16: For a given list of LipidX lipid identifiers return the list of corresponding LIPID MAPS IDs. Output should include LipidX ID, the corresponding SwissLipids ID and name, plus the LIPID MAPS ID. This query first identifies SwissLipids identifiers for a given list of LipidX identifiers. It then retrieves the corresponding Isomeric subspecies and from them the required LIPID MAPS identifiers. Extends ID mapping to LipidX identifiers and by using the hierarchy. extends ex:15

SELECT ?TODO WHERE {?TODO a ?TODO}Use

17: For a given list of LipidX lipid identifiers return the list of corresponding HMDB IDs. Output should include LipidX ID, the corresponding SwissLipids ID and name, plus the HMDB ID. This query first identifies SwissLipids identifiers for a given list of LipidX identifiers. It then retrieves the corresponding Isomeric subspecies and from them the required HMDB identifiers. Extends ID mapping to LipidX identifiers and by using the hierarchy. extends ex:16

SELECT ?TODO WHERE {?TODO a ?TODO}Use

18: For a given list of LipidX lipid identifiers return the list of corresponding ChEBI IDs. Output should include LipidX ID, the corresponding SwissLipids ID and name, plus the HMDB ID. This query first identifies SwissLipids identifiers for a given list of LipidX identifiers. It then retrieves the required ChEBI identifiers from them. Extends ID mapping to LipidX identifiers and by using the hierarchy. extends ex:15

SELECT ?TODO WHERE {?TODO a ?TODO}Use

19: For a given list of LipidX lipid identifiers return the list of possible structures and relevant enzymes. Output should include the LipidX ID, the corresponding SwissLipids ID(s) and name(s), and the name(s) and ID(s) of the proteins. This query first identifies SwissLipids identifiers for a given list of LipidX identifiers. It then retrieves the corresponding Isomeric subspecies, and from them retrieves the list of reactions in which they participate, and the enzymes that catalyze them. extends ex:16

SELECT ?TODO WHERE {?TODO a ?TODO}Use

20: Returns the list of lipid analytes identified in a list of tissues (UBERON lipid identifiers). Output should include the corresponding SwissLipids ID(s) and name(s), and the name(s) and ID(s) of the tissues. A simple query which does not traverse the hierarchy.

SELECT ?TODO WHERE {?TODO a ?TODO}Use

21: Returns the list of possible lipid structures for a list of tissues (UBERON lipid identifiers). Output should include the corresponding SwissLipids ID(s) and name(s), and the name(s) and ID(s) of the tissues. This query first retrieves SwissLipids identifiers for a given list of UBERON identifiers. It then retrieves the corresponding Isomeric subspecies and returns those. Extends ex:20

SELECT ?TODO WHERE {?TODO a ?TODO}Use

22: Returns the list of possible lipid structures for a list of tissues (UBERON lipid identifiers), but considers only those lipids associated with one or more publications. Output should include the corresponding SwissLipids ID(s) and name(s), and the name(s) and ID(s) of the tissues. This query first retrieves SwissLipids identifiers for a given list of UBERON identifiers. It then retrieves the corresponding Isomeric subspecies and returns those that are linked to at least one PMID. As that PMID does not necessarily reflect association to the tissue in question we don’t return that. Extends ex:3, ex:23

SELECT ?TODO WHERE {?TODO a ?TODO}Use

23: Returns the list of lipid analytes associated with a list of one or more subcellular locations (GO cellular components). Output should include the corresponding SwissLipids ID(s) and name(s), and the name(s) and ID(s) of the cellular components.

SELECT ?TODO WHERE {?TODO a ?TODO}Use

24: Returns the list of possible lipid structures associated with a list of one or more subcellular locations (GO cellular components). Output should include the corresponding SwissLipids ID(s) and name(s), and the name(s) and ID(s) of the cellular components. This query first retrieves SwissLipids identifiers for a given list of GO cellular component identifiers. It then retrieves the corresponding Isomeric subspecies and returns those. Extends ex:25

SELECT ?TODO WHERE {?TODO a ?TODO}Use

25: Returns the list of possible lipid structures associated with a list of one or more subcellular locations (GO cellular components), but considers only those lipids associated with one or more publications. Output should include the corresponding SwissLipids ID(s) and name(s), and the name(s) and ID(s) of the cellular components. This query first identifies SwissLipids identifiers for a given list of GO cellular component identifiers. It then retrieves the corresponding Isomeric subspecies and returns those that are linked to at least one PMID. As that PMID does not necessarily reflect association to the cellular compartment in question we don’t return that. Extends ex:3, ex:25

SELECT ?TODO WHERE {?TODO a ?TODO}Use

26: Returns the list of lipid analytes associated with a list of one or more organisms (NCBI taxonomic IDs). Output should include the corresponding SwissLipids ID(s) and name(s), and the name(s) and ID(s) of the organisms.

SELECT ?TODO WHERE {?TODO a ?TODO}Use

27: Returns the list of possible lipid structures associated with a list of one or more organisms (NCBI taxonomic IDs). Output should include the corresponding SwissLipids ID(s) and name(s), and the name(s) and ID(s) of the organisms. This query first identifies SwissLipids identifiers for a given list of NCBI taxonomic IDs. It then retrieves the corresponding Isomeric subspecies and returns those. Extends ex:26

SELECT ?TODO WHERE {?TODO a ?TODO}Use

28: Returns the list of possible lipid structures associated with a list of one or more organisms (NCBI taxonomic IDs), but considers only those lipids associated with one or more publications. Output should include the corresponding SwissLipids ID(s) and name(s), and the name(s) and ID(s) of the organisms. This query first identifies SwissLipids identifiers for a given list of NCBI taxonomic IDs. It then retrieves the corresponding Isomeric subspecies and returns those that are linked to at least one PMID. As that PMID does not necessarily reflect association to the cellular compartment in question we don’t return that. Extends ex:3, ex:28

SELECT ?TODO WHERE {?TODO a ?TODO}Use

29: Returns the list of possible lipid structures for a list of tissues (UBERON lipid identifiers), but considers only those lipids associated with LIPID MAPS identifers. Output should include the corresponding SwissLipids ID(s) and name(s), LIPID MAPS identifiers, and the name(s) and ID(s) of the tissues. This query first retrieves SwissLipids identifiers for a given list of UBERON identifiers. It then retrieves the corresponding Isomeric subspecies and returns those that are linked to LIPID MAPS.

SELECT ?TODO WHERE {?TODO a ?TODO}Use

30: Returns the list of possible lipid structures for a list of tissues (UBERON lipid identifiers), but considers only those lipids associated with LIPID MAPS identifers. Output should include the corresponding SwissLipids ID(s) and name(s), LIPID MAPS identifiers, and the name(s) and ID(s) of the tissues. This query first retrieves SwissLipids identifiers for a given list of UBERON identifiers. It then retrieves the corresponding Isomeric subspecies and returns those that are linked to LIPID MAPS.

SELECT ?TODO WHERE {?TODO a ?TODO}Use

31: Returns the list of possible lipid structures associated with a list of one or more subcellular locations (GO cellular components), but considers only those lipids associated with LIPID MAPS identifers. Output should include the corresponding SwissLipids ID(s) and name(s), LIPID MAPS identifiers, and the name(s) and ID(s) of the subcellular locations (GO cellular components). This query first retrieves SwissLipids identifiers for a given list of subcellular locations (GO cellular component identifiers). It then retrieves the corresponding Isomeric subspecies and returns those that are linked to LIPID MAPS.

SELECT ?TODO WHERE {?TODO a ?TODO}Use

32: Returns the list of possible lipid structures associated with a list of one or more organisms (NCBI taxonomic IDs) but considers only those lipids associated with LIPID MAPS identifers. Output should include the corresponding SwissLipids ID(s) and name(s), LIPID MAPS identifiers, and the name(s) and NCBI taxonomic ID(s) of the organisms. This query first retrieves SwissLipids identifiers for a given list of organisms (NCBI taxonomic IDs). It then retrieves the corresponding Isomeric subspecies and returns those that are linked to LIPID MAPS.

SELECT ?TODO WHERE {?TODO a ?TODO}Use

33: Returns the list of possible lipid structures associated with a list of one or more subcellular locations (GO cellular components), but considers only those lipids associated with LIPID MAPS identifers. Output should include the corresponding SwissLipids ID(s) and name(s), LIPID MAPS identifiers, and the name(s) and ID(s) of the subcellular locations (GO cellular components). This query first retrieves SwissLipids identifiers for a given list of subcellular locations (GO cellular component identifiers). It then retrieves the corresponding Isomeric subspecies and returns those that are linked to LIPID MAPS.

SELECT ?TODO WHERE {?TODO a ?TODO}Use

34: Returns the list of possible lipid structures associated with a list of one or more organisms (NCBI taxonomic IDs) but considers only those lipids associated with LIPID MAPS identifers. Output should include the corresponding SwissLipids ID(s) and name(s), LIPID MAPS identifiers, and the name(s) and NCBI taxonomic ID(s) of the organisms. This query first retrieves SwissLipids identifiers for a given list of organisms (NCBI taxonomic IDs). It then retrieves the corresponding Isomeric subspecies and returns those that are linked to LIPID MAPS.

SELECT ?TODO WHERE {?TODO a ?TODO}Use

35: Returns the list of isomeric subspecies containing a specific combination of fatty acids at defined positions. If the user supplies a single fatty acid and position (e.g. hexadecanoate at sn1), find all lipids with that fatty acid at that position, irrespective of whether or not there are other fatty acids at positions (here sn2, sn3). could generalize this query to allow logical combinations of fatty acids (e.g. hexadecanoate at sn1 AND (9Z)-octadecenoate at sn2, hexadecanoate at sn1 AND NOT (9Z)-octadecenoate at sn2, etc) Output should include the corresponding SwissLipids ID(s) and name(s).

SELECT ?TODO WHERE {?TODO a ?TODO}Use

36: Returns the list of isomeric subspecies containing a specific combination of fatty acids at defined positions, but only those isomeric subspecies that are associated with a publication. If the user supplies a single fatty acid and position (e.g. hexadecanoate at sn1), find all lipids with that fatty acid at that position, irrespective of whether or not there are other fatty acids at positions (here sn2, sn3). could generalize this query to allow logical combinations of fatty acids (e.g. hexadecanoate at sn1 AND (9Z)-octadecenoate at sn2, hexadecanoate at sn1 AND NOT (9Z)-octadecenoate at sn2, etc) Output should include the corresponding SwissLipids ID(s) and name(s) and PMIDs.

SELECT ?startId ?startName ?tail1 ?tailName1 ?tail2 ?tailName2 ?id ?name ?pubmed WHERE { VALUES ?startId { SLM:000121946 } ?startId rdfs:label ?startName . # tail components ?startId SLM:haspart ?tail1 . ?startId SLM:haspart ?tail2 . FILTER(!sameTerm(?tail1, ?tail2)) ?tail1 rdfs:label ?tailName1 . ?tail2 rdfs:label ?tailName2 . # Retrieve lipids with similar tails ?id SLM:haspart ?tail1 , ?tail2 . # Restrict to isomeric subspecies with PubMed citation(s) ?id SLM:rank SLM:Isomeric_Subspecies . ?id SLM:citation ?pubmed . # Retrieve name ?id rdfs:label ?name . } ORDER BY ?id ?tail1 ?tail2Use

37: Returns the list of isomeric subspecies that contain the same fatty acid component(s) at the same position(s) as a user-defined lipid. The user supplies a lipid ID, from which we first retrieve the fatty acids and their positions, after which we search for other lipids with the same combination of fatty acids at the same positions. This query could be useful in the website (classification tab): for a given lipid, provide a list of the other lipids with the same “tail” e.g. for PA(16:0/18:1(9Z)) => hexadecanoate@sn1 AND (9Z)-octadecenoate@sn2 => PC(16:0/18:1(9Z)), PE(16:0/18:1(9Z)), PG(16:0/18:1(9Z)), PI(16:0/18:1(9Z)), PIP[3](16:0/18:1(9Z)), PIP[4](16:0/18:1(9Z)), PIP[5](16:0/18:1(9Z)), PI2P[3,4](16:0/18:1(9Z)), PI2P[4,5](16:0/18:1(9Z)), PI2P[3,5](16:0/18:1(9Z)), PI3P[3,4,5](16:0/18:1(9Z)), PS(16:0/18:1(9Z))… Output should include the corresponding SwissLipids ID(s) and name(s).

# Example 37 SELECT ?startId ?startName ?tail1 ?tailName1 ?tail2 ?tailName2 ?id ?name WHERE { VALUES ?startId { SLM:000121946 } ?startId rdfs:label ?startName . # tail components ?startId SLM:haspart ?tail1 . ?startId SLM:haspart ?tail2 . FILTER(!sameTerm(?tail1, ?tail2)) ?tail1 rdfs:label ?tailName1 . ?tail2 rdfs:label ?tailName2 . # Retrieve lipids with similar tails ?id SLM:haspart ?tail1 , ?tail2 . # Restrict to isomeric subspecies with PubMed citation(s) ?id SLM:rank SLM:Isomeric_Subspecies . # Retrieve name ?id rdfs:label ?name . } ORDER BY ?id ?tail1 ?tail2Use

38: Returns the list of isomeric subspecies that contain the same fatty acid component(s) at the same position(s) as a user-defined lipid, but limits the output to published lipids linked to a PMID. Output should include the corresponding SwissLipids ID(s) and name(s) and the PMID(s) for each. Extends ex:36 Output should include the corresponding SwissLipids ID(s) and name(s).

# Example 38 SELECT ?startId ?startName ?tail1 ?tailName1 ?tail2 ?tailName2 ?id ?name ?pubmed WHERE { VALUES ?startId { SLM:000121946 } ?startId rdfs:label ?startName . # tail components ?startId SLM:haspart ?tail1 . ?startId SLM:haspart ?tail2 . FILTER(!sameTerm(?tail1, ?tail2)) ?tail1 rdfs:label ?tailName1 . ?tail2 rdfs:label ?tailName2 . # Retrieve lipids with similar tails ?id SLM:haspart ?tail1 , ?tail2 . # Restrict to isomeric subspecies with PubMed citation(s) ?id SLM:rank SLM:Isomeric_Subspecies . ?id SLM:citation ?pubmed . # Retrieve name ?id rdfs:label ?name . } ORDER BY ?id ?tail1 ?tail2Use