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 LIPID MAPS ID (LMID). Returns full lipid record includi…

LipidMaps_get_compound_by_id tool specification

Tool Information:

  • Name: LipidMaps_get_compound_by_id

  • Type: LipidMapsTool

  • Description: Get lipid structure and classification by LIPID MAPS ID (LMID). Returns full lipid record including name, formula, exact mass, SMILES, InChI, cross-references to KEGG/HMDB/ChEBI/PubChem. Example: ‘LMFA08040013’ returns Palmitoyl-EA.

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)

Look up a LIPID MAPS Structure Database (LMSD) record from an external cross-reference identifier…

LipidMaps_get_compound_by_xref tool specification

Tool Information:

  • Name: LipidMaps_get_compound_by_xref

  • Type: LipidMapsTool

  • Description: Look up a LIPID MAPS Structure Database (LMSD) record from an external cross-reference identifier, resolving any common metabolite/lipid ID to its LIPID MAPS lm_id plus all of its cross-references. Set xref_type to the namespace of input_value: ‘kegg_id’, ‘hmdb_id’, ‘chebi_id’, ‘pubchem_cid’, ‘inchi_key’, or ‘abbrev_chains’ (a structure-resolved lipid abbreviation such as ‘PC(16:0/18:1)’). Examples: kegg_id ‘C00157’ -> lm_id LMGP01010000 (PC), hmdb_id HMDB00564, chebi_id 57643; hmdb_id ‘HMDB0000564’ -> lm_id LMGP01010564 (PC 16:0/16:0); abbrev_chains ‘PC(16:0/18:1)’ -> lm_id LMGP01010005. Sends a browser User-Agent so the JSON route passes Cloudflare.

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 lipids by molecular formula in LIPID MAPS Structure Database. Returns all lipids matching …

LipidMaps_search_by_formula tool specification

Tool Information:

  • Name: LipidMaps_search_by_formula

  • Type: LipidMapsTool

  • Description: Search lipids by molecular formula in LIPID MAPS Structure Database. Returns all lipids matching the given formula. Example: ‘C22H32O2’ finds DHA and related C22:6 fatty acids.

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 for lipids by exact abbreviation in LIPID MAPS Structure Database. IMPORTANT: Only exact l…

LipidMaps_search_by_name tool specification

Tool Information:

  • Name: LipidMaps_search_by_name

  • Type: LipidMapsTool

  • Description: Search for lipids by exact abbreviation in LIPID MAPS Structure Database. IMPORTANT: Only exact lipidomics abbreviations work (e.g., ‘DHA’, ‘EPA’, ‘PC 16:0/18:1’, ‘SM 34:1’). Class names like ‘ceramide’ or ‘sphingomyelin’ will NOT match — use LipidMaps_search_by_formula for class-level searches. Returns matching lipid records with structures and classification.

Parameters:

  • input_value (string) (required) Exact lipid abbreviation used in lipidomics (e.g., ‘DHA’, ‘EPA’, ‘PC 16:0/18:1’, ‘SM 34:1’). Class names like ‘ceramide’ will not match — use exact abbreviations only.

  • 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)