Biosamples Tools

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

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

Available Tools

BioSamples_get_facets (Type: BioSamplesTool)

Faceted aggregation discovery over EBI BioSamples: given a free-text query, return the available …

BioSamples_get_facets tool specification

Tool Information:

  • Name: BioSamples_get_facets

  • Type: BioSamplesTool

  • Description: Faceted aggregation discovery over EBI BioSamples: given a free-text query, return the available attribute facets (organism, status, SRA accession, external reference, release date range, …) with sample counts plus the top values per facet, so a scientist learns which filterable attribute keys/values exist before running a structured filter search (BioSamples_search_by_filter). Also returns external-reference data facets (e.g. ENA). Example: text=’cancer’ returns organism (count 59585), SRA accession (54248), status (59590), external reference (54524), release date range (59590), and ENA external-reference facet (53344). No authentication required.

Parameters:

  • text (string) (required) Free-text query to compute facets over. Examples: ‘cancer’, ‘liver’, ‘Homo sapiens’.

  • max_values ([‘integer’, ‘null’]) (optional) Maximum number of top values to return per facet (1-50, default 10).

Example Usage:

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

BioSamples_get_relationships (Type: BioSamplesTool)

Retrieve the relationship/provenance graph of a BioSample: the sample-to-sample lineage edges (e….

BioSamples_get_relationships tool specification

Tool Information:

  • Name: BioSamples_get_relationships

  • Type: BioSamplesTool

  • Description: Retrieve the relationship/provenance graph of a BioSample: the sample-to-sample lineage edges (e.g. ‘derived from’, ‘has member’, ‘child of’, ‘same as’, ‘recurated into’) that the standard BioSamples_get_sample parser drops. Each edge reports source, type, target, and the direction relative to the queried sample, so processed-sample -> source-tissue and sample-group -> member-sample provenance becomes reachable. Example: SAMEA4451312 returns edges [SAMEA4451312 derived from SAMEA4451117] and [SAMEG315830 has member SAMEA4451312]. No authentication required.

Parameters:

  • accession (string) (required) BioSamples accession. Formats: SAMEA* (EBI), SAMN* (NCBI), SAMD* (DDBJ), SAMEG* (sample group). Example: ‘SAMEA4451312’.

Example Usage:

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

BioSamples_get_sample (Type: BioSamplesTool)

Get detailed metadata for a specific biological sample from the EBI BioSamples database by access…

BioSamples_get_sample tool specification

Tool Information:

  • Name: BioSamples_get_sample

  • Type: BioSamplesTool

  • Description: Get detailed metadata for a specific biological sample from the EBI BioSamples database by accession. Returns sample name, organism, tissue, disease, experimental context, and links to associated data archives (ENA, ArrayExpress, EVA). BioSamples contains 60+ million samples from all major sequence and functional genomics archives. Example: SAMEA104228123 returns a metagenomic sample from the Qiita microbiome project.

Parameters:

  • accession (string) (required) BioSamples accession. Formats: SAMEA* (EBI), SAMN* (NCBI), SAMD* (DDBJ). Examples: ‘SAMEA104228123’, ‘SAMD00000603’.

Example Usage:

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

BioSamples_search (Type: BioSamplesTool)

Search the EBI BioSamples database by text query across 60+ million biological samples. Returns m…

BioSamples_search tool specification

Tool Information:

  • Name: BioSamples_search

  • Type: BioSamplesTool

  • Description: Search the EBI BioSamples database by text query across 60+ million biological samples. Returns matching samples with accessions, names, organisms, and key characteristics. Useful for finding source material metadata for sequencing, proteomics, and other experiments. Example: searching ‘breast cancer’ returns thousands of tumor samples with tissue/disease annotations.

Parameters:

  • query (string) (required) Free-text search query. Examples: ‘breast cancer’, ‘liver tissue’, ‘CRISPR screen’, ‘Mus musculus brain’.

  • limit ([‘integer’, ‘null’]) (optional) Maximum results to return (1-50, default 10).

  • page ([‘integer’, ‘null’]) (optional) Page number (0-indexed, default 0).

Example Usage:

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

BioSamples_search_by_filter (Type: BioSamplesTool)

Search the EBI BioSamples database with structured attribute filters. More precise than text sear…

BioSamples_search_by_filter tool specification

Tool Information:

  • Name: BioSamples_search_by_filter

  • Type: BioSamplesTool

  • Description: Search the EBI BioSamples database with structured attribute filters. More precise than text search - filters by specific metadata fields like organism, tissue, or disease. Example: attribute=’organism’, value=’Homo sapiens’ returns human samples; attribute=’disease’, value=’melanoma’ returns melanoma-specific samples.

Parameters:

  • attribute (string) (required) Attribute name to filter on. Common attributes: ‘organism’, ‘tissue’, ‘disease’, ‘cell type’, ‘sex’, ‘age’.

  • value (string) (required) Value to match for the attribute. Examples: ‘Homo sapiens’, ‘liver’, ‘melanoma’, ‘female’.

  • limit ([‘integer’, ‘null’]) (optional) Maximum results to return (1-50, default 10).

Example Usage:

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