Knowledge Beacon Aggregator (KBA) Client

This is a simple command line interface client and associated Python library to access the Translator Knowledge Beacon Aggregator ("KBA") web service.

KBA provides integrated access to a pool of Translator Knowledge Beacon API wrapped knowledge sources publishing concepts and relationship statements. KBA 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. Most of the endpoints of the KBA API are designed for asynchronous management of long running queries.

This Python package is automatically generated by the Swagger Codegen project:

• API version: 1.1.3
• Package version: 1.0.0
• Build package: io.swagger.codegen.languages.PythonClientCodegen

Requirements.

Python 2.7 and 3.5+

Installation & Usage

pip install

You can install from PyPI:

python3 -m pip install kba

Then import the package:

import kba

Command Line Interface

This package comes with a CLI that can be used to query the Beacon Aggregator. The --help flag can be used with any command to see documentation.

$ kba --help
Usage: kba [OPTIONS] COMMAND [ARGS]...

Options:
  --help  Show this message and exit.

Commands:
  beacons     Retrieves all beacons
  categories  Retrieves all categories
  concept     Initiates a concept query with the given search parameters
  dump        Retrieves the results of a query (by default the last query)
  kmap        Retrieves the knowledge map
  ping        Retrieves the status of a query (by default the last query)
  predicates  Retrieves all predicates
  statement   Initiates a statement query with the given search parameters

Initiate a concept query:

$ kba concept --keywords caffeine --categories "chemical substance" --categories pathway
Query ID:	eyUiFRZWVN5dD01VMQS1

Get the status of the last query posted:

$ kba ping
Last query:	eyUiFRZWVN5dD01VMQS1
Beacon 1 finished with 0 records
Beacon 2 finished with 204 records
Beacon 3 finished with 15 records
Beacon 4 has not yet returned
Beacon 5 finished with 43 records
Beacon 6 has not yet returned
Beacon 7 has not yet returned
Beacon 8 finished with 9 records

Get pages of records from the last query, saving it to file:

$ kba dump --page 1 --size 500 --out caffeine.json
Last query:	eyUiFRZWVN5dD01VMQS1
Saved response to caffeine.json

Getting Started

Please follow the installation procedure and then run the following:

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)

Documentation for API Endpoints

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

Class	Method	HTTP request	Description
ConceptsApi	get_cliques	GET /cliques/data/{queryId}
ConceptsApi	get_cliques_query_status	GET /cliques/status/{queryId}
ConceptsApi	get_concept_details	GET /concepts/details/{cliqueId}
ConceptsApi	get_concepts	GET /concepts/data/{queryId}
ConceptsApi	get_concepts_query_status	GET /concepts/status/{queryId}
ConceptsApi	post_cliques_query	POST /cliques
ConceptsApi	post_concepts_query	POST /concepts
MetadataApi	get_beacons	GET /beacons
MetadataApi	get_concept_categories	GET /categories
MetadataApi	get_error_log	GET /errorlog
MetadataApi	get_knowledge_map	GET /kmap
MetadataApi	get_predicates	GET /predicates
StatementsApi	get_statement_details	GET /statements/details/{statementId}
StatementsApi	get_statements	GET /statements/data/{queryId}
StatementsApi	get_statements_query_status	GET /statements/status/{queryId}
StatementsApi	post_statements_query	POST /statements

Documentation For Models

• ServerBeaconConceptCategory
• ServerBeaconPredicate
• ServerClique
• ServerCliquesQuery
• ServerCliquesQueryBeaconStatus
• ServerCliquesQueryResult
• ServerCliquesQueryStatus
• ServerConcept
• ServerConceptCategoriesByBeacon
• ServerConceptCategory
• ServerConceptDetail
• ServerConceptWithDetails
• ServerConceptWithDetailsBeaconEntry
• ServerConceptsQuery
• ServerConceptsQueryBeaconStatus
• ServerConceptsQueryResult
• ServerConceptsQueryStatus
• ServerKnowledgeBeacon
• ServerKnowledgeMap
• ServerKnowledgeMapObject
• ServerKnowledgeMapPredicate
• ServerKnowledgeMapStatement
• ServerKnowledgeMapSubject
• ServerLogEntry
• ServerPredicate
• ServerPredicatesByBeacon
• ServerStatement
• ServerStatementAnnotation
• ServerStatementCitation
• ServerStatementDetails
• ServerStatementObject
• ServerStatementPredicate
• ServerStatementSubject
• ServerStatementsQuery
• ServerStatementsQueryBeaconStatus
• ServerStatementsQueryResult
• ServerStatementsQueryStatus

Documentation For Authorization

All endpoints do not require authorization.

Authors

• lancehannestad@gmail.com
• richard@starinformatics.com