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knowledge-beacon-api.yaml
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swagger: '2.0'
info:
title: Translator Knowledge Beacon API
version: 1.1.1
contact:
url: 'http://starinformatics.com'
email: richard@starinformatics.com
description: >
This is the Translator Knowledge Beacon web service application programming
interface (API).
license:
name: MIT License
url: 'http://opensource.org/licenses/MIT'
schemes:
- https
produces:
- application/json
tags:
- name: metadata
description: Queries about global characteristics of the knowledge source
- name: concepts
description: Queries relating to concepts
- name: statements
description: Queries relating to concept-relationship statements and their evidence
paths:
/categories:
get:
description: >
Get a list of concept categories and number of their concept instances
documented by the knowledge source. These types should be mapped onto
the Translator-endorsed Biolink Model concept type classes with local
types, explicitly added as mappings to the Biolink Model YAML file.
tags:
- metadata
operationId: getConceptCategories
responses:
'200':
schema:
type: array
items:
title: BeaconConceptCategory
type: object
properties:
id:
type: string
description: the CURIE of the concept category
uri:
type: string
description: >-
The category URI which should generally resolves to the
full semantic description of the category
category:
type: string
description: 'human readable name ("rdfs:label")'
local_id:
type: string
description: the locally designated CURIE of the concept category
local_uri:
type: string
description: >-
This locally designated category URI should generally
resolve to the full semantic description of the category
local_category:
type: string
description: 'human readable local semantic type name ("rdfs:label")'
description:
type: string
description: human readable name definition of the category
frequency:
type: integer
description: >-
the number of concept entries of the specified type in the
beacon knowledge base
description: |
Successful response with categories and frequency returned
examples:
application/json:
- id: 'biolink:CellularComponent'
uri: 'http://bioentity.io/vocab/CellularComponent'
category: cellular component
local_id: 'GO:0005575'
local_uri: 'http://amigo.geneontology.org/amigo/term/GO:0005575'
local_category: cellular_component
description: |
The part of a cell, extracellular environment or virus in
which a gene product is located.
frequency: 12355
/predicates:
get:
description: >
Get a list of predicates used in statements issued by the knowledge
source
tags:
- metadata
operationId: getPredicates
responses:
'200':
schema:
type: array
items:
title: BeaconPredicate
type: object
properties:
id:
type: string
description: |
CURIE-encoded identifier of predicate relation
uri:
type: string
description: >-
The predicate URI which should generally resolves to the
full semantic description of the predicate relation
edge_label:
type: string
description: >
A predicate edge label which must be taken from the minimal
predicate ('slot') list of the [Biolink
Model](https://biolink.github.io/biolink-model).
relation:
type: string
description: >
The predicate relation, with the preferred format being a
CURIE where one exists, but strings/labels acceptable. This
relation may be equivalent to the edge_label (e.g.
edge_label: has_phenotype, relation: RO:0002200), or a more
specific relation in cases where the source provides more
granularity (e.g. edge_label: molecularly_interacts_with,
relation: RO:0002447)
local_id:
type: string
description: >
CURIE-encoded identifier of the locally defined predicate
relation. Such terms should be formally documented as
mappings in the [Biolink
Model](https://biolink.github.io/biolink-model)
local_uri:
type: string
description: >-
The predicate URI which should generally resolves to the
local predicate relation
local_relation:
type: string
description: >
human readable name of the locally defined predicate
relation
description:
type: string
description: >
human readable definition of predicate relation provided by
this beacon
frequency:
type: integer
description: >-
the number of statement entries using the specified
predicate in the given beacon knowledge base
description: >
Successful response with predicates with CURIE and definitions
indexed by beacons which support the relation
examples:
application/json:
- id: 'biolink:has_phenotype'
uri: 'http://bioentity.io/vocab/has_phenotype'
edge_label: has_phenotype
relation: 'RO:001279'
local_id: 'SIO:000983'
local_uri: 'http://semanticscience.org/resource/SIO_001279'
local_relation: has phenotype
description: |
has phenotype is a relation between an object and an
observable/measurable characteristic
frequency: 1234
/kmap:
get:
description: >
Get a high level knowledge map of the all the beacons by subject
semantic type, predicate and semantic object type
tags:
- metadata
operationId: getKnowledgeMap
responses:
'200':
schema:
type: array
items:
title: BeaconKnowledgeMapStatement
type: object
properties:
subject:
title: BeaconKnowledgeMapSubject
type: object
properties:
category:
type: string
description: >
the concept semantic type of a statement subject. This
should be specified as Biolink concept semantic type
names like gene, pathway, etc. (see [Biolink
Model](https://biolink.github.io/biolink-model) for the
full list of terms)
prefixes:
type: array
items:
type: string
description: >
the prefix of the namespace of statement subject
concept identifiers which may conceivably be bound to
the given relationship
predicate:
title: BeaconKnowledgeMapPredicate
type: object
properties:
edge_label:
type: string
description: >
Human readable name of the 'minimal' standard Biolink
Model predicate relationship name. See [Biolink
Model](https://biolink.github.io/biolink-model) for the
full list of terms.
relation:
type: string
description: >
Human readable name of a 'maximal' Biolink Model or
beacon-specific (or Reasoner-specific) predicate
relationship name.
negated:
type: boolean
object:
title: BeaconKnowledgeMapObject
type: object
properties:
category:
type: string
description: >
the concept semantic type of a statement object. This
should be specified as Biolink concept semantic type
names
like gene, pathway, etc. (see [Biolink
Model](https://biolink.github.io/biolink-model) for the
full list of terms)
prefixes:
type: array
items:
type: string
description: >
the prefix of the namespace of statement object
concept identifiers which may conceivably be bound to
the given relationship
frequency:
type: integer
description: >
the frequency of statements of the specified relationship
within the given beacon
description:
type: string
description: |
a description of the nature of the relationship
description: |
Successful response with categories and frequency returned
examples:
application/json:
- subject:
category: gene
prefixes:
- DRUGBANK
- CHEMBL
- UNIPROT
predicate:
relation: gene_associated_with_condition
object:
category: disease or phenotypic feature
prefixes:
- MP
- HP
- DOID
count: 500
description: >
a gene that is capable of some activity that affects the
magnitude or nature of a pathological process, phenotype or
disease
/concepts:
get:
description: |
Retrieves a list of whose concept in the
beacon knowledge base with names and/or synonyms
matching a set of keywords or substrings.
The results returned should generally
be returned in order of the quality of the match,
that is, the highest ranked concepts should exactly
match the most keywords, in the same order as the
keywords were given. Lower quality hits with fewer
keyword matches or out-of-order keyword matches,
should be returned lower in the list.
tags:
- concepts
parameters:
- name: keywords
in: query
description: >-
an array of keywords or substrings against which to match concept
names and synonyms
required: true
type: array
items:
type: string
- name: categories
in: query
description: >
an array set of concept categories - specified as Biolink name
labels codes gene, pathway, etc. - to which to constrain concepts
matched by the main keyword search (see [Biolink
Model](https://biolink.github.io/biolink-model) for the full list of
terms)
required: false
type: array
items:
type: string
- name: size
in: query
description: >
maximum number of concept entries requested by the client; if this
argument is omitted, then the query is expected to returned all the
available data for the query
required: false
type: integer
operationId: getConcepts
responses:
'200':
schema:
type: array
items:
title: BeaconConcept
type: object
properties:
id:
type: string
description: >
local object CURIE for the concept in the specified
knowledge source database
name:
type: string
description: |
canonical human readable name of the concept
categories:
type: array
items:
type: string
description: >
concept semantic type 'category'. Should be specified from
the
[Biolink Model](https://biolink.github.io/biolink-model).
description:
type: string
description: |
(optional) narrative concept definition
description: |
Successful response with list of core concept data returned
examples:
application/json:
- id: 'wd:Q6591532'
name: 'WRN protein, human'
category: protein
description: >-
Werner syndrome ATP-dependent helicase (1432 aa, ~162 kDa) is
encoded by the human WRN gene. This protein plays a role in
both magnesium and ATP-dependent DNA-helicase activity and
3\'->5\' exonuclease activity towards double-stranded DNA with
a 5\'-overhang.
'/concepts/{conceptId}':
get:
description: >
Retrieves details for a specified concepts in the system, as specified
by a (url-encoded) CURIE identifier of a concept known the given
knowledge source.
tags:
- concepts
parameters:
- name: conceptId
in: path
description: (url-encoded) CURIE identifier of concept of interest
required: true
type: string
operationId: getConceptDetails
responses:
'200':
schema:
title: BeaconConceptWithDetails
type: object
properties:
id:
type: string
description: >
local object CURIE for the concept in the specified knowledge
source database
uri:
type: string
description: |
(optional) equivalent to expansion of the CURIE
name:
type: string
description: |
canonical human readable name of the concept
symbol:
type: string
description: |
(optional) symbol, used for genomic data
categories:
type: array
items:
type: string
description: |
concept semantic type 'category'. Should be specified from the
[Biolink Model](https://biolink.github.io/biolink-model).
description:
type: string
description: |
(optional) narrative concept definition
synonyms:
type: array
description: |
list of synonyms for concept
items:
type: string
exact_matches:
description: >
List of [CURIE](https://www.w3.org/TR/curie/) identifiers of
concepts thought to be exactly matching concepts,
[*sensa*-SKOS](http://www.w3.org/2004/02/skos/core#exactMatch).
This is generally the same list returned by the /exact_matches
endpoint (given the concept 'id' as input)
type: array
items:
type: string
details:
type: array
items:
title: BeaconConceptDetail
type: object
properties:
tag:
type: string
description: |
property name
value:
type: string
description: |
property value
description: |
Any other metadata returned by the beacon as tag = value
description: |
Successful response with concept details returned
examples:
application/json:
- id: 'wd:Q6591532'
name: 'WRN protein, human'
category: protein
symbol: WRN
synonyms:
- RecQ3
- Werner Syndrome ATP-Dependent Helicase
- 'RECQL2 protein, human'
- EC 3.1.-.-
- 'WRN protein, human'
- WRN
- Exonuclease WRN
- Werner Syndrome Protein
- RecQ Protein-Like 2
- EC 3.6.4.12
- 'RECQ3 protein, human'
- 'Werner syndrome helicase, human'
- WRN Protein
- 'DNA Helicase, RecQ-Like Type 3'
description: >-
Werner syndrome ATP-dependent helicase (1432 aa, ~162 kDa) is
encoded by the human WRN gene. This protein plays a role in
both magnesium and ATP-dependent DNA-helicase activity and
3\'->5\' exonuclease activity towards double-stranded DNA with
a 5\'-overhang.
details:
- tag: taxon
value: '9606'
- tag: phenotype
value: progeria
/exactmatches:
get:
description: >
Given an input array of [CURIE](https://www.w3.org/TR/curie/)
identifiers of known exactly matched concepts
[*sensa*-SKOS](http://www.w3.org/2004/02/skos/core#exactMatch),
retrieves the list of [CURIE](https://www.w3.org/TR/curie/) identifiers
of additional concepts that are deemed by the given knowledge source to
be exact matches to one or more of the input concepts **plus** whichever
concept identifiers from the input list were specifically matched to
these additional concepts, thus giving the whole known set of equivalent
concepts known to this particular knowledge source. If an empty set is
returned, the it can be assumed that the given knowledge source does
not know of any new equivalent concepts matching the input set. The
caller of this endpoint can then decide whether or not to treat its
input identifiers as its own equivalent set.
tags:
- concepts
parameters:
- name: c
in: query
description: >
an array set of [CURIE-encoded](https://www.w3.org/TR/curie/)
identifiers of concepts thought to be exactly matching concepts, to
be used in a search for additional exactly matching concepts
[*sensa*-SKOS](http://www.w3.org/2004/02/skos/core#exactMatch).
required: true
type: array
items:
type: string
operationId: getExactMatchesToConceptList
responses:
'200':
description: >
Successful response returns a set of
[CURIE-encoded](https://www.w3.org/TR/curie/) identifiers of
concepts (with supporting evidence code and reference) matching at
least one identifier in the input list of known exactly matched
concepts
[*sensa*-SKOS](http://www.w3.org/2004/02/skos/core#exactMatch). Each
concept identifier is returned with the full list of any additional
associated [CURIE-encoded](https://www.w3.org/TR/curie/) identifiers
of exact match concepts known to the given Knowledge Source.
schema:
type: array
items:
title: ExactMatchResponse
type: object
properties:
id:
type: string
description: |
A given [CURIE](https://www.w3.org/TR/curie/) identifier.
within_domain:
type: boolean
description: >
True if the knowledge source is aware of this identifier,
and has the capacity to return the identified concept.
Otherwise, false.
has_exact_matches:
description: >
List of [CURIE](https://www.w3.org/TR/curie/) identifiers of
a exactly matching concepts.
type: array
items:
type: string
examples:
application/json:
- 'wd:Q14883734'
- 'NCBIGene:7486'
/statements:
get:
description: >
Given a specified set of [CURIE-encoded](https://www.w3.org/TR/curie/)
source ('s') concept identifiers, retrieves a list of relationship
statements where either the subject or object concept matches any of the
input 'source' concepts provided. Optionally, a set of target ('t')
concept identifiers may also be given, in which case a member of the
'target' identifier set should match the concept opposing the 'source'
in the statement, that is, if the'source' matches a subject, then the
'target' should match the object of a given statement (or vice versa).
tags:
- statements
parameters:
- name: s
in: query
description: >
an array set of [CURIE-encoded](https://www.w3.org/TR/curie/)
identifiers of 'source' concepts possibly known to the beacon.
Unknown CURIES should simply be ignored (silent match failure).
required: true
type: array
items:
type: string
- name: edge_label
in: query
description: >
(Optional) A predicate edge label against which to constrain the
search for statements ('edges') associated with the given query seed
concept. The predicate edge_names for this parameter should be as
published by the /predicates API endpoint and must be taken from the
minimal predicate ('slot') list of the [Biolink
Model](https://biolink.github.io/biolink-model).
required: false
type: string
- name: relation
in: query
description: >
(Optional) A predicate relation against which to constrain the
search for statements ('edges') associated with the given query seed
concept. The predicate relations for this parameter should be as
published by the /predicates API endpoint and the preferred format
is a CURIE where one exists, but strings/labels acceptable. This
relation may be equivalent to the edge_label (e.g. edge_label:
has_phenotype, relation: RO:0002200), or a more specific relation
in cases where the source provides more granularity (e.g.
edge_label: molecularly_interacts_with, relation: RO:0002447)
required: false
type: string
- name: t
in: query
description: >
(optional) an array set of
[CURIE-encoded](https://www.w3.org/TR/curie/) identifiers of
'target' concepts possibly known to the beacon. Unknown CURIEs
should simply be ignored (silent match failure).
required: false
type: array
items:
type: string
- name: keywords
in: query
description: >-
an array of keywords or substrings against which to filter concept
names and synonyms
required: false
type: array
items:
type: string
- name: categories
in: query
description: >
an array set of concept categories (specified as Biolink name labels
codes gene, pathway, etc.) to which to constrain concepts matched by
the main keyword search (see [Biolink
Model](https://biolink.github.io/biolink-model) for the full list of
codes)
required: false
type: array
items:
type: string
- name: size
in: query
description: >
maximum number of concept entries requested by the client; if this
argument is omitted, then the query is expected to returned all the
available data for the query
required: false
type: integer
operationId: getStatements
responses:
'200':
description: >
Successful response returns a list of concept-relations where there
is an exact match of an input concept identifier either to the
subject or object concepts of the statement
schema:
type: array
items:
title: BeaconStatement
type: object
properties:
id:
type: string
description: >-
CURIE-encoded identifier for statement (can be used to
retrieve associated evidence)
subject:
title: BeaconStatementSubject
type: object
properties:
id:
type: string
description: |
CURIE-encoded identifier of concept
name:
type: string
description: human readable label of subject concept
categories:
type: array
items:
type: string
description: >
a semantic group for the subject concept (specified as a
code gene, pathway, disease, etc. - see [Biolink
Model](https://biolink.github.io/biolink-model) for the
full list of categories)
predicate:
title: BeaconStatementPredicate
type: object
properties:
edge_label:
type: string
description: >
The predicate edge label associated with this statement,
which should be as published by the /predicates API
endpoint and must be taken from the minimal predicate
('slot') list of the [Biolink
Model](https://biolink.github.io/biolink-model).
relation:
type: string
description: >-
The predicate relation associated with this statement,
which should be as published by the /predicates API
endpoint with the preferred format being a CURIE where
one exists, but strings/labels acceptable. This relation
may be equivalent to the edge_label (e.g. edge_label:
has_phenotype, relation: RO:0002200), or a more specific
relation in cases where the source provides more
granularity (e.g. edge_label:
molecularly_interacts_with, relation: RO:0002447)
negated:
type: boolean
description: >
(Optional) a boolean that if set to true, indicates the
edge statement is negated i.e. is not true
object:
title: BeaconStatementObject
type: object
properties:
id:
type: string
description: |
CURIE-encoded identifier of object concept
name:
type: string
description: human readable label of object concept
categories:
type: array
items:
type: string
description: >
a semantic group for the object concept (specified as a
code gene, pathway, disease, etc. - see [Biolink
Model](https://biolink.github.io/biolink-model) for the
full list of categories)
examples:
application/json:
- source: semmeddb
id: 'kb:12345'
subject:
id:
- 'wd:Q14912054'
name: KCNJ11
category: gene
predicate:
edge_label: has_phenotype
relation: 'RO:0002200'
negated: false
object:
id:
- 'wd:Q2898645'
name: Neonatal diabetes mellitus
category: disease
'/statements/{statementId}':
get:
description: >
Retrieves a details relating to a specified concept-relationship
statement include 'is_defined_by and 'provided_by' provenance; extended
edge properties exported as tag = value; and any associated annotations
(publications, etc.) cited as evidence for the given statement.
tags:
- statements
parameters:
- name: statementId
in: path
description: >
(url-encoded) CURIE identifier of the concept-relationship statement
("assertion", "claim") for which associated evidence is sought
required: true
type: string
- name: keywords
in: query
description: >-
an array of keywords or substrings against which to filter
annotation names (e.g. publication titles).
required: false
type: array
items:
type: string
- name: size
in: query
description: >
maximum number of concept entries requested by the client; if this
argument is omitted, then the query is expected to returned all the
available data for the query
required: false
type: integer
operationId: getStatementDetails
responses:
'200':
schema:
title: BeaconStatementWithDetails
type: object
properties:
id:
type: string
description: >
Statement identifier of the statement made in an edge (echoed
back)
is_defined_by:
type: string
description: >
A CURIE/URI for the translator group that wrapped this
knowledge source ('beacon') that publishes the statement made
in an edge.
provided_by:
type: string
description: >
A CURIE prefix, e.g. Pharos, MGI, Monarch. The group that
curated/asserted the statement made in an edge.
qualifiers:
type: array
description: >
(Optional) terms representing qualifiers that modify or
qualify the meaning of the statement made in an edge.
items:
type: string
annotation:
type: array
description: >
Extra edge properties, generally compliant with Translator
Knowledge Graph Standard Specification
items:
title: BeaconStatementAnnotation
type: object
properties:
tag:
type: string
description: |
property name
value:
type: string
description: |
property value
description: |
Statement edge properties returned as tag = value pairs
evidence:
type: array
items:
title: BeaconStatementCitation
type: object
properties:
id:
type: string
description: >
CURIE-encoded identifier to a citation to evidence
supporting the given statement (e.g. PMID of a pubmed
abstract)
uri:
type: string
description: |
(optional) expansion of the citation CURIE
name:
type: string
description: >
canonical human readable and searchable name of the
citation (i.e. publication title, comment, etc.)
evidence_type:
type: string
description: >
class of evidence supporting the statement made in an
edge - typically a class from the ECO ontology (e.g.
ECO:0000220 'sequencing assay evidence', see [Evidence
Ontology](http://purl.obolibrary.org/obo/eco.owl)
date:
type: string
description: >
publication date of annotation (generally of format
'yyyy-mm-dd')
description: |
successful call with statement details returned
examples:
application/json:
id: 'kb:12345'
is_defined_by: 'http://starinformatics.com'
provided_by: 'https://skr3.nlm.nih.gov/SemMedDB/'
qualifiers: []
annotation:
- tag: stage
value: neo-natal
evidence:
- id: 'PMID:22781086'
uri: 'https://www.ncbi.nlm.nih.gov/pubmed/?term=22781086'
name: >-
Neonatal diabetes mellitus and congenital diaphragmatic
hernia coincidence or concurrent etiology?
evidence_type: ECO_0000033
date: '2012-07-10T00:00:00.000Z'