Marrvel Tools#

Configuration File: marrvel_tools.json Tool Type: Local Tools Count: 2

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

Available Tools#

MARRVEL_get_gene (Type: MARRVELGeneTool)#

Get a complete normalized MARRVEL human-gene record by symbol: HGNC/Ensembl/Entrez/UniProt cross-…

MARRVEL_get_gene tool specification

Tool Information:

  • Name: MARRVEL_get_gene

  • Type: MARRVELGeneTool

  • Description: Get a complete normalized MARRVEL human-gene record by symbol: HGNC/Ensembl/Entrez/UniProt cross-references, GRCh38 and hg19 coordinates, cytogenetic location, aliases, status/update date, summaries, and Pharos ligand/target IDs. The wrapper verifies the returned symbol and duplicate HGNC/Pharos fields before success. It intentionally excludes the upstream xref.omimId because that field is a confirmed invalid placeholder; use MARRVEL_get_omim_phenotypes for the verified gene MIM number. MARRVEL indexes only current approved HGNC symbols, so a retired symbol or alias (e.g. ‘RP20’/’LCA2’ for RPE65) is resolved once via HGNC and re-queried; when that happens the substitution is disclosed in metadata.resolved_symbol and metadata.resolved_note, and metadata.query_symbol keeps the symbol you asked for. MARRVEL currently serves this API only over unencrypted HTTP because its HTTPS certificate does not match api.marrvel.org; metadata makes that transport limitation explicit. No API key required.

Parameters:

  • symbol (string) (optional) HGNC gene symbol, e.g. ‘CFTR’, ‘BRCA1’. Input is normalized to uppercase because the MARRVEL gene endpoint is case-sensitive and otherwise returns a silent empty object.

  • gene_symbol (string) (optional) Alias for symbol. If multiple aliases are supplied, all must identify the same symbol.

  • gene (string) (optional) Alias for symbol. If multiple aliases are supplied, all must identify the same symbol.

Example Usage:

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

MARRVEL_get_omim_phenotypes (Type: MARRVELOmimTool)#

Get the complete OMIM phenotype association list for a human gene via MARRVEL, including phenotyp…

MARRVEL_get_omim_phenotypes tool specification

Tool Information:

  • Name: MARRVEL_get_omim_phenotypes

  • Type: MARRVELOmimTool

  • Description: Get the complete OMIM phenotype association list for a human gene via MARRVEL, including phenotype name, verified gene/phenotype MIM numbers, inheritance, mapping key, and phenotypic series. Use to enumerate the Mendelian diseases linked to a gene and their inheritance patterns. Metadata preserves the OMIM title, description, status, update time, phenotype count, and the count of adjacent allelic-variant records. Allelic-variant narratives are not returned by this phenotype-focused tool, and metadata states that limitation explicitly. MARRVEL indexes only current approved HGNC symbols, so a retired symbol or alias (e.g. ‘RP20’/’LCA2’ for RPE65) is resolved once via HGNC and re-queried; when that happens the substitution is disclosed in metadata.resolved_symbol and metadata.resolved_note. The upstream API currently uses unencrypted HTTP. No API key required.

Parameters:

  • symbol (string) (optional) HGNC gene symbol, e.g. ‘CFTR’, ‘BRCA1’. Input is normalized to uppercase for consistent MARRVEL lookup semantics.

  • gene_symbol (string) (optional) Alias for symbol. Multiple supplied aliases must agree.

  • gene (string) (optional) Alias for symbol. Multiple supplied aliases must agree.

Example Usage:

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