Biothings Gateway Tools#

Configuration File: biothings_gateway_tools.json Tool Type: Local Tools Count: 4

This page contains all tools defined in the biothings_gateway_tools.json configuration file.

Available Tools#

BioThings_get_entity (Type: BioThingsGatewayTool)#

Retrieve one record from a BioThings API by its _id, as returned in BioThings_query results. Exam…

BioThings_get_entity tool specification

Tool Information:

  • Name: BioThings_get_entity

  • Type: BioThingsGatewayTool

  • Description: Retrieve one record from a BioThings API by its _id, as returned in BioThings_query results. Example: api=’mondo’, entity_id=’MONDO:0010329’. Uses the API’s typed annotation route and falls back to an _id query when that route is not exposed.

Parameters:

  • api (string) (required) API slug, e.g. ‘mondo’. See BioThings_list_apis.

  • entity_id (string) (required) Record _id from a BioThings_query result, e.g. ‘MONDO:0010329’.

Example Usage:

query = {
    "name": "BioThings_get_entity",
    "arguments": {
        "api": "example_value",
        "entity_id": "example_value"
    }
}
result = tu.run(query)

BioThings_get_metadata (Type: BioThingsGatewayTool)#

Describe a BioThings API: record counts, build date and version, upstream sources, and optionally…

BioThings_get_metadata tool specification

Tool Information:

  • Name: BioThings_get_metadata

  • Type: BioThingsGatewayTool

  • Description: Describe a BioThings API: record counts, build date and version, upstream sources, and optionally the full list of queryable field names. Call this before writing a fielded BioThings_query so you use field names the API actually has. Example: api=’semmeddb’, include_fields=true.

Parameters:

  • api (string) (required) API slug, e.g. ‘semmeddb’. See BioThings_list_apis.

  • include_fields ([‘boolean’, ‘null’]) (optional) If true, also fetch the full list of queryable field names.

Example Usage:

query = {
    "name": "BioThings_get_metadata",
    "arguments": {
        "api": "example_value"
    }
}
result = tu.run(query)

BioThings_list_apis (Type: BioThingsGatewayTool)#

List the ~50 biomedical APIs reachable through the BioThings gateway, with a one-line description…

BioThings_list_apis tool specification

Tool Information:

  • Name: BioThings_list_apis

  • Type: BioThingsGatewayTool

  • Description: List the ~50 biomedical APIs reachable through the BioThings gateway, with a one-line description of each. Includes resources with no other ToolUniverse coverage such as DDInter (drug-drug interactions), repoDB (drug repurposing), IDISK (dietary supplements), TTD, GMMAD2, denovo-db, BioMuta, PFOCR, SEMMEDDB, Disbiome, InnateDB, CCLE, and PheWAS. Entries that duplicate a dedicated ToolUniverse tool are flagged in preferred_tooluniverse_tool; prefer the dedicated tool in those cases. Call this before BioThings_query to pick an api slug.

Parameters:

  • keyword ([‘string’, ‘null’]) (optional) Filter APIs by substring in the slug or description, e.g. ‘drug’, ‘microbiome’.

  • only_without_dedicated_tool ([‘boolean’, ‘null’]) (optional) If true, list only APIs that have no dedicated ToolUniverse equivalent.

Example Usage:

query = {
    "name": "BioThings_list_apis",
    "arguments": {
    }
}
result = tu.run(query)

BioThings_query (Type: BioThingsGatewayTool)#

Search any BioThings-hosted API with an Elasticsearch-style query. Use ‘*’ to match everything, a…

BioThings_query tool specification

Tool Information:

  • Name: BioThings_query

  • Type: BioThingsGatewayTool

  • Description: Search any BioThings-hosted API with an Elasticsearch-style query. Use ‘*’ to match everything, a bare term for full-text search, or a fielded query such as ‘subject.name:aspirin’. Example: api=’ddinter’, q=’drug_a.name:warfarin’ finds drug-drug interactions involving warfarin. Returns matching records with their _id, which BioThings_get_entity accepts. Use BioThings_list_apis to choose an api and BioThings_get_metadata to discover field names.

Parameters:

  • api (string) (required) API slug, e.g. ‘ddinter’, ‘repodb’, ‘semmeddb’. See BioThings_list_apis.

  • q (string) (required) Query string. ‘*’ for all, a bare term for full-text, or ‘field:value’ for fielded search.

  • size ([‘integer’, ‘null’]) (optional) Maximum records to return (default 10, max 100).

  • skip ([‘integer’, ‘null’]) (optional) Number of records to skip, for paging through large result sets.

  • fields ([‘string’, ‘null’]) (optional) Comma-separated fields to return, e.g. ‘subject,object,predicate’. Omit for all.

Example Usage:

query = {
    "name": "BioThings_query",
    "arguments": {
        "api": "example_value",
        "q": "example_value"
    }
}
result = tu.run(query)