Zooma Tools

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

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

Available Tools

ZOOMA_annotate_text (Type: ZoomaTool)

Map a free-text term (e.g. a sample attribute, phenotype, organism name, anatomical part, or dise…

ZOOMA_annotate_text tool specification

Tool Information:

  • Name: ZOOMA_annotate_text

  • Type: ZoomaTool

  • Description: Map a free-text term (e.g. a sample attribute, phenotype, organism name, anatomical part, or disease label) to ontology terms using EBI ZOOMA. Returns matched ontology terms as semantic-tag IRIs (OBO/EFO PURLs) with a confidence rating (HIGH/GOOD/MEDIUM/LOW), the curation source, the evidence type, and OLS lookup links. Use this when you have arbitrary text and need the most likely standardized ontology term(s) — for instance normalizing experiment metadata or resolving a disease/tissue name to an ontology ID. Optionally restrict matches to one or more ontologies (e.g. ‘efo’, ‘mondo’, ‘uberon’), give a property type hint, set a minimum confidence, and cap the number of results.

Parameters:

  • property_value (string) (required) Free text to annotate to ontology terms, e.g. ‘bone marrow’, ‘asthma’, ‘Homo sapiens’. Required.

  • property_type ([‘string’, ‘null’]) (optional) Optional property-type hint that narrows the annotation context, e.g. ‘disease’, ‘organism part’, ‘cell type’, ‘organism’. Leave unset to let ZOOMA infer it.

  • ontologies ([‘string’, ‘null’]) (optional) Optional comma-separated ontology source filter restricting matches to these ontologies, e.g. ‘efo’ or ‘efo,uberon’ or ‘mondo’. Leave unset to search all sources.

  • min_confidence ([‘string’, ‘null’]) (optional) Optional minimum confidence to keep, one of ‘LOW’, ‘MEDIUM’, ‘GOOD’, ‘HIGH’. Annotations below this level are dropped. Leave unset to keep all.

  • max_results ([‘integer’, ‘null’]) (optional) Maximum number of annotations to return (default 10). ZOOMA can return 100+ fuzzy matches for common terms.

Example Usage:

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

ZOOMA_list_datasources (Type: ZoomaTool)

List the curated annotation datasources that EBI ZOOMA draws on when mapping free text to ontolog…

ZOOMA_list_datasources tool specification

Tool Information:

  • Name: ZOOMA_list_datasources

  • Type: ZoomaTool

  • Description: List the curated annotation datasources that EBI ZOOMA draws on when mapping free text to ontology terms. Returns each datasource’s short name, type (DATABASE or ONTOLOGY), and home URI - for example ‘uniprot’, ‘eva-clinvar’, ‘atlas’ (Expression Atlas), ‘cbi’ (BioSamples), ‘metabolights’. Use this to discover valid source identifiers for provenance interpretation or to understand which curated resources back a given ZOOMA annotation. Takes no arguments.

Parameters:

No parameters required.

Example Usage:

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