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biolink-model.yaml
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id: "http://bioentity.io/json-schema/biolink.json"
name: biolink model
description: Entity and association taxonomy and datamodel for life-sciences data
prefixes:
OBAN: http://purl.org/oban/
SIO: http://semanticscience.org/resource/SIO_
wgs: http://www.w3.org/2003/01/geo/wgs84_pos
types:
- name: identifier type
typeof: string
description: >-
A string that is intended to uniquely identify a thing
May be URI in full or compact (CURIE) form
- name: label type
typeof: string
description: >-
A string that provides a human-readable name for a thing
- name: symbol type
typeof: string
- name: biological sequence
typeof: string
slots:
- name: id
identifier: true
abstract: true
domain: named thing
range: identifier type
- name: label
domain: named thing
range: label type
description: >-
A human-readable name for a thing
mappings:
- "rdfs:label"
- name: full name
domain: named thing
range: label type
description: >-
a long-form human readable name for a thing
- name: description
domain: named thing
range: string
description: >-
a human-readable description of a thing
- name: systematic synonym
domain: named thing
range: label type
description: >-
more commonly used for gene symbols in yeast
- name: association slot
abstract: true
domain: association
description: >-
any slot that relates an association to another entity
- name: subject
is_a: association slot
description: >-
connects an association to the subject of the association.
For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.
required: true
mappings:
- rdf:subject
- owl:annotatedSource
- oban:association_has_subject
- name: object
is_a: association slot
description: >-
connects an association to the object of the association.
For example, in a gene-to-phenotype association, the gene is subject and phenotype is object.
required: true
mappings:
- rdf:object
- owl:annotatedTarget
- oban:association_has_object
- name: relation
is_a: association slot
description: >-
the relationship type by which a subject is connected to an object in an association
range: relationship type
required: true
mappings:
- "rdf:predicate"
- "owl:annotatedProperty"
- "oban:association_has_predicate"
- name: negated
is_a: association slot
range: boolean
description: >-
if set to true, then the association is negated i.e. is not true
- name: has confidence level
is_a: association slot
range: confidence level
description: >-
connects an association to a qualitative term denoting the level of confidence
- name: has evidence
is_a: association slot
range: evidence instance
description: >-
connects an association to an instance of supporting evidence
- name: provided by
is_a: association slot
range: provider
description: >-
connects an association to the agent (person, organization or group) that provided it
mappings:
- prov:providedBy
- name: association type
is_a: association slot
range: ontology class
description: >-
connects an association to the type of association (e.g. gene to phenotype)
mappings:
- rdf:type
- name: creation date
range: date
description: >-
date on which thing was created
mappings:
- dc:created
- name: in taxon
domain: thing with taxon
range: organism taxon
description: >-
connects a thing to a class representing a taxon
mappings:
- "RO:0002162"
- name: latitude
range: float
description: >-
latitude
mappings:
- wgs:lat
- name: longitude
range: float
description: >-
longitude
mappings:
- wgs:long
- name: timepoint
range: xsd:time
description: >-
a point in time
- name: stage qualifier
is_a: association slot
range: life stage
path: "object/during"
description: >-
stage at which expression takes place
- name: quantifier qualifier
is_a: association slot
range: quantifier
description: >-
A measurable quantity for the object of the association
- name: qualifiers
singular_name: qualifier
description: >-
connects an association to qualifiers that modify or qualify the meaning of that association
is_a: association slot
multivalued: true
range: ontology class
- name: frequency qualifier
description: >-
a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject
is_a: association slot
range: frequency value
- name: severity qualifier
description: >-
a qualifier used in a phenotypic association to state how severe the phenotype is in the subject
is_a: association slot
range: severity value
- name: onset qualifier
description: >-
a qualifier used in a phenotypic association to state when the phenotype appears is in the subject
is_a: association slot
range: life stage
- name: publications
singular_name: publication
description: >-
connects an association to publications supporting the association
is_a: association slot
multivalued: true
range: publication
## genotypes
- name: has gene
description: >-
connects and entity to a single gene
range: gene
- name: has zygosity
domain: single locus feature complement
range: zygosity
- name: filler
range: named thing
description: >-
The value in a property-value tuple
- name: phase
description: >-
TODO
- name: genome build
description: >-
TODO
- name: interbase coordinate
description: >-
TODO
- name: start interbase coordinate
is_a: interbase coordinate
- name: end interbase coordinate
is_a: interbase coordinate
## ------
## OTHER
## ------
- name: associations
multivalued: true
range: association
classes:
## ------
## RELATIONSHIP TYPES
## ------
- name: relationship type
description: >-
An OWL property used as an edge label
## ------
## THINGS
## ------
- name: severity value
description: >-
describes the severity of a phenotypic feature or disease
is_a: attribute
- name: frequency value
description: >-
describes the frequency of occurrence of an event or condition
is_a: attribute
- name: named thing
description: "a databased entity or concept/class"
slots:
- id
- label
slot_usage:
- name: id
required: true
- name: biological entity
is_a: named thing
abstract: true
- name: ontology class
description: "a concept or class in an ontology, vocabulary or thesaurus"
mixin: true
- name: gene ontology class
description: >-
an ontology class that describes a functional aspect of a gene, gene prodoct or complex
mixin: true
is_a: ontology class
flags:
- testing
- name: thing with taxon
abstract: true
mixin: true
description: >-
A mixin that can be used on any entity with a taxon
slots:
- in taxon
- name: organism taxon
is_a: organismal entity
mixins:
- ontology class
values_from:
- ncbitaxon
- name: organismal entity
description: >-
A named entity that is either a part of an organism, a whole organism, population or clade of organisms, excluding molecular entities
abstract: true
is_a: biological entity
- name: individual organism
mixins:
- thing with taxon
is_a: organismal entity
subclass_of: "NCBITaxon:1"
mappings:
- SIO:010000
- name: case
aliases: ['patient', 'proband']
is_a: individual organism
description: >-
An individual organism that has a patient role in some clinical context.
- name: population of individual organisms
mixins:
- thing with taxon
is_a: organismal entity
- name: biosample
aliases: ['biospecimen', 'sample']
mixins:
- thing with taxon
is_a: organismal entity
- name: disease or phenotypic feature
aliases: ['phenome']
is_a: biological entity
description: >-
Either one of a disease or an individual phenotypic feature. Some knowledge resources such as Monarch treat these as distinct, others such as MESH conflate.
mixins:
- thing with taxon
union_of:
- disease
- phenotypic feature
- name: disease
aliases: ['condition', 'disorder']
is_a: disease or phenotypic feature
mappings:
- "MONDO:0000001"
- name: phenotypic feature
aliases: ['sign', 'symptom', 'phenotype', 'trait']
is_a: disease or phenotypic feature
mappings:
- "UPHENO:0000001"
- name: environment
aliases: ['environment', 'exposure', 'experimental condition']
is_a: biological entity
description: >-
A feature of the environment of an organism that influences one or more phenotypic features
of that organism, potentially mediated by genes
- name: information content entity
aliases: ['information', 'information artefact', 'information entity']
abstract: true
is_a: named thing
description: >-
a piece of information that typically describes some piece of biology or is used as support.
mappings:
- "IAO:0000030"
- name: confidence level
is_a: information content entity
description: >-
Level of confidence in a statement
values_from:
- cio
mappings:
- "CIO:0000028"
- name: evidence type
is_a: information content entity
aliases: ['evidence code']
description: >-
Class of evidence that supports an association
values_from:
- eco
mappings:
- "ECO:0000000"
- name: publication
is_a: information content entity
aliases: ['reference']
description: >-
Any published piece of information. Can refer to a whole publication,
or to a part of it (e.g. a figure, figure legend, or section highlighted by NLP).
The scope is intended to be general and include information published on the web as well as journals.
mappings:
- "IAO:0000311"
- name: administrative entity
abstract: true
- name: provider
is_a: administrative entity
aliases: ['agent', 'group']
description: >-
person, group, organization or project that provides a piece of information
- name: molecular entity
is_a: biological entity
mixins:
- thing with taxon
aliases: ['bioentity']
description: "A gene, gene product, small molecule or macromolecule (including protein complex)"
- name: chemical substance
is_a: molecular entity
description: >-
may be a chemical entity or a formulation with a chemical entity as active ingredient, or a complex
material with multiple chemical entities as part
subclass_of: "CHEBI:24431"
mappings:
- SIO:010004
- name: attribute
subclass_of: PATO:0000001
description: >-
A property or characteristic of an entity
- name: anatomical entity
is_a: organismal entity
mixins:
- thing with taxon
subclass_of: UBERON:0001062
description: >-
A subcellular location, cell type or gross anatomical part
- name: life stage
is_a: organismal entity
mixins:
- thing with taxon
subclass_of: UBERON:0000105
description: >-
A stage of development or growth of an organism, including post-natal adult stages
- name: planetary entity
is_a: named thing
description: >-
Any entity or process that exists at the level of the whole planet
- name: environmental process
is_a: planetary entity
mixins:
- occurrent
subclass_of: ENVO:02500000
- name: environmental feature
is_a: planetary entity
subclass_of: ENVO:00002297
- name: clinical entity
is_a: named thing
description: >-
Any entity or process that exists in the clinical domain and outside the biological realm. Diseases are placed under biological entities
- name: clinical trial
is_a: clinical entity
- name: clinical intervention
is_a: clinical entity
- name: genomic entity
is_a: molecular entity
aliases: ['sequence feature']
description: >-
an entity that can either be directly located on a genome (gene, transcript, exon, regulatory region) or is encoded in a genome (protein)
mappings: ['SO:0000110']
- name: genome
is_a: genomic entity
description: >-
A genome is the sum of genetic material within a cell or virion.
mappings: ['SO:0001026']
- name: transcript
is_a: genomic entity
description: >-
An RNA synthesized on a DNA or RNA template by an RNA polymerase
mappings: ['SO:0000673']
- name: exon
is_a: genomic entity
description: >-
A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing
mappings: ['SO:0000147']
- name: coding sequence
is_a: genomic entity
mappings: ['SO:0000316']
- name: gene or gene product
is_a: genomic entity
union_of:
- gene
- gene product
description: >-
a union of genes or gene products.
Frequently an identifier for one will be used as proxy for another
slot_usage:
- name: label
range: symbol type
description: >-
genes are typically designated by a short symbol and a full name. We map the symbol to the default display label
and use an additional slot for full name
- name: gene
is_a: gene or gene product
aliases: ['locus']
id_prefixes:
- NCBIGene
- ENSEMBL
- HGNC
- MGI
- ZFIN
mappings:
- "SO:0000704"
- "SIO:010035"
- name: gene product
is_a: gene or gene product
description: >-
The functional molecular product of a single gene. Gene products are either proteins or functional RNA molecules
union_of:
- protein
- RNA product
- name: protein
is_a: gene product
mappings:
- "PR:000000001"
- "SIO:010043"
id_prefixes:
- UniProtKB
- PR
- ENSEMBL
- name: RNA product
is_a: gene product
mappings:
- "CHEBI:33697"
id_prefixes:
- RNAcentral
- name: noncoding RNA product
is_a: RNA product
id_prefixes:
- RNAcentral
- name: microRNA
is_a: noncoding RNA product
mappings:
- "SO:0000276"
id_prefixes:
- MIR
- name: macromolecular complex
is_a: molecular entity
mappings:
- "GO:0032991"
- "SIO:010046"
id_prefixes:
- IntAct
- name: gene grouping
abstract: true
mixin: true
description: >-
any grouping of multiple genes or gene products
- name: gene family
is_a: molecular entity
mappings:
- "NCIT:C20130"
mixins:
- gene grouping
description: >-
any grouping of multiple genes or gene products related by common descent
id_prefixes:
- PANTHER
- name: zygosity
is_a: attribute
mappings:
- "GENO:0000133"
- name: genotype
is_a: genomic entity
description: >-
An information content entity that describes a genome by specifying the total variation in genomic sequence and/or gene expression, relative to some extablished background
comment: >-
Consider renaming as genotypic entity
slots:
- has zygosity
mapping:
- "GENO:0000536"
- name: allele
is_a: genotype
description: >-
A genomic feature representing one of a set of coexisting sequence variants at a particular genomic locus
alt_descriptions:
- description: "An enitity that describes a single affected, endogenous allele. These can be of any type that matches that definition"
source: AGR
slots:
- has gene
slot_usage:
- slot: has gene
multivalued: true
description: Each allele can be associated with any number of genes
- slot: id
examples:
- value: ZFIN:ZDB-ALT-980203-1091
description: ti282a allele from ZFIN
mapping:
- "GENO:0000512"
- name: sequence variant
aliases: ['allele']
is_a: genomic entity
description: >-
A genomic feature representing one of a set of coexisting sequence variants at a particular genomic locus.
mappings:
- "GENO:0000512"
- name: drug exposure
aliases: ['drug intake', 'drug dose']
is_a: environment
description: >-
A drug exposure is an intake of a particular chemical substance
slots:
- drug
slot_usage:
- name: drug
range: chemical entity
required: true
multivalued: true
mappings:
- "ECTO:0000509"
- name: treatment
aliases: ['medical action']
is_a: environment
description: >-
A treatment is targeted at a disease or phenotype and may involve multiple drug 'exposures'
slots:
- treats
- has exposure parts
slot_usage:
- name: treats
range: disease or phenotypic feature
required: true
- name: has exposure parts
multivalued: true
range: drug exposure
required: true
mappings:
- "OGMS:0000090"
- name: geographic location
is_a: planetary entity
description: >-
a location that can be described in lat/long coordinates
slots:
- latitude
- longitude
- name: geographic location at time
is_a: planetary entity
description: >-
a location that can be described in lat/long coordinates, for a particular time
slots:
- latitude
- longitude
- timepoint
## ------
## ASSOCIATIONS
## ------
- name: association
abstract: true
is_a: information content entity
description: >-
A typed association between two entities, supported by evidence
comment: This is roughly the model used by biolink and ontobio at the moment
slots:
- association type
- subject
- negated
- relation
- object
- qualifiers
- publications
- provided by
mappings:
- "OBAN:association"
- "rdf:Statement"
- "owl:Axiom"
- name: genotype to genotype part association
is_a: association
defining_slots:
- subject
- object
description: >-
Any association between one genotype and a genotypic entity that is a sub-component of it
slot_usage:
- name: relation
subproperty_of: "GENO:0000382"
- name: subject
range: genotype
description: >-
parent genotype
definitional: true
- name: object
range: genotype
description: >-
child genotype
definitional: true
- name: genotype to gene association
is_a: association
defining_slots:
- subject
- object
description: >-
Any association between a genotype and a gene.
The genotype have have multiple variants in that gene or a single one. There is no assumption of cardinality
slot_usage:
- name: relation
description: >-
the relationship type used to connect genotype to gene
- name: subject
range: genotype
description: >-
parent genotype
definitional: true
- name: object
range: gene
description: >-
gene implicated in genotype
definitional: true
- name: genotype to variant association
is_a: association
defining_slots:
- subject
- object
description: >-
Any association between a genotype and a sequence variant.
slot_usage:
- name: relation
description: >-
the relationship type used to connect genotype to gene
- name: subject
range: genotype
description: >-
parent genotype
definitional: true
- name: object
range: sequence variant
description: >-
gene implicated in genotype
definitional: true
- name: gene to gene association
aliases: ['molecular or genetic interaction']
abstract: true
is_a: association
defining_slots:
- subject
- object
description: >-
abstract parent class for different kinds of gene-gene or gene product to gene product relationships.
Includes homology and interaction.
slot_usage:
- name: subject
range: gene or gene product
description: >-
the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary.
We allow a gene product to stand as proxy for the gene or vice versa
definitional: true
- name: object
range: gene or gene product
description: >-
the object gene in the association. If the relation is symmetric, subject vs object is arbitrary.
We allow a gene product to stand as proxy for the gene or vice versa
definitional: true
- name: gene to gene homology association
is_a: gene to gene association
defining_slots:
- subject
- object
- relation
description: >-
A homology association between two genes. May be orthology (in which case the species of subject and object
should differ) or paralogy (in which case the species may be the same)
symmetric: true
slot_usage:
- name: relation
subproperty_of: "RO:HOM0000001"
values_from:
- ro
description: >-
homology relationship type
definitional: true
- name: molecular interaction
is_a: association
mixin: true
abstract: true
description: >-
An interaction at the molecular level between two physical entities
slot_usage:
- name: relation
subproperty_of: "RO:0002436"
values_from:
- ro
- mi
description: "interaction relationship type"
definitional: true
- slot: interacting molecules category
range: class
subclass_of: "MI:1046"
examples:
- value: MI:1048
description: smallmolecule-protein
- name: pairwise gene or protein interaction association
is_a: gene to gene association
defining_slots:
- subject
- object
- relation
mixins:
- molecular interaction
description: >-
An interaction between two genes or two gene products.
May be physical (e.g. protein binding) or genetic (between genes).
May be symmetric (e.g. protein interaction) or directed (e.g. phosphorylation)
symmetric: true
slot_usage:
- name: relation
subproperty_of: "RO:0002436"
values_from:
- ro
- mi
description: "interaction relationship type"
definitional: true
- name: chemical to thing association
is_a: association
defining_slots:
- subject
abstract: true
description: >-
An interaction between a chemical entity and another entity
slot_usage:
- name: subject
range: chemical substance
description: "the chemical substance or entity that is an interactor"
definitional: true
- name: case to thing association
is_a: association
defining_slots:
- subject
abstract: true
description: >-
An abstract association for use where the case is the subject
slot_usage:
- name: subject
range: case
description: "the case (e.g. patient) that has the property"
definitional: true
- name: chemical to gene association
is_a: association
defining_slots:
- subject
- object
mixins:
- chemical to thing association
description: >-
An interaction between a chemical entity or substance and a gene or gene product. The chemical substance may
be a drug with the gene being a target of the drug.
slot_usage:
- name: object
range: gene product
description: "the gene or gene product with which the chemical interacts"
definitional: true
- name: chemical to disease or phenotypic feature association
is_a: association
mappings:
- SIO:000993
defining_slots:
- subject
- object
mixins:
- chemical to thing association
- thing to disease or phenotypic feature association
description: >-
An interaction between a chemical entity and a phenotype or disease, where the presence of the chemical gives rise to
or exacerbates the phenotype
slot_usage:
- name: object
range: disease or phenotypic feature
description: "the disease or phenotype that is affected by the chemical"
definitional: true
- name: chemical to pathway association
is_a: association
mappings:
- SIO:001250
defining_slots:
- subject
- object
mixins:
- chemical to thing association
description: >-
An interaction between a chemical entity and a biological process or pathway
slot_usage:
- name: object
range: pathway
description: "the pathway that is affected by the chemical"
definitional: true
- name: chemical to gene association
is_a: association
mappings:
- SIO:001257
defining_slots:
- subject
- object
mixins:
- chemical to thing association
description: >-
An interaction between a chemical entity and a gene or gene product
slot_usage:
- name: object
range: gene or gene product
description: "the gene or gene product that is affected by the chemical"
definitional: true
- name: biosample to thing association
is_a: association
defining_slots:
- subject
abstract: true
description: >-
An association between a biosample and something
slot_usage:
- name: subject
range: biosample
description: >-
the biosample being described
definitional: true
- name: biosample to disease or phenotypic feature association
is_a: association
defining_slots:
- subject
- object
mixins:
- biosample to thing association