Services

LIPID MAPS® SPARQL Endpoint

The LIPID MAPS® SPARQL Endpoint, enables federated queries over LIPID MAPS and our partners.

Documentation on how to use SPARQL can be found here.

We gratefully acknowledge members of the ELIXIR 2021 Hackathon “FAIR lipids” for collaborative working on this project, with specific mention of Maksim Kolchin, Jerven Bolleman (SIB), Denise Slenter (WikiPathways) and Egon Willighagen (WikiPathways).

Code example

You can use the following Python script to programmatically try out the SPARQL Endpoint.

            
            from SPARQLWrapper import SPARQLWrapper, JSON
            import pandas as pd

            sparql = SPARQLWrapper(
                "https://lipidmaps.org/sparql"
            )
            sparql.setReturnFormat(JSON)

            # For example, retrieve the  name, category and formula of the first 5 lipids via a SPARQL endpoint 
            sparql.setQuery("""
                PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
                PREFIX chebi: <http://purl.obolibrary.org/obo/chebi/>
                
                SELECT ?name ?category ?formula
                WHERE {
                    SERVICE <https://lipidmaps.org/sparql> {    
                        ?lipidmaps rdfs:label ?name .	 
                        ?lipidmaps rdfs:subClassOf ?category .    
                        ?lipidmaps chebi:formula ?formula .    
                    }
                }
                LIMIT 5
                """
            )
            try:
                res = sparql.queryAndConvert()
                
                for i in res["results"]["bindings"]:
                    print(i)
                    
            except Exception as e:
                print(e)

Objects properties

It is possible to query the LIPID MAPS database with the following specifying objects:

Prefix lipidmaps-o: abbrev and abbrevChains
Prefix rdfs: label and subClassOf
Prefix obo: equivalentClass
Prefix chebi: formula, inchi, inchikey and monoisotopicmass

Examples

Example Request	Example query	Example results
Fetch all lipids, categories and formulas in LIPID MAPS	`PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX chebi: <http://purl.obolibrary.org/obo/chebi/> SELECT ?name ?category ?formula WHERE { SERVICE <https://lipidmaps.org/sparql> { ?lipidmaps rdfs:label ?name . ?lipidmaps rdfs:subClassOf ?category . ?lipidmaps chebi:formula ?formula . } FILTER(?formula="C18H36O") }`	SEE RESULT
Fetch all lipids in LIPID MAPS and SwissLipids	`PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX chebi: <http://purl.obolibrary.org/obo/chebi/> SELECT ?name ?category ?formula ?externalMolecule WHERE { SERVICE <https://lipidmaps.org/sparql> { ?lipidmaps rdfs:label ?name ; rdfs:subClassOf ?category ; chebi:formula ?formula ; owl:equivalentClass ?externalMolecule . } SERVICE <https://beta.sparql.swisslipids.org/sparql> { ?externalMolecule chebi:smiles ?smileCode ; rdfs:seeAlso ?seeAlso . } FILTER(?formula="C18H36O") }`	SEE RESULT