Biothings Tools

Configuration File: biothings_tools.json Tool Type: Local Tools Count: 7

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

Available Tools

MyChem_get_chemical_annotation (Type: MyChemTool)

Get detailed annotation for a specific chemical/drug by its InChIKey or other ID. Returns compreh…

MyChem_get_chemical_annotation tool specification

Tool Information:

  • Name: MyChem_get_chemical_annotation

  • Type: MyChemTool

  • Description: Get detailed annotation for a specific chemical/drug by its InChIKey or other ID. Returns comprehensive drug information including mechanisms, targets, interactions, and indications.

Parameters:

  • chem_id (string) (required) Chemical ID. InChIKey recommended (e.g., ‘BSYNRYMUTXBXSQ-UHFFFAOYSA-N’ for aspirin). Also accepts DrugBank ID or ChEMBL ID.

  • fields (string) (optional) Fields to return. Useful: drugbank (comprehensive), chebi, pubchem, chembl, drugcentral, aeolus (adverse events).

Example Usage:

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

MyChem_query_chemicals (Type: MyChemTool)

Search for chemicals and drugs by name, structure (InChIKey, SMILES), or database ID. Returns ann…

MyChem_query_chemicals tool specification

Tool Information:

  • Name: MyChem_query_chemicals

  • Type: MyChemTool

  • Description: Search for chemicals and drugs by name, structure (InChIKey, SMILES), or database ID. Returns annotations from sources like DrugBank, ChEMBL, ChEBI, and PubChem.

Parameters:

  • query (string) (required) Search query. Examples: ‘aspirin’ (name), ‘BSYNRYMUTXBXSQ-UHFFFAOYSA-N’ (InChIKey), ‘drugbank.id:DB00945’, ‘chembl.molecule_chembl_id:CHEMBL25’.

  • fields (string) (optional) Comma-separated fields to return. Common: drugbank, chebi, pubchem, chembl, drugcentral, unii.

  • size (integer) (optional) Maximum number of results (1-100).

Example Usage:

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

MyGene_batch_query (Type: MyGeneTool)

Query multiple genes at once using a list of gene identifiers. Efficient for retrieving annotatio…

MyGene_batch_query tool specification

Tool Information:

  • Name: MyGene_batch_query

  • Type: MyGeneTool

  • Description: Query multiple genes at once using a list of gene identifiers. Efficient for retrieving annotations for a gene set or performing ID mapping between different gene ID types.

Parameters:

  • gene_ids (array) (required) List of gene IDs to query. Can mix different ID types (Entrez, Ensembl, symbols).

  • species (string) (optional) Species filter for the query.

  • fields (string) (optional) Comma-separated list of fields to return for each gene.

Example Usage:

query = {
    "name": "MyGene_batch_query",
    "arguments": {
        "gene_ids": ["item1", "item2"]
    }
}
result = tu.run(query)

MyGene_get_gene_annotation (Type: MyGeneTool)

Get detailed annotation for a specific gene by its ID (Entrez or Ensembl). Returns comprehensive …

MyGene_get_gene_annotation tool specification

Tool Information:

  • Name: MyGene_get_gene_annotation

  • Type: MyGeneTool

  • Description: Get detailed annotation for a specific gene by its ID (Entrez or Ensembl). Returns comprehensive information including gene ontology, pathways, protein domains, and literature references.

Parameters:

  • gene_id (string) (required) Gene ID to query. Can be Entrez Gene ID (e.g., ‘1017’ for CDK2) or Ensembl ID (e.g., ‘ENSG00000123374’).

  • fields (string) (optional) Comma-separated list of fields to return. Available fields include: symbol, name, summary, go (gene ontology), pathway (KEGG/Reactome), interpro (protein domains), generif (gene references), pdb, uniprot.

Example Usage:

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

MyGene_query_genes (Type: MyGeneTool)

Search for genes by keyword, symbol, name, or other identifiers. Returns gene annotations from 30…

MyGene_query_genes tool specification

Tool Information:

  • Name: MyGene_query_genes

  • Type: MyGeneTool

  • Description: Search for genes by keyword, symbol, name, or other identifiers. Returns gene annotations from 30+ sources including Entrez Gene, Ensembl, UniProt, HGNC. Useful for finding gene IDs, symbols, descriptions, and basic annotations.

Parameters:

  • query (string) (required) Search query. Can be gene symbol (e.g., ‘CDK2’), name (‘cyclin dependent kinase’), Entrez ID (‘1017’), or Ensembl ID (‘ENSG00000123374’). Supports wildcards (*) and boolean operators (AND, OR, NOT).

  • species (string) (optional) Species filter. Use common name or NCBI taxonomy ID. Examples: ‘human’, ‘mouse’, ‘9606’ (human), ‘all’.

  • fields (string) (optional) Comma-separated list of fields to return. Common fields: symbol, name, entrezgene, ensembl.gene, summary, go, pathway, interpro.

  • size (integer) (optional) Maximum number of results to return (1-100).

Example Usage:

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

MyVariant_get_variant_annotation (Type: MyVariantTool)

Get detailed annotations for a specific variant by its HGVS ID (e.g., ‘chr1:g.2186318G>A’). Retur…

MyVariant_get_variant_annotation tool specification

Tool Information:

  • Name: MyVariant_get_variant_annotation

  • Type: MyVariantTool

  • Description: Get detailed annotations for a specific variant by its HGVS ID (e.g., ‘chr1:g.2186318G>A’). Returns information from dbSNP, ClinVar, CADD, and other sources.

Parameters:

  • variant_id (string) (required) HGVS variant ID (e.g., ‘chr1:g.2186318G>A’ or ‘rs123’).

  • fields (string) (optional) Fields to return. Useful fields: dbsnp, clinvar, cadd, gnomad_genome, gnomad_exome, dbnsfp (functional predictions).

Example Usage:

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

MyVariant_query_variants (Type: MyVariantTool)

Search for genetic variants by various criteria including rsID, gene, chromosome position, or cli…

MyVariant_query_variants tool specification

Tool Information:

  • Name: MyVariant_query_variants

  • Type: MyVariantTool

  • Description: Search for genetic variants by various criteria including rsID, gene, chromosome position, or clinical significance. Returns variant annotations from sources like dbSNP, ClinVar, gnomAD, and CADD.

Parameters:

  • query (string) (required) Search query. Examples: ‘rs58991260’ (rsID), ‘chr7:g.55249071G>A’ (HGVS), ‘clinvar.gene:BRCA1’ (gene in ClinVar), ‘cadd.phred:>30’ (high CADD score).

  • fields (string) (optional) Comma-separated fields to return. Common: dbsnp, clinvar, cadd, gnomad_genome, dbnsfp.

  • size (integer) (optional) Maximum number of results (1-100).

Example Usage:

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