Pubtator Tools

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

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

Available Tools

PubTator3_EntityAutocomplete (Type: PubTatorTool)

Provides suggestions for the best‐matching standardized PubTator IDs for a partial biomedical ter…

PubTator3_EntityAutocomplete tool specification

Tool Information:

  • Name: PubTator3_EntityAutocomplete

  • Type: PubTatorTool

  • Description: Provides suggestions for the best‐matching standardized PubTator IDs for a partial biomedical term (gene, disease, chemical, or variant). Use this tool first to convert free‐text names into the stable @IDs required by the other PubTator APIs.

Parameters:

  • text (string) (required) A few characters or the full name of the biomedical concept you are trying to look up (e.g. “BRAF V6”).

  • entity_type (string) (optional) Optional filter to restrict suggestions to a single category such as GENE, DISEASE, CHEMICAL, or VARIANT.

  • max_results (integer) (optional) Maximum number of suggestions to return (1 - 50, default = 10).

Example Usage:

query = {
    "name": "PubTator3_EntityAutocomplete",
    "arguments": {
        "text": "example_value"
    }
}
result = tu.run(query)

PubTator3_LiteratureSearch (Type: PubTatorTool)

Find PubMed articles that match a keyword, a PubTator entity ID (e.g. “@GENE_BRAF”), or an entity…

PubTator3_LiteratureSearch tool specification

Tool Information:

  • Name: PubTator3_LiteratureSearch

  • Type: PubTatorTool

  • Description: Find PubMed articles that match a keyword, a PubTator entity ID (e.g. “@GENE_BRAF”), or an entity-to-entity relation expression (e.g. “relations:treat|@CHEMICAL_Doxorubicin|@DISEASE_Neoplasms”).

Parameters:

  • query (string) (required) What you want to search for. This can be plain keywords, a single PubTator ID, or the special relation syntax shown above.

  • page (integer) (optional) Zero-based results page (optional; default = 0).

  • page_size (integer) (optional) How many PMIDs to return per page (optional; default = 20, maximum = 200).

Example Usage:

query = {
    "name": "PubTator3_LiteratureSearch",
    "arguments": {
        "query": "example_value"
    }
}
result = tu.run(query)