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beacon-aggregator-api.yaml
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swagger: '2.0'
info:
title: Translator Knowledge Beacon Aggregator API
version: 1.1.3
contact:
url: 'http://starinformatics.com'
email: richard@starinformatics.com
description: >
This is the Translator Knowledge Beacon Aggregator web service application
programming interface (API) that provides integrated access to a pool of
knowledge sources publishing concepts and relations through the Translator
Knowledge Beacon API. This API is similar to that of the latter mentioned
API with the addition of some extra informative endpoints plus session
identifier and beacon indices. These latter identifiers are locally assigned
numeric indices provided to track the use of specific registered beacons
within the aggregator API itself.
license:
name: MIT License
url: 'http://opensource.org/licenses/MIT'
host: kba.ncats.io
basePath: /
schemes:
- https
produces:
- application/json
tags:
- name: metadata
description: Queries about global characteristics of the knowledge beacon network
paths:
/beacons:
get:
description: |
Get a list of all of the knowledge beacons that the aggregator can query
tags:
- metadata
operationId: getBeacons
responses:
'200':
schema:
type: array
items:
title: ServerKnowledgeBeacon
type: object
properties:
beacon:
type: integer
description: |
aggregator assigned beacon index identifier
name:
type: string
description: |
beacon name
url:
type: string
description: |
URL used to execute API calls on the beacon
description:
type: string
description: |
beacon description
contact:
type: string
description: |
name of the person responsible for this beacon
wraps:
type: string
description: |
URL of this beacon's data source
repo:
type: string
description: |
URL of this beacon's repository
description: |
Successful response with beacons
examples:
application/json:
- id: 1
name: SemMedDB
url: 'https://rkb.ncats.io'
description: ''
/categories:
get:
description: >
Get a list of semantic categories and number of instances in each
available knowledge beacon, including associated beacon-specific
metadata
tags:
- metadata
parameters:
- name: beacons
in: query
description: >
set of aggregator indices of beacons to constrain categories
returned
required: false
type: array
items:
type: integer
operationId: getConceptCategories
responses:
'200':
schema:
type: array
items:
title: ServerConceptCategory
type: object
properties:
id:
type: string
description: >-
the CURIE of the concept category (see [Biolink Model
Classes](https://biolink.github.io/biolink-model)
uri:
type: string
description: >-
the URI of the concept category (see [Biolink Model
Classes](https://biolink.github.io/biolink-model) for the
full list of URI)
category:
type: string
description: >
the human readable label of the concept category (see
[Biolink Model
Classes](https://biolink.github.io/biolink-model) for the
full list of concept categories)
description:
type: string
description: >
human readable definition assigned by the beacon for the
specified concept category
beacons:
type: array
description: >
list of metadata for beacons that support the use of this
concept category
items:
title: ServerConceptCategoriesByBeacon
type: object
properties:
beacon:
type: integer
description: |
Aggregator index identifier of the given beacon
categories:
type: array
items:
title: ServerBeaconConceptCategory
type: object
description: |
Single local concept categories from a given beacon
properties:
id:
type: string
description: >
the 'local' CURIE-encoded identifier of the
given concept category, as published by the
given beacon
uri:
type: string
description: >
the 'local' URI of the given concept category,
as published by the given beacon
category:
type: string
description: >
the 'local' human readable label of the given
concept category, as published by the given
beacon
frequency:
type: integer
description: >
the number of instances of the specified concept
category is used in statements within the given
beacon
description: |
Successful response with concept categories and frequency returned
examples:
application/json:
- id: 'BLM:Gene'
uri: 'http://bioentity.io/vocab/Gene'
category: gene
description: >
A region (or regions) that includes all of the sequence
elements necessary to encode a functional transcript. A gene
may include regulatory regions, transcribed regions and/or
other functional sequence regions.
beacons:
- beacon: 1
categories:
- id: 'UMLSSG:GENE'
uri: 'https://metamap.nlm.nih.gov/Docs/SemGroups_2013#GENE'
category: GENE
frequency: 1234
- beacon: 5
categories:
- id: 'SO:0000704'
uri: 'http://www.sequenceontology.org/0000704'
category: gene
frequency: 5678
/predicates:
get:
description: >
Get a list of predicates used in statements issued by the knowledge
source
tags:
- metadata
parameters:
- name: beacons
in: query
description: >
set of aggregator indices of beacons to constrain predicates
returned
required: false
type: array
items:
type: integer
operationId: getPredicates
responses:
'200':
schema:
type: array
items:
title: ServerPredicate
type: object
properties:
id:
type: string
description: >-
the CURIE of the predicate relation (see [Biolink
Model](https://biolink.github.io/biolink-model)
uri:
type: string
description: >-
the URI of the predicate relation (see [Biolink
Model](https://biolink.github.io/biolink-model) for the full
list of URI)
edge_label:
type: string
description: >-
the human readable 'edge label' of the 'minimal' predicate
(see [Biolink
Model](https://biolink.github.io/biolink-model) for the full
list of Biolink Model minimal predicates)
description:
type: string
description: >
human readable definition assigned by the beacon for the
predicate relation
beacons:
type: array
description: >
list of metadata for beacons that support the use of this
predicate relation
items:
title: ServerPredicatesByBeacon
type: object
properties:
beacon:
type: integer
description: |
aggregator index of the given beacon
predicates:
type: array
items:
title: ServerBeaconPredicate
type: object
description: |
Local predicate definition from a given beacon
properties:
id:
type: string
description: >
the 'local' CURIE-encoded identifier of a
maximal predicate relation, as published by the
given beacon
uri:
type: string
description: >
the 'local' URI of a maximal predicate
relation, as published by the given beacon
relation:
type: string
description: >
the human readable 'relation of the 'maximal'
predicate (see the [Biolink
Model](https://biolink.github.io/biolink-model)
for a list of Biolink maximal predicates; this
field may map onto beacon-specific non-Biolink
relations
description:
type: string
description: >
human readable definition of the given
predicate relation
frequency:
type: integer
description: >
the number of instances of the specified
predicate relation is used in statements within
the given beacon
description: >
Successful response with predicates with CURIE and definitions
indexed by beacons which support the relation
examples:
application/json:
- id: 'BLM:affects_risk_for'
uri: 'http://bioentity.io/vocab/affects_risk_for'
edge_label: affects_risk_for
description: |
holds between two entities where exposure to one entity
alters the chance of developing the other
beacons:
- beacon: 1
predicates:
- id: 'SEMMEDDB:PREDISPOSES'
uri: 'https://metamap.nlm.nih.gov/predicate/PREDISPOSES'
relation: PREDISPOSES
description: >-
agent which predisposes individual to a given
condition
frequency: 123
/kmap:
get:
description: >
Get a high level knowledge map of the all the beacons specified by
triplets of subject concept category, relationship predicate and concept
object category
tags:
- metadata
parameters:
- name: beacons
in: query
description: >
set of aggregator indices of beacons constraining knowledge maps
returned
required: false
type: array
items:
type: integer
operationId: getKnowledgeMap
responses:
'200':
schema:
type: array
items:
title: ServerKnowledgeMap
type: object
properties:
beacon:
type: integer
description: |
aggregator assigned beacon index identifier
statements:
type: array
items:
title: ServerKnowledgeMapStatement
type: object
properties:
subject:
title: ServerKnowledgeMapSubject
type: object
properties:
category:
type: string
description: >
the human readable label of the concept category
of a statement subject
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: ServerKnowledgeMapPredicate
type: object
properties:
edge_label:
type: string
description: >-
the human readable edge label of the 'minimal'
predicate of the given relationship
relation:
type: string
description: >-
the human readable label of the 'maximal'
predicate of the given relationship
negated:
type: boolean
object:
title: ServerKnowledgeMapObject
type: object
properties:
category:
type: string
description: >
the human readable label of the concept category
of a statement object
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:
- beacon: 1
statements:
- subject:
category: gene
prefixes:
- DRUGBANK
- CHEMBL
- UNIPROT
predicate:
edge_label: is substance that treats
relation: 'RO:0002606'
object:
category: disease or phenotypic feature
prefixes:
- MP
- HP
- DOID
count: 500
description: >
a small molecule or compound that is capable of some
activity that negative regulates or decreases the
magnitude of a pathological process, phenotype or disease
- subject:
category: drug
prefixes:
- DRUGBANK
- CHEMBL
predicate:
edge_label: chemical_to_pathway_association
relation: 'SIO:001250'
object:
category: pathway
prefixes:
- KEGG
count: 100
description: |
Drug interacts with a given pathway
/errorlog:
get:
description: |
Get a log of the system errors associated with a specified query
tags:
- metadata
parameters:
- name: queryId
in: query
description: |
query identifier returned from a POSTed query
required: true
type: string
operationId: getErrorLog
responses:
'200':
schema:
type: array
items:
title: ServerLogEntry
type: object
properties:
queryId:
type: string
description: |
session identifier of initiated query
timestamp:
type: string
description: |
timestamp
beacon:
type: integer
description: |
aggregator assigned beacon index identifier
query:
type: string
description: |
URL of the API call executed by the aggregator
message:
type: string
description: |
error message
description: |
Successful response with most recent errors
examples:
application/json:
- queryId: AB123
timestamp: '2018-12-31 15:09:24.614'
beacon: 2
query: 'https://wikidata.ncats.io/concepts?keywords=WRN'
message: Bad Gateway
/concepts:
post:
description: |
Posts the query parameters to retrieves a list of
concepts from the system
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: >
a subset array of concept categories (specified as 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: beacons
in: query
description: >
subset of aggregator indices of beacons to be used as knowledge
sources for the query (if omitted, then the all beacons are queried)
required: false
type: array
items:
type: integer
operationId: postConceptsQuery
responses:
'200':
schema:
title: ServerConceptsQuery
type: object
properties:
queryId:
type: string
description: |
session identifier of initiated query
keywords:
type: array
items:
type: string
description: |
'keywords' string parameter to API call, echoed back
categories:
type: array
items:
type: string
description: |
'categories' string parameter to API call, echoed back
description: >
Successful concept query initialization, with initial query status
returned
examples:
application/json:
queryId: XRBTu9CgfiXEhcfMdr4y
keywords:
- Werner
- Syndrome
categories:
- gene
- protein
- disease
'/concepts/status/{queryId}':
get:
description: >
Retrieves the status of a given keyword search query about the concepts
in the system
tags:
- concepts
parameters:
- name: queryId
in: path
description: >-
an active query identifier as returned by a POST of concept query
parameters.
required: true
type: string
- name: beacons
in: query
description: >
subset of aggregator indices of beacons whose status is being polled
(if omitted, then the status of all beacons from the query are
returned)
required: false
type: array
items:
type: integer
operationId: getConceptsQueryStatus
responses:
'200':
schema:
title: ServerConceptsQueryStatus
type: object
properties:
queryId:
type: string
description: >
session identifier of a query previously initiated by
/concepts
status:
type: array
description: |
array of beacon-specific query status reports
items:
title: ServerConceptsQueryBeaconStatus
type: object
properties:
beacon:
type: integer
description: |
Index number of beacon providing these concept details
status:
type: integer
description: >
Http code status of beacon API - 200 means 'data ready',
102 means 'query in progress', other codes (e.g. 500)
are server errors. Once a beacon has a '200' success
code, then the /concepts/data endpoint may be used to
retrieve it.
discovered:
type: integer
description: >
A count of how many items a beacon has returned. This
number will not always be the same as the final number
of results since we merge duplicate items.
processed:
type: integer
description: >
A count of how many of the beacon responses have been
processed and are ready for consumption.
count:
type: integer
description: >
When a 200 status code is returned, this integer
designates the number of concepts matched by the query
for the given beacon.
description: |
Current query status returned
examples:
application/json:
queryId: XRBTu9CgfiXEhcfMdr4y
status:
- beacon: 1
status: 200
discovered: 3
processed: 3
count: 3
- beacon: 2
status: 500
discovered: null
processed: null
count: null
- beacon: 5
status: 102
discovered: 37
processed: 10
count: null
'/concepts/data/{queryId}':
get:
description: >
Retrieves a (paged) list of basic equivalent concept clique data from
beacons
'data ready' from a previously /concepts posted query parameter
submission
tags:
- concepts
parameters:
- name: queryId
in: path
description: >-
the query identifier of a concepts query previously posted by the
/concepts endpoint
required: true
type: string
- name: beacons
in: query
description: |
set of aggregator indices of beacons whose data are to be retrieved
required: false
type: array
items:
type: integer
- name: pageNumber
in: query
description: |
(1-based) number of the page to be returned in a paged set of query
results. Defaults to '1'.
required: false
type: integer
- name: pageSize
in: query
description: |
number of concepts per page to be returned in a paged set of query
results. Defaults to '10'.
required: false
type: integer
operationId: getConcepts
responses:
'200':
schema:
title: ServerConceptsQueryResult
type: object
properties:
queryId:
type: string
description: |
session identifier of the query returning the results
beacons:
type: array
items:
type: integer
description: >
subset of aggregator indices of beacons whose concepts are
to be retrieved
pageNumber:
type: integer
description: |
'pageNumber' string parameter to API call, echoed back
pageSize:
type: integer
description: |
'pageSize' string parameter to API call, echoed back
results:
type: array
items:
title: ServerConcept
type: object
properties:
clique:
type: string
description: >
CURIE identifying the inferred equivalent concept clique
to which the concept belongs. This is assigned by an
identifier precedence heuristic by the beacon-aggregator
name:
type: string
description: |
Canonical human readable name of the concept
categories:
type: array
items:
type: string
description: >
Concept categories associated with the given concept
((see [Biolink
Model](https://biolink.github.io/biolink-model) for the
full list of categories).
description: |
Successful response with concept list returned
examples:
application/json:
queryId: XRBTu9CgfiXEhcfMdr4y
beacons:
- 1
- 5
pageNumber: 1
pageSize: 4
results:
- clique: 'UNIPROT:Q14191'
name: 'WRN protein, human'
category: protein
- clique: 'NCBIGENE:56897'
name: WRNIP1
category: gene
- clique: 'NCBIGENE:7486'
name: WRN
category: gene
- clique: 'DOID:5686'
name: Werner Syndrome
category: disease
/cliques:
post:
description: >
Retrieves the beacon aggregator assigned cliques of equivalent concepts
that includes the specified (url-encoded) CURIE identifiers. Note that
the clique to which a given concept CURIE belongs may change over time
as the aggregator progressively discovers the members of the clique. Any
unmatched identifiers will be ignored (e.g. the id couldn't be found in
any of the beacons)
tags:
- concepts
parameters:
- name: ids
in: query
description: >-
an array of [CURIE-encoded](https://www.w3.org/TR/curie/)
identifiers of interest to be resolved to a list of concept cliques
required: true
type: array
items:
type: string
operationId: postCliquesQuery
responses:
'200':
schema:
title: ServerCliquesQuery
type: object
properties:
queryId:
type: string
description: |
session identifier of initiated query
ids:
type: array
items:
type: string
description: |
'ids' string parameter to call, echoed back
description: >
Successful clique query initialization, with initial query status
returned
examples:
application/json:
queryId: XRBTu9CgfiXEhcfMdr4y
ids:
- 'NCIT:C34942'
- 'MONDO:0005406'
'/cliques/status/{queryId}':
get:
description: |
Retrieves the status of a given query about the cliques in the system
tags:
- concepts
parameters:
- name: queryId
in: path
description: >-
an active query identifier as returned by a POST of clique query
parameters.
required: true
type: string
operationId: getCliquesQueryStatus
responses:
'200':
schema:
title: ServerCliquesQueryStatus
type: object
properties:
queryId:
type: string
description: |
session identifier of a query previously initiated by /cliques
status:
type: array
description: |
array of beacon-specific query status reports
items:
title: ServerCliquesQueryBeaconStatus
type: object
properties:
beacon:
type: integer
description: |
Index number of beacon providing these concept details
status:
type: integer
description: >
Http code status of beacon API - 200 means 'data ready',
102 means 'query in progress', other codes (e.g. 500)
are server errors. Once a beacon has a '200' success
code, then the /cliques/data endpoint may be used to
retrieve it
count:
type: integer
description: >
When a 200 status code is returned, this integer
designates the number of ids matched by the query for
the given beacon.
description: |
Current query status returned
examples:
application/json:
queryId: XRBTu9CgfiXEhcfMdr4y
status:
- beacon: 1
status: 200
count: 10
- beacon: 2
status: 500
count: null
- beacon: 5
status: 102
count: null
'/cliques/data/{queryId}':
get:
description: >
Retrieves a list of concept cliques based on 'data ready' from a
previously /cliques posted query parameter submission
tags:
- concepts
parameters:
- name: queryId
in: path
description: >-
the query identifier of a concepts query previously posted by the
/cliques endpoint
required: true
type: string
operationId: getCliques
responses:
'200':
schema:
title: ServerCliquesQueryResult
type: object
properties:
queryId:
type: string
description: |
session identifier of the query returning the results
results:
type: array
items:
title: ServerClique
type: object
properties:
id:
type: string
description: >
CURIE identifying the concept whose concept clique is
being resolved
cliqueId:
type: string
description: >
CURIE identifying the equivalent concept clique to which
the input concept CURIE belongs.
description: |
Successful response with clique identifiers returned
examples:
application/json:
queryId: XRBTu9CgfiXEhcfMdr4y
results:
- id: 'NCBIGENE:2176'
cliqueId: 'NCBIGENE:2176'
- id: 'MONDO:0005406'
cliqueId: 'NCIT:C34942'
'/concepts/details/{cliqueId}':
get:
description: >
Retrieves details for a specified clique of equivalent concepts in the
system, as specified by a (url-encoded) CURIE identifier of a clique
known to the aggregator
tags:
- concepts
parameters:
- name: cliqueId
in: path
description: >-
a [CURIE-encoded](https://www.w3.org/TR/curie/) identifier, as
returned by any other endpoint of the beacon aggregator API, of an
exactly matching concept clique of interest.
required: true
type: string
- name: beacons
in: query
description: >
set of aggregator indices of beacons to be used as knowledge sources
for the query
required: false
type: array
items:
type: integer
operationId: getConceptDetails
responses:
'200':
schema:
title: ServerConceptWithDetails
type: object
description: |
A single record of a given concept clique with details
properties:
clique:
type: string
description: >
CURIE identifying the equivalent concept clique to which the
concept belongs.
name:
type: string
description: |