SwissLipids

• Find the list of SwissLipids for all organisms and their Isomeric subspecies
• For a given (list of) lipid Species identifier(s) (e.g. SWISSLIPID:000056420 (Phosphatidylcholine (20:2)) SWISSLIPID:000308470 (Triacylglycerol (64:6))), return a list of the corresponding Molecular subspecies (if any), Structural subspecies (if any), and Isomeric subspecies. The query should return the lipid recommended names as well as identifiers. The list should be sorted by level in the hierarchy (Isomeric subspecies last). Future versions of this query should be generic enough to work from any start point (Species, Molecular subspecies, Structural subspecies). Recapitulates the “browse lipid analytes” function of the website (in batch).
• For a given (list of) lipid Species identifiers (e.g. SWISSLIPID:000056493, Phosphatidylcholine (32:0)), return a list of the corresponding Molecular subspecies (if any), Structural subspecies (if any), and Isomeric subspecies (if any) which are associated with at least one citation (PMID: PubMed id). The query should return the lipid identifiers (?id), recommended names (?name), and PMIDs (?citation). Future versions of this query should be generic enough to work from any start point (Species, Molecular subspecies, Structural subspecies).
• For a given (list of) lipid classes (e.g. SWISSLIPID:000399814 (Ceramide) SWISSLIPID:000000007 (Sphingomyelin (iso-d17:1(4E))), return a list of the corresponding Isomeric subspecies. The query should return the lipid recommended names (?name) as well as identifiers (?id). Recapitulates the “browse lipid classes” function of the website (in batch).
• For a given lipid (SWISSLIPID:000399814, Ceramide), return a list of all corresponding reactions (Rhea IDs and equation), as well as their enzymes as annotated in UniProtKB/Swiss-Prot) enzymes themselves (ID and protein name). This query does not consider the hierarchy: it looks for reactions and enzymes only for the specified lipid.
• For a given lipid (SWISSLIPID:000399814, Ceramide), return a list of all corresponding reactions (Rhea IDs and equation). This query does consider the hierarchy: it looks for reactions involving the specified lipid and/or its more specific forms.
• For a given lipid (SWISSLIPID:000399814, Ceramide), return a list of all enzymes in UniProtKB/Swiss-Prot annotated to catalyze reactions involving that lipid. This query does not consider the hierarchy: it looks for reactions and enzymes only for the specified lipid.
• For a given list of ChEBI identifiers return the list of corresponding SwissLipids identifiers. Output should include SwissLipids identifier and name plus the HMDB identifier. This query considers only the cross references in the SwissLipids entry – it does not attempt to query other levels to find links between parents or children. Recapitulates one ID mapping function on the website.
• For a given list of HMDB identifiers return the list of corresponding SwissLipids identifiers. Output should include SwissLipids identifier and name plus the HMDB identifier. This query considers only the cross references in the SwissLipids entry – it does not attempt to query other levels to find links between parents or children. Recapitulates one ID mapping function on the website.
• For a given list of LIPID MAPS identifiers return the list of corresponding ChEBI IDs. Output should include LIPID MAPS ID, the corresponding SwissLipids ID and name, plus the ChEBI ID. This query first identifies SwissLipids identifiers for a given list of HMDB identifiers. It then retrieves all children and from them the required LIPID MAPS identifiers. extends ex:9
• For a given list of LIPID MAPS identifiers return the list of corresponding SwissLipids identifiers. Output should include SwissLipids identifier and name plus the LIPID MAPS identifier. This query considers only the cross references in the SwissLipids entry – it does not attempt to query other levels to find links between parents or children. Recapitulates one ID mapping function on the website
• For a given list of LipidX lipid identifiers return the list of published Isomeric subspecies. Output should include the LipidX ID and the corresponding SwissLipids ID(s) and name(s) plus PubMed ID(s). This query first identifies SwissLipids identifiers for a given list of LipidX identifiers. It then retrieves the corresponding Isomeric subspecies that are linked to at least one publication, and the corresponding PMIDs. extends ex:15
• For a given list of lipid Species, return a list of the corresponding Isomeric subspecies for that particular lipid that are linked to an enzyme as annotated in UniProtKB (UniProt AC and recommended name). This question would allow a user with (a list of) very high level MS identifications to immediately narrow them to the most likely potential lipid structures and protein targets as in this example: SWISSLIPID:000056871 / PC(O-36:4) (target species of interest) -> SWISSLIPID:000028143 / PC(O-16:0/20:4(5Z,8Z,11Z,14Z)) -> LPCAT4, PLA2G4A, PLA2G4C, PLA2G4F (target proteins)
• Lipids affected by human enzymes
• Lipids by fatty acid component (hexadecanoate) at position sn1
• Lipids produced in different organisms
• Retrieve mapping between SwissLipids lipid identifiers and their corresponding ChEBI identifiers. Output should include SwissLipids identifier and name plus the ChEBI identifier.
• Retrieve mapping between SwissLipids lipid identifiers and their corresponding HMDB identifiers. Output should include SwissLipids identifier and name plus the HMDB identifier.
• Retrieve mapping between SwissLipids lipid identifiers and their corresponding LIPID MAPS identifiers. Output should include SwissLipids identifier and name plus the LIPID MAPS identifier.
• 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.
• 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).
• [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)), PIP3, PIP4, PIP5, PI2P3,4, PI2P4,5, PI2P3,5, PI3P3,4,5, PS(16:0/18:1(9Z))… Output should include the corresponding SwissLipids ID(s) and name(s).](./37.md)
• Select the SwissLipids categories and their labels.