LIPID MAPS REST service

The LIPID MAPS REST service enables access to a variety of data (including lipid structures and lipid-related genes/proteins) using HTTP requests. These requests may be carried out using a web browser or may be embedded in 3rd party applications or scripts to enable programmatic access. Most modern programming languages including PHP, Perl, Python, Java and Javascript have the capability to create HTTP request and interact with datasets such as this REST service.

The REST URL is composed of 3 main parts:

  1. The invariant base URL (in this case "https://www.lipidmaps.org/rest")

  2. The input specification is composed of 3 required parameters separated by forward slashes. The first parameter is the context, either "compound", "gene" or "protein", each of which has a separate list of input items associated with it (2nd parameter). The 3rd parameter is an appropriate input value for the chosen item.

    Examples of an input specification are:

    • /compound/pubchem_cid/985/
    • /compound/formula/C20H34O/
    • /gene/gene_id/31/gene_name/
    • /protein/uniprot_id/Q13085/all/

  3. The output specification is composed of a required output item parameter and an optional output format parameter. The list of possible output items depends on the value chosen for the context. In the case of the "compound" context one or more (separated by commas) of 'formula', 'exactmass', 'inchi_key', 'name', 'sys_name', 'smiles', 'lm_id', 'pubchem_cid', 'hmdb_id', 'kegg_id', 'chebi_id', 'metacyc_id' may be specified. More conveniently, an output type of 'all' may be specified to retrieve all compound-related fields. Also an output type of 'classification' retrieves the LIPID MAPS classification hierarchy. In the case of the "gene" and "protein"contexts, allowed output types include 'gene_id', 'gene_name', 'gene_symbol', 'gene_synonyms', 'alt_names', 'mrna_id', 'refseq_id', 'protein_gi', 'uniprot_id', 'protein_entry', 'protein_name', 'seqlength' and 'seq'. The default output format is JSON which is amenable to manipulation and parsing by various programming languages. Optionally a text output format may be specified with each field displayed in a separate row, for example: /compound/pubchem_cid/311/all/textAll or part of the LIPID MAPS Structure Database (LMSD) may be downloaded by specifying the "download" (tabular) option as the output format, for example:
    https://www.lipidmaps.org/rest/compound/lm_id/LMFA/all/download generates a table of all lipids in the "Fatty Acyls" category. This format contains SMILES strings and InChI Keys but does not contain the structure molfiles (which are available as SD file downloads on the LMSD Download page).

    The interactive "REST url" creator below shows the complete list of currently available options for this service.

    Interactive "REST url" Creator


    Base URL /Context /Input item /Input value /Output item /Output format
    https://www.lipidmaps.org/rest / / / / /

    (What is REST?) (What is JSON?)


    Examples

    Example Request Example URL
    Fetch compound name from LM_IDhttps://www.lipidmaps.org/rest/compound/lm_id/LMFA01010001/name
    Fetch all compound fields from LM_IDhttps://www.lipidmaps.org/rest/compound/lm_id/LMFA01010001/all
    Fetch all compound fields as text from LM_IDhttps://www.lipidmaps.org/rest/compound/lm_id/LMFA01010001/all/txt
    Fetch compound smiles from PubChem CIDhttps://www.lipidmaps.org/rest/compound/pubchem_cid/985/smiles
    Fetch compound sytematic name from inchi keyhttps://www.lipidmaps.org/rest/compound/inchi_key/IPCSVZSSVZVIGE-UHFFFAOYSA-N/sys_name
    Fetch compound physicochemical properties from inchi keyhttps://www.lipidmaps.org/rest/compound/inchi_key/IPCSVZSSVZVIGE-UHFFFAOYSA-N/physchem
    Fetch all compound fields from formula (multiple records)https://www.lipidmaps.org/rest/compound/formula/C20H34O/all
    Fetch compound classification hierarchy from PubChem CIDhttps://www.lipidmaps.org/rest/compound/pubchem_cid/985/classification
    Download compound molfile from LM_IDhttps://www.lipidmaps.org/rest/compound/lm_id/LMFA01010001/molfile
    Draw structure from abbreviation (?)https://www.lipidmaps.org/rest/compound/abbrev/PC(16:0_20:4(5Z,8Z,11Z,14Z))/structure
    Fetch all compound fields from bulk abbreviationhttps://www.lipidmaps.org/rest/compound/abbrev/PA(38:0)/all/txt
    Fetch all compound fields from chain abbreviationhttps://www.lipidmaps.org/rest/compound/abbrev_chains/PC(16:0_18:0)/all/txt
    Download table of all Prostaglandins in LMSDhttps://www.lipidmaps.org/rest/compound/lm_id/LMFA0301/all/download
    Download table of all Eicosanoids in LMSDhttps://www.lipidmaps.org/rest/compound/lm_id/LMFA03/all/download
    Download table of all Glycerophospholipids in LMSDhttps://www.lipidmaps.org/rest/compound/lm_id/LMGP/all/download
    Download table of all lipids in LMSDhttps://www.lipidmaps.org/rest/compound/lm_id/LM/all/download
    Fetch all gene fields from gene symbolhttps://www.lipidmaps.org/rest/gene/gene_symbol/acaca/all
    Fetch gene name from Entrez gene idhttps://www.lipidmaps.org/rest/gene/gene_id/31/gene_name
    Fetch all protein fields from UniProt idhttps://www.lipidmaps.org/rest/protein/uniprot_id/Q13085/all
    Fetch all protein fields from Entrez gene idhttps://www.lipidmaps.org/rest/protein/gene_id/19/all
    Fetch mRNA id from protein Refseq idhttps://www.lipidmaps.org/rest/protein/refseq_id/NP_005493/mrna_id
    Perform MS precursor ion search on LIPIDS virtual database with m/z 635.52, ion-type M+H and mass tolerance of 0.5 and output as texthttps://www.lipidmaps.org/rest/moverz/LIPIDS/635.52/M+H/0.5/txt
    Perform MS precursor ion search on LIPIDS virtual database with m/z 513.45, ion-type M-2H (2-) and mass tolerance of 0.2 and output as texthttps://www.lipidmaps.org/rest/moverz/LIPIDS/513.45/M-2H/0.2/txt


    REST (REpresentational State Transfer) is an architectural style consisting of a coordinated set of architectural constraints applied to components, connectors, and data elements, within a distributed hypermedia system. REST ignores the details of component implementation and protocol syntax in order to focus on the roles of components, the constraints upon their interaction with other components, and their interpretation of significant data elements.
    Fielding, Roy T. (2000). "Chapter 5: Representational State Transfer (REST)". Architectural Styles and the Design of Network-based Software Architectures (Ph.D.). University of California, Irvine.
    Fielding, Roy T.; Taylor, Richard N. (May 2002), "Principled Design of the Modern Web Architecture" (PDF), ACM Transactions on Internet Technology (TOIT) (New York: Association for Computing Machinery) 2 (2): 115-150, doi:10.1145/514183.514185, ISSN 1533-5399
    REST Wikipedia page


    JSON (JavaScript Object Notation) is a lightweight data-interchange format which human readable and also convenient for computers to parse and generate. JSON is a text format that is completely language independent but uses conventions that are familiar to most common programming languages.
    Official JSON website