Lipidmaps Tools#

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

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

Available Tools#

LipidMaps_get_compound_by_id (Type: LipidMapsTool)#

Get lipid structure and classification by exact LIPID MAPS ID (LMID). The wrapper validates outpu…

LipidMaps_get_compound_by_id tool specification

Tool Information:

  • Name: LipidMaps_get_compound_by_id

  • Type: LipidMapsTool

  • Description: Get lipid structure and classification by exact LIPID MAPS ID (LMID). The wrapper validates output fields before network access, requires JSON, verifies the returned LMID, and reports result-set and field-scope completeness. Example: LMFA08040013 returns Palmitoyl-EA with structure and external cross-references.

Parameters:

  • input_value (string) (required) LIPID MAPS ID (LMID), e.g., ‘LMFA08040013’. Format: LM + 2-letter category + 8-digit number.

  • output_item (string) (optional) Type of output. Options: ‘all’ (complete record), ‘name’, ‘formula’, ‘exactmass’, ‘smiles’, ‘classification’, ‘molfile’.

Example Usage:

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

LipidMaps_get_compound_by_xref (Type: LipidMapsTool)#

Resolve a KEGG, HMDB, ChEBI, PubChem, InChIKey, or chain-resolved abbreviation to every matching …

LipidMaps_get_compound_by_xref tool specification

Tool Information:

  • Name: LipidMaps_get_compound_by_xref

  • Type: LipidMapsTool

  • Description: Resolve a KEGG, HMDB, ChEBI, PubChem, InChIKey, or chain-resolved abbreviation to every matching LIPID MAPS structure record. Namespace aliases cannot conflict, all path segments are encoded, output fields are validated, and the complete unpaginated match set is explicit. Slash chain forms are normalized to the API’s underscore representation before request.

Parameters:

  • input_value (string) (required) The cross-reference identifier value to resolve, e.g. ‘C00157’ (KEGG), ‘HMDB0000564’ (HMDB), ‘57643’ (ChEBI), or ‘PC(16:0/18:1)’ (abbrev_chains).

  • xref_type (string) (optional) Namespace of input_value. One of: ‘kegg_id’, ‘hmdb_id’, ‘chebi_id’, ‘pubchem_cid’, ‘inchi_key’, ‘abbrev_chains’.

  • output_item (string) (optional) Type of output. Options: ‘all’ (complete record with all cross-refs), ‘name’, ‘formula’, ‘exactmass’, ‘smiles’, ‘classification’.

Example Usage:

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

LipidMaps_search_by_formula (Type: LipidMapsTool)#

Search the LIPID MAPS Structure Database by exact molecular formula. Returns the complete unpagin…

LipidMaps_search_by_formula tool specification

Tool Information:

  • Name: LipidMaps_search_by_formula

  • Type: LipidMapsTool

  • Description: Search the LIPID MAPS Structure Database by exact molecular formula. Returns the complete unpaginated set and rejects malformed or non-JSON responses instead of silently dropping rows. Live C22H32O2 currently returns seven lipid records.

Parameters:

  • input_value (string) (required) Molecular formula (e.g., ‘C22H32O2’, ‘C16H32O2’). Standard chemical formula format.

  • output_item (string) (optional) Type of output. Options: ‘all’, ‘name’, ‘smiles’, ‘classification’.

Example Usage:

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

LipidMaps_search_by_name (Type: LipidMapsTool)#

Search exact lipidomics abbreviations in LIPID MAPS. Sum compositions use abbrev (e.g. PC 34:1); …

LipidMaps_search_by_name tool specification

Tool Information:

  • Name: LipidMaps_search_by_name

  • Type: LipidMapsTool

  • Description: Search exact lipidomics abbreviations in LIPID MAPS. Sum compositions use abbrev (e.g. PC 34:1); an acyl-chain slash form such as PC 16:0/18:1 is normalized before the first request to abbrev_chains=PC 16:0_18:1, avoiding the upstream router’s 404. Sphingolipid sums require the ;O2-style suffix. Returns the complete unpaginated match set with explicit field-scope metadata; class names are not abbreviation searches.

Parameters:

  • input_value (string) (required) Exact lipid abbreviation used in lipidomics (e.g., ‘DHA’, ‘EPA’, ‘PC 34:1’, ‘PC 16:0/18:1’, ‘SM 34:1;O2’). Class names like ‘ceramide’ will not match — use exact abbreviations only. Sphingolipid sum-composition abbreviations must include the ‘;O2’-style hydroxyl-count suffix.

  • output_item (string) (optional) Type of output. Options: ‘all’, ‘name’, ‘formula’, ‘exactmass’, ‘smiles’, ‘classification’.

Example Usage:

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