Pubtator3 Ext Tools#

Configuration File: pubtator3_ext_tools.json Tool Type: Local Tools Count: 2

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

Available Tools#

PubTator3_GetEntityRelations (Type: BaseRESTTool)#

Query the NCBI PubTator3 relation graph for a normalized biomedical entity. PubTator returns the …

PubTator3_GetEntityRelations tool specification

Tool Information:

  • Name: PubTator3_GetEntityRelations

  • Type: BaseRESTTool

  • Description: Query the NCBI PubTator3 relation graph for a normalized biomedical entity. PubTator returns the full ranked edge array and has no server pagination, so ToolUniverse applies exact client-side pagination: start with offset=0 and continue with metadata.next_offset while metadata.has_more is true. metadata.total_results is exact. Edges retain publication-count ranking. Entities use @TYPE_Name format.

Parameters:

  • e1 (string) (required) Primary normalized PubTator entity in @TYPE_Name format. Examples: ‘@GENE_BRAF’, ‘@DISEASE_Melanoma’, ‘@CHEMICAL_Doxorubicin’, ‘@CHEMICAL_Vemurafenib’. Required.

  • type ([‘string’, ‘null’]) (optional) Optional relation type filter to restrict edges. Examples: ‘treat’, ‘cause’, ‘associate’, ‘prevent’, ‘inhibit’, ‘stimulate’, ‘interact’, ‘compare’, ‘drug_interact’, ‘negative_correlate’, ‘positive_correlate’. Omit to return all relation types.

  • e2 ([‘string’, ‘null’]) (optional) Optional second normalized PubTator entity (@TYPE_Name) to query a specific pair relationship between e1 and e2, e.g. e1=’@CHEMICAL_Doxorubicin’, type=’treat’, e2=’@DISEASE_Neoplasms’. Omit for a one-entity neighborhood query.

  • limit ([‘integer’, ‘null’]) (optional) Number of ranked relation edges in this client-side page (default 50).

  • offset (integer) (optional) Zero-based ranked-edge offset. Continue with metadata.next_offset while metadata.has_more is true.

Example Usage:

query = {
    "name": "PubTator3_GetEntityRelations",
    "arguments": {
        "e1": "example_value"
    }
}
result = tu.run(query)

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)