Ncbi Datasets Tools

Configuration File: ncbi_datasets_tools.json Tool Type: Local Tools Count: 5

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

Available Tools

NCBIDatasets_get_gene (Type: NCBIDatasetsTool)

Get comprehensive gene information from NCBI by Gene ID. Returns gene symbol, description, chromo…

NCBIDatasets_get_gene tool specification

Tool Information:

  • Name: NCBIDatasets_get_gene

  • Type: NCBIDatasetsTool

  • Description: Get comprehensive gene information from NCBI by Gene ID. Returns gene symbol, description, chromosomal location, genomic coordinates, cross-references to UniProt/Ensembl/OMIM, synonyms, and annotation details. Covers all organisms in NCBI Gene database. Example: gene_id 7157 returns TP53 (tumor protein p53) on chromosome 17.

Parameters:

  • gene_id (string) (required) NCBI Gene ID (numeric). Examples: ‘7157’ (TP53), ‘672’ (BRCA1), ‘3630’ (INS), ‘22059’ (mouse Trp53).

Example Usage:

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

NCBIDatasets_get_gene_by_symbol (Type: NCBIDatasetsTool)

Look up gene information by gene symbol and organism. Searches NCBI Gene database using official …

NCBIDatasets_get_gene_by_symbol tool specification

Tool Information:

  • Name: NCBIDatasets_get_gene_by_symbol

  • Type: NCBIDatasetsTool

  • Description: Look up gene information by gene symbol and organism. Searches NCBI Gene database using official gene symbols. Specify the taxon as common name (human, mouse, rat) or taxonomy ID. Returns gene ID, description, chromosomal location, and database cross-references.

Parameters:

  • symbol (string) (required) Gene symbol. Examples: ‘TP53’, ‘BRCA1’, ‘INS’, ‘EGFR’.

  • taxon (string) (optional) Organism as common name or taxonomy ID. Examples: ‘human’, ‘mouse’, ‘rat’, ‘9606’, ‘10090’. Default: ‘human’.

Example Usage:

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

NCBIDatasets_get_orthologs (Type: NCBIDatasetsTool)

Get orthologous genes across species for a given NCBI Gene ID. Returns orthologs identified by NC…

NCBIDatasets_get_orthologs tool specification

Tool Information:

  • Name: NCBIDatasets_get_orthologs

  • Type: NCBIDatasetsTool

  • Description: Get orthologous genes across species for a given NCBI Gene ID. Returns orthologs identified by NCBI’s Ortholog pipeline, including gene symbols, species, and gene types for each ortholog. Useful for comparative genomics and cross-species gene function studies. Example: gene_id 7157 (TP53) returns mouse Trp53, rat Tp53, zebrafish tp53, etc.

Parameters:

  • gene_id (string) (required) NCBI Gene ID (numeric). Examples: ‘7157’ (TP53), ‘672’ (BRCA1), ‘3630’ (INS).

  • page_size (integer) (optional) Maximum number of orthologs to return (1-100). Default: 20.

Example Usage:

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

NCBIDatasets_get_taxonomy (Type: NCBIDatasetsTool)

Get detailed taxonomy information from NCBI by taxonomy ID. Returns organism name, rank, full lin…

NCBIDatasets_get_taxonomy tool specification

Tool Information:

  • Name: NCBIDatasets_get_taxonomy

  • Type: NCBIDatasetsTool

  • Description: Get detailed taxonomy information from NCBI by taxonomy ID. Returns organism name, rank, full lineage, counts of genes/assemblies/RNA types, and child taxa. Covers all organisms in NCBI Taxonomy including bacteria, archaea, eukaryotes, and viruses. Example: tax_id 9606 returns Homo sapiens with 20,625 protein-coding genes.

Parameters:

  • tax_id (string) (required) NCBI Taxonomy ID (numeric). Examples: ‘9606’ (Homo sapiens), ‘10090’ (Mus musculus), ‘7227’ (Drosophila melanogaster), ‘562’ (E. coli).

Example Usage:

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

NCBIDatasets_suggest_taxonomy (Type: NCBIDatasetsTool)

Suggest taxonomic names matching a query string. Searches NCBI Taxonomy for organisms by partial …

NCBIDatasets_suggest_taxonomy tool specification

Tool Information:

  • Name: NCBIDatasets_suggest_taxonomy

  • Type: NCBIDatasetsTool

  • Description: Suggest taxonomic names matching a query string. Searches NCBI Taxonomy for organisms by partial name, returning matching scientific names, taxonomy IDs, common names, and ranks. Useful for finding taxonomy IDs from partial organism names. Example: ‘drosophila’ returns D. melanogaster (7227), D. simulans (7240), etc.

Parameters:

  • query (string) (required) Partial organism name to search. Examples: ‘drosophila’, ‘escherichia’, ‘arabidopsis’, ‘saccharomyces’.

Example Usage:

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