search_bioentities
Search for bioentities (genes/proteins) across organisms using name, taxonomy, type, and source filters, with pagination.
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 |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
No arguments | |||