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 free text to ontology terms with EBI ZOOMA and exact local pagination over the complete upstr…

ZOOMA_annotate_text tool specification

Tool Information:

  • Name: ZOOMA_annotate_text

  • Type: ZoomaTool

  • Description: Map free text to ontology terms with EBI ZOOMA and exact local pagination over the complete upstream annotation array. Returns semantic-tag IRIs/CURIEs, confidence, provenance and OLS links. metadata.total_matches is the exact count after min_confidence filtering; continue with metadata.next_offset while has_more is true. Optionally restrict ontology sources or provide a property-type hint.

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 (unknown) (optional) Ontology source filter as a comma-separated string or string array, e.g. ‘efo,uberon’ or [‘efo’,’uberon’].

  • min_confidence ([‘string’, ‘null’]) (optional) Optional minimum confidence to keep, one of LOW, MEDIUM, GOOD, HIGH. Invalid values are rejected rather than silently disabling the filter.

  • max_results ([‘integer’, ‘null’]) (optional) Legacy alias for limit. Maximum annotations on this page; defaults to 10.

  • limit ([‘integer’, ‘null’]) (optional) Maximum annotations on this local page, 1-1000. Takes precedence over max_results and defaults to 10.

  • offset ([‘integer’, ‘null’]) (optional) Zero-based offset into the exact match set after min_confidence filtering. Continue with metadata.next_offset.

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)