attributes.yaml

# This file extends biolink.yaml with additional node and edge properties created as placeholders so that they can be used in knowledge graphs and pass KGX validation which requires Biolink compliance.
# They will remain here until such time as we can evaluate their utility, and how they should be modeled, before deciding if/what to move into Biolink proper.
# The convention for naming such properties is to begin with the name/infores code for the source of the property, and then use the name of the property as defined by the source.
# e.g. we created an edge property to hold the 'interaction score' from  DGIdb - which we name "dgidb interaction score"
---
id: https://w3id.org/biolink/biolink-model/attributes
name: Attributes
description: Attributes as candidates for inclusion in Biolink Model
license: https://creativecommons.org/publicdomain/zero/1.0/

prefixes:
  AGRKB: 'https://www.alliancegenome.org/'
  apollo: 'https://github.com/GMOD/Apollo'
  AspGD: 'http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid='
  bioschemas: 'https://bioschemas.org/'
  linkml: 'https://w3id.org/linkml/'
  CAID: 'http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid='
   # Placeholder: just points to GMOD Chado wiki
  CHADO: 'http://gmod.org/wiki/Chado/'
   # Placeholders: not sure how 'chembio'and CHEMBL.MECHANISM really resolve
  ChemBank: 'http://chembank.broadinstitute.org/chemistry/viewMolecule.htm?cbid='
  CHEMBL.MECHANISM: 'https://www.ebi.ac.uk/chembl/mechanism/inspect/'
  CID: 'http://pubchem.ncbi.nlm.nih.gov/compound/'
  CLINVAR: 'http://identifiers.org/clinvar'
  COAR_RESOURCE: 'http://purl.org/coar/resource_type/'
  COG: 'https://www.ncbi.nlm.nih.gov/research/cog-project/'
  ComplexPortal: 'https://www.ebi.ac.uk/complexportal/complex/'
  CPT: 'https://www.ama-assn.org/practice-management/cpt/'
  CTD.CHEMICAL: 'http://ctdbase.org/detail.go?type=chem&acc='
  CTD.DISEASE: 'http://ctdbase.org/detail.go?type=disease&db=MESH&acc='
  CTD.GENE: 'http://ctdbase.org/detail.go?type=gene&acc='
  CTD: 'http://ctdbase.org/'
  DGIdb: 'https://www.dgidb.org/interaction_types'
  dcat: 'http://www.w3.org/ns/dcat#'
  dct: 'http://purl.org/dc/terms/'
  dcid: 'https://datacommons.org/browser/'
  doi: 'https://doi.org/'
  DOID-PROPERTY: 'http://purl.obolibrary.org/obo/doid#'
  DrugCentral: 'http://drugcentral.org/drugcard/'
  ECTO: 'http://purl.obolibrary.org/obo/ECTO_'
  EDAM-DATA: 'http://edamontology.org/data_'
  EDAM-FORMAT: 'http://edamontology.org/format_'
  EDAM-OPERATION: 'http://edamontology.org/operation_'
  EDAM-TOPIC: 'http://edamontology.org/topic_'
  EFO: 'http://www.ebi.ac.uk/efo/EFO_'
  ExO: 'http://purl.obolibrary.org/obo/ExO_'
  fabio: 'http://purl.org/spar/fabio/'
  FMA: 'http://purl.obolibrary.org/obo/FMA_'
  foaf: 'http://xmlns.com/foaf/0.1/'
  foodb.compound: 'http://foodb.ca/compounds/'
  foodb.food: 'http://foodb.ca/foods/'
  FYECO: 'https://www.pombase.org/term/'
  FYPO: 'http://purl.obolibrary.org/obo/FYPO_'   # Fission Yeast Phenotype Ontology
  gff3: 'https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md#'
  GOREL: 'http://purl.obolibrary.org/obo/GOREL_'
   # GOP: Gene Ontology Property (not really a GO term but an associated metadatum)
  GOP: 'http://purl.obolibrary.org/obo/go#'
  gpi: 'https://github.com/geneontology/go-annotation/blob/master/specs/gpad-gpi-2-0.md#'
  GSID: 'https://scholar.google.com/citations?user='
  GTEx: 'https://www.gtexportal.org/home/gene/'
  GTOPDB: 'https://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId='
  gtpo: 'https://rdf.guidetopharmacology.org/ns/gtpo#'
  HANCESTRO: 'http://www.ebi.ac.uk/ancestro/ancestro_'
  HCPCS: 'http://purl.bioontology.org/ontology/HCPCS/'
  HsapDv: 'http://purl.obolibrary.org/obo/HsapDv_'
  ICD10: 'https://icd.who.int/browse10/2016/en#/'
  ICD9: 'http://translator.ncats.nih.gov/ICD9_'
  icd11: 'http://id.who.int/icd/entity/'
  icd11.foundation: 'http://id.who.int/icd/entity/'
  interpro: 'https://www.ebi.ac.uk/interpro/entry/'
  INO: 'http://purl.obolibrary.org/obo/INO_'
  isbn: 'https://www.isbn-international.org/identifier/'  # note: a resolvable base URI not available from isbn-international
  isni: 'https://isni.org/isni/'
  issn: 'https://portal.issn.org/resource/ISSN/'
  ncats.drug: 'https://drugs.ncats.io/drug/'
  KEGG.BRITE: 'https://bioregistry.io/kegg.brite:'
  KEGG: 'http://www.kegg.jp/entry/'
  KEGG.GENES: 'https://bioregistry.io/kegg.genes:bsu:'
  KEGG.PATHWAY: 'https://bioregistry.io/kegg.pathway:'
  KEGG.RCLASS: 'https://www.genome.jp/dbget-bin/www_bget?rc:'
  LOINC: 'http://loinc.org/rdf/'
  MAXO: 'http://purl.obolibrary.org/obo/MAXO_'
  medgen: 'https://www.ncbi.nlm.nih.gov/medgen/'
  metacyc.reaction: 'http://identifiers.org/metacyc.reaction:'
  METANETX.REACTION: 'https://www.metanetx.org/equa_info/'
  MESH: 'http://id.nlm.nih.gov/mesh/'
  MI: 'http://purl.obolibrary.org/obo/MI_'
  mirbase: 'http://identifiers.org/mirbase'
  mmmp.biomaps: 'https://bioregistry.io/mmmp.biomaps:'
  MmusDv: 'http://purl.obolibrary.org/obo/MMUSDV_'
  MSigDB: 'https://www.gsea-msigdb.org/gsea/msigdb/'
  NBO-PROPERTY: 'http://purl.obolibrary.org/obo/nbo#'
  ncats.bioplanet: 'https://tripod.nih.gov/bioplanet/detail.jsp?pid='
  NCBIGene: 'http://identifiers.org/ncbigene/'
  NCIT-OBO: 'http://purl.obolibrary.org/obo/ncit#'
  NDDF: 'http://purl.bioontology.org/ontology/NDDF/'
  NLMID: 'https://www.ncbi.nlm.nih.gov/nlmcatalog/?term='
  OBAN: 'http://purl.org/oban/'
  OMIM.PS: 'https://www.omim.org/phenotypicSeries/'
  ORCID: 'https://orcid.org/'
  ORDO: 'http://www.orpha.net/ORDO/'
  os: 'https://github.com/cmungall/owlstar/blob/master/owlstar.ttl'
  PANTHER.FAMILY: 'http://www.pantherdb.org/panther/family.do?clsAccession='
  PathWhiz: 'http://smpdb.ca/pathways/#'   #  See also https://smpdb.ca/pathwhiz/
  pav: 'http://purl.org/pav/'
  PHARMGKB.DRUG: 'https://www.pharmgkb.org/chemical/'
  PHARMGKB.DISEASE: 'https://www.pharmgkb.org/disease/'
  PHARMGKB.GENE: 'https://www.pharmgkb.org/gene/'
  PHARMGKB.PATHWAYS: 'https://www.pharmgkb.org/pathway/'
  PHARMGKB.VARIANT: 'https://www.pharmgkb.org/variant/'
  PHAROS: 'http://pharos.nih.gov'
  PomBase: 'https://www.pombase.org/gene/'
  prov: 'http://www.w3.org/ns/prov#'
  qud: 'http://qudt.org/1.1/schema/qudt#'
  REPODB: 'http://apps.chiragjpgroup.org/repoDB/'
  ResearchID: 'https://publons.com/researcher/'
  RO: 'http://purl.obolibrary.org/obo/RO_'
  RXNORM: 'http://purl.bioontology.org/ontology/RXNORM/'
  RXCUI: 'https://mor.nlm.nih.gov/RxNav/search?searchBy=RXCUI&searchTerm='
  schema: 'http://schema.org/'
  ScopusID: 'https://www.scopus.com/authid/detail.uri?authorId='
  SEED.REACTION: 'https://modelseed.org/biochem/reactions/'
  SEMMEDDB: 'https://skr3.nlm.nih.gov/SemMedDB'
  SIO: 'http://semanticscience.org/resource/SIO_'
  SNOMEDCT: 'http://snomed.info/id/'
  SPDI: 'https://api.ncbi.nlm.nih.gov/variation/v0/spdi/'
  UBERGRAPH: 'http://translator.renci.org/ubergraph-axioms.ofn#'
  UBERON_CORE: 'http://purl.obolibrary.org/obo/uberon/core#'
  UBERON_NONAMESPACE: 'http://purl.obolibrary.org/obo/core#'
  STY: 'http://purl.bioontology.org/ontology/STY/'
  UMLSSG: 'https://lhncbc.nlm.nih.gov/semanticnetwork/download/sg_archive/SemGroups-v04.txt'
  UniProtKB: 'http://purl.uniprot.org/uniprot/'
  UNIPROT.ISOFORM: 'http://purl.uniprot.org/isoforms/'
  VANDF: 'https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/VANDF/'
  UO-PROPERTY: 'http://purl.obolibrary.org/obo/uo#'
  VMC: 'https://github.com/ga4gh/vr-spec/'
  WBls: 'http://purl.obolibrary.org/obo/WBls_'
  WBbt: 'http://purl.obolibrary.org/obo/WBbt_'
  WBVocab: 'http://bio2rdf.org/wormbase_vocabulary'
  WIKIDATA: 'https://www.wikidata.org/entity/'             #  Wikidata Entity
  WIKIDATA_PROPERTY: 'https://www.wikidata.org/prop/'
  wgs: 'http://www.w3.org/2003/01/geo/wgs84_pos'
  XPO: 'http://purl.obolibrary.org/obo/XPO_'   #  Xenopus Phenotype Ontology
  Xenbase: 'http://www.xenbase.org/gene/showgene.do?method=display&geneId='
  PMC: 'http://europepmc.org/articles/PMC'

default_range: string
default_prefix: biolink

default_curi_maps:
  - obo_context
  - idot_context
  - monarch_context
  - semweb_context

emit_prefixes:
  - rdf
  - rdfs
  - xsd
  - skos
  - oboInOwl
  - BIOGRID
  - SO

imports:
  - linkml:types

classes:

slots:

  information content:
    description: Information content (IC) value for a term, primarily from Automats.
    range: float

  equivalent identifiers:
    description: >-
      A set of identifiers that are considered equivalent to the primary identifier of the entity. This attribute is
      used to represent a collection of identifiers that are considered equivalent to the primary identifier
      of an entity. These equivalent identifiers may come from different databases, ontologies, or naming
      conventions, but they all refer to the same underlying concept or entity. This attribute is particularly
      useful in data integration and interoperability scenarios, where it is important to recognize and link
      different representations of the same entity across various sources.
    range: uriorcurie
    multivalued: true
    see_also:
      - biolink:xref
      - biolink:synonyms

  chembl drug warning:
    description: Text describing warnings for use of chemicals as therapeutics.
    range: string

  chembl prodrug:
    description: Flag indicating if a drug is a prodrug that is active only after being metabolized by the body.
    range: boolean

  chembl chirality:
    description: Tern indicating the chirality of the chemical entity.
    range: string

  chembl black box warning:
    description: Text describing black box warnings for use of chemicals as therapeutics.
    range: string

  chembl natural product:
    description: Flag indicating if a chemical entity is a natural product.
    range: boolean

  chembl availability type:
    description: Text indicating the availability type of the chemical entity.
    range: string

  chembl binding site name:
    description: Text indicating the name of the binding site for a chemical entity.
    range: string

  chembl binding site comment:
    description: Text describing the binding site for a chemical entity.
    range: string

  chembl mechanism of action description:
    description: Text describing the mechanism of action for a chemical entity.
    range: string

  chembl mechanism of action comment:
    description: Additional comments regarding the mechanism of action.
    range: string

  chembl mutation:
    description: Text describing mutations associated with a chemical entity.
    range: string

  chembl mutation accession:
    description: Accession identifier for a mutation associated with a chemical entity.
    range: string

  chembl selectivity comment:
    description: Additional comments regarding the selectivity of the drug.
    range: string

  chembl assay description:
    description: Text describing the assay associated with a chemical entity.
    range: string

  chembl confidence score:
    description: >-
      A score defined by ChEMBL that represents the confidence level of a particular drug-target 
      interaction, based on the type and quality of evidence supporting the interaction. The score 
      ranges from 0 to 9, with higher scores indicating stronger evidence for the interaction.
    range: integer

  dgidb relative drug specificity score:
    description: >-
      A score defined by DGIdb that quantifies the gene-interaction specificity of a given drug - representing the ratio of average
      known gene partners for all drugs to the known partners for the given drug. See https://dgidb.org/about/overview/interaction-score.
    range: float

  dgidb relative gene specificity score:
    description: >-
      A score defined by DGIdb that quantifies the drug-interaction specificity of a given gene - representing the ratio of average
      known drug partners for all genes to the known partners for the given gene. See https://dgidb.org/about/overview/interaction-score.
    range: float

  intact confidence value:
    aliases: ['intact miscore', 'intact interaction score']
    description: >-
      A score defined by MI / IntAct that represents the degree of confidence in the existence of a particular interaction by assessing
      the annotation of that specific interaction in a standards-compliant dataset. The score given to an interaction will increase as
      the number of experimental evidences supporting that interaction increases. Experimental evidences contribute more highly to the final
      score than evidences derived by predictive algorithms or literature text-mining methods. Range is 0-1, with higher scores indicated more
      confidence. See here for details: https://www.ebi.ac.uk/intact/documentation/user-guide#interaction_scoring.

  dgidb interaction score:
    description: >-
      A score defined by DGIdb that is used to rank interaction record results in DGIdb, which  combines their evidence
      score  (based on total supporting sources and pubs), with their relative gene specificity score and relative drug specificity
      score. See https://dgidb.org/about/overview/interaction-score.
    range: float

  dgidb evidence score:
    description: >-
      A score defined by DGIdb that is used to report the amount of evidence supporting a given interaction statement, which is
      simply the sum of all supporting sources and publications. See https://dgidb.org/about/overview/interaction-score.
    range: integer

  diseases confidence score:
    description: >-
      A score defined by Jensen Lab Diseases that reports confidence level in an association on a scale of 1-5 stars. 
      It is based on different inputs for curated knowledge associations vs text-mined associations vs experimental/GWAS based associations,
      but adjusts/caps scores for these types of knowledge such that they are comparable on a single scale.
    range: float
  
  drug_rep_hub disease area:
    description: >-
      A term used by Drug Repurposing Hub to describe the disease area associated with a drug.
    range: string

  gene2phenotype confidence category:
    description: >-
      A term used by EBI Gene2Phenotype to describe the confidence that the association is real.
      GenCC confidence terms are used for different levels of confidence (enum). 
      See https://www.ebi.ac.uk/gene2phenotype/about/terminology#g2p-confidence-section.
    range: string

  signor confidence score:
    description: >-
      A score defined by SIGNOR Lab Diseases that reports confidence level in a curated interaction. Scores are based on four factors:
      number of supporting publications, occurrence in curated SIGNOR pathways, support in Reactome interaction data, co-mentions in UniProt
      records. Scores range 0-1, and reflect a relative measure of evidence support, not an absolute probability or statistical confidence measure. 
    range: float

  stringdb combined score:
    description: >-
      A confidence score assigned by STRING representing the estimated
      likelihood that two proteins are functionally associated, based on the
      probabilistic integration of all available evidence channels (e.g.,
      curated databases, experiments, co-expression, evolutionary evidence,
      and text mining). Higher scores indicate greater confidence in the
      existence of a biologically meaningful functional association.
    range: float

  stringdb experimental score:
    description: >-
      A confidence score assigned by STRING representing the estimated
      likelihood that two proteins are functionally associated based solely on
      experimental evidence, including laboratory measurements of physical
      interactions or protein associations. Higher scores indicate stronger
      experimental support for a biological association between the proteins.
    range: float

  stringdb coexpression score:
    description: >-
      A confidence score assigned by STRING representing the estimated
      likelihood that two proteins are functionally associated based solely on
      evidence that their encoding genes exhibit correlated expression
      patterns across one or more transcriptomic datasets. Higher scores
      indicate stronger support for a biological association inferred from
      gene co-expression.
    range: float