LIPID MAPS® REST service
The REST URL is composed of 3 main parts:
- The invariant base URL (in this case "https://www.lipidmaps.org/rest")
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:
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/text
All 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).
Interactive "REST url" Creator
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