search_bioentities

Search for genes and proteins using Gene Ontology data with taxonomic and source filtering to find biological entities across organisms.

Instructions

Search for bioentities (genes/proteins) using Gene Ontology data.

Searches across gene and protein names/labels with optional taxonomic filtering. Provides access to comprehensive bioentity information from GOlr.

Args: text: Text search across names and labels (e.g., "insulin", "kinase") taxon: Organism filter - accepts NCBI Taxon ID with or without prefix (e.g., "9606", "NCBITaxon:9606" for human) bioentity_type: Type filter (e.g., "protein", "gene") source: Source database filter (e.g., "UniProtKB", "MGI", "RGD") limit: Maximum number of results to return (default: 10) offset: Starting offset for pagination (default: 0)

Returns: Dictionary containing search results with bioentity information

Examples: # Search for human insulin proteins results = search_bioentities( text="insulin", taxon="9606", bioentity_type="protein" )

# Find mouse kinases from MGI results = search_bioentities( text="kinase", taxon="NCBITaxon:10090", source="MGI", limit=20 ) # Search for any human genes/proteins results = search_bioentities( taxon="9606", limit=50 ) # Find specific protein types results = search_bioentities( text="receptor", bioentity_type="protein", limit=25 ) # Search across all organisms results = search_bioentities(text="p53") # Pagination example page1 = search_bioentities(text="kinase", limit=10, offset=0) page2 = search_bioentities(text="kinase", limit=10, offset=10) # Common organisms: # Human: "9606" or "NCBITaxon:9606" # Mouse: "10090" or "NCBITaxon:10090" # Rat: "10116" or "NCBITaxon:10116" # Fly: "7227" or "NCBITaxon:7227" # Worm: "6239" or "NCBITaxon:6239" # Yeast: "559292" or "NCBITaxon:559292"

Notes: - Results include ID, name, type, organism, and source information - Text search covers both short names/symbols and full descriptions - Taxon IDs automatically handle NCBITaxon: prefix normalization - Use pagination for large result sets - Sources include UniProtKB, MGI, RGD, ZFIN, SGD, and others

Input Schema

Name	Required	Description	Default
`text`	No
`taxon`	No
`bioentity_type`	No
`source`	No
`limit`	No
`offset`	No

Input Schema (JSON Schema)

{ "properties": { "bioentity_type": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null }, "limit": { "default": 10, "type": "integer" }, "offset": { "default": 0, "type": "integer" }, "source": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null }, "taxon": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null }, "text": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null } }, "type": "object" }

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