Bioportal Tools#

Configuration File: bioportal_tools.json Tool Type: Local Tools Count: 4

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

Available Tools#

BioPortal_annotate_text (Type: BioPortalTool)#

Annotate biomedical text with ontology terms using BioPortal’s Annotator (named entity recognitio…

BioPortal_annotate_text tool specification

Tool Information:

  • Name: BioPortal_annotate_text

  • Type: BioPortalTool

  • Description: Annotate biomedical text with ontology terms using BioPortal’s Annotator (named entity recognition). Scans free text and identifies mentions of biomedical concepts from 900+ ontologies. Useful for extracting disease mentions, drug names, gene functions, phenotypes, and anatomical terms from clinical notes, papers, or abstracts. Example: annotate ‘Melanoma is a malignant tumor of melanocytes’ to find DOID:1909 (melanoma) and DOID:162 (cancer).

Parameters:

  • text (string) (required) Biomedical text to annotate. Can be a sentence, abstract, or clinical note. Maximum recommended length: 500 words.

  • ontologies ([‘string’, ‘null’]) (optional) Comma-separated ontology acronyms to restrict annotation. If null, uses all ontologies. Common: ‘DOID,HP,CHEBI,GO,NCIT,MESH’.

  • longest_only ([‘boolean’, ‘null’]) (optional) If true (default), only return longest matching spans. Set false for all possible matches.

Example Usage:

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

BioPortal_get_concept (Type: BioPortalTool)#

Get detailed information about a specific concept from a BioPortal ontology, including full defin…

BioPortal_get_concept tool specification

Tool Information:

  • Name: BioPortal_get_concept

  • Type: BioPortalTool

  • Description: Get detailed information about a specific concept from a BioPortal ontology, including full definition, synonyms, CUI codes, and semantic types. Requires knowing the ontology acronym and concept IRI. Use BioPortal_search_ontology_terms first to find concept IDs, then use this tool for complete details. Example: get details for DOID:1909 (melanoma) from the DOID ontology, or GO:0006915 (apoptotic process) from the GO ontology.

Parameters:

Example Usage:

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

BioPortal_get_hierarchy (Type: BioPortalTool)#

Get children, parents, or ancestors of a specific concept in a BioPortal ontology, including ever…

BioPortal_get_hierarchy tool specification

Tool Information:

  • Name: BioPortal_get_hierarchy

  • Type: BioPortalTool

  • Description: Get children, parents, or ancestors of a specific concept in a BioPortal ontology, including every synonym supplied for each returned concept and synonym_count. Use the 1-based page parameter to retrieve complete high-cardinality hierarchies; metadata reports total_count, page_count, has_more, and next_page.

Parameters:

  • ontology (string) (required) Ontology acronym in BioPortal. Examples: ‘GO’, ‘HP’, ‘DOID’, ‘CHEBI’, ‘UBERON’, ‘NCIT’.

  • concept_id (string) (required) Full IRI of the concept. Example: ‘http://purl.obolibrary.org/obo/DOID_9351’ for diabetes mellitus.

  • direction ([‘string’, ‘null’]) (optional) Direction of hierarchy traversal: ‘children’ (narrower terms, default), ‘parents’ (direct broader terms), or ‘ancestors’ (all broader terms to root).

  • page_size ([‘integer’, ‘null’]) (optional) Number of results to return (default: 25, max: 100).

  • page (integer) (optional) One-based result page number (default: 1). Continue with metadata.next_page while metadata.has_more is true.

Example Usage:

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

BioPortal_search_ontology_terms (Type: BioPortalTool)#

Search across 900+ biomedical ontologies in BioPortal (NCBO) for concepts matching a query. Retur…

BioPortal_search_ontology_terms tool specification

Tool Information:

  • Name: BioPortal_search_ontology_terms

  • Type: BioPortalTool

  • Description: Search across 900+ biomedical ontologies in BioPortal (NCBO) for concepts matching a query. Returns every synonym supplied for each result, plus synonym_count, labels, IDs, definitions, and match metadata. Optionally filter by ontology and use the 1-based page parameter to retrieve every result page; metadata reports total_count, page_count, has_more, and next_page.

Parameters:

  • query (string) (required) Search query for finding ontology terms. Can be disease names, gene functions, phenotypes, chemical names, anatomical terms, etc. Examples: ‘melanoma’, ‘apoptosis’, ‘seizure’, ‘aspirin’, ‘hippocampus’.

  • ontologies ([‘string’, ‘null’]) (optional) Comma-separated list of ontology acronyms to search within. If null, searches all ontologies. Common ontologies: GO (Gene Ontology), HP (Human Phenotype), DOID (Disease Ontology), CHEBI (Chemical Entities), UBERON (Anatomy), NCIT (NCI Thesaurus), MESH (Medical Subject Headings), SNOMEDCT (SNOMED CT), RXNORM (Drug Names).

  • page_size ([‘integer’, ‘null’]) (optional) Number of results to return (default: 10, max: 50).

  • page (integer) (optional) One-based result page number (default: 1). Continue with metadata.next_page while metadata.has_more is true.

  • exact_match ([‘boolean’, ‘null’]) (optional) If true, only return exact matches (default: false).

Example Usage:

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