Ncbi Datasets Tools

Configuration File: ncbi_datasets_tools.json Tool Type: Local Tools Count: 8

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_genome_assembly (Type: NCBIDatasetsTool)

Get genome assembly metadata for an assembly accession (RefSeq GCF_ or GenBank GCA_) from the NCB…

NCBIDatasets_get_genome_assembly tool specification

Tool Information:

  • Name: NCBIDatasets_get_genome_assembly

  • Type: NCBIDatasetsTool

  • Description: Get genome assembly metadata for an assembly accession (RefSeq GCF_ or GenBank GCA_) from the NCBI Datasets v2 API. Returns organism/strain, assembly name/level/status, RefSeq category (e.g. reference genome), release date, submitter, BioProject, and assembly statistics (total length, chromosome count, contig/scaffold N50, GC%, annotation provider). Use to characterize a specific genome assembly across any organism (bacteria, fungi, plant, animal). No API key required.

Parameters:

  • accession (string) (required) Assembly accession, e.g. ‘GCF_000005845.2’ (E. coli K-12) or ‘GCF_000001405.40’ (human GRCh38.p14).

Example Usage:

query = {
    "name": "NCBIDatasets_get_genome_assembly",
    "arguments": {
        "accession": "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_sequence_reports (Type: NCBIDatasetsTool)

Get per-sequence (chromosome/plasmid/scaffold) reports for a genome assembly via the NCBI Dataset…

NCBIDatasets_get_sequence_reports tool specification

Tool Information:

  • Name: NCBIDatasets_get_sequence_reports

  • Type: NCBIDatasetsTool

  • Description: Get per-sequence (chromosome/plasmid/scaffold) reports for a genome assembly via the NCBI Datasets v2 API. Returns each molecule’s chromosome name, role, location type, RefSeq and GenBank accessions, length, and GC%. Use to map an assembly to its individual sequence accessions (e.g. resolve E. coli K-12 to NC_000913.3, or human chromosomes to their RefSeq NC_ accessions). No API key required.

Parameters:

  • accession (string) (required) Assembly accession, e.g. ‘GCF_000005845.2’.

Example Usage:

query = {
    "name": "NCBIDatasets_get_sequence_reports",
    "arguments": {
        "accession": "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_list_genomes_by_taxon (Type: NCBIDatasetsTool)

List genome assemblies available for a taxon (NCBI tax id or scientific name) via the NCBI Datase…

NCBIDatasets_list_genomes_by_taxon tool specification

Tool Information:

  • Name: NCBIDatasets_list_genomes_by_taxon

  • Type: NCBIDatasetsTool

  • Description: List genome assemblies available for a taxon (NCBI tax id or scientific name) via the NCBI Datasets v2 API. Returns a summary list of assemblies (accession, assembly name/level, RefSeq category, release date, total length, N50, GC%) plus the total count available. Use to discover what genomes exist for an organism or clade, e.g. all Escherichia coli or Mycobacterium tuberculosis assemblies. Set reference_only to restrict to reference/representative genomes. No API key required.

Parameters:

  • taxon (string) (required) NCBI tax id or scientific name, e.g. ‘562’, ‘Escherichia coli’, ‘Saccharomyces cerevisiae’.

  • limit ([‘integer’, ‘null’]) (optional) Max assemblies to return (default 20, max 100).

  • reference_only ([‘boolean’, ‘null’]) (optional) If true, return only reference/representative genomes.

Example Usage:

query = {
    "name": "NCBIDatasets_list_genomes_by_taxon",
    "arguments": {
        "taxon": "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)