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 ClinVar clinical-control variants overlapping a MaveDB score set for functional-score calibra…
MaveDB_get_clinical_controls tool specification
Tool Information:
Name:
MaveDB_get_clinical_controlsType:
MaveDBToolDescription: Get ClinVar clinical-control variants overlapping a MaveDB score set for functional-score calibration. Returns identifiers, gene, clinical significance, review status, version, and linked MaveDB variant URNs. The significance filter is applied before exact total counts and recoverable limit/offset pagination; continue with next_offset while has_more is true.
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 clinical controls on this page. Set to 0 or null to return everything from offset onward.offset(integer) (optional) Zero-based offset after the optional significance filter. Continue with data.next_offset.
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_matrixType:
MaveDBToolDescription: 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 identifier, …
MaveDB_get_gnomad_variants tool specification
Tool Information:
Name:
MaveDB_get_gnomad_variantsType:
MaveDBToolDescription: Get gnomAD population-frequency variants observed within a MaveDB score set. Returns identifier, version, allele count/number/frequency, and linked genomic VRS alleles. Exact totals and recoverable limit/offset pagination are reported; continue with next_offset while has_more is true.
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 gnomAD variants on this page. Set to 0 or null to return everything from offset onward.offset(integer) (optional) Zero-based offset in the complete gnomAD overlap list. Continue with data.next_offset.
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_variantsType:
MaveDBToolDescription: Get genomically-mapped variant coordinates (GA4GH VRS Allele + ClinGen Allele ID) for a MaveDB score set. Each variant includes genomic SequenceLocation when mapped, ClinGen canonical Allele ID, alignment status, and mapping errors. The API returns the full list internally; limit/offset provide recoverable local pagination. Continue with next_offset while has_more is true. 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 mapped variants on this page. Set to 0 or null to return everything from offset onward.offset(integer) (optional) Zero-based offset in the complete mapped-variant list. Continue with data.next_offset.
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_setType:
MaveDBToolDescription: 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_scoresType:
MaveDBToolDescription: 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_experimentsType:
MaveDBToolDescription: 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_setsType:
MaveDBToolDescription: Search MaveDB for variant effect score sets from Multiplexed Assays of Variant Effect (MAVE) experiments, including deep mutational scanning. Returns score set URNs, target genes, titles, variant counts, and publication dates. Metadata exposes the exact total and next_offset so every result from MaveDB’s full search response is reachable.
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.offset(integer) (optional) Zero-based result offset. Continue with metadata.next_offset while has_more is true.
Example Usage:
query = {
"name": "MaveDB_search_score_sets",
"arguments": {
"query": "example_value"
}
}
result = tu.run(query)