kba.ConceptsApi

All URIs are relative to https://kba.ncats.io

Method	HTTP request	Description
get_cliques	GET /cliques/data/{queryId}
get_cliques_query_status	GET /cliques/status/{queryId}
get_concept_details	GET /concepts/details/{cliqueId}
get_concepts	GET /concepts/data/{queryId}
get_concepts_query_status	GET /concepts/status/{queryId}
post_cliques_query	POST /cliques
post_concepts_query	POST /concepts

get_cliques

ServerCliquesQueryResult get_cliques(query_id)

Retrieves a list of concept cliques based on 'data ready' from a previously /cliques posted query parameter submission

Example

from __future__ import print_function
import time
import kba
from kba.rest import ApiException
from pprint import pprint

# create an instance of the API class
api_instance = kba.ConceptsApi()
query_id = 'query_id_example' # str | the query identifier of a concepts query previously posted by the /cliques endpoint

try:
    api_response = api_instance.get_cliques(query_id)
    pprint(api_response)
except ApiException as e:
    print("Exception when calling ConceptsApi->get_cliques: %s\n" % e)

Parameters

Name	Type	Description	Notes
query_id	str	the query identifier of a concepts query previously posted by the /cliques endpoint

Return type

ServerCliquesQueryResult

Authorization

No authorization required

HTTP request headers

Content-Type: Not defined
Accept: application/json

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get_cliques_query_status

ServerCliquesQueryStatus get_cliques_query_status(query_id)

Retrieves the status of a given query about the cliques in the system

Example

from __future__ import print_function
import time
import kba
from kba.rest import ApiException
from pprint import pprint

# create an instance of the API class
api_instance = kba.ConceptsApi()
query_id = 'query_id_example' # str | an active query identifier as returned by a POST of clique query parameters.

try:
    api_response = api_instance.get_cliques_query_status(query_id)
    pprint(api_response)
except ApiException as e:
    print("Exception when calling ConceptsApi->get_cliques_query_status: %s\n" % e)

Parameters

Name	Type	Description	Notes
query_id	str	an active query identifier as returned by a POST of clique query parameters.

Return type

ServerCliquesQueryStatus

Authorization

No authorization required

HTTP request headers

Content-Type: Not defined
Accept: application/json

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get_concept_details

ServerConceptWithDetails get_concept_details(clique_id, beacons=beacons)

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

Example

from __future__ import print_function
import time
import kba
from kba.rest import ApiException
from pprint import pprint

# create an instance of the API class
api_instance = kba.ConceptsApi()
clique_id = 'clique_id_example' # str | 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.
beacons = [56] # list[int] | set of aggregator indices of beacons to be used as knowledge sources for the query  (optional)

try:
    api_response = api_instance.get_concept_details(clique_id, beacons=beacons)
    pprint(api_response)
except ApiException as e:
    print("Exception when calling ConceptsApi->get_concept_details: %s\n" % e)

Parameters

Name	Type	Description	Notes
clique_id	str	a CURIE-encoded identifier, as returned by any other endpoint of the beacon aggregator API, of an exactly matching concept clique of interest.
beacons	list[int]	set of aggregator indices of beacons to be used as knowledge sources for the query	[optional]

Return type

ServerConceptWithDetails

Authorization

No authorization required

HTTP request headers

Content-Type: Not defined
Accept: application/json

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get_concepts

ServerConceptsQueryResult get_concepts(query_id, beacons=beacons, page_number=page_number, page_size=page_size)

Retrieves a (paged) list of basic equivalent concept clique data from beacons 'data ready' from a previously /concepts posted query parameter submission

Example

from __future__ import print_function
import time
import kba
from kba.rest import ApiException
from pprint import pprint

# create an instance of the API class
api_instance = kba.ConceptsApi()
query_id = 'query_id_example' # str | the query identifier of a concepts query previously posted by the /concepts endpoint
beacons = [56] # list[int] | set of aggregator indices of beacons whose data are to be retrieved  (optional)
page_number = 56 # int | (1-based) number of the page to be returned in a paged set of query results. Defaults to '1'.  (optional)
page_size = 56 # int | number of concepts per page to be returned in a paged set of query results. Defaults to '10'.  (optional)

try:
    api_response = api_instance.get_concepts(query_id, beacons=beacons, page_number=page_number, page_size=page_size)
    pprint(api_response)
except ApiException as e:
    print("Exception when calling ConceptsApi->get_concepts: %s\n" % e)

Parameters

Name	Type	Description	Notes
query_id	str	the query identifier of a concepts query previously posted by the /concepts endpoint
beacons	list[int]	set of aggregator indices of beacons whose data are to be retrieved	[optional]
page_number	int	(1-based) number of the page to be returned in a paged set of query results. Defaults to '1'.	[optional]
page_size	int	number of concepts per page to be returned in a paged set of query results. Defaults to '10'.	[optional]

Return type

ServerConceptsQueryResult

Authorization

No authorization required

HTTP request headers

Content-Type: Not defined
Accept: application/json

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get_concepts_query_status

ServerConceptsQueryStatus get_concepts_query_status(query_id, beacons=beacons)

Retrieves the status of a given keyword search query about the concepts in the system

Example

from __future__ import print_function
import time
import kba
from kba.rest import ApiException
from pprint import pprint

# create an instance of the API class
api_instance = kba.ConceptsApi()
query_id = 'query_id_example' # str | an active query identifier as returned by a POST of concept query parameters.
beacons = [56] # list[int] | subset of aggregator indices of beacons whose status is being polled (if omitted, then the status of all beacons from the query are returned)  (optional)

try:
    api_response = api_instance.get_concepts_query_status(query_id, beacons=beacons)
    pprint(api_response)
except ApiException as e:
    print("Exception when calling ConceptsApi->get_concepts_query_status: %s\n" % e)

Parameters

Name	Type	Description	Notes
query_id	str	an active query identifier as returned by a POST of concept query parameters.
beacons	list[int]	subset of aggregator indices of beacons whose status is being polled (if omitted, then the status of all beacons from the query are returned)	[optional]

Return type

ServerConceptsQueryStatus

Authorization

No authorization required

HTTP request headers

Content-Type: Not defined
Accept: application/json

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post_cliques_query

ServerCliquesQuery post_cliques_query(ids)

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)

Example

from __future__ import print_function
import time
import kba
from kba.rest import ApiException
from pprint import pprint

# create an instance of the API class
api_instance = kba.ConceptsApi()
ids = ['ids_example'] # list[str] | an array of [CURIE-encoded](https://www.w3.org/TR/curie/) identifiers of interest to be resolved to a list of concept cliques

try:
    api_response = api_instance.post_cliques_query(ids)
    pprint(api_response)
except ApiException as e:
    print("Exception when calling ConceptsApi->post_cliques_query: %s\n" % e)

Parameters

Name	Type	Description	Notes
ids	list[str]	an array of CURIE-encoded identifiers of interest to be resolved to a list of concept cliques

Return type

ServerCliquesQuery

Authorization

No authorization required

HTTP request headers

Content-Type: Not defined
Accept: application/json

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post_concepts_query

ServerConceptsQuery post_concepts_query(keywords, categories=categories, beacons=beacons)

Posts the query parameters to retrieves a list of concepts from the system

Example

from __future__ import print_function
import time
import kba
from kba.rest import ApiException
from pprint import pprint

# create an instance of the API class
api_instance = kba.ConceptsApi()
keywords = ['keywords_example'] # list[str] | an array of keywords or substrings against which to match concept names and synonyms
categories = ['categories_example'] # list[str] | 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)  (optional)
beacons = [56] # list[int] | subset of aggregator indices of beacons to be used as knowledge sources for the query (if omitted, then the all beacons are queried)  (optional)

try:
    api_response = api_instance.post_concepts_query(keywords, categories=categories, beacons=beacons)
    pprint(api_response)
except ApiException as e:
    print("Exception when calling ConceptsApi->post_concepts_query: %s\n" % e)

Parameters

Name	Type	Description	Notes
keywords	list[str]	an array of keywords or substrings against which to match concept names and synonyms
categories	list[str]	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 for the full list of codes)	[optional]
beacons	list[int]	subset of aggregator indices of beacons to be used as knowledge sources for the query (if omitted, then the all beacons are queried)	[optional]

Return type

ServerConceptsQuery

Authorization

No authorization required

HTTP request headers

Content-Type: Not defined
Accept: application/json

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Files

ConceptsApi.md

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ConceptsApi.md

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kba.ConceptsApi

get_cliques

Example

Parameters

Return type

Authorization

HTTP request headers

get_cliques_query_status

Example

Parameters

Return type

Authorization

HTTP request headers

get_concept_details

Example

Parameters

Return type

Authorization

HTTP request headers

get_concepts

Example

Parameters

Return type

Authorization

HTTP request headers

get_concepts_query_status

Example

Parameters

Return type

Authorization

HTTP request headers

post_cliques_query

Example

Parameters

Return type

Authorization

HTTP request headers

post_concepts_query

Example

Parameters

Return type

Authorization

HTTP request headers