Harmonizome Tools

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

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

Available Tools

Harmonizome_get_gene (Type: HarmonizomeTool)

Get comprehensive gene information from Harmonizome (Ma’ayan Lab), which integrates data from 100…

Harmonizome_get_gene tool specification

Tool Information:

  • Name: Harmonizome_get_gene

  • Type: HarmonizomeTool

  • Description: Get comprehensive gene information from Harmonizome (Ma’ayan Lab), which integrates data from 100+ genomics datasets covering gene expression, protein interactions, pathways, diseases, drug targets, and more. Returns gene symbol, name, NCBI Entrez ID, description, synonyms, and linked protein identifiers. Useful as a quick gene summary with curated descriptions from RefSeq. Example: TP53 returns description about tumor suppressor protein, NCBI ID 7157, synonyms [TRP53, LFS1, P53, BMFS5, BCC7], and linked UniProt protein P53_HUMAN.

Parameters:

  • gene_symbol (string) (required) Official gene symbol (case-insensitive). Examples: ‘TP53’, ‘BRCA1’, ‘EGFR’, ‘KRAS’, ‘CDK2’.

Example Usage:

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

Harmonizome_list_datasets (Type: HarmonizomeTool)

List all 100+ integrated genomics datasets available in Harmonizome (Ma’ayan Lab). Returns datase…

Harmonizome_list_datasets tool specification

Tool Information:

  • Name: Harmonizome_list_datasets

  • Type: HarmonizomeTool

  • Description: List all 100+ integrated genomics datasets available in Harmonizome (Ma’ayan Lab). Returns dataset names that can be used to explore gene-gene set associations. Covers gene expression (Allen Brain Atlas, GTEx, BioGPS, CCLE, TCGA), pathways (BioCarta, KEGG, Reactome, WikiPathways), protein interactions (BioGRID, PPI Hub), gene regulation (ChEA, ENCODE, JASPAR), drug targets (DrugBank, CTD), disease associations (OMIM, ClinVar, GAD, GWAS), phenotypes (MGI, HPO), and more. Provides a high-level catalog of all data sources integrated in Harmonizome.

Parameters:

No parameters required.

Example Usage:

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