Compound Gene Disease Tools#

Configuration File: compound_gene_disease_tools.json Tool Type: Local Tools Count: 1

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

Available Tools#

gather_gene_disease_associations (Type: CompoundGeneDiseaseAssociationTool)#

Query multiple gene-disease databases (DisGeNET, OMIM, OpenTargets, GenCC, ClinVar) in a single c…

gather_gene_disease_associations tool specification

Tool Information:

  • Name: gather_gene_disease_associations

  • Type: CompoundGeneDiseaseAssociationTool

  • Description: Query multiple gene-disease databases (DisGeNET, OMIM, OpenTargets, GenCC, ClinVar) in a single call. Returns a cross-referenced comparison table showing which sources agree on each association, with concordance scores. Use when you need to compare gene-disease evidence across databases or find associations unique to one source. Each association carries ‘concordance’ (how many sources named it) with two denominators: ‘total_sources_queried’ (all five, including any that failed) and ‘total_sources_with_data’ (those that actually contributed) – use the latter, since a source with no API key configured otherwise looks like a source that disagreed. ‘associations’ is paged by limit/offset (default 50) and ‘per_source_results’ by source_limit/source_offset (default 10 rows per source); ‘num_associations’, ‘truncated’ and ‘per_source_result_counts’ give the untruncated figures and ‘notes’ names any truncation that applied. Use next_association_offset as offset for the next association page and per_source_pagination[source].next_offset as source_offset for source rows.

Parameters:

  • gene ([‘string’, ‘null’]) (optional) Gene symbol (e.g., ‘TP53’, ‘BRCA1’). At least one of gene or disease required.

  • disease ([‘string’, ‘null’]) (optional) Disease name (e.g., ‘breast cancer’, ‘distal renal tubular acidosis’). At least one of gene or disease required.

  • limit (integer) (optional) Associations per page (1-500; default 50).

  • offset (integer) (optional) Zero-based concordance association offset.

  • source_limit (integer) (optional) Rows returned per source (1-500; default 10).

  • source_offset (integer) (optional) Zero-based offset applied independently to every source list.

Example Usage:

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