Bvbrc Tools

Configuration File: bvbrc_tools.json Tool Type: Local Tools Count: 13

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

Available Tools

BVBRC_get_genome (Type: BVBRCTool)

Get the complete genome record exposed by BV-BRC, including all assembly, quality, CheckM, access…

BVBRC_get_genome tool specification

Tool Information:

• Name: BVBRC_get_genome

• Type: BVBRCTool

• Description: Get the complete genome record exposed by BV-BRC, including all assembly, quality, CheckM, accession, sequencing, host, disease, and isolation fields. Set include_related=true to additionally retrieve the first explicitly paginated page of AMR phenotypes and specialty genes for the exact genome under related_records; metadata then reports independent totals and next offsets. Example: ‘83332.12’ returns Mycobacterium tuberculosis H37Rv.

Parameters:

• genome_id (string) (required) BV-BRC genome identifier (taxon_id.version format). Examples: ‘83332.12’ (M. tuberculosis H37Rv), ‘511145.12’ (E. coli K-12 MG1655), ‘93061.5’ (S. aureus NCTC 8325).

• include_related (boolean) (optional) Also retrieve paginated AMR phenotype and specialty-gene records for this exact genome. Default: false, because each related collection costs an extra request; metadata.related_data names the dedicated tools to call instead.

• related_limit (integer) (optional) Maximum AMR and specialty-gene records returned per related collection.

• related_offset (integer) (optional) Zero-based offset for both related collections. Their independent next offsets are reported in metadata.related_pagination.

Example Usage:

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

BVBRC_get_protein_structure (Type: BVBRCTool)

Get detailed pathogen protein structure information from BV-BRC by PDB ID. Returns structure meta…

BVBRC_get_protein_structure tool specification

Tool Information:

• Name: BVBRC_get_protein_structure

• Type: BVBRCTool

• Description: Get detailed pathogen protein structure information from BV-BRC by PDB ID. Returns structure metadata including title, resolution, method, gene, organism, UniProt accession, PMID references, sequence, and taxonomic lineage. Useful for structural biology research on pathogen proteins. Example: ‘6VSB’ returns the SARS-CoV-2 spike glycoprotein structure.

Parameters:

• pdb_id (string) (required) PDB identifier for the protein structure. Examples: ‘6VSB’ (SARS-CoV-2 spike), ‘7CMD’ (SARS-CoV-2 PLpro), ‘6VW1’ (SARS-CoV-2 RBD-ACE2 complex).

Example Usage:

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

BVBRC_get_taxonomy (Type: BVBRCTool)

Get detailed taxonomy information for a pathogen from BV-BRC by NCBI Taxonomy ID. Returns taxon n…

BVBRC_get_taxonomy tool specification

Tool Information:

• Name: BVBRC_get_taxonomy

• Type: BVBRCTool

• Description: Get detailed taxonomy information for a pathogen from BV-BRC by NCBI Taxonomy ID. Returns taxon name, rank, lineage, alternative names, and genome counts. Useful for resolving pathogen taxonomy and understanding classification hierarchy. Example: ‘2697049’ returns SARS-CoV-2 taxonomy with full lineage from Viruses to species.

Parameters:

• taxon_id (string) (required) NCBI Taxonomy ID. Examples: ‘2697049’ (SARS-CoV-2), ‘1773’ (M. tuberculosis), ‘1280’ (S. aureus), ‘11320’ (Influenza A).

Example Usage:

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

BVBRC_search_amr (Type: BVBRCTool)

Search for ANTIBACTERIAL resistance (AMR) phenotype data in BV-BRC – bacteria tested against ant…

BVBRC_search_amr tool specification

Tool Information:

• Name: BVBRC_search_amr

• Type: BVBRCTool

• Description: Search for ANTIBACTERIAL resistance (AMR) phenotype data in BV-BRC – bacteria tested against antibiotics (e.g. ‘methicillin’, ‘ciprofloxacin’), NOT antiviral drug-resistance mutations (for influenza/viral antiviral resistance, use Pathoplexus_get_mutations or literature search instead). Returns resistance/susceptibility data for pathogens against specific antibiotics, including MIC values, testing methods, and evidence. Results are explicitly paginated; metadata reports the true total, truncation state, and next offset. Filter by ‘antibiotic’, ‘resistant_phenotype’, and/or a specific BV-BRC ‘genome_id’. There is no organism/species parameter: to scope results to one organism, first obtain its genome_id(s) and pass genome_id here.

Parameters:

• antibiotic ([‘string’, ‘null’]) (optional) Antibiotic name to search for. Examples: ‘methicillin’, ‘vancomycin’, ‘ciprofloxacin’, ‘amikacin’, ‘isoniazid’.

• genome_id ([‘string’, ‘null’]) (optional) BV-BRC genome ID to get AMR data for a specific genome. Example: ‘83332.12’.

• resistant_phenotype ([‘string’, ‘null’]) (optional) Filter by resistance phenotype. Options: ‘Resistant’, ‘Susceptible’, ‘Intermediate’.

• limit ([‘integer’, ‘null’]) (optional) Maximum number of results per page. Default: 25. Max: 100.

• offset ([‘integer’, ‘null’]) (optional) Zero-based result offset. Use metadata.next_offset to retrieve the next page. Default: 0.

Example Usage:

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

BVBRC_search_epitopes (Type: BVBRCTool)

Search for pathogen epitopes (B-cell and T-cell) in BV-BRC with explicit pagination. Metadata rep…

BVBRC_search_epitopes tool specification

Tool Information:

• Name: BVBRC_search_epitopes

• Type: BVBRCTool

• Description: Search for pathogen epitopes (B-cell and T-cell) in BV-BRC with explicit pagination. Metadata reports the true total and next offset.

Parameters:

• taxon_id ([‘string’, ‘null’]) (optional) NCBI Taxonomy ID for the pathogen organism. Examples: ‘2697049’ (SARS-CoV-2), ‘11320’ (Influenza A), ‘1773’ (M. tuberculosis).

• protein_name ([‘string’, ‘null’]) (optional) Target protein name to filter epitopes. Examples: ‘Spike glycoprotein’, ‘Nucleocapsid protein’, ‘Replicase polyprotein 1ab’.

• epitope_type ([‘string’, ‘null’]) (optional) Type of epitope. Options: ‘Linear peptide’, ‘Discontinuous peptide’. Most epitopes are linear peptides.

• organism ([‘string’, ‘null’]) (optional) Organism name keyword to search across epitope records. Example: ‘coronavirus’, ‘influenza’.

• limit ([‘integer’, ‘null’]) (optional) Maximum number of results. Default: 25. Max: 100.

• offset ([‘integer’, ‘null’]) (optional) Zero-based result offset. Use metadata.next_offset to continue.

Example Usage:

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

BVBRC_search_genome_features (Type: BVBRCTool)

Search for genome features (genes, proteins, CDS) in BV-BRC pathogen genomes with explicit pagina…

BVBRC_search_genome_features tool specification

Tool Information:

• Name: BVBRC_search_genome_features

• Type: BVBRCTool

• Description: Search for genome features (genes, proteins, CDS) in BV-BRC pathogen genomes with explicit pagination. Metadata reports the true Content-Range total, truncation state, and next offset.

Parameters:

• gene ([‘string’, ‘null’]) (optional) Gene name to search for. Examples: ‘mecA’ (methicillin resistance), ‘blaTEM’ (beta-lactamase), ‘katG’ (isoniazid resistance).

• product ([‘string’, ‘null’]) (optional) Gene product keyword to search. Examples: ‘beta-lactamase’, ‘penicillin-binding protein’, ‘DNA gyrase’.

• genome_id ([‘string’, ‘null’]) (optional) Restrict search to a specific genome. Example: ‘83332.12’.

• limit ([‘integer’, ‘null’]) (optional) Maximum number of results. Default: 10. Max: 100.

• keyword ([‘string’, ‘null’]) (optional) Alias for product: gene product keyword to search (e.g., ‘spike protein’, ‘beta-lactamase’).

• offset ([‘integer’, ‘null’]) (optional) Zero-based result offset. Use metadata.next_offset to continue.

Example Usage:

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

BVBRC_search_genomes (Type: BVBRCTool)

Search for pathogen genomes in BV-BRC by organism name or keyword, with explicit pagination and o…

BVBRC_search_genomes tool specification

Tool Information:

• Name: BVBRC_search_genomes

• Type: BVBRCTool

• Description: Search for pathogen genomes in BV-BRC by organism name or keyword, with explicit pagination and optional genome status, quality, CheckM, and collection-date filters. The response metadata reports the true total from BV-BRC’s Content-Range header, whether the page is truncated, and the next offset. Example: ‘Staphylococcus aureus’ returns S. aureus genome assemblies.

Parameters:

• keyword (string) (required) Search keyword - organism name, strain, or pathogen. Examples: ‘Staphylococcus aureus’, ‘Escherichia coli’, ‘Salmonella enterica’, ‘SARS-CoV-2’.

• limit ([‘integer’, ‘null’]) (optional) Maximum number of results to return per page. Default: 10. Max: 100.

• offset ([‘integer’, ‘null’]) (optional) Zero-based result offset. Use metadata.next_offset to retrieve the next page. Default: 0.

• genome_status ([‘string’, ‘null’]) (optional) Exact BV-BRC genome status filter, such as ‘Complete’ or ‘WGS’.

• genome_quality ([‘string’, ‘null’]) (optional) Exact BV-BRC genome quality classification filter, such as ‘Good’.

• min_checkm_completeness ([‘number’, ‘null’]) (optional) Minimum CheckM completeness percentage.

• max_checkm_contamination ([‘number’, ‘null’]) (optional) Maximum CheckM contamination percentage.

• collection_date_start ([‘string’, ‘null’]) (optional) Inclusive lower bound for collection_date, in the date format accepted by BV-BRC.

• collection_date_end ([‘string’, ‘null’]) (optional) Inclusive upper bound for collection_date, in the date format accepted by BV-BRC.

Example Usage:

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

BVBRC_search_pathways (Type: BVBRCTool)

Search for metabolic pathways in BV-BRC with explicit pagination. Metadata reports the true row t…

BVBRC_search_pathways tool specification

Tool Information:

• Name: BVBRC_search_pathways

• Type: BVBRCTool

• Description: Search for metabolic pathways in BV-BRC with explicit pagination. Metadata reports the true row total and next offset; distinct gene/annotation rows remain distinguishable.

Parameters:

• taxon_id ([‘string’, ‘null’]) (optional) NCBI Taxonomy ID. Examples: ‘1773’ (M. tuberculosis), ‘562’ (E. coli), ‘1280’ (S. aureus).

• pathway_name ([‘string’, ‘null’]) (optional) Pathway name keyword. Examples: ‘Glycolysis’, ‘Fatty acid’, ‘Amino acid’, ‘Sulfur metabolism’.

• ec_number ([‘string’, ‘null’]) (optional) Enzyme Commission number. Examples: ‘1.11.1.6’ (catalase), ‘2.7.1.1’ (hexokinase).

• genome_id ([‘string’, ‘null’]) (optional) Restrict to a specific genome. Example: ‘83332.12’ (M. tuberculosis H37Rv).

• limit ([‘integer’, ‘null’]) (optional) Maximum number of results. Default: 25. Max: 100.

• offset ([‘integer’, ‘null’]) (optional) Zero-based result offset. Use metadata.next_offset to continue.

Example Usage:

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

BVBRC_search_protein_structures (Type: BVBRCTool)

Search for pathogen protein structures in BV-BRC by organism, gene, or method, with explicit pagi…

BVBRC_search_protein_structures tool specification

Tool Information:

• Name: BVBRC_search_protein_structures

• Type: BVBRCTool

• Description: Search for pathogen protein structures in BV-BRC by organism, gene, or method, with explicit pagination and true totals.

Parameters:

• taxon_id ([‘string’, ‘null’]) (optional) NCBI Taxonomy ID. Examples: ‘2697049’ (SARS-CoV-2), ‘1773’ (M. tuberculosis), ‘11320’ (Influenza A).

• gene ([‘string’, ‘null’]) (optional) Gene name filter. Examples: ‘S’ (spike), ‘rep’ (replicase), ‘N’ (nucleocapsid).

• method ([‘string’, ‘null’]) (optional) Experimental method. Examples: ‘X-ray diffraction’, ‘Electron microscopy’, ‘Solution NMR’.

• limit ([‘integer’, ‘null’]) (optional) Maximum number of results. Default: 10. Max: 100.

• offset ([‘integer’, ‘null’]) (optional) Zero-based result offset. Use metadata.next_offset to continue.

Example Usage:

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

BVBRC_search_specialty_genes (Type: BVBRCTool)

Search for specialty genes in BV-BRC including virulence factors, antibiotic resistance genes, dr…

BVBRC_search_specialty_genes tool specification

Tool Information:

• Name: BVBRC_search_specialty_genes

• Type: BVBRCTool

• Description: Search for specialty genes in BV-BRC including virulence factors, antibiotic resistance genes, drug targets, and human homologs. Filter by exact genome_id, taxon, gene, property, or source. Results are explicitly paginated and metadata reports the true total and next offset.

Parameters:

• gene ([‘string’, ‘null’]) (optional) Gene name to search. Examples: ‘mecA’ (methicillin resistance), ‘katG’ (isoniazid resistance), ‘drrC’ (efflux pump).

• property ([‘string’, ‘null’]) (optional) Specialty gene property category. Options: ‘Antibiotic Resistance’, ‘Virulence Factor’, ‘Drug Target’, ‘Transporter’, ‘Human Homolog’.

• source ([‘string’, ‘null’]) (optional) Source database for annotation. Options: ‘CARD’, ‘NDARO’, ‘PATRIC_VF’, ‘VFDB’, ‘DrugBank’, ‘TTD’, ‘Human’.

• taxon_id ([‘string’, ‘null’]) (optional) NCBI Taxonomy ID. Examples: ‘1280’ (S. aureus), ‘1773’ (M. tuberculosis), ‘562’ (E. coli).

• genome_id ([‘string’, ‘null’]) (optional) Exact BV-BRC genome ID, such as ‘83332.12’. Use this to retrieve specialty genes for one assembly rather than every genome in a taxon.

• limit ([‘integer’, ‘null’]) (optional) Maximum number of results per page. Default: 25. Max: 100.

• offset ([‘integer’, ‘null’]) (optional) Zero-based result offset. Use metadata.next_offset to continue.

Example Usage:

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

BVBRC_search_subsystems (Type: BVBRCTool)

Search for functional subsystems in BV-BRC with explicit pagination and true Content-Range totals.

BVBRC_search_subsystems tool specification

Tool Information:

• Name: BVBRC_search_subsystems

• Type: BVBRCTool

• Description: Search for functional subsystems in BV-BRC with explicit pagination and true Content-Range totals.

Parameters:

• taxon_id ([‘string’, ‘null’]) (optional) NCBI Taxonomy ID. Examples: ‘1773’ (M. tuberculosis), ‘1280’ (S. aureus), ‘562’ (E. coli).

• superclass ([‘string’, ‘null’]) (optional) Top-level functional category. Options include: ‘METABOLISM’, ‘STRESS RESPONSE, DEFENSE, VIRULENCE’, ‘ENERGY’, ‘CELLULAR PROCESSES’, ‘DNA PROCESSING’, ‘PROTEIN PROCESSING’, ‘CELL ENVELOPE’, ‘RNA PROCESSING’.

• subsystem_name ([‘string’, ‘null’]) (optional) Subsystem name keyword. Examples: ‘mycothiol’, ‘iron acquisition’, ‘beta-lactam resistance’.

• role_name ([‘string’, ‘null’]) (optional) Specific functional role keyword. Examples: ‘catalase’, ‘penicillin-binding protein’.

• genome_id ([‘string’, ‘null’]) (optional) Restrict to a specific genome. Example: ‘83332.12’.

• limit ([‘integer’, ‘null’]) (optional) Maximum number of results. Default: 25. Max: 100.

• offset ([‘integer’, ‘null’]) (optional) Zero-based result offset. Use metadata.next_offset to continue.

Example Usage:

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

BVBRC_search_surveillance (Type: BVBRCTool)

Search influenza and pathogen surveillance data in BV-BRC with explicit pagination and true Conte…

BVBRC_search_surveillance tool specification

Tool Information:

• Name: BVBRC_search_surveillance

• Type: BVBRCTool

• Description: Search influenza and pathogen surveillance data in BV-BRC with explicit pagination and true Content-Range totals.

Parameters:

• subtype ([‘string’, ‘null’]) (optional) Influenza subtype to search for. Examples: ‘H5N1’, ‘H1N1’, ‘H3N2’, ‘H7N9’. Common in surveillance tracking.

• geographic_group ([‘string’, ‘null’]) (optional) Geographic region filter. Options: ‘North America’, ‘Europe’, ‘Asia’, ‘Africa’, ‘South America’, ‘Oceania’.

• host_group ([‘string’, ‘null’]) (optional) Host organism group. Options: ‘Human’, ‘Animal’, ‘Avian’, ‘Swine’, ‘Environment’.

• collection_country ([‘string’, ‘null’]) (optional) Country of sample collection. Examples: ‘USA’, ‘China’, ‘Egypt’, ‘Vietnam’.

• limit ([‘integer’, ‘null’]) (optional) Maximum number of results. Default: 25. Max: 100.

• offset ([‘integer’, ‘null’]) (optional) Zero-based result offset. Use metadata.next_offset to continue.

Example Usage:

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

BVBRC_search_taxonomy (Type: BVBRCTool)

Search for pathogen taxonomy entries in BV-BRC by keyword, with explicit pagination and true Cont…

BVBRC_search_taxonomy tool specification

Tool Information:

• Name: BVBRC_search_taxonomy

• Type: BVBRCTool

• Description: Search for pathogen taxonomy entries in BV-BRC by keyword, with explicit pagination and true Content-Range totals.

Parameters:

• keyword (string) (required) Taxonomy search keyword. Examples: ‘Mycobacterium’, ‘coronavirus’, ‘Salmonella’, ‘influenza’, ‘Ebola’.

• limit ([‘integer’, ‘null’]) (optional) Maximum number of results. Default: 10. Max: 100.

• offset ([‘integer’, ‘null’]) (optional) Zero-based result offset. Use metadata.next_offset to continue.

Example Usage:

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

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