: Standard Reactome pathway name from_schema: https://cair2015.github.io/als-kg mappings: - schema:name slot_uri: schema:name alias: pathway_name owner: Pathway domain_of: - Pathway range: string pathway__pathway_definition: name: pathway__pathway_definition description: Reactome pathway description or summary when available from_schema: https://cair2015.github.io/als-kg mappings: - IAO:0000115 slot_uri: IAO:0000115 alias: pathway_definition owner: Pathway domain_of: - Pathway range: string pathway__species: name: pathway__species description: Species for the Reactome pathway; expected to be Homo sapiens for human ALS KG assertions from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:species alias: species owner: Pathway domain_of: - Pathway range: string pathway__parent_pathway: name: pathway__parent_pathway description: Parent Reactome pathway CURIE when available from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:parent_pathway alias: parent_pathway owner: Pathway domain_of: - Pathway range: ReactomeIdentifier multivalued: true diseaseSubtype__subtype_id: name: diseaseSubtype__subtype_id description: Custom subtype identifier from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:subtype_id alias: subtype_id owner: DiseaseSubtype domain_of: - DiseaseSubtype range: string diseaseSubtype__cluster_method: name: diseaseSubtype__cluster_method description: Clustering approach (NMF, WGCNA, scRNA-seq, consensus) from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:cluster_method alias: cluster_method owner: DiseaseSubtype domain_of: - DiseaseSubtype range: string diseaseSubtype__cluster_id: name: diseaseSubtype__cluster_id description: Cluster number from analysis from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:cluster_id alias: cluster_id owner: DiseaseSubtype domain_of: - DiseaseSubtype range: integer diseaseSubtype__signature_genes: name: diseaseSubtype__signature_genes description: Top discriminative genes for subtype from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:signature_genes alias: signature_genes owner: DiseaseSubtype domain_of: - DiseaseSubtype range: string multivalued: true diseaseSubtype__n_patients: name: diseaseSubtype__n_patients description: Number of patients in subtype from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:n_patients alias: n_patients owner: DiseaseSubtype domain_of: - DiseaseSubtype range: integer diseaseSubtype__cohort: name: diseaseSubtype__cohort description: Source patient cohort (AnswerALS, NYGC, PRO-ACT) from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:cohort alias: cohort owner: DiseaseSubtype domain_of: - DiseaseSubtype range: string diseaseSubtype__clinical_correlate: name: diseaseSubtype__clinical_correlate description: Associated clinical feature or phenotype from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:clinical_correlate alias: clinical_correlate owner: DiseaseSubtype domain_of: - DiseaseSubtype range: string diseaseSubtype__median_survival_months: name: diseaseSubtype__median_survival_months description: Median survival from symptom onset from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:median_survival_months alias: median_survival_months owner: DiseaseSubtype domain_of: - DiseaseSubtype range: float diseaseSubtype__source_publication: name: diseaseSubtype__source_publication description: DOI or PMID reference from_schema: https://cair2015.github.io/als-kg mappings: - dcterms:bibliographicCitation slot_uri: dcterms:bibliographicCitation alias: source_publication owner: DiseaseSubtype domain_of: - DiseaseSubtype range: string association__association_id: name: association__association_id description: Stable identifier for the association record from_schema: https://cair2015.github.io/als-kg mappings: - schema:identifier slot_uri: schema:identifier alias: association_id owner: Association domain_of: - Association range: uriorcurie association__association_label: name: association__association_label description: Human-readable summary of the association from_schema: https://cair2015.github.io/als-kg mappings: - rdfs:label slot_uri: rdfs:label alias: association_label owner: Association domain_of: - Association range: string association__subject: name: association__subject description: Subject entity IRI or CURIE used to materialize a direct edge from_schema: https://cair2015.github.io/als-kg mappings: - rdf:subject slot_uri: rdf:subject alias: subject owner: Association domain_of: - Association range: string required: true association__predicate: name: association__predicate description: Direct object property represented by this association from_schema: https://cair2015.github.io/als-kg mappings: - rdf:predicate slot_uri: rdf:predicate alias: predicate owner: Association domain_of: - Association range: string required: true association__object: name: association__object description: Object entity IRI or CURIE used to materialize a direct edge from_schema: https://cair2015.github.io/als-kg mappings: - rdf:object slot_uri: rdf:object alias: object owner: Association domain_of: - Association range: string required: true association__source: name: association__source description: Data source for this association from_schema: https://cair2015.github.io/als-kg mappings: - dcterms:source slot_uri: dcterms:source alias: source owner: Association domain_of: - Association range: string association__source_version: name: association__source_version description: Data source version or release date from_schema: https://cair2015.github.io/als-kg mappings: - dcterms:hasVersion slot_uri: dcterms:hasVersion alias: source_version owner: Association domain_of: - Association range: string association__evidence_type: name: association__evidence_type description: Type of supporting evidence from_schema: https://cair2015.github.io/als-kg mappings: - ECO:0000000 slot_uri: ECO:0000000 alias: evidence_type owner: Association domain_of: - Association range: string association__evidence_source: name: association__evidence_source description: Publication, study, database record, or extraction artifact supporting the association from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:evidence_source alias: evidence_source owner: Association domain_of: - Association range: string association__confidence: name: association__confidence description: Normalized confidence score from 0 to 1 from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:confidence alias: confidence owner: Association domain_of: - Association range: string association__ingest_date: name: association__ingest_date description: Date this association was ingested from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:ingest_date alias: ingest_date owner: Association domain_of: - Association range: string association__last_updated: name: association__last_updated description: Date this association was last modified from_schema: https://cair2015.github.io/als-kg mappings: - dcterms:modified slot_uri: dcterms:modified alias: last_updated owner: Association domain_of: - Association range: string diseasePhenotypeAssociation__has_disease: name: diseasePhenotypeAssociation__has_disease from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:has_disease alias: has_disease owner: DiseasePhenotypeAssociation domain_of: - DiseasePhenotypeAssociation range: Disease required: true diseasePhenotypeAssociation__has_phenotype: name: diseasePhenotypeAssociation__has_phenotype from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:has_phenotype alias: has_phenotype owner: DiseasePhenotypeAssociation domain_of: - DiseasePhenotypeAssociation range: Phenotype required: true diseasePhenotypeAssociation__predicate: name: diseasePhenotypeAssociation__predicate from_schema: https://cair2015.github.io/als-kg mappings: - rdf:predicate slot_uri: rdf:predicate ifabsent: alskb:disease_manifests_as_phenotype alias: predicate owner: DiseasePhenotypeAssociation domain_of: - DiseasePhenotypeAssociation range: string diseasePhenotypeAssociation__frequency: name: diseasePhenotypeAssociation__frequency description: Frequency in affected population or cohort from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:frequency alias: frequency owner: DiseasePhenotypeAssociation domain_of: - DiseasePhenotypeAssociation range: string diseasePhenotypeAssociation__severity: name: diseasePhenotypeAssociation__severity description: Typical severity or severity distribution from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:severity alias: severity owner: DiseasePhenotypeAssociation domain_of: - DiseasePhenotypeAssociation range: string diseasePhenotypeAssociation__onset_type: name: diseasePhenotypeAssociation__onset_type description: Onset pattern when phenotype is onset-specific from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:onset_type alias: onset_type owner: DiseasePhenotypeAssociation domain_of: - DiseasePhenotypeAssociation range: OnsetTypeEnum diseasePhenotypeAssociation__cohort: name: diseasePhenotypeAssociation__cohort description: Cohort or study population supporting this phenotype annotation from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:cohort alias: cohort owner: DiseasePhenotypeAssociation domain_of: - DiseasePhenotypeAssociation range: string geneDiseaseAssociation__has_gene: name: geneDiseaseAssociation__has_gene from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:has_gene alias: has_gene owner: GeneDiseaseAssociation domain_of: - GeneDiseaseAssociation range: Gene required: true geneDiseaseAssociation__has_disease: name: geneDiseaseAssociation__has_disease from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:has_disease alias: has_disease owner: GeneDiseaseAssociation domain_of: - GeneDiseaseAssociation range: Disease required: true geneDiseaseAssociation__predicate: name: geneDiseaseAssociation__predicate from_schema: https://cair2015.github.io/als-kg mappings: - rdf:predicate slot_uri: rdf:predicate ifabsent: alskb:gene_associated_with_disease alias: predicate owner: GeneDiseaseAssociation domain_of: - GeneDiseaseAssociation range: string geneDiseaseAssociation__association_type: name: geneDiseaseAssociation__association_type description: causal, risk_factor, protective, modifier, biomarker, or correlative from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:association_type alias: association_type owner: GeneDiseaseAssociation domain_of: - GeneDiseaseAssociation range: string geneDiseaseAssociation__association_score: name: geneDiseaseAssociation__association_score description: Source-specific gene-disease association score from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:association_score alias: association_score owner: GeneDiseaseAssociation domain_of: - GeneDiseaseAssociation range: float geneDiseaseAssociation__p_value: name: geneDiseaseAssociation__p_value description: Statistical significance when available from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:p_value alias: p_value owner: GeneDiseaseAssociation domain_of: - GeneDiseaseAssociation range: float geneDiseaseAssociation__odds_ratio: name: geneDiseaseAssociation__odds_ratio description: Genetic association odds ratio when available from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:odds_ratio alias: odds_ratio owner: GeneDiseaseAssociation domain_of: - GeneDiseaseAssociation range: float geneDiseaseAssociation__effect_direction: name: geneDiseaseAssociation__effect_direction description: increased_risk, decreased_risk, protective, upregulated, downregulated, or unknown from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:effect_direction alias: effect_direction owner: GeneDiseaseAssociation domain_of: - GeneDiseaseAssociation range: string geneDiseaseAssociation__evidence_count: name: geneDiseaseAssociation__evidence_count description: Number of supporting studies or records from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:evidence_count alias: evidence_count owner: GeneDiseaseAssociation domain_of: - GeneDiseaseAssociation range: integer variantDiseaseAssociation__has_variant: name: variantDiseaseAssociation__has_variant from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:has_variant alias: has_variant owner: VariantDiseaseAssociation domain_of: - VariantDiseaseAssociation range: Variant required: true variantDiseaseAssociation__has_disease: name: variantDiseaseAssociation__has_disease from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:has_disease alias: has_disease owner: VariantDiseaseAssociation domain_of: - VariantDiseaseAssociation range: Disease required: true variantDiseaseAssociation__predicate: name: variantDiseaseAssociation__predicate from_schema: https://cair2015.github.io/als-kg mappings: - rdf:predicate slot_uri: rdf:predicate ifabsent: alskb:variant_associated_with_disease alias: predicate owner: VariantDiseaseAssociation domain_of: - VariantDiseaseAssociation range: string variantDiseaseAssociation__clinical_significance: name: variantDiseaseAssociation__clinical_significance description: ClinVar/ACMG or ALS-specific clinical interpretation from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:clinical_significance alias: clinical_significance owner: VariantDiseaseAssociation domain_of: - VariantDiseaseAssociation range: string variantDiseaseAssociation__inheritance_mode: name: variantDiseaseAssociation__inheritance_mode description: autosomal_dominant, autosomal_recessive, X_linked, mitochondrial, complex, or unknown from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:inheritance_mode alias: inheritance_mode owner: VariantDiseaseAssociation domain_of: - VariantDiseaseAssociation range: string variantDiseaseAssociation__penetrance: name: variantDiseaseAssociation__penetrance description: Complete, reduced, age-dependent, or unknown penetrance from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:penetrance alias: penetrance owner: VariantDiseaseAssociation domain_of: - VariantDiseaseAssociation range: string variantDiseaseAssociation__association_type: name: variantDiseaseAssociation__association_type description: causal, risk_factor, modifier, protective, or uncertain from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:association_type alias: association_type owner: VariantDiseaseAssociation domain_of: - VariantDiseaseAssociation range: string variantProteinEffectAssociation__has_variant: name: variantProteinEffectAssociation__has_variant from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:has_variant alias: has_variant owner: VariantProteinEffectAssociation domain_of: - VariantProteinEffectAssociation range: Variant required: true variantProteinEffectAssociation__has_protein: name: variantProteinEffectAssociation__has_protein from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:has_protein alias: has_protein owner: VariantProteinEffectAssociation domain_of: - VariantProteinEffectAssociation range: Protein required: true variantProteinEffectAssociation__predicate: name: variantProteinEffectAssociation__predicate from_schema: https://cair2015.github.io/als-kg mappings: - rdf:predicate slot_uri: rdf:predicate ifabsent: alskb:variant_affects_protein alias: predicate owner: VariantProteinEffectAssociation domain_of: - VariantProteinEffectAssociation range: string variantProteinEffectAssociation__functional_consequence: name: variantProteinEffectAssociation__functional_consequence description: missense, frameshift, nonsense, splice_site, synonymous, repeat_expansion, or structural from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:functional_consequence alias: functional_consequence owner: VariantProteinEffectAssociation domain_of: - VariantProteinEffectAssociation range: string variantProteinEffectAssociation__predicted_effect: name: variantProteinEffectAssociation__predicted_effect description: loss_of_function, gain_of_function, dominant_negative, aggregation_prone, no_change, or unknown from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:predicted_effect alias: predicted_effect owner: VariantProteinEffectAssociation domain_of: - VariantProteinEffectAssociation range: string variantProteinEffectAssociation__assay: name: variantProteinEffectAssociation__assay description: Functional assay or computational method supporting the effect from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:assay alias: assay owner: VariantProteinEffectAssociation domain_of: - VariantProteinEffectAssociation range: string proteinProteinInteractionAssociation__protein_1: name: proteinProteinInteractionAssociation__protein_1 from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:protein_1 alias: protein_1 owner: ProteinProteinInteractionAssociation domain_of: - ProteinProteinInteractionAssociation range: Protein required: true proteinProteinInteractionAssociation__protein_2: name: proteinProteinInteractionAssociation__protein_2 from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:protein_2 alias: protein_2 owner: ProteinProteinInteractionAssociation domain_of: - ProteinProteinInteractionAssociation range: Protein required: true proteinProteinInteractionAssociation__predicate: name: proteinProteinInteractionAssociation__predicate from_schema: https://cair2015.github.io/als-kg mappings: - rdf:predicate slot_uri: rdf:predicate ifabsent: alskb:protein_interacts_with_protein alias: predicate owner: ProteinProteinInteractionAssociation domain_of: - ProteinProteinInteractionAssociation range: string proteinProteinInteractionAssociation__interaction_score: name: proteinProteinInteractionAssociation__interaction_score description: Source-specific confidence score such as STRING combined score from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:interaction_score alias: interaction_score owner: ProteinProteinInteractionAssociation domain_of: - ProteinProteinInteractionAssociation range: float proteinProteinInteractionAssociation__interaction_type: name: proteinProteinInteractionAssociation__interaction_type description: direct, indirect, physical, genetic, colocalization, pathway, or predicted from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:interaction_type alias: interaction_type owner: ProteinProteinInteractionAssociation domain_of: - ProteinProteinInteractionAssociation range: string proteinProteinInteractionAssociation__assay: name: proteinProteinInteractionAssociation__assay description: Assay or method supporting the interaction from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:assay alias: assay owner: ProteinProteinInteractionAssociation domain_of: - ProteinProteinInteractionAssociation range: string proteinPathwayAssociation__has_protein: name: proteinPathwayAssociation__has_protein from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:has_protein alias: has_protein owner: ProteinPathwayAssociation domain_of: - ProteinPathwayAssociation range: Protein required: true proteinPathwayAssociation__has_pathway: name: proteinPathwayAssociation__has_pathway from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:has_pathway alias: has_pathway owner: ProteinPathwayAssociation domain_of: - ProteinPathwayAssociation range: Pathway required: true proteinPathwayAssociation__predicate: name: proteinPathwayAssociation__predicate from_schema: https://cair2015.github.io/als-kg mappings: - rdf:predicate slot_uri: rdf:predicate ifabsent: alskb:protein_participates_in_pathway alias: predicate owner: ProteinPathwayAssociation domain_of: - ProteinPathwayAssociation range: string proteinPathwayAssociation__reactome_evidence_code: name: proteinPathwayAssociation__reactome_evidence_code description: Reactome evidence code or inferred/electronic/manual annotation category when available from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:reactome_evidence_code alias: reactome_evidence_code owner: ProteinPathwayAssociation domain_of: - ProteinPathwayAssociation range: string proteinPathwayAssociation__pathway_role: name: proteinPathwayAssociation__pathway_role description: participant, catalyst, regulator, input, output, or member, when this detail is available from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:pathway_role alias: pathway_role owner: ProteinPathwayAssociation domain_of: - ProteinPathwayAssociation range: string proteinPathwayAssociation__species: name: proteinPathwayAssociation__species description: Species context for the Reactome protein-pathway annotation from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:species alias: species owner: ProteinPathwayAssociation domain_of: - ProteinPathwayAssociation range: string drugTargetAssociation__has_drug: name: drugTargetAssociation__has_drug from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:has_drug alias: has_drug owner: DrugTargetAssociation domain_of: - DrugTargetAssociation range: Drug required: true drugTargetAssociation__target: name: drugTargetAssociation__target description: Gene or protein target from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:target alias: target owner: DrugTargetAssociation domain_of: - DrugTargetAssociation range: MolecularEntity required: true inlined: true inlined_as_list: true drugTargetAssociation__predicate: name: drugTargetAssociation__predicate from_schema: https://cair2015.github.io/als-kg mappings: - rdf:predicate slot_uri: rdf:predicate ifabsent: alskb:drug_targets_molecular_entity alias: predicate owner: DrugTargetAssociation domain_of: - DrugTargetAssociation range: string drugTargetAssociation__action_type: name: drugTargetAssociation__action_type description: inhibitor, activator, binder, antagonist, agonist, modulator, ASO_knockdown, or unknown from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:action_type alias: action_type owner: DrugTargetAssociation domain_of: - DrugTargetAssociation range: string drugTargetAssociation__binding_affinity_nm: name: drugTargetAssociation__binding_affinity_nm description: Binding affinity in nanomolar when available from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:binding_affinity_nm alias: binding_affinity_nm owner: DrugTargetAssociation domain_of: - DrugTargetAssociation range: float drugTargetAssociation__mechanism: name: drugTargetAssociation__mechanism description: Mechanistic description of target modulation from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:mechanism alias: mechanism owner: DrugTargetAssociation domain_of: - DrugTargetAssociation range: string drugDiseaseTherapeuticAssociation__has_drug: name: drugDiseaseTherapeuticAssociation__has_drug from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:has_drug alias: has_drug owner: DrugDiseaseTherapeuticAssociation domain_of: - DrugDiseaseTherapeuticAssociation range: Drug required: true drugDiseaseTherapeuticAssociation__has_disease: name: drugDiseaseTherapeuticAssociation__has_disease from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:has_disease alias: has_disease owner: DrugDiseaseTherapeuticAssociation domain_of: - DrugDiseaseTherapeuticAssociation range: Disease required: true drugDiseaseTherapeuticAssociation__predicate: name: drugDiseaseTherapeuticAssociation__predicate from_schema: https://cair2015.github.io/als-kg mappings: - rdf:predicate slot_uri: rdf:predicate ifabsent: alskb:drug_treats_or_modulates_disease alias: predicate owner: DrugDiseaseTherapeuticAssociation domain_of: - DrugDiseaseTherapeuticAssociation range: string drugDiseaseTherapeuticAssociation__relation_type: name: drugDiseaseTherapeuticAssociation__relation_type description: treats, disease_modifying, symptomatic, palliative, contraindicated, off_label, or investigational from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:relation_type alias: relation_type owner: DrugDiseaseTherapeuticAssociation domain_of: - DrugDiseaseTherapeuticAssociation range: string drugDiseaseTherapeuticAssociation__approval_status: name: drugDiseaseTherapeuticAssociation__approval_status description: approved, investigational, withdrawn, off_label, failed_trial, or unknown from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:approval_status alias: approval_status owner: DrugDiseaseTherapeuticAssociation domain_of: - DrugDiseaseTherapeuticAssociation range: string drugDiseaseTherapeuticAssociation__clinical_phase: name: drugDiseaseTherapeuticAssociation__clinical_phase description: Highest clinical development phase for ALS or ALS subtype from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:clinical_phase alias: clinical_phase owner: DrugDiseaseTherapeuticAssociation domain_of: - DrugDiseaseTherapeuticAssociation range: string drugDiseaseTherapeuticAssociation__outcome_measure: name: drugDiseaseTherapeuticAssociation__outcome_measure description: ALSFRS-R, survival, respiratory function, biomarker, or other endpoint from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:outcome_measure alias: outcome_measure owner: DrugDiseaseTherapeuticAssociation domain_of: - DrugDiseaseTherapeuticAssociation range: string exposureDiseaseAssociation__exposure: name: exposureDiseaseAssociation__exposure from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:exposure alias: exposure owner: ExposureDiseaseAssociation domain_of: - ExposureDiseaseAssociation range: ExposureOrStressor required: true exposureDiseaseAssociation__has_disease: name: exposureDiseaseAssociation__has_disease from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:has_disease alias: has_disease owner: ExposureDiseaseAssociation domain_of: - ExposureDiseaseAssociation range: Disease required: true exposureDiseaseAssociation__predicate: name: exposureDiseaseAssociation__predicate from_schema: https://cair2015.github.io/als-kg mappings: - rdf:predicate slot_uri: rdf:predicate ifabsent: alskb:exposure_associated_with_disease alias: predicate owner: ExposureDiseaseAssociation domain_of: - ExposureDiseaseAssociation range: string exposureDiseaseAssociation__association_type: name: exposureDiseaseAssociation__association_type description: risk_factor, protective, trigger, modifier, or correlative from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:association_type alias: association_type owner: ExposureDiseaseAssociation domain_of: - ExposureDiseaseAssociation range: string exposureDiseaseAssociation__mechanism: name: exposureDiseaseAssociation__mechanism description: Proposed biological mechanism from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:mechanism alias: mechanism owner: ExposureDiseaseAssociation domain_of: - ExposureDiseaseAssociation range: string exposureDiseaseAssociation__epidemiological_support: name: exposureDiseaseAssociation__epidemiological_support from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:epidemiological_support alias: epidemiological_support owner: ExposureDiseaseAssociation domain_of: - ExposureDiseaseAssociation range: boolean exposureDiseaseAssociation__odds_ratio: name: exposureDiseaseAssociation__odds_ratio description: Epidemiological odds ratio or equivalent effect estimate from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:odds_ratio alias: odds_ratio owner: ExposureDiseaseAssociation domain_of: - ExposureDiseaseAssociation range: float exposureDiseaseAssociation__population: name: exposureDiseaseAssociation__population description: Population, geography, occupation, or cohort context from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:population alias: population owner: ExposureDiseaseAssociation domain_of: - ExposureDiseaseAssociation range: string transcriptionFactorRegulationAssociation__transcription_factor: name: transcriptionFactorRegulationAssociation__transcription_factor from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:transcription_factor alias: transcription_factor owner: TranscriptionFactorRegulationAssociation domain_of: - TranscriptionFactorRegulationAssociation range: TranscriptionFactor required: true transcriptionFactorRegulationAssociation__target_gene: name: transcriptionFactorRegulationAssociation__target_gene from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:target_gene alias: target_gene owner: TranscriptionFactorRegulationAssociation domain_of: - TranscriptionFactorRegulationAssociation range: Gene required: true transcriptionFactorRegulationAssociation__predicate: name: transcriptionFactorRegulationAssociation__predicate from_schema: https://cair2015.github.io/als-kg mappings: - rdf:predicate slot_uri: rdf:predicate ifabsent: alskb:transcription_factor_regulates_gene alias: predicate owner: TranscriptionFactorRegulationAssociation domain_of: - TranscriptionFactorRegulationAssociation range: string transcriptionFactorRegulationAssociation__regulation_type: name: transcriptionFactorRegulationAssociation__regulation_type description: activation, repression, bidirectional, context_dependent, or unknown from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:regulation_type alias: regulation_type owner: TranscriptionFactorRegulationAssociation domain_of: - TranscriptionFactorRegulationAssociation range: string transcriptionFactorRegulationAssociation__confidence_level: name: transcriptionFactorRegulationAssociation__confidence_level description: Source-specific confidence level such as DoRothEA A-D from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:confidence_level alias: confidence_level owner: TranscriptionFactorRegulationAssociation domain_of: - TranscriptionFactorRegulationAssociation range: string transcriptionFactorRegulationAssociation__tissue_or_cell_type: name: transcriptionFactorRegulationAssociation__tissue_or_cell_type description: Tissue or cell type context for the regulatory relationship from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:tissue_or_cell_type alias: tissue_or_cell_type owner: TranscriptionFactorRegulationAssociation domain_of: - TranscriptionFactorRegulationAssociation range: string geneExpressionAssociation__has_gene: name: geneExpressionAssociation__has_gene from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:has_gene alias: has_gene owner: GeneExpressionAssociation domain_of: - GeneExpressionAssociation range: Gene required: true geneExpressionAssociation__has_anatomy: name: geneExpressionAssociation__has_anatomy from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:has_anatomy alias: has_anatomy owner: GeneExpressionAssociation domain_of: - GeneExpressionAssociation range: Anatomy required: true geneExpressionAssociation__predicate: name: geneExpressionAssociation__predicate from_schema: https://cair2015.github.io/als-kg mappings: - rdf:predicate slot_uri: rdf:predicate ifabsent: alskb:gene_expressed_in_anatomy alias: predicate owner: GeneExpressionAssociation domain_of: - GeneExpressionAssociation range: string geneExpressionAssociation__expression_level: name: geneExpressionAssociation__expression_level description: high, medium, low, absent, upregulated, downregulated, or not_detected from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:expression_level alias: expression_level owner: GeneExpressionAssociation domain_of: - GeneExpressionAssociation range: string geneExpressionAssociation__specificity_index: name: geneExpressionAssociation__specificity_index description: Tissue-specificity score from 0 to 1 from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:specificity_index alias: specificity_index owner: GeneExpressionAssociation domain_of: - GeneExpressionAssociation range: float geneExpressionAssociation__log2_fold_change: name: geneExpressionAssociation__log2_fold_change description: Differential expression log2 fold change when available from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:log2_fold_change alias: log2_fold_change owner: GeneExpressionAssociation domain_of: - GeneExpressionAssociation range: float geneExpressionAssociation__adjusted_p_value: name: geneExpressionAssociation__adjusted_p_value description: Multiple-testing-adjusted p-value when available from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:adjusted_p_value alias: adjusted_p_value owner: GeneExpressionAssociation domain_of: - GeneExpressionAssociation range: float geneExpressionAssociation__tissue_or_cell_type: name: geneExpressionAssociation__tissue_or_cell_type description: Tissue or cell-type context from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:tissue_or_cell_type alias: tissue_or_cell_type owner: GeneExpressionAssociation domain_of: - GeneExpressionAssociation range: string geneExpressionAssociation__disease_stage: name: geneExpressionAssociation__disease_stage description: Disease stage or clinical context from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:disease_stage alias: disease_stage owner: GeneExpressionAssociation domain_of: - GeneExpressionAssociation range: string diseaseDiseaseAssociation__disease_1: name: diseaseDiseaseAssociation__disease_1 from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:disease_1 alias: disease_1 owner: DiseaseDiseaseAssociation domain_of: - DiseaseDiseaseAssociation range: Disease required: true diseaseDiseaseAssociation__disease_2: name: diseaseDiseaseAssociation__disease_2 from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:disease_2 alias: disease_2 owner: DiseaseDiseaseAssociation domain_of: - DiseaseDiseaseAssociation range: Disease required: true diseaseDiseaseAssociation__predicate: name: diseaseDiseaseAssociation__predicate from_schema: https://cair2015.github.io/als-kg mappings: - rdf:predicate slot_uri: rdf:predicate ifabsent: alskb:disease_related_to_disease alias: predicate owner: DiseaseDiseaseAssociation domain_of: - DiseaseDiseaseAssociation range: string diseaseDiseaseAssociation__relation_type: name: diseaseDiseaseAssociation__relation_type description: comorbidity, shared_pathway, shared_gene, phenotypic_similarity, differential_diagnosis, or disease_subtype from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:relation_type alias: relation_type owner: DiseaseDiseaseAssociation domain_of: - DiseaseDiseaseAssociation range: string diseaseDiseaseAssociation__similarity_score: name: diseaseDiseaseAssociation__similarity_score description: Semantic similarity or clinical overlap score from 0 to 1 from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:similarity_score alias: similarity_score owner: DiseaseDiseaseAssociation domain_of: - DiseaseDiseaseAssociation range: float diseaseDiseaseAssociation__shared_mechanism: name: diseaseDiseaseAssociation__shared_mechanism description: Shared biological mechanism, pathway, or clinical rationale from_schema: https://cair2015.github.io/als-kg slot_uri: alskb:shared_mechanism alias: shared_mechanism owner: DiseaseDiseaseAssociation domain_of: - DiseaseDiseaseAssociation range: string classes: NamedEntity: name: NamedEntity definition_uri: https://cair2015.github.io/als-kg/elements/NamedEntity description: Root class for all named entities in the ALS-KG ontology. Provides core ontology metadata (id, label, definition, synonyms, xrefs). from_schema: https://cair2015.github.io/als-kg mappings: - biolink:NamedThing abstract: true slots: - namedEntity__id - namedEntity__label - namedEntity__definition - namedEntity__synonym - namedEntity__xref - namedEntity__comment - namedEntity__is_obsolete - namedEntity__source - namedEntity__last_updated attributes: id: name: id description: Persistent unique identifier (IRI) slot_uri: schema:identifier required: true label: name: label description: Preferred human-readable label slot_uri: rdfs:label required: true definition: name: definition description: Formal textual definition slot_uri: IAO:0000115 synonym: name: synonym description: Alternative names slot_uri: oboInOwl:hasRelatedSynonym xref: name: xref description: Cross-references to external ontologies slot_uri: oboInOwl:hasDbXref comment: name: comment description: Informal notes or comments slot_uri: rdfs:comment is_obsolete: name: is_obsolete description: Deprecation flag slot_uri: owl:deprecated ifabsent: 'false' source: name: source description: Original source/database slot_uri: dcterms:source last_updated: name: last_updated description: Last modification timestamp slot_uri: dcterms:modified class_uri: biolink:NamedThing OntologyClass: name: OntologyClass definition_uri: https://cair2015.github.io/als-kg/elements/OntologyClass description: Abstract base for entity classes (nodes in knowledge graph). Inherits from NamedEntity with semantic web compatible metadata. from_schema: https://cair2015.github.io/als-kg mappings: - owl:Class is_a: NamedEntity abstract: true slots: - namedEntity__id - namedEntity__label - namedEntity__definition - namedEntity__synonym - namedEntity__xref - namedEntity__comment - namedEntity__is_obsolete - namedEntity__source - namedEntity__last_updated - ontologyClass__source_version - ontologyClass__ingest_date attributes: source_version: name: source_version description: Source database/ontology version slot_uri: dcterms:hasVersion ingest_date: name: ingest_date description: When entity was imported into ALS-KG class_uri: owl:Class Relationship: name: Relationship definition_uri: https://cair2015.github.io/als-kg/elements/Relationship description: 'Abstract base for reified relationships (edges with explicit properties). Follows RDF triple pattern: subject, predicate, object. Can carry additional metadata (confidence, evidence, provenance).' from_schema: https://cair2015.github.io/als-kg mappings: - rdf:Statement abstract: true slots: - relationship__subject - relationship__predicate - relationship__object - relationship__source - relationship__confidence - relationship__evidence_type - relationship__evidence_source - relationship__ingest_date attributes: subject: name: subject description: Subject resource IRI slot_uri: rdf:subject required: true predicate: name: predicate description: Relationship type IRI slot_uri: rdf:predicate required: true object: name: object description: Object resource IRI slot_uri: rdf:object required: true source: name: source description: Data source for this relationship slot_uri: dcterms:source confidence: name: confidence description: Confidence score (0-1) evidence_type: name: evidence_type description: Type of evidence supporting relationship slot_uri: ECO:0000000 evidence_source: name: evidence_source description: Citation or study ID ingest_date: name: ingest_date description: Ingest date class_uri: rdf:Statement DiseaseOrPhenotype: name: DiseaseOrPhenotype definition_uri: https://cair2015.github.io/als-kg/elements/DiseaseOrPhenotype description: Abstract parent class for all disease/phenotype entities. Following MONDO and HPO ontology patterns. from_schema: https://cair2015.github.io/als-kg mappings: - biolink:DiseaseOrPhenotypicFeature is_a: OntologyClass abstract: true slots: - namedEntity__id - namedEntity__label - namedEntity__definition - namedEntity__synonym - namedEntity__xref - namedEntity__comment - namedEntity__is_obsolete - namedEntity__source - namedEntity__last_updated - ontologyClass__source_version - ontologyClass__ingest_date - diseaseOrPhenotype__mondo_id - diseaseOrPhenotype__hpo_id attributes: mondo_id: name: mondo_id description: MONDO cross-reference range: MondoIdentifier hpo_id: name: hpo_id description: HPO cross-reference range: HpoIdentifier class_uri: biolink:DiseaseOrPhenotypicFeature Disease: name: Disease definition_uri: https://cair2015.github.io/als-kg/elements/Disease description: Disease entity. Encompasses ALS (MONDO:0007743), related neurodegenerative disorders (FTD, PLS, PMA, SMA), and comorbidities. Follows MONDO disease hierarchy via is_a relationships. from_schema: https://cair2015.github.io/als-kg mappings: - biolink:Disease is_a: DiseaseOrPhenotype slots: - namedEntity__id - namedEntity__label - namedEntity__definition - namedEntity__synonym - namedEntity__xref - namedEntity__comment - namedEntity__is_obsolete - namedEntity__source - namedEntity__last_updated - ontologyClass__source_version - ontologyClass__ingest_date - diseaseOrPhenotype__hpo_id - disease__mondo_id - disease__name - disease__disease_type - disease__onset_type - disease__umls_cui - disease__omim_id - disease__orphanet_id - disease__icd10_code attributes: mondo_id: name: mondo_id identifier: true range: MondoIdentifier required: true name: name: name description: Disease name (preferred from MONDO) slot_uri: schema:name disease_type: name: disease_type range: DiseaseTypeEnum onset_type: name: onset_type range: OnsetTypeEnum umls_cui: name: umls_cui description: UMLS Concept Unique Identifier omim_id: name: omim_id description: OMIM (Online Mendelian Inheritance in Man) ID orphanet_id: name: orphanet_id description: Orphanet rare disease identifier icd10_code: name: icd10_code description: ICD-10-CM code for billing/clinical use class_uri: biolink:Disease Phenotype: name: Phenotype definition_uri: https://cair2015.github.io/als-kg/elements/Phenotype description: Phenotypic feature (HPO term). Represents observable/measurable characteristics associated with diseases. Distinct from drug side effects which are modeled via DrugCausesPhenotype relationships. from_schema: https://cair2015.github.io/als-kg mappings: - biolink:PhenotypicFeature is_a: DiseaseOrPhenotype slots: - namedEntity__id - namedEntity__label - namedEntity__definition - namedEntity__synonym - namedEntity__xref - namedEntity__comment - namedEntity__is_obsolete - namedEntity__source - namedEntity__last_updated - ontologyClass__source_version - ontologyClass__ingest_date - diseaseOrPhenotype__mondo_id - phenotype__hpo_id - phenotype__frequency - phenotype__severity attributes: hpo_id: name: hpo_id identifier: true range: HpoIdentifier required: true frequency: name: frequency description: Frequency of phenotype in affected individuals (e.g. Frequent 75-99%) range: string severity: name: severity description: Severity scale range: string class_uri: biolink:PhenotypicFeature Anatomy: name: Anatomy definition_uri: https://cair2015.github.io/als-kg/elements/Anatomy description: 'Anatomical structure (UBERON ontology). ALS-specific relevance: motor cortex, spinal cord, anterior horn cells, neuromuscular junction. Linked to gene expression and disease manifestation.' from_schema: https://cair2015.github.io/als-kg mappings: - biolink:AnatomicalEntity is_a: OntologyClass slots: - namedEntity__id - namedEntity__label - namedEntity__definition - namedEntity__synonym - namedEntity__xref - namedEntity__comment - namedEntity__is_obsolete - namedEntity__source - namedEntity__last_updated - ontologyClass__source_version - ontologyClass__ingest_date - anatomy__uberon_id - anatomy__bto_id - anatomy__mesh_id - anatomy__anatomical_system attributes: uberon_id: name: uberon_id identifier: true range: UberonIdentifier required: true bto_id: name: bto_id description: Brenda Tissue Ontology ID mesh_id: name: mesh_id description: MeSH cross-reference anatomical_system: name: anatomical_system description: Anatomical system classification class_uri: biolink:AnatomicalEntity MolecularEntity: name: MolecularEntity definition_uri: https://cair2015.github.io/als-kg/elements/MolecularEntity description: Abstract base for molecular-level entities (genes, proteins, variants). Directly related to disease mechanisms via molecular interactions. from_schema: https://cair2015.github.io/als-kg mappings: - biolink:MolecularEntity is_a: OntologyClass abstract: true slots: - namedEntity__id - namedEntity__label - namedEntity__definition - namedEntity__synonym - namedEntity__xref - namedEntity__comment - namedEntity__is_obsolete - namedEntity__source - namedEntity__last_updated - ontologyClass__source_version - ontologyClass__ingest_date class_uri: biolink:MolecularEntity Gene: name: Gene definition_uri: https://cair2015.github.io/als-kg/elements/Gene description: 'Human gene entity (Entrez/NCBI model). Separate from protein product to properly distinguish genotype from phenotype. Key ALS genes: C9orf72, SOD1, TARDBP, FUS, TBK1, NEK1, SQSTM1, VCP, OPTN.' from_schema: https://cair2015.github.io/als-kg mappings: - biolink:Gene is_a: MolecularEntity slots: - namedEntity__id - namedEntity__label - namedEntity__definition - namedEntity__synonym - namedEntity__xref - namedEntity__comment - namedEntity__is_obsolete - namedEntity__source - namedEntity__last_updated - ontologyClass__source_version - ontologyClass__ingest_date - gene__ncbi_gene_id - gene__hgnc_symbol - gene__ensembl_id - gene__chromosome - gene__genomic_pos_start - gene__genomic_pos_end - gene__als_risk_tier attributes: ncbi_gene_id: name: ncbi_gene_id identifier: true range: NcbiGeneIdentifier required: true hgnc_symbol: name: hgnc_symbol description: Official HGNC gene symbol ensembl_id: name: ensembl_id description: Ensembl gene identifier chromosome: name: chromosome description: Cytogenetic location (e.g. 21q22.11 for SOD1) genomic_pos_start: name: genomic_pos_start description: GRCh38 start coordinate (1-based) range: integer genomic_pos_end: name: genomic_pos_end description: GRCh38 end coordinate range: integer als_risk_tier: name: als_risk_tier description: Evidence tier for ALS association (ALSoD classification) - definitive, strong, moderate, or candidate range: string class_uri: biolink:Gene TranscriptionFactor: name: TranscriptionFactor definition_uri: https://cair2015.github.io/als-kg/elements/TranscriptionFactor description: 'Gene encoding a transcription factor (TF). Subclass of Gene, carries both :Gene and :TranscriptionFactor labels. Source: DoRothEA + ENCODE TF annotations.' from_schema: https://cair2015.github.io/als-kg is_a: Gene slots: - namedEntity__id - namedEntity__label - namedEntity__definition - namedEntity__synonym - namedEntity__xref - namedEntity__comment - namedEntity__is_obsolete - namedEntity__source - namedEntity__last_updated - ontologyClass__source_version - ontologyClass__ingest_date - gene__ncbi_gene_id - gene__hgnc_symbol - gene__ensembl_id - gene__chromosome - gene__genomic_pos_start - gene__genomic_pos_end - gene__als_risk_tier - transcriptionFactor__tf_family - transcriptionFactor__dorothea_confidence attributes: tf_family: name: tf_family description: Structural family (C2H2-ZF, bHLH, Homeodomain, etc.) dorothea_confidence: name: dorothea_confidence description: DoRothEA confidence level (A=high, D=low) class_uri: alskb:TranscriptionFactor Protein: name: Protein definition_uri: https://cair2015.github.io/als-kg/elements/Protein description: 'Protein product (UniProt model). Distinct from Gene entity to capture protein-specific properties: aggregation propensity, prion-like domains, subcellular localization.' from_schema: https://cair2015.github.io/als-kg mappings: - biolink:Protein is_a: MolecularEntity slots: - namedEntity__id - namedEntity__label - namedEntity__definition - namedEntity__synonym - namedEntity__xref - namedEntity__comment - namedEntity__is_obsolete - namedEntity__source - namedEntity__last_updated - ontologyClass__source_version - ontologyClass__ingest_date - protein__uniprot_id - protein__protein_name - protein__hgnc_symbol - protein__molecular_weight_kda - protein__protein_family - protein__subcellular_location - protein__aggregation_prone - protein__has_prion_like_domain attributes: uniprot_id: name: uniprot_id slot_uri: 'UniProtKB:' identifier: true range: UniprotIdentifier required: true protein_name: name: protein_name description: Protein name (UniProt recommended name) slot_uri: schema:name hgnc_symbol: name: hgnc_symbol description: Gene name (cross-reference to Gene entity) molecular_weight_kda: name: molecular_weight_kda description: Molecular weight in kDa range: float protein_family: name: protein_family description: Protein family classification (Pfam) subcellular_location: name: subcellular_location description: Cellular compartment(s) where protein is localized (e.g. mitochondrion, nucleus, axon) multivalued: true aggregation_prone: name: aggregation_prone description: Known to form aggregates (TDP-43, SOD1, FUS) range: boolean has_prion_like_domain: name: has_prion_like_domain description: Contains intrinsically disordered prion-like region range: boolean class_uri: biolink:Protein Variant: name: Variant definition_uri: https://cair2015.github.io/als-kg/elements/Variant description: Genetic sequence variant (ClinVar model). Includes SNVs, indels, repeat expansions (C9orf72), and structural variants. Links to genes, proteins, and disease associations. from_schema: https://cair2015.github.io/als-kg mappings: - biolink:SequenceVariant is_a: MolecularEntity slots: - namedEntity__id - namedEntity__label - namedEntity__definition - namedEntity__synonym - namedEntity__xref - namedEntity__comment - namedEntity__is_obsolete - namedEntity__source - namedEntity__last_updated - ontologyClass__source_version - ontologyClass__ingest_date - variant__clinvar_id - variant__rsid - variant__hgvs_c - variant__hgvs_p - variant__variant_type - variant__clinical_significance - variant__als_class - variant__maf attributes: clinvar_id: name: clinvar_id identifier: true range: ClinvarIdentifier required: true rsid: name: rsid description: dbSNP reference SNP ID hgvs_c: name: hgvs_c description: HGVS coding sequence notation (e.g. c.10A>G) hgvs_p: name: hgvs_p description: HGVS protein notation (e.g. p.Ala4Val) variant_type: name: variant_type range: VariantTypeEnum clinical_significance: name: clinical_significance description: ClinVar clinical interpretation als_class: name: als_class description: ALS-specific classification (causal, risk, modifier, protective) maf: name: maf description: Minor allele frequency in gnomAD non-neuro cohort range: float minimum_value: 0.0 maximum_value: 1.0 class_uri: biolink:SequenceVariant ChemicalEntity: name: ChemicalEntity definition_uri: https://cair2015.github.io/als-kg/elements/ChemicalEntity description: Abstract base for chemical and pharmacological entities (drugs, exposures, metabolites). from_schema: https://cair2015.github.io/als-kg mappings: - biolink:ChemicalEntity is_a: OntologyClass abstract: true slots: - namedEntity__id - namedEntity__label - namedEntity__definition - namedEntity__synonym - namedEntity__xref - namedEntity__comment - namedEntity__is_obsolete - namedEntity__source - namedEntity__last_updated - ontologyClass__source_version - ontologyClass__ingest_date class_uri: biolink:ChemicalEntity Drug: name: Drug definition_uri: https://cair2015.github.io/als-kg/elements/Drug description: 'Pharmaceutical compound (DrugBank model). ALS-approved drugs: Riluzole, Edaravone, Tofersen, AMX0035. Includes mechanism, targets, side effects.' from_schema: https://cair2015.github.io/als-kg mappings: - biolink:Drug is_a: ChemicalEntity slots: - namedEntity__id - namedEntity__label - namedEntity__definition - namedEntity__synonym - namedEntity__xref - namedEntity__comment - namedEntity__is_obsolete - namedEntity__source - namedEntity__last_updated - ontologyClass__source_version - ontologyClass__ingest_date - drug__drugbank_id - drug__drug_name - drug__chembl_id - drug__inchi_key - drug__smiles - drug__drug_type - drug__als_approved - drug__trial_status - drug__mechanism - drug__indication attributes: drugbank_id: name: drugbank_id identifier: true range: DrugBankIdentifier required: true drug_name: name: drug_name description: Preferred drug name slot_uri: schema:name chembl_id: name: chembl_id description: ChEMBL compound ID inchi_key: name: inchi_key description: Standard InChIKey hash smiles: name: smiles description: Canonical SMILES string drug_type: name: drug_type description: Categorization (small molecule, biologic, ASO, cell therapy, gene therapy) als_approved: name: als_approved description: FDA approval status for ALS treatment range: boolean trial_status: name: trial_status description: Highest clinical trial phase reached mechanism: name: mechanism description: Known mechanism of action indication: name: indication description: Clinical indication class_uri: biolink:Drug ExposureOrStressor: name: ExposureOrStressor definition_uri: https://cair2015.github.io/als-kg/elements/ExposureOrStressor description: 'Environmental exposure or chemical stressor from CTD ontology. ALS-relevant: BMAA, organophosphate pesticides, heavy metals, solvents.' from_schema: https://cair2015.github.io/als-kg mappings: - biolink:ChemicalSubstance is_a: ChemicalEntity slots: - namedEntity__id - namedEntity__label - namedEntity__definition - namedEntity__synonym - namedEntity__xref - namedEntity__comment - namedEntity__is_obsolete - namedEntity__source - namedEntity__last_updated - ontologyClass__source_version - ontologyClass__ingest_date - exposureOrStressor__ctd_id - exposureOrStressor__exposure_name - exposureOrStressor__exposure_type - exposureOrStressor__mesh_id - exposureOrStressor__cas_number - exposureOrStressor__als_relevance attributes: ctd_id: name: ctd_id identifier: true range: CtdIdentifier required: true exposure_name: name: exposure_name description: Standard name of exposure/stressor slot_uri: schema:name exposure_type: name: exposure_type description: Category (chemical, metal, pesticide, radiation, biological, other) mesh_id: name: mesh_id description: MeSH ID for exposure agent cas_number: name: cas_number description: CAS Registry number als_relevance: name: als_relevance description: Flagged as ALS-relevant in literature range: boolean class_uri: biolink:ChemicalSubstance BiologicalConcept: name: BiologicalConcept definition_uri: https://cair2015.github.io/als-kg/elements/BiologicalConcept description: Abstract base for functional/biological concepts from GO and related ontologies. Represents processes, functions, and compartments involved in ALS pathology. from_schema: https://cair2015.github.io/als-kg is_a: OntologyClass abstract: true slots: - namedEntity__id - namedEntity__label - namedEntity__definition - namedEntity__synonym - namedEntity__xref - namedEntity__comment - namedEntity__is_obsolete - namedEntity__source - namedEntity__last_updated - ontologyClass__source_version - ontologyClass__ingest_date class_uri: alskb:BiologicalConcept BiologicalProcess: name: BiologicalProcess definition_uri: https://cair2015.github.io/als-kg/elements/BiologicalProcess description: 'Gene Ontology Biological Process term. ALS-relevant: protein aggregation, oxidative stress, neuroinflammation, axonal transport, neurodegeneration, apoptosis.' from_schema: https://cair2015.github.io/als-kg mappings: - biolink:BiologicalProcess is_a: BiologicalConcept slots: - namedEntity__id - namedEntity__label - namedEntity__definition - namedEntity__synonym - namedEntity__xref - namedEntity__comment - namedEntity__is_obsolete - namedEntity__source - namedEntity__last_updated - ontologyClass__source_version - ontologyClass__ingest_date - biologicalProcess__go_id - biologicalProcess__process_name - biologicalProcess__go_definition attributes: go_id: name: go_id identifier: true range: GoIdentifier required: true process_name: name: process_name description: Standard process name from GO slot_uri: schema:name go_definition: name: go_definition description: GO textual definition slot_uri: IAO:0000115 class_uri: biolink:BiologicalProcess MolecularFunction: name: MolecularFunction definition_uri: https://cair2015.github.io/als-kg/elements/MolecularFunction description: Gene Ontology Molecular Function term. Describes biochemical activities (catalytic, binding, etc.) performed by gene products. from_schema: https://cair2015.github.io/als-kg mappings: - biolink:MolecularActivity is_a: BiologicalConcept slots: - namedEntity__id - namedEntity__label - namedEntity__definition - namedEntity__synonym - namedEntity__xref - namedEntity__comment - namedEntity__is_obsolete - namedEntity__source - namedEntity__last_updated - ontologyClass__source_version - ontologyClass__ingest_date - molecularFunction__go_id - molecularFunction__function_name - molecularFunction__go_definition attributes: go_id: name: go_id identifier: true range: GoIdentifier required: true function_name: name: function_name description: Molecular function name from GO slot_uri: schema:name go_definition: name: go_definition description: GO textual definition slot_uri: IAO:0000115 class_uri: biolink:MolecularActivity CellularComponent: name: CellularComponent definition_uri: https://cair2015.github.io/als-kg/elements/CellularComponent description: 'Gene Ontology Cellular Component term. ALS-critical compartments: stress granule, P-body, cytoplasm, nucleus, axon, neuromuscular junction, mitochondrion.' from_schema: https://cair2015.github.io/als-kg mappings: - biolink:CellularComponent is_a: BiologicalConcept slots: - namedEntity__id - namedEntity__label - namedEntity__definition - namedEntity__synonym - namedEntity__xref - namedEntity__comment - namedEntity__is_obsolete - namedEntity__source - namedEntity__last_updated - ontologyClass__source_version - ontologyClass__ingest_date - cellularComponent__go_id - cellularComponent__component_name - cellularComponent__go_definition attributes: go_id: name: go_id identifier: true range: GoIdentifier required: true component_name: name: component_name description: Cellular component name from GO slot_uri: schema:name go_definition: name: go_definition description: GO textual definition slot_uri: IAO:0000115 class_uri: biolink:CellularComponent Pathway: name: Pathway definition_uri: https://cair2015.github.io/als-kg/elements/Pathway description: Reactome pathway entity representing a curated biological pathway or reaction-level pathway context relevant to ALS mechanisms, including neuroinflammation, RNA metabolism, protein homeostasis, mitochondrial dysfunction, and axonal transport. from_schema: https://cair2015.github.io/als-kg mappings: - biolink:Pathway is_a: BiologicalConcept slots: - namedEntity__id - namedEntity__label - namedEntity__definition - namedEntity__synonym - namedEntity__xref - namedEntity__comment - namedEntity__is_obsolete - namedEntity__source - namedEntity__last_updated - ontologyClass__source_version - ontologyClass__ingest_date - pathway__reactome_id - pathway__pathway_name - pathway__pathway_definition - pathway__species - pathway__parent_pathway attributes: reactome_id: name: reactome_id identifier: true range: ReactomeIdentifier required: true pathway_name: name: pathway_name description: Standard Reactome pathway name slot_uri: schema:name pathway_definition: name: pathway_definition description: Reactome pathway description or summary when available slot_uri: IAO:0000115 species: name: species description: Species for the Reactome pathway; expected to be Homo sapiens for human ALS KG assertions parent_pathway: name: parent_pathway description: Parent Reactome pathway CURIE when available range: ReactomeIdentifier multivalued: true class_uri: biolink:Pathway DiseaseSubtype: name: DiseaseSubtype definition_uri: https://cair2015.github.io/als-kg/elements/DiseaseSubtype description: Molecularly-defined disease subtype derived from clustering analysis (transcriptomics, proteomics, multi-omics). Represents cohort stratification. Links to Disease via is_a relationship; carries distinct clinical correlates. from_schema: https://cair2015.github.io/als-kg is_a: Disease slots: - namedEntity__id - namedEntity__label - namedEntity__definition - namedEntity__synonym - namedEntity__xref - namedEntity__comment - namedEntity__is_obsolete - namedEntity__source - namedEntity__last_updated - ontologyClass__source_version - ontologyClass__ingest_date - diseaseOrPhenotype__hpo_id - disease__mondo_id - disease__name - disease__disease_type - disease__onset_type - disease__umls_cui - disease__omim_id - disease__orphanet_id - disease__icd10_code - diseaseSubtype__subtype_id - diseaseSubtype__cluster_method - diseaseSubtype__cluster_id - diseaseSubtype__signature_genes - diseaseSubtype__n_patients - diseaseSubtype__cohort - diseaseSubtype__clinical_correlate - diseaseSubtype__median_survival_months - diseaseSubtype__source_publication attributes: subtype_id: name: subtype_id description: Custom subtype identifier cluster_method: name: cluster_method description: Clustering approach (NMF, WGCNA, scRNA-seq, consensus) cluster_id: name: cluster_id description: Cluster number from analysis range: integer signature_genes: name: signature_genes description: Top discriminative genes for subtype multivalued: true n_patients: name: n_patients description: Number of patients in subtype range: integer cohort: name: cohort description: Source patient cohort (AnswerALS, NYGC, PRO-ACT) clinical_correlate: name: clinical_correlate description: Associated clinical feature or phenotype median_survival_months: name: median_survival_months description: Median survival from symptom onset range: float source_publication: name: source_publication description: DOI or PMID reference slot_uri: dcterms:bibliographicCitation class_uri: alskb:DiseaseSubtype Association: name: Association definition_uri: https://cair2015.github.io/als-kg/elements/Association description: Abstract base for optional evidence-bearing associations. Use when a relationship cannot be represented sufficiently by a direct object property because the edge needs provenance, evidence, confidence, or additional qualifiers. The subject/predicate/object fields allow the association to be materialized as an RDF triple or property-graph edge. from_schema: https://cair2015.github.io/als-kg mappings: - biolink:Association is_a: Relationship abstract: true slots: - association__association_id - association__association_label - association__subject - association__predicate - association__object - association__source - association__source_version - association__evidence_type - association__evidence_source - association__confidence - association__ingest_date - association__last_updated attributes: association_id: name: association_id description: Stable identifier for the association record slot_uri: schema:identifier range: uriorcurie association_label: name: association_label description: Human-readable summary of the association slot_uri: rdfs:label subject: name: subject description: Subject entity IRI or CURIE used to materialize a direct edge slot_uri: rdf:subject required: true predicate: name: predicate description: Direct object property represented by this association slot_uri: rdf:predicate required: true object: name: object description: Object entity IRI or CURIE used to materialize a direct edge slot_uri: rdf:object required: true source: name: source description: Data source for this association slot_uri: dcterms:source source_version: name: source_version description: Data source version or release date slot_uri: dcterms:hasVersion evidence_type: name: evidence_type description: Type of supporting evidence slot_uri: ECO:0000000 evidence_source: name: evidence_source description: Publication, study, database record, or extraction artifact supporting the association confidence: name: confidence description: Normalized confidence score from 0 to 1 ingest_date: name: ingest_date description: Date this association was ingested last_updated: name: last_updated description: Date this association was last modified slot_uri: dcterms:modified class_uri: biolink:Association DiseasePhenotypeAssociation: name: DiseasePhenotypeAssociation definition_uri: https://cair2015.github.io/als-kg/elements/DiseasePhenotypeAssociation description: Optional association for Disease -> Phenotype when the clinical feature requires edge metadata such as frequency, onset, severity, source cohort, or evidence. Materializes to disease_manifests_as_phenotype. from_schema: https://cair2015.github.io/als-kg is_a: Association slots: - association__association_id - association__association_label - association__subject - association__object - association__source - association__source_version - association__evidence_type - association__evidence_source - association__confidence - association__ingest_date - association__last_updated - diseasePhenotypeAssociation__has_disease - diseasePhenotypeAssociation__has_phenotype - diseasePhenotypeAssociation__predicate - diseasePhenotypeAssociation__frequency - diseasePhenotypeAssociation__severity - diseasePhenotypeAssociation__onset_type - diseasePhenotypeAssociation__cohort attributes: has_disease: name: has_disease range: Disease required: true has_phenotype: name: has_phenotype range: Phenotype required: true predicate: name: predicate slot_uri: rdf:predicate ifabsent: alskb:disease_manifests_as_phenotype frequency: name: frequency description: Frequency in affected population or cohort severity: name: severity description: Typical severity or severity distribution onset_type: name: onset_type description: Onset pattern when phenotype is onset-specific range: OnsetTypeEnum cohort: name: cohort description: Cohort or study population supporting this phenotype annotation class_uri: alskb:DiseasePhenotypeAssociation GeneDiseaseAssociation: name: GeneDiseaseAssociation definition_uri: https://cair2015.github.io/als-kg/elements/GeneDiseaseAssociation description: Optional association for Gene -> Disease when causal/risk/protective or correlative gene-disease edges need evidence, scores, statistics, or source-specific qualifiers. Materializes to gene_associated_with_disease. from_schema: https://cair2015.github.io/als-kg is_a: Association slots: - association__association_id - association__association_label - association__subject - association__object - association__source - association__source_version - association__evidence_type - association__evidence_source - association__confidence - association__ingest_date - association__last_updated - geneDiseaseAssociation__has_gene - geneDiseaseAssociation__has_disease - geneDiseaseAssociation__predicate - geneDiseaseAssociation__association_type - geneDiseaseAssociation__association_score - geneDiseaseAssociation__p_value - geneDiseaseAssociation__odds_ratio - geneDiseaseAssociation__effect_direction - geneDiseaseAssociation__evidence_count attributes: has_gene: name: has_gene range: Gene required: true has_disease: name: has_disease range: Disease required: true predicate: name: predicate slot_uri: rdf:predicate ifabsent: alskb:gene_associated_with_disease association_type: name: association_type description: causal, risk_factor, protective, modifier, biomarker, or correlative association_score: name: association_score description: Source-specific gene-disease association score range: float p_value: name: p_value description: Statistical significance when available range: float odds_ratio: name: odds_ratio description: Genetic association odds ratio when available range: float effect_direction: name: effect_direction description: increased_risk, decreased_risk, protective, upregulated, downregulated, or unknown evidence_count: name: evidence_count description: Number of supporting studies or records range: integer class_uri: alskb:GeneDiseaseAssociation VariantDiseaseAssociation: name: VariantDiseaseAssociation definition_uri: https://cair2015.github.io/als-kg/elements/VariantDiseaseAssociation description: Optional association for Variant -> Disease when variant-level evidence, clinical significance, inheritance, penetrance, or source assertions are needed. Materializes to variant_associated_with_disease. from_schema: https://cair2015.github.io/als-kg is_a: Association slots: - association__association_id - association__association_label - association__subject - association__object - association__source - association__source_version - association__evidence_type - association__evidence_source - association__confidence - association__ingest_date - association__last_updated - variantDiseaseAssociation__has_variant - variantDiseaseAssociation__has_disease - variantDiseaseAssociation__predicate - variantDiseaseAssociation__clinical_significance - variantDiseaseAssociation__inheritance_mode - variantDiseaseAssociation__penetrance - variantDiseaseAssociation__association_type attributes: has_variant: name: has_variant range: Variant required: true has_disease: name: has_disease range: Disease required: true predicate: name: predicate slot_uri: rdf:predicate ifabsent: alskb:variant_associated_with_disease clinical_significance: name: clinical_significance description: ClinVar/ACMG or ALS-specific clinical interpretation inheritance_mode: name: inheritance_mode description: autosomal_dominant, autosomal_recessive, X_linked, mitochondrial, complex, or unknown penetrance: name: penetrance description: Complete, reduced, age-dependent, or unknown penetrance association_type: name: association_type description: causal, risk_factor, modifier, protective, or uncertain class_uri: alskb:VariantDiseaseAssociation VariantProteinEffectAssociation: name: VariantProteinEffectAssociation definition_uri: https://cair2015.github.io/als-kg/elements/VariantProteinEffectAssociation description: Optional association for Variant -> Protein when protein consequence, predicted effect, assay result, or functional evidence is needed. Materializes to variant_affects_protein. from_schema: https://cair2015.github.io/als-kg is_a: Association slots: - association__association_id - association__association_label - association__subject - association__object - association__source - association__source_version - association__evidence_type - association__evidence_source - association__confidence - association__ingest_date - association__last_updated - variantProteinEffectAssociation__has_variant - variantProteinEffectAssociation__has_protein - variantProteinEffectAssociation__predicate - variantProteinEffectAssociation__functional_consequence - variantProteinEffectAssociation__predicted_effect - variantProteinEffectAssociation__assay attributes: has_variant: name: has_variant range: Variant required: true has_protein: name: has_protein range: Protein required: true predicate: name: predicate slot_uri: rdf:predicate ifabsent: alskb:variant_affects_protein functional_consequence: name: functional_consequence description: missense, frameshift, nonsense, splice_site, synonymous, repeat_expansion, or structural predicted_effect: name: predicted_effect description: loss_of_function, gain_of_function, dominant_negative, aggregation_prone, no_change, or unknown assay: name: assay description: Functional assay or computational method supporting the effect class_uri: alskb:VariantProteinEffectAssociation ProteinProteinInteractionAssociation: name: ProteinProteinInteractionAssociation definition_uri: https://cair2015.github.io/als-kg/elements/ProteinProteinInteractionAssociation description: Optional association for Protein -> Protein when interaction score, interaction type, database evidence, or assay metadata are needed. Materializes to protein_interacts_with_protein. from_schema: https://cair2015.github.io/als-kg is_a: Association slots: - association__association_id - association__association_label - association__subject - association__object - association__source - association__source_version - association__evidence_type - association__evidence_source - association__confidence - association__ingest_date - association__last_updated - proteinProteinInteractionAssociation__protein_1 - proteinProteinInteractionAssociation__protein_2 - proteinProteinInteractionAssociation__predicate - proteinProteinInteractionAssociation__interaction_score - proteinProteinInteractionAssociation__interaction_type - proteinProteinInteractionAssociation__assay attributes: protein_1: name: protein_1 range: Protein required: true protein_2: name: protein_2 range: Protein required: true predicate: name: predicate slot_uri: rdf:predicate ifabsent: alskb:protein_interacts_with_protein interaction_score: name: interaction_score description: Source-specific confidence score such as STRING combined score range: float interaction_type: name: interaction_type description: direct, indirect, physical, genetic, colocalization, pathway, or predicted assay: name: assay description: Assay or method supporting the interaction class_uri: alskb:ProteinProteinInteractionAssociation ProteinPathwayAssociation: name: ProteinPathwayAssociation definition_uri: https://cair2015.github.io/als-kg/elements/ProteinPathwayAssociation description: Optional association for Protein -> Pathway when Reactome evidence code, source release, pathway hierarchy, species, or annotation provenance are needed. Materializes to protein_participates_in_pathway. from_schema: https://cair2015.github.io/als-kg is_a: Association slots: - association__association_id - association__association_label - association__subject - association__object - association__source - association__source_version - association__evidence_type - association__evidence_source - association__confidence - association__ingest_date - association__last_updated - proteinPathwayAssociation__has_protein - proteinPathwayAssociation__has_pathway - proteinPathwayAssociation__predicate - proteinPathwayAssociation__reactome_evidence_code - proteinPathwayAssociation__pathway_role - proteinPathwayAssociation__species attributes: has_protein: name: has_protein range: Protein required: true has_pathway: name: has_pathway range: Pathway required: true predicate: name: predicate slot_uri: rdf:predicate ifabsent: alskb:protein_participates_in_pathway reactome_evidence_code: name: reactome_evidence_code description: Reactome evidence code or inferred/electronic/manual annotation category when available pathway_role: name: pathway_role description: participant, catalyst, regulator, input, output, or member, when this detail is available species: name: species description: Species context for the Reactome protein-pathway annotation class_uri: alskb:ProteinPathwayAssociation DrugTargetAssociation: name: DrugTargetAssociation definition_uri: https://cair2015.github.io/als-kg/elements/DrugTargetAssociation description: Optional association for Drug -> MolecularEntity when action type, binding affinity, target class, or mechanism evidence is needed. Materializes to drug_targets_molecular_entity. from_schema: https://cair2015.github.io/als-kg is_a: Association slots: - association__association_id - association__association_label - association__subject - association__object - association__source - association__source_version - association__evidence_type - association__evidence_source - association__confidence - association__ingest_date - association__last_updated - drugTargetAssociation__has_drug - drugTargetAssociation__target - drugTargetAssociation__predicate - drugTargetAssociation__action_type - drugTargetAssociation__binding_affinity_nm - drugTargetAssociation__mechanism attributes: has_drug: name: has_drug range: Drug required: true target: name: target description: Gene or protein target range: MolecularEntity required: true predicate: name: predicate slot_uri: rdf:predicate ifabsent: alskb:drug_targets_molecular_entity action_type: name: action_type description: inhibitor, activator, binder, antagonist, agonist, modulator, ASO_knockdown, or unknown binding_affinity_nm: name: binding_affinity_nm description: Binding affinity in nanomolar when available range: float mechanism: name: mechanism description: Mechanistic description of target modulation class_uri: alskb:DrugTargetAssociation DrugDiseaseTherapeuticAssociation: name: DrugDiseaseTherapeuticAssociation definition_uri: https://cair2015.github.io/als-kg/elements/DrugDiseaseTherapeuticAssociation description: Optional association for Drug -> Disease when therapeutic indication, approval status, clinical-trial evidence, or outcome metadata are needed. Materializes to drug_treats_or_modulates_disease. from_schema: https://cair2015.github.io/als-kg is_a: Association slots: - association__association_id - association__association_label - association__subject - association__object - association__source - association__source_version - association__evidence_type - association__evidence_source - association__confidence - association__ingest_date - association__last_updated - drugDiseaseTherapeuticAssociation__has_drug - drugDiseaseTherapeuticAssociation__has_disease - drugDiseaseTherapeuticAssociation__predicate - drugDiseaseTherapeuticAssociation__relation_type - drugDiseaseTherapeuticAssociation__approval_status - drugDiseaseTherapeuticAssociation__clinical_phase - drugDiseaseTherapeuticAssociation__outcome_measure attributes: has_drug: name: has_drug range: Drug required: true has_disease: name: has_disease range: Disease required: true predicate: name: predicate slot_uri: rdf:predicate ifabsent: alskb:drug_treats_or_modulates_disease relation_type: name: relation_type description: treats, disease_modifying, symptomatic, palliative, contraindicated, off_label, or investigational approval_status: name: approval_status description: approved, investigational, withdrawn, off_label, failed_trial, or unknown clinical_phase: name: clinical_phase description: Highest clinical development phase for ALS or ALS subtype outcome_measure: name: outcome_measure description: ALSFRS-R, survival, respiratory function, biomarker, or other endpoint class_uri: alskb:DrugDiseaseTherapeuticAssociation ExposureDiseaseAssociation: name: ExposureDiseaseAssociation definition_uri: https://cair2015.github.io/als-kg/elements/ExposureDiseaseAssociation description: Optional association for ExposureOrStressor -> Disease when epidemiology, mechanism, dose, duration, population, or study design metadata are needed. Materializes to exposure_associated_with_disease. from_schema: https://cair2015.github.io/als-kg is_a: Association slots: - association__association_id - association__association_label - association__subject - association__object - association__source - association__source_version - association__evidence_type - association__evidence_source - association__confidence - association__ingest_date - association__last_updated - exposureDiseaseAssociation__exposure - exposureDiseaseAssociation__has_disease - exposureDiseaseAssociation__predicate - exposureDiseaseAssociation__association_type - exposureDiseaseAssociation__mechanism - exposureDiseaseAssociation__epidemiological_support - exposureDiseaseAssociation__odds_ratio - exposureDiseaseAssociation__population attributes: exposure: name: exposure range: ExposureOrStressor required: true has_disease: name: has_disease range: Disease required: true predicate: name: predicate slot_uri: rdf:predicate ifabsent: alskb:exposure_associated_with_disease association_type: name: association_type description: risk_factor, protective, trigger, modifier, or correlative mechanism: name: mechanism description: Proposed biological mechanism epidemiological_support: name: epidemiological_support range: boolean odds_ratio: name: odds_ratio description: Epidemiological odds ratio or equivalent effect estimate range: float population: name: population description: Population, geography, occupation, or cohort context class_uri: alskb:ExposureDiseaseAssociation TranscriptionFactorRegulationAssociation: name: TranscriptionFactorRegulationAssociation definition_uri: https://cair2015.github.io/als-kg/elements/TranscriptionFactorRegulationAssociation description: Optional association for TranscriptionFactor -> Gene when direction, confidence, tissue/cell context, or assay evidence are needed. Materializes to transcription_factor_regulates_gene. from_schema: https://cair2015.github.io/als-kg is_a: Association slots: - association__association_id - association__association_label - association__subject - association__object - association__source - association__source_version - association__evidence_type - association__evidence_source - association__confidence - association__ingest_date - association__last_updated - transcriptionFactorRegulationAssociation__transcription_factor - transcriptionFactorRegulationAssociation__target_gene - transcriptionFactorRegulationAssociation__predicate - transcriptionFactorRegulationAssociation__regulation_type - transcriptionFactorRegulationAssociation__confidence_level - transcriptionFactorRegulationAssociation__tissue_or_cell_type attributes: transcription_factor: name: transcription_factor range: TranscriptionFactor required: true target_gene: name: target_gene range: Gene required: true predicate: name: predicate slot_uri: rdf:predicate ifabsent: alskb:transcription_factor_regulates_gene regulation_type: name: regulation_type description: activation, repression, bidirectional, context_dependent, or unknown confidence_level: name: confidence_level description: Source-specific confidence level such as DoRothEA A-D tissue_or_cell_type: name: tissue_or_cell_type description: Tissue or cell type context for the regulatory relationship class_uri: alskb:TranscriptionFactorRegulationAssociation GeneExpressionAssociation: name: GeneExpressionAssociation definition_uri: https://cair2015.github.io/als-kg/elements/GeneExpressionAssociation description: Optional association for Gene -> Anatomy when expression level, specificity, tissue, cell type, disease stage, or differential-expression qualifiers are needed. Materializes to gene_expressed_in_anatomy. from_schema: https://cair2015.github.io/als-kg is_a: Association slots: - association__association_id - association__association_label - association__subject - association__object - association__source - association__source_version - association__evidence_type - association__evidence_source - association__confidence - association__ingest_date - association__last_updated - geneExpressionAssociation__has_gene - geneExpressionAssociation__has_anatomy - geneExpressionAssociation__predicate - geneExpressionAssociation__expression_level - geneExpressionAssociation__specificity_index - geneExpressionAssociation__log2_fold_change - geneExpressionAssociation__adjusted_p_value - geneExpressionAssociation__tissue_or_cell_type - geneExpressionAssociation__disease_stage attributes: has_gene: name: has_gene range: Gene required: true has_anatomy: name: has_anatomy range: Anatomy required: true predicate: name: predicate slot_uri: rdf:predicate ifabsent: alskb:gene_expressed_in_anatomy expression_level: name: expression_level description: high, medium, low, absent, upregulated, downregulated, or not_detected specificity_index: name: specificity_index description: Tissue-specificity score from 0 to 1 range: float log2_fold_change: name: log2_fold_change description: Differential expression log2 fold change when available range: float adjusted_p_value: name: adjusted_p_value description: Multiple-testing-adjusted p-value when available range: float tissue_or_cell_type: name: tissue_or_cell_type description: Tissue or cell-type context disease_stage: name: disease_stage description: Disease stage or clinical context class_uri: alskb:GeneExpressionAssociation DiseaseDiseaseAssociation: name: DiseaseDiseaseAssociation definition_uri: https://cair2015.github.io/als-kg/elements/DiseaseDiseaseAssociation description: Optional association for Disease -> Disease when disease-disease edges need relation type, similarity score, shared mechanism, or comorbidity statistics. Materializes to disease_related_to_disease. from_schema: https://cair2015.github.io/als-kg is_a: Association slots: - association__association_id - association__association_label - association__subject - association__object - association__source - association__source_version - association__evidence_type - association__evidence_source - association__confidence - association__ingest_date - association__last_updated - diseaseDiseaseAssociation__disease_1 - diseaseDiseaseAssociation__disease_2 - diseaseDiseaseAssociation__predicate - diseaseDiseaseAssociation__relation_type - diseaseDiseaseAssociation__similarity_score - diseaseDiseaseAssociation__shared_mechanism attributes: disease_1: name: disease_1 range: Disease required: true disease_2: name: disease_2 range: Disease required: true predicate: name: predicate slot_uri: rdf:predicate ifabsent: alskb:disease_related_to_disease relation_type: name: relation_type description: comorbidity, shared_pathway, shared_gene, phenotypic_similarity, differential_diagnosis, or disease_subtype similarity_score: name: similarity_score description: Semantic similarity or clinical overlap score from 0 to 1 range: float shared_mechanism: name: shared_mechanism description: Shared biological mechanism, pathway, or clinical rationale class_uri: alskb:DiseaseDiseaseAssociation metamodel_version: 1.7.0 source_file: als_kg.yaml source_file_date: '2026-04-28T23:22:28' source_file_size: 42252 generation_date: '2026-04-28T23:22:38'