Mavedb Tools

Configuration File: mavedb_tools.json Tool Type: Local Tools Count: 4

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

Available Tools

MaveDB_get_score_set (Type: MaveDBTool)

Get detailed information about a specific MaveDB score set by its URN identifier. Returns the tar…

MaveDB_get_score_set tool specification

Tool Information:

  • Name: MaveDB_get_score_set

  • Type: MaveDBTool

  • Description: Get detailed information about a specific MaveDB score set by its URN identifier. Returns the target gene, experimental methods, variant count, publications, and license. Score sets contain functional impact scores from deep mutational scanning or saturation genome editing experiments.

Parameters:

  • urn (string) (required) MaveDB score set URN (e.g., ‘urn:mavedb:00000001-a-1’). Obtain URNs from MaveDB_search_score_sets.

Example Usage:

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

MaveDB_get_variant_scores (Type: MaveDBTool)

Get functional variant effect scores from a MaveDB score set. Returns HGVS-annotated variants wit…

MaveDB_get_variant_scores tool specification

Tool Information:

  • Name: MaveDB_get_variant_scores

  • Type: MaveDBTool

  • Description: Get functional variant effect scores from a MaveDB score set. Returns HGVS-annotated variants with their functional scores from deep mutational scanning or other MAVE assays. Scores indicate variant effect on protein function (interpretation depends on the specific assay - check score set metadata). Optionally filter by HGVS protein notation (e.g., ‘Arg175’ to find all R175 substitutions).

Parameters:

  • urn (string) (required) MaveDB score set URN (e.g., ‘urn:mavedb:00001234-c-1’). Obtain from MaveDB_search_score_sets.

  • hgvs_pro (string) (optional) Optional filter: HGVS protein notation substring (e.g., ‘Arg175’, ‘p.Arg175His’). Case-insensitive partial match on protein-level HGVS.

  • limit (integer) (optional) Maximum variants to return (default 50, max 500).

Example Usage:

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

MaveDB_search_experiments (Type: MaveDBTool)

Search MaveDB for experiments (groups of related score sets from the same study). Each experiment…

MaveDB_search_experiments tool specification

Tool Information:

  • Name: MaveDB_search_experiments

  • Type: MaveDBTool

  • Description: Search MaveDB for experiments (groups of related score sets from the same study). Each experiment may contain multiple score sets from different replicates, conditions, or analysis methods. Returns experiment URNs, titles, associated score sets, and publications. Search by gene name, protein, or assay keywords.

Parameters:

  • query (string) (required) Search query: gene symbol (e.g., ‘TP53’, ‘BRCA1’), protein name, or keywords describing the experiment.

Example Usage:

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

MaveDB_search_score_sets (Type: MaveDBTool)

Search MaveDB for variant effect score sets from Multiplexed Assays of Variant Effect (MAVE) expe…

MaveDB_search_score_sets tool specification

Tool Information:

  • Name: MaveDB_search_score_sets

  • Type: MaveDBTool

  • Description: Search MaveDB for variant effect score sets from Multiplexed Assays of Variant Effect (MAVE) experiments, including deep mutational scanning. Returns score set URNs, titles, variant counts, and publication dates. Use gene names or protein names as search terms.

Parameters:

  • query (string) (required) Search text - gene name (e.g., ‘BRCA1’, ‘TP53’), protein name, or keyword. Searches titles and descriptions of score sets.

  • limit (integer) (optional) Maximum number of results to return.

Example Usage:

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