Lipidmaps Gene Tools

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

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

Available Tools

LipidMaps_get_gene (Type: LipidMapsGeneTool)

Look up a lipid-metabolism gene in the LIPID MAPS Proteome Database (LMPD). Resolves a gene to it…

LipidMaps_get_gene tool specification

Tool Information:

  • Name: LipidMaps_get_gene

  • Type: LipidMapsGeneTool

  • Description: Look up a lipid-metabolism gene in the LIPID MAPS Proteome Database (LMPD). Resolves a gene to its LMPD record (gene name, synonyms, alternative names, chromosome, cytogenetic map location, NCBI summary, and species). Set input_item to the namespace of input_value: ‘gene_symbol’ (e.g. ‘FASN’), ‘gene_id’ (NCBI Gene ID, e.g. ‘2194’), ‘gene_name’ (exact gene-name substring), or ‘lmp_id’ (LIPID MAPS protein id, e.g. ‘LMP002507’). A gene_symbol may match multiple species (e.g. ‘FASN’ returns mouse LMP001577 and human LMP002507); all matches are returned as a list. Use this for lipid-related enzymes such as fatty acid synthase (FASN) or stearoyl-CoA desaturase (SCD). Complements the LipidMaps_get_compound_* structure tools, which cover lipids, not the genes/enzymes that make them.

Parameters:

  • input_value (string) (required) The gene identifier value to resolve, e.g. ‘FASN’ (gene symbol), ‘2194’ (NCBI Gene ID), or ‘LMP002507’ (LIPID MAPS protein id).

  • input_item (string) (optional) Namespace of input_value. One of: ‘gene_symbol’, ‘gene_id’, ‘gene_name’, ‘lmp_id’.

  • output_item (string) (optional) Which fields to return. ‘all’ (default) returns the complete record; a single field name (e.g. ‘gene_name’, ‘summary’, ‘chromosome’) returns just that field.

Example Usage:

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

LipidMaps_get_protein (Type: LipidMapsGeneTool)

Look up a lipid-metabolism protein/enzyme in the LIPID MAPS Proteome Database (LMPD). Resolves a …

LipidMaps_get_protein tool specification

Tool Information:

  • Name: LipidMaps_get_protein

  • Type: LipidMapsGeneTool

  • Description: Look up a lipid-metabolism protein/enzyme in the LIPID MAPS Proteome Database (LMPD). Resolves a protein to its LMPD record including gene symbol/name, species, and cross-references (UniProt accession, RefSeq protein id, mRNA RefSeq id, protein GI, UniProt entry name) plus the amino-acid sequence. Set input_item to the namespace of input_value: ‘uniprot_id’ (e.g. ‘P49327’), ‘gene_symbol’ (e.g. ‘SCD’), ‘gene_id’ (NCBI Gene ID), ‘refseq_id’ (RefSeq protein id, e.g. ‘NP_004095’), ‘mrna_id’ (RefSeq mRNA id), ‘protein_entry’ (UniProt entry name, e.g. ‘FAS_HUMAN’), or ‘lmp_id’ (LIPID MAPS protein id). A gene_symbol may match multiple species; all matches are returned as a list. Use this to map a lipid-related enzyme (e.g. fatty acid synthase, stearoyl-CoA desaturase) to its sequence and database cross-references.

Parameters:

  • input_value (string) (required) The protein identifier value to resolve, e.g. ‘P49327’ (UniProt), ‘NP_004095’ (RefSeq protein), ‘SCD’ (gene symbol), or ‘LMP002507’ (LIPID MAPS protein id).

  • input_item (string) (optional) Namespace of input_value. One of: ‘uniprot_id’, ‘gene_symbol’, ‘gene_id’, ‘gene_name’, ‘refseq_id’, ‘mrna_id’, ‘protein_entry’, ‘lmp_id’.

  • output_item (string) (optional) Which fields to return. ‘all’ (default) returns the complete record; a single field name (e.g. ‘uniprot_id’, ‘protein_name’, ‘seq’) returns just that field.

Example Usage:

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