Pubtator3 Ext Tools

Configuration File: pubtator3_ext_tools.json Tool Type: Local Tools Count: 1

This page contains all tools defined in the pubtator3_ext_tools.json configuration file.

Available Tools

PubTator3_get_annotations (Type: BaseRESTTool)

Extract biomedical entity annotations from PubMed articles using NCBI PubTator3. Given one or mor…

PubTator3_get_annotations tool specification

Tool Information:

  • Name: PubTator3_get_annotations

  • Type: BaseRESTTool

  • Description: Extract biomedical entity annotations from PubMed articles using NCBI PubTator3. Given one or more PubMed IDs (PMIDs), returns text-mined entities including genes, diseases, chemicals, species, mutations, and cell lines with their normalized identifiers (NCBI Gene ID, MeSH, NCBI Taxonomy, etc.) and text positions. Useful for extracting structured biomedical knowledge from literature. Provide PMIDs as a comma-separated string.

Parameters:

  • pmids (string) (required) Comma-separated PubMed IDs (e.g., ‘33205991’, ‘33205991,34234088’). Maximum ~100 PMIDs per request.

  • concepts (string) (optional) Comma-separated entity types to extract: gene, disease, chemical, species, mutation, cellline (default: all types)

Example Usage:

query = {
    "name": "PubTator3_get_annotations",
    "arguments": {
        "pmids": "example_value"
    }
}
result = tu.run(query)