Mavedb Tools

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

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

Available Tools

MaveDB_get_clinical_controls (Type: MaveDBTool)

Get clinical-control variants (ClinVar pathogenic/benign/VUS) that overlap a MaveDB score set, us…

MaveDB_get_clinical_controls tool specification

Tool Information:

• Name: MaveDB_get_clinical_controls

• Type: MaveDBTool

• Description: Get clinical-control variants (ClinVar pathogenic/benign/VUS) that overlap a MaveDB score set, used to calibrate MAVE functional scores into clinically-interpretable thresholds. Returns ClinVar entries with dbIdentifier, gene symbol, clinical significance (e.g. ‘Uncertain significance’, ‘Pathogenic’), review status, ClinVar version (e.g. ‘01_2025’), and the MaveDB variant URN(s) sharing the same genomic coordinate. Optionally filter by clinical_significance. This is the reference set for building functional-score evidence (e.g. ACMG PS3/BS3). Obtain the URN from MaveDB_search_score_sets.

Parameters:

• urn (string) (required) MaveDB score set URN (e.g., ‘urn:mavedb:00001263-a-2’ for BRCA2 SGE). Obtain from MaveDB_search_score_sets.

• clinical_significance ([‘string’, ‘null’]) (optional) Optional exact-match filter on ClinVar clinical significance (case-insensitive), e.g. ‘Pathogenic’, ‘Benign’, ‘Uncertain significance’.

• limit ([‘integer’, ‘null’]) (optional) Maximum number of clinical controls to return (client-side truncation). Set to 0 or null to return all.

Example Usage:

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

MaveDB_get_effect_matrix (Type: MaveDBTool)

One-shot DMS data loader: fetch a MaveDB score set, parse HGVS to (ref_aa, position, alt_aa), fil…

MaveDB_get_effect_matrix tool specification

Tool Information:

• Name: MaveDB_get_effect_matrix

• Type: MaveDBTool

• Description: One-shot DMS data loader: fetch a MaveDB score set, parse HGVS to (ref_aa, position, alt_aa), filter to single missense, optionally verify position numbering against a UniProt canonical sequence, and reshape into a (20 amino acids × n_positions) effect matrix ready for downstream analysis. Hides the boilerplate that variant-effect-prediction benchmarking and residue-mechanism interpretation skills used to inline. Returns the matrix, the position list, the standard amino acid order, and explicit numbering / drop / score-field metadata so the caller can audit what was loaded.

Parameters:

• urn (string) (required) MaveDB score set URN (e.g., ‘urn:mavedb:00000115-a-7’). Obtain from MaveDB_search_score_sets.

• uniprot_id ([‘string’, ‘null’]) (optional) Optional UniProt accession (e.g., ‘P01116’ for KRAS). If supplied, the tool fetches the canonical sequence and verifies the MaveDB position numbering against it via a landmark check; sets numbering_offset and surfaces a warning in numbering_check if the positions don’t match (silent off-by-N is the #1 silent bug in DMS analysis).

• score_field ([‘string’, ‘null’]) (optional) Optional explicit column name to use as the variant score (e.g., ‘score’, ‘ddG’, ‘fitness’). If omitted, tries ‘score’ → ‘ddG’ → ‘fitness’ → first numeric non-HGVS field in that order. The actual field used is reported in data.score_field_used.

Example Usage:

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

MaveDB_get_gnomad_variants (Type: MaveDBTool)

Get gnomAD population-frequency variants observed within a MaveDB score set. Returns gnomAD varia…

MaveDB_get_gnomad_variants tool specification

Tool Information:

• Name: MaveDB_get_gnomad_variants

• Type: MaveDBTool

• Description: Get gnomAD population-frequency variants observed within a MaveDB score set. Returns gnomAD variants with dbIdentifier (e.g. ‘13-32319097-A-C’), gnomAD version (e.g. ‘v4.1’), allele count, allele number, and allele frequency, each linked to the MaveDB mapped variant via a genomic VRS Allele. Cross-reference allele frequency with the measured MAVE functional score: rare variants with strong functional impact are candidate disease alleles. Obtain the URN from MaveDB_search_score_sets.

Parameters:

• urn (string) (required) MaveDB score set URN (e.g., ‘urn:mavedb:00001263-a-2’ for BRCA2 SGE). Obtain from MaveDB_search_score_sets.

• limit ([‘integer’, ‘null’]) (optional) Maximum number of gnomAD variants to return (client-side truncation). Set to 0 or null to return all.

Example Usage:

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

MaveDB_get_mapped_variants (Type: MaveDBTool)

Get genomically-mapped variant coordinates (GA4GH VRS Allele + ClinGen Allele ID) for a MaveDB sc…

MaveDB_get_mapped_variants tool specification

Tool Information:

• Name: MaveDB_get_mapped_variants

• Type: MaveDBTool

• Description: Get genomically-mapped variant coordinates (GA4GH VRS Allele + ClinGen Allele ID) for a MaveDB score set. Each MAVE variant is mapped to a postMapped VRS Allele carrying a genomic SequenceLocation (chromosome + start/end on the reference assembly, e.g. NC_000013.11 for chr13) plus the ClinGen canonical Allele ID (e.g. CA387754009), which links the functional score to ClinVar, dbSNP, and gnomAD. Intronic or unmappable variants have post_mapped=null and an error_message. Use this to translate raw MAVE scores into genome coordinates for downstream variant annotation. Obtain the URN from MaveDB_search_score_sets.

Parameters:

• urn (string) (required) MaveDB score set URN (e.g., ‘urn:mavedb:00001263-a-2’ for BRCA2 SGE). Obtain from MaveDB_search_score_sets.

• limit ([‘integer’, ‘null’]) (optional) Maximum number of mapped variants to return (client-side truncation). Set to 0 or null to return all (the API returns the full list in one call).

Example Usage:

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

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). The /scores endpoint returns every variant in one CSV; limit is client-side truncation only — set limit=0 (or omit) to receive ALL variants in one call (use this for whole-protein DMS analyses, e.g. KRAS folding ΔΔG has ~2200 variants).

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’, ‘null’]) (optional) Maximum variants to return after client-side filtering. Set to 0 or null to return all variants in the score set (default — needed for whole-protein DMS workflows). Set to a positive integer to truncate. The MaveDB API returns the full CSV in one HTTP call regardless, so ‘unlimited’ has no extra cost.

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)

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