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biolink-model.yaml
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biolink-model.yaml
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id: https://w3id.org/biolink/biolink-model
name: Biolink-Model
description: Entity and association taxonomy and datamodel for life-sciences data
license: https://creativecommons.org/publicdomain/zero/1.0/
# Version should be kept in sync with primary Git repository release tag
version: 2.2.16
## ------------
## PREFIXES
## ------------
# CURIE namespaces (prefixes/base URI's) mappings of prefixes used in the body of the Biolink Model specification
# are resolved using a specific precedence order, for use in the generation of the Biolink Model context.jsonld
# mappings to namespaces. Any prefixes encountered in the Biolink Model but not resolved by the following
# precedence sources, are anonymously declared by linkml as http://example.org/UNKNOWN/ rooted base URI's
# which should ideally be repaired in one of the precedence lists.
#
# 1. The following 'prefixes:' delimited list has first precedence in resolution.
#
prefixes:
alliancegenome: 'https://www.alliancegenome.org/'
apollo: 'https://github.com/GMOD/Apollo'
AspGD: 'http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid='
biolink: 'https://w3id.org/biolink/vocab/'
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/'
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/'
foaf: 'http://xmlns.com/foaf/0.1/'
foodb.compound: 'http://foodb.ca/compounds/'
FYPO: 'http://purl.obolibrary.org/obo/FYPO_' # Fission Yeast Phenotype Ontology
GAMMA: 'http://translator.renci.org/GAMMA_'
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.codes/icd9cm/'
ICD9: 'http://translator.ncats.nih.gov/ICD9_'
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/'
KEGG.BRITE: 'http://www.kegg.jp/entry/'
KEGG.DGROUP: 'http://www.kegg.jp/entry/'
KEGG.ENZYME: 'http://www.kegg.jp/entry/'
KEGG.GENE: 'http://www.kegg.jp/entry/'
KEGG.PATHWAY: 'https://www.kegg.jp/entry/'
KEGG.RCLASS: 'http://www.kegg.jp/entry/'
LOINC: 'http://loinc.org/rdf/'
MAXO: 'http://purl.obolibrary.org/obo/MAXO_'
medgen: 'https://www.ncbi.nlm.nih.gov/medgen/'
metacyc.reaction: 'https://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:'
MSigDB: 'https://www.gsea-msigdb.org/gsea/msigdb/'
NBO-PROPERTY: 'http://purl.obolibrary.org/obo/nbo#'
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/'
oboformat: 'http://www.geneontology.org/formats/oboInOwl#'
OMIM.PS: 'https://www.omim.org/phenotypicSeries/'
OBOREL: 'http://purl.obolibrary.org/obo/RO_'
ORCID: 'https://orcid.org/'
ORPHA: 'http://www.orpha.net/ORDO/Orphanet_'
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/'
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_'
SNOMED: 'http://www.snomedbrowser.com/Codes/Details/'
SNOMEDCT: 'http://www.snomedbrowser.com/Codes/Details/'
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#'
# The UMLS Semantic types and groups namespaces don't have a directly
# resolvable Base URI, but we point to a pair of sensible web documents
STY: 'http://purl.bioontology.org/ontology/STY/'
UMLSSG: 'https://lhncbc.nlm.nih.gov/semanticnetwork/download/sg_archive/SemGroups-v04.txt'
VANDF: 'https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/VANDF/'
UO-PROPERTY: 'http://purl.obolibrary.org/obo/uo#'
# The "Variation Modelling Collaboration" (VMC) is not (yet) a conventional namespace so we point to its Github repo
# See also: https://www.ga4gh.org/work_stream/genomic-knowledge-standards/#existing-standards and
# https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7153148/
VMC: 'https://github.com/ga4gh/vr-spec/'
WBVocab: 'http://bio2rdf.org/wormbase_vocabulary'
WIKIDATA: 'https://www.wikidata.org/wiki/' # Wikidata Entity
WIKIDATA_PROPERTY: 'https://www.wikidata.org/wiki/Property:' # Wikidata Property - not a conventional namespace prefix
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='
default_prefix: biolink
default_range: string
# 2. The following prefix maps are retrieved from the
# specified contexts defined at https://prefixcommons.org/
default_curi_maps:
- obo_context
- idot_context
- monarch_context
- semweb_context
# The following 'standard' prefixes are also used.
emit_prefixes:
- rdf
- rdfs
- xsd
- skos
- OIO
- BIOGRID
- SO
## ------------
## SUBSETS
## ------------
enums:
logical_interpretation_enum:
permissible_values:
SomeSome:
description: >-
A modifier on a triple that causes the triple to be interpreted as a some-some statement
meaning: os:SomeSomeInterpretation
AllSome:
description: >-
A modifier on a triple that causes the triple to be interpreted as an all-some statement.
meaning: os:AllSomeInterpretation
InverseAllSome:
reaction_direction_enum:
permissible_values:
left_to_right:
right_to_left:
bidirectional:
neutral:
reaction_side_enum:
permissible_values:
left:
right:
phase_enum:
description: phase
permissible_values:
0:
1:
2:
strand_enum:
description: strand
permissible_values:
"+":
description: Positive
"-":
description: Negative
".":
description: Unstranded
"?":
description: Unknown
sequence_enum:
description: type of sequence
permissible_values:
"NA":
description: nucleic acid
"AA":
description: amino acid
predicate_qualifier_enum:
description: >-
constrained list of qualifying terms that soften or expand the definition of the predicate used.
can be used to constrain or qualify any predicate (any child of related_to).
permissible_values:
"predicted":
"possibly":
"hypothesized":
"validated":
"supported by real-world evidence":
"supported by clinical evidence":
druggable_gene_category_enum:
permissible_values:
"Tclin":
description: >-
These targets have activities in DrugCentral (ie. approved drugs) with known mechanism of action.
"Tbio":
description: >-
These targets have activities in ChEMBL, Guide to Pharmacology or DrugCentral that satisfy
the activity thresholds detailed below.
"Tchem":
description: >-
These targets do not have known drug or small molecule activities that satisfy the activity
thresholds detailed below AND satisfy one or more of the following criteria:
target is above the cutoff criteria for Tdark
target is annotated with a Gene Ontology Molecular Function or Biological Process leaf term(s)
with an Experimental Evidence code
"Tdark":
description: >-
These are targets about which virtually nothing is known. They do not have known drug or small
molecule activities that satisfy the activity thresholds detailed below AND satisfy two or
more of the following criteria:
A PubMed text-mining score from Jensen Lab less than 5, greater than or equal TO 3 Gene RIFs, or
less than or equal to 50 Antibodies available according to http://antibodypedia.com.
drug_availability_enum:
description: >-
permissible_values:
"over the counter":
description: >-
chemical entity is available over the counter without a prescription.
"prescription":
description:
chemical entity is available by prescription.
drug_delivery_enum:
permissible_values:
"inhalation":
"oral":
"absorbtion through the skin":
"intravenous injection":
FDA_approval_status_enum:
description: >-
permissible_values:
"Discovery & Development Phase":
description: >-
Discovery & Development Phase. Discovery involves researchers finding new possibilities
for medication through testing molecular compounds, noting unexpected effects from existing treatments,
or the creation of new technology that allows novel ways of targeting medical products to sites in the body.
Drug development occurs after researchers identify potential compounds for experiments.
"Preclinical Research Phase":
description: >-
Preclinical Research Phase. Once researchers have examined the possibilities a new drug may contain,
they must do preliminary research to determine its potential for harm (toxicity).
This is categorized as preclinical research and can be one of two types: in vitro or in vivo.
"FDA Clinical Research Phase":
description: >-
Clinical Research Phase. Clinical research involves trials of the drug on people,
and it is one of the most involved stages in the drug development and approval process.
Clinical trials must answer specific questions and follow a protocol determined by
the drug researcher or manufacturer.
"FDA Review Phase 4":
description: >-
FDA Review
"FDA Post-Market Safety Monitoring":
description: >-
FDA Post-Market Safety Monitoring. The last phase of drug approval is an ongoing one
while the drug is on the marketplace. If a developer wants to change anything about the
drug formulation or approve it for a new use, they must apply with the FDA. The FDA also
frequently reviews the drug’s advertising and its manufacturing facility to make sure
everything involved in its creation and marketing is in compliance with regulations.
"FDA Clinical Research Phase 1":
description: >-
In the FDA Clinical Research Phase, the Clinical Research Phase 1 involves 20 – 100 study participants and
lasts several months. This phase is used to determine the safety and dosage of the drug,
and about 70% of these drugs move on to the next clinical research phase.
"FDA Clinical Research Phase 2":
description: >-
In the FDA Clinical Research Phase, the Clinical Research Phase 2 involves up to several hundred people,
who must have the disease or condition the drug supposes to treat. This phase can last
from a few months to two years, and its purpose is to monitor the efficacy of the drug,
as well as note side effects that may occur.
"FDA Clinical Research Phase 3":
description: >-
In the FDA Clinical Research Phase, the Clinical Research Phase 3 involves 300 – 3000 volunteers
and can last up to four years. It is used to continue monitoring the efficacy of
the drug, as well as exploring any longer-term adverse reactions.
"FDA Clinical Research Phase 4":
description: >-
In the FDA Clinical Research Phase, the Clinical Research Phase 4 involves several thousands of
volunteers who have the disease or condition and continues to monitor safety and efficacy.
If a drug passes this phase, it goes on to FDA review.
"FDA Fast Track":
description: >-
Fast track is a process designed to facilitate the development, and expedite the
review of drugs to treat serious conditions and fill an unmet medical need.
The purpose is to get important new drugs to the patient earlier. Fast Track
addresses a broad range of serious conditions. For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/fast-track
"FDA Breakthrough Therapy":
description: >-
Breakthrough Therapy designation is a process designed to expedite the
development and review of drugs that are intended to treat a serious
condition and preliminary clinical evidence indicates that the drug may
demonstrate substantial improvement over available therapy on a clinically significant endpoint(s).
For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/breakthrough-therapy
"FDA Accelerated Approval":
description: >-
When studying a new drug, it can sometimes take many years to learn whether a drug actually
provides a real effect on how a patient survives, feels, or functions. A positive therapeutic
effect that is clinically meaningful in the context of a given disease is known as “clinical benefit”.
Mindful of the fact that it may take an extended period of time to measure a drug’s intended clinical
benefit, in 1992 FDA instituted the Accelerated Approval regulations. These regulations allowed drugs
for serious conditions that filled an unmet medical need to be approved based on a surrogate endpoint.
Using a surrogate endpoint enabled the FDA to approve these drugs faster.
For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/accelerated-approval
"FDA Priority Review":
description: >-
Prior to approval, each drug marketed in the United States must go through a detailed FDA review process.
In 1992, under the Prescription Drug User Act (PDUFA), FDA agreed to specific goals for improving
the drug review time and created a two-tiered system of review times – Standard Review and Priority
Review. A Priority Review designation means FDA’s goal is to take action on an application
within 6 months (compared to 10 months under standard review).
For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/priority-review
"Regular FDA Approval":
"Post-Approval Withdrawal":
subsets:
model_organism_database:
description: >-
Subset that is relevant for a typical Model Organism Database (MOD)
translator_minimal:
description: >-
Minimum subset of translator work
samples:
description: >-
Sample/biosample datamodel
testing:
description: >-
TBD
## ------------
## TYPES
## ------------
imports:
- linkml:types
types:
chemical formula value:
uri: xsd:string
base: str
description: A chemical formula
notes:
- Should be implemented as a stronger type
category type:
typeof: uriorcurie
description: >-
A primitive type in which the value denotes a class within the biolink model.
The value must be a URI or a CURIE. In a Neo4j representation, the value should
be the CURIE for the biolink class, for example biolink:Gene. For an RDF representation,
the value should be a URI such as https://w3id.org/biolink/vocab/Gene
iri type:
typeof: uriorcurie
description: >-
An IRI
label type:
typeof: string
description: >-
A string that provides a human-readable name for an entity
predicate type:
typeof: uriorcurie
description: >-
A CURIE from the biolink related_to hierarchy.
For example, biolink:related_to, biolink:causes, biolink:treats.
narrative text:
typeof: string
description: >-
A string that provides a human-readable description of something
symbol type:
typeof: string
frequency value:
typeof: string
uri: UO:0000105
percentage frequency value:
typeof: double
uri: UO:0000187
quotient:
aliases: ['ratio']
typeof: double
uri: UO:0010006
unit:
typeof: string
uri: UO:0000000
id_prefixes:
- UO
exact_mappings:
- qud:Unit
time type:
typeof: time
biological sequence:
typeof: string
## ------------
## SLOTS
## ------------
slots:
## ---------------
## ATTRIBUTE SLOTS
## ---------------
has attribute:
description: >-
connects any entity to an attribute
domain: entity
range: attribute
multivalued: true
in_subset:
- samples
close_mappings:
# RTX term meaning 'specifies value of' tagged as inverse of 'biolink:has attribute'
- OBI:0001927
exact_mappings:
- SIO:000008
narrow_mappings:
# if 'has attribute' annotates a NamedThing as subject or
# object of an association, these OBAN mappings may apply
- OBAN:association_has_subject_property
- OBAN:association_has_object_property
- CPT:has_possibly_included_panel_element
- DRUGBANK:category
# RTX contributed terms. Could perhaps review for more semantically precise mappings?
- EFO:is_executed_in
- HANCESTRO:0301
- LOINC:has_action_guidance
- LOINC:has_adjustment
- LOINC:has_aggregation_view
- LOINC:has_approach_guidance
- LOINC:has_divisor
- LOINC:has_exam
- LOINC:has_method
- LOINC:has_modality_subtype
- LOINC:has_object_guidance
- LOINC:has_scale
- LOINC:has_suffix
- LOINC:has_time_aspect
- LOINC:has_time_modifier
- LOINC:has_timing_of
# disease is stage
- NCIT:R88
- NCIT:eo_disease_has_property_or_attribute
- NCIT:has_data_element
- NCIT:has_pharmaceutical_administration_method
- NCIT:has_pharmaceutical_basic_dose_form
- NCIT:has_pharmaceutical_intended_site
- NCIT:has_pharmaceutical_release_characteristics
- NCIT:has_pharmaceutical_state_of_matter
- NCIT:has_pharmaceutical_transformation
- NCIT:is_qualified_by
- NCIT:qualifier_applies_to
- NCIT:role_has_domain
- NCIT:role_has_range
- INO:0000154
- HANCESTRO:0308
- OMIM:has_inheritance_type
- ORPHA:C016
- ORPHA:C017
- RO:0000053
# RTX tagged a few RO terms as 'biolink:related_to' but semantics suggest a better mapping here
- RO:0000086
- RO:0000087
- SNOMED:has_access
- SNOMED:has_clinical_course
- SNOMED:has_count_of_base_of_active_ingredient
- SNOMED:has_dose_form_administration_method
- SNOMED:has_dose_form_release_characteristic
- SNOMED:has_dose_form_transformation
- SNOMED:has_finding_context
- SNOMED:has_finding_informer
- SNOMED:has_inherent_attribute
- SNOMED:has_intent
- SNOMED:has_interpretation
- SNOMED:has_laterality
- SNOMED:has_measurement_method
- SNOMED:has_method
- SNOMED:has_priority
- SNOMED:has_procedure_context
- SNOMED:has_process_duration
- SNOMED:has_property
- SNOMED:has_revision_status
- SNOMED:has_scale_type
- SNOMED:has_severity
- SNOMED:has_specimen
- SNOMED:has_state_of_matter
- SNOMED:has_subject_relationship_context
- SNOMED:has_surgical_approach
- SNOMED:has_technique
- SNOMED:has_temporal_context
- SNOMED:has_time_aspect
- SNOMED:has_units
- UMLS:has_structural_class
- UMLS:has_supported_concept_property
- UMLS:has_supported_concept_relationship
- UMLS:may_be_qualified_by
has attribute type:
description: >-
connects an attribute to a class that describes it
domain: attribute
range: ontology class
multivalued: false
required: true
in_subset:
- samples
narrow_mappings:
- LOINC:has_modality_type
- LOINC:has_view_type
# TRAPI Attribute schema alignment:
# value: NamedThing.name
# value_type: NamedThing.category
# value_type_name: quantity_value.NamedThing.name
has qualitative value:
description: >-
connects an attribute to a value
domain: attribute
range: named thing
multivalued: false
in_subset:
- samples
# TRAPI Attribute schema alignment:
# value: quantity_value.has_numeric_value[double] - may be a vector?
# value_type: quantity_value.has_unit.unit.uri
# value_type_name: quantity_value.has_unit.unit.name[string]
has quantitative value:
description: >-
connects an attribute to a value
domain: attribute
range: quantity value
multivalued: true
exact_mappings:
- qud:quantityValue
narrow_mappings:
- SNOMED:has_concentration_strength_numerator_value
- SNOMED:has_presentation_strength_denominator_value
- SNOMED:has_presentation_strength_numerator_value
in_subset:
- samples
has numeric value:
description: >-
connects a quantity value to a number
domain: quantity value
range: double
multivalued: false
exact_mappings:
- qud:quantityValue
in_subset:
- samples
has unit:
description: >-
connects a quantity value to a unit
domain: quantity value
range: unit
multivalued: false
close_mappings:
# These RTX contributed terms mean "is unit of" which is the semantic inverse of this biolink:has_unit term
- EFO:0001697
- UO-PROPERTY:is_unit_of
exact_mappings:
- qud:unit
- IAO:0000039
narrow_mappings:
- SNOMED:has_concentration_strength_denominator_unit
- SNOMED:has_concentration_strength_numerator_unit
- SNOMED:has_presentation_strength_denominator_unit
- SNOMED:has_presentation_strength_numerator_unit
- SNOMED:has_unit_of_presentation
in_subset:
- samples
base coordinate:
is_a: sequence localization attribute
aliases: [ 'one-based', 'fully-closed' ]
description: >-
A position in the base coordinate system. Base coordinates start at position 1 instead of position 0.
range: integer
## --------------------
## NODE PROPERTY SLOTS
## --------------------
node property:
description: >-
A grouping for any property that holds between a node and a value
domain: named thing
id:
identifier: true
description: >-
A unique identifier for an entity.
Must be either a CURIE shorthand for a URI or a complete URI
in_subset:
- translator_minimal
required: true
exact_mappings:
- alliancegenome:primaryId
- gff3:ID
- gpi:DB_Object_ID
iri:
description: >-
An IRI for an entity. This is determined by the id using expansion rules.
range: iri type
in_subset:
- translator_minimal
- samples
exact_mappings:
- WIKIDATA_PROPERTY:P854
type:
slot_uri: rdf:type
exact_mappings:
- alliancegenome:soTermId
- gff3:type
- gpi:DB_Object_Type
category:
is_a: type
domain: entity
range: category type
designates_type: true
description: >-
Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the
biolink entity type class.
* In a neo4j database this MAY correspond to the neo4j label tag.
* In an RDF database it should be a biolink model class URI.
This field is multi-valued. It should include values for ancestors of the biolink class; for example,
a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`, ...
In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink
class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f`
may have a rdf:type assertion to a SO class such as TF_binding_site,
which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity,
biolink:MolecularEntity, biolink:NamedThing}
is_class_field: true
multivalued: true
in_subset:
- translator_minimal
name:
aliases: [ 'label', 'display name', 'title' ]
description: >-
A human-readable name for an attribute or entity.
range: label type
in_subset:
- translator_minimal
- samples
#
# linkML doesn't like this name slot to be "required: true".
# Besides, some entity nodes/attributes may not have names?
# required: true
slot_uri: rdfs:label
exact_mappings:
- gff3:Name
- gpi:DB_Object_Name
narrow_mappings:
- dct:title
- WIKIDATA_PROPERTY:P1476
source:
deprecated: true
stoichiometry:
description: >-
the relationship between the relative quantities of substances taking part in a reaction or
forming a compound, typically a ratio of whole integers.
is_a: association slot
range: integer
reaction direction:
description: >-
the direction of a reaction as constrained by the direction_enum (ie: left_to_right, neutral, etc.)
is_a: association slot
range: reaction_direction_enum
narrow_mappings:
- NCIT:C42677
reaction balanced:
is_a: association slot
range: boolean
reaction side:
description: >-
the side of a reaction being modeled (ie: left or right)
is_a: association slot
range: reaction_side_enum
symbol:
is_a: node property
domain: named thing
description: >-
Symbol for a particular thing
exact_mappings:
- alliancegenome:symbol
- gpi:DB_Object_Symbol
synonym:
is_a: node property
aliases: ['alias']
domain: named thing
range: label type
description: >-
Alternate human-readable names for a thing
multivalued: true
in_subset:
- translator_minimal
narrow_mappings:
# there is an interesting debate here: are these terms "narrower" a.k.a. more specialized instances of
# 'biolink:synonym' or should they be binned into their respective namesake class of mappings?
# namely, is 'oboInOwl:hasExactSynonym' an instance 'exact_mappings', etc.
- skos:altLabel
- gff3:Alias
- alliancegenome:synonyms
- gpi:DB_Object_Synonyms
- oboInOwl:hasExactSynonym
- oboInOwl:hasNarrowSynonym
- oboInOwl:hasBroadSynonym
- oboInOwl:hasRelatedSynonym
# TODO: RTX contributed terms mapped here... May need review?
- HANCESTRO:0330
- IAO:0000136
- RXNORM:has_tradename
has topic:
aliases: ['topic', 'descriptors']
is_a: node property
range: ontology class
exact_mappings:
- foaf:topic
description: >-
Connects a node to a vocabulary term or ontology class that describes some aspect of the entity. In general specific characterization is preferred.
See https://github.com/biolink/biolink-model/issues/238
xref:
is_a: node property
aliases: ['dbxref', 'Dbxref', 'DbXref']
domain: named thing
range: uriorcurie
description: >-
Alternate CURIEs for a thing
multivalued: true
in_subset:
- translator_minimal
narrow_mappings:
- gff3:Dbxref
- gpi:DB_Xrefs
full name:
is_a: node property
domain: named thing
range: label type
description: >-
a long-form human readable name for a thing
description:
aliases: ['definition']
range: narrative text
description: >-
a human-readable description of an entity
in_subset:
- translator_minimal
slot_uri: dct:description
exact_mappings:
- IAO:0000115
- skos:definitions
narrow_mappings:
- gff3:Description
systematic synonym:
is_a: node property
domain: named thing
range: label type
multivalued: true
slot_uri: GOP:systematic_synonym
description: >-
more commonly used for gene symbols in yeast
affiliation:
is_a: node property
description: >-
a professional relationship between one provider (often a person) within another provider (often an organization).
Target provider identity should be specified by a CURIE. Providers may have multiple affiliations.
domain: agent
range: uriorcurie
multivalued: true
address:
is_a: node property
description: >-
the particulars of the place where someone or an organization is situated. For now, this slot is a
simple text "blob" containing all relevant details of the given location for fitness of purpose.
For the moment, this "address" can include other contact details such as email and phone number(?).
## Space
latitude:
is_a: node property
range: float
description: >-
latitude
exact_mappings:
- wgs:lat
longitude:
is_a: node property
range: float
description: >-
longitude
exact_mappings:
- wgs:long
## Time
timepoint:
is_a: node property
aliases: ['duration']
range: time type
description: >-
a point in time
creation date:
is_a: node property
aliases: ['publication date']
range: date
description: >-
date on which an entity was created. This can be applied to nodes or edges
exact_mappings:
- dct:createdOn
- WIKIDATA_PROPERTY:P577
update date:
is_a: node property
range: date
description: >-
date on which an entity was updated. This can be applied to nodes or edges
## Statistics
aggregate statistic:
is_a: node property
abstract: true
has count:
description: >-
number of things with a particular property
is_a: aggregate statistic
range: integer
exact_mappings:
- LOINC:has_count
has total:
description: >-
total number of things in a particular reference set
is_a: aggregate statistic
range: integer
has quotient:
is_a: aggregate statistic
range: double
has percentage:
description: >-
equivalent to has quotient multiplied by 100
is_a: aggregate statistic
range: double
## Properties for Information Content Entity and Publication Nodes
has taxonomic rank:
is_a: node property
range: taxonomic rank
multivalued: false
mappings:
- WIKIDATA:P105
has dataset:
is_a: node property
domain: dataset version
range: dataset
slot_uri: dct:source
source web page:
is_a: node property
domain: dataset summary
broad_mappings:
- dct:source
source logo:
is_a: node property
domain: dataset summary
slot_uri: schema:logo
retrieved on:
is_a: node property
domain: dataset
range: date
exact_mappings:
- pav:retrievedOn
version of:
is_a: node property
domain: dataset version
range: dataset summary
exact_mappings:
- dct:isVersionOf
version:
is_a: node property
domain: dataset
broad_mappings:
- pav:version
- owl:versionInfo
license:
is_a: node property
domain: information content entity
exact_mappings:
- dct:license
narrow_mappings:
- WIKIDATA_PROPERTY:P275
rights:
is_a: node property
domain: information content entity
exact_mappings:
- dct:rights
format:
is_a: node property
domain: information content entity