Harmonizome Tools#

Configuration File: harmonizome_tools.json Tool Type: Local Tools Count: 6

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

Available Tools#

Harmonizome_get_dataset (Type: HarmonizomeTool)#

Get Harmonizome dataset metadata plus a recoverable page of its gene-set catalog. Large datasets …

Harmonizome_get_dataset tool specification

Tool Information:

  • Name: Harmonizome_get_dataset

  • Type: HarmonizomeTool

  • Description: Get Harmonizome dataset metadata plus a recoverable page of its gene-set catalog. Large datasets contain thousands of gene sets; start at gene_set_offset=0 and continue with metadata.next_gene_set_offset while has_more_gene_sets is true. Metadata.total_gene_sets is exact.

Parameters:

  • dataset_name (string) (required) Exact dataset name from Harmonizome. Examples: ‘CTD Gene-Disease Associations’, ‘KEGG Pathways’, ‘BioGRID Protein-Protein Interactions’. Use Harmonizome_list_datasets to find names.

  • gene_set_limit (integer) (optional) Gene set names per page (default 50, max 1000).

  • gene_set_offset (integer) (optional) Zero-based offset into the complete gene-set catalog. Continue with metadata.next_gene_set_offset.

Example Usage:

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

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_get_gene_set_members (Type: HarmonizomeTool)#

Retrieve Harmonizome gene-set members or per-gene associations. Both modes are recoverably pagina…

Harmonizome_get_gene_set_members tool specification

Tool Information:

  • Name: Harmonizome_get_gene_set_members

  • Type: HarmonizomeTool

  • Description: Retrieve Harmonizome gene-set members or per-gene associations. Both modes are recoverably paginated with limit/offset and metadata.next_offset; metadata.total_associations is the complete count.

Parameters:

  • mode (string) (optional) ‘gene_set’ for member genes of an attribute set (requires attribute + dataset); ‘gene’ for a gene’s full association table (requires gene_symbol).

  • attribute (string) (optional) Attribute/gene-set name for mode=’gene_set’ (e.g. ‘heart’, ‘liver’, a cell type or disease). Spaces are auto-encoded.

  • dataset (string) (optional) Dataset name for mode=’gene_set’ (e.g. ‘GTEx Tissue Gene Expression Profiles’). Use Harmonizome_list_datasets to find names.

  • gene_symbol (string) (optional) Gene symbol for mode=’gene’ (e.g. ‘DTD2’, ‘TP53’).

  • limit (integer) (optional) Maximum number of association rows to return (default 100). Sets can have thousands of members.

  • offset (integer) (optional) Zero-based association offset. Continue with metadata.next_offset.

Example Usage:

query = {
    "name": "Harmonizome_get_gene_set_members",
    "arguments": {
    }
}
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.

Parameters:

No parameters required.

Example Usage:

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

Harmonizome_search (Type: HarmonizomeTool)#

Search Harmonizome across genes, datasets, or attributes. Results are recoverably paginated: star…

Harmonizome_search tool specification

Tool Information:

  • Name: Harmonizome_search

  • Type: HarmonizomeTool

  • Description: Search Harmonizome across genes, datasets, or attributes. Results are recoverably paginated: start with offset=0 and continue with metadata.next_offset while metadata.has_more is true; dataset/attribute metadata includes the complete total. Gene search resolves Harmonizome’s mixed-entity suggestions one by one: expected non-gene 404s are counted in rejected_non_gene_suggestions, while transport, HTTP, or malformed-data failures return an error instead of a plausible incomplete gene page.

Parameters:

  • query (string) (required) Search query. Examples: ‘TP53’, ‘BRCA1’, ‘kinase’, ‘expression’, ‘pathway’.

  • entity_type (string) (optional) What to search for: ‘gene’ (default), ‘dataset’, or ‘attribute’.

  • limit (integer) (optional) Maximum results to return (default: 20).

  • offset (integer) (optional) Zero-based result offset. Continue with metadata.next_offset.

Example Usage:

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

Harmonizome_search_genes (Type: HarmonizomeTool)#

Resolve Harmonizome genes by exact symbol and symbol-like suggestions. The upstream /gene collect…

Harmonizome_search_genes tool specification

Tool Information:

  • Name: Harmonizome_search_genes

  • Type: HarmonizomeTool

  • Description: Resolve Harmonizome genes by exact symbol and symbol-like suggestions. The upstream /gene collection silently ignores text filters, so this tool does not use it and will return no records for unsupported descriptive terms rather than unrelated catalog rows. Results support offset continuation when metadata.has_more is true; exact total count is unavailable for suggestions.

Parameters:

  • query (string) (required) Gene symbol or symbol prefix. Examples: ‘TP53’, ‘BRCA1’, ‘CDK’. Descriptive terms such as ‘kinase’ are not a supported gene-symbol search.

  • limit (integer) (optional) Maximum results to return (default: 20).

  • offset (integer) (optional) Zero-based offset over gene-resolvable symbol suggestions. Continue with metadata.next_offset.

Example Usage:

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