Humanmine Tools

Configuration File: humanmine_tools.json Tool Type: Local Tools Count: 4

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

Available Tools

HumanMine_search (Type: BaseRESTTool)

Search HumanMine (InterMine) for genes, proteins, pathways, diseases, and other biological entiti…

HumanMine_search tool specification

Tool Information:

  • Name: HumanMine_search

  • Type: BaseRESTTool

  • Description: Search HumanMine (InterMine) for genes, proteins, pathways, diseases, and other biological entities related to human, mouse, and rat. HumanMine integrates data from 30+ sources including NCBI Gene, UniProt, Ensembl, GO, KEGG, Reactome, OMIM, and GWAS Catalog. Returns entity IDs, types, names, symbols, and organism information. Use the facet_Category parameter to filter results to a specific type (Gene, Protein, Pathway, Disease, Publication, etc.).

Parameters:

  • q (string) (required) Search query: gene symbol (e.g., ‘TP53’, ‘BRCA1’), gene name, disease name, pathway name, or any biological term

  • size ([‘integer’, ‘null’]) (optional) Maximum number of results to return (default 10, max 100)

  • facet_Category ([‘string’, ‘null’]) (optional) Filter by entity type: ‘Gene’, ‘Protein’, ‘Pathway’, ‘Disease’, ‘Publication’, ‘GWASResult’, ‘GOTerm’, ‘ProteinDomain’, etc.

Example Usage:

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

HumanMine_search_genes (Type: BaseRESTTool)

Search HumanMine specifically for genes by symbol, name, or ID across human, mouse, and rat. Huma…

HumanMine_search_genes tool specification

Tool Information:

  • Name: HumanMine_search_genes

  • Type: BaseRESTTool

  • Description: Search HumanMine specifically for genes by symbol, name, or ID across human, mouse, and rat. HumanMine integrates gene data from NCBI Gene, Ensembl, UniProt, and other sources. Returns gene symbols, Entrez IDs, Ensembl IDs, gene names, and organism information. More focused than HumanMine_search as it pre-filters to Gene category only.

Parameters:

  • q (string) (required) Gene search query: gene symbol (e.g., ‘EGFR’, ‘TP53’), gene name (e.g., ‘tumor protein p53’), or Entrez Gene ID

  • size ([‘integer’, ‘null’]) (optional) Maximum number of results to return (default 10, max 100)

Example Usage:

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

HumanMine_search_pathways (Type: BaseRESTTool)

Search HumanMine specifically for biological pathways by name or identifier. Integrates pathway d…

HumanMine_search_pathways tool specification

Tool Information:

  • Name: HumanMine_search_pathways

  • Type: BaseRESTTool

  • Description: Search HumanMine specifically for biological pathways by name or identifier. Integrates pathway data from Reactome, KEGG, and other sources. Returns pathway names, identifiers (Reactome IDs like R-HSA-109581), and associated organisms. Useful for finding pathway IDs for downstream enrichment analysis.

Parameters:

  • q (string) (required) Pathway search query: pathway name (e.g., ‘apoptosis’, ‘cell cycle’, ‘PI3K-Akt signaling’), or Reactome ID

  • size ([‘integer’, ‘null’]) (optional) Maximum number of results to return (default 10, max 100)

Example Usage:

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

InterMine_run_pathquery (Type: BaseRESTTool)

Run an arbitrary InterMine PathQuery against HumanMine (an InterMine data warehouse) to traverse …

InterMine_run_pathquery tool specification

Tool Information:

  • Name: InterMine_run_pathquery

  • Type: BaseRESTTool

  • Description: Run an arbitrary InterMine PathQuery against HumanMine (an InterMine data warehouse) to traverse the data model graph: gene->pathways, gene->protein domains, region->features, etc. The ‘query’ argument is an InterMine XML PathQuery string (with model, view columns, and constraints) — results come back as JSON rows in the order of the ‘view’ columns. Example: query ‘<query model=”genomic” view=”Gene.symbol Gene.pathways.name Gene.pathways.dataSets.name”><constraint path=”Gene.symbol” op=”=” value=”PAX6”/></query>’ returns PAX6 Reactome pathways like ‘Activation of HOX genes during differentiation’. A second view ‘Gene.proteins.proteinDomainRegions.proteinDomain.name’ returns protein domains such as ‘Homeobox domain’.

Parameters:

  • query (string) (required) InterMine XML PathQuery. Must include model, view (space-separated paths), and constraints. Example: ‘<query model=”genomic” view=”Gene.symbol Gene.pathways.name”><constraint path=”Gene.symbol” op=”=” value=”PAX6”/></query>’.

Example Usage:

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