New Robot form request for Lee IH PMID 36482414

[earlEBI]

Robot form request for plasma metabolite terms. I've mentioned blood plasma in the definition, if that's okay. I've also added a synonym column and there are four columns at the end which contain source codes for HMDB, KEGG, LM and/or T3DB. These are from ST1 and ST6. https://docs.google.com/spreadsheets/d/1dk_whJPpX31ee5H5yEnGO2fPHMRn_L8o4t0O5Ous1PQ/edit?usp=sharing

Any problems, please let me know

[ar-ibrahim]

Hey Lizzy @earlEBI :) The following terms are already in EFO. I'll add these exact synonyms to the existing terms. If you have any comments please let me know.

Term requested	Database x-ref	Notes
malic acid measurement	HMDB0000156||KEGG COMPOUND:C00149	EFO:0021622 (L-Malic acid measurement, exact synonym)
octanoate measurement	HMDB0000482||HMDB0304443	EFO:0021831 (caprylic acid measurement; exact synonym)
trehalose measurement	HMDB0000975||KEGG COMPOUND:C01083	EFO:0021592 (D-trehalose measurement; exact synonym)
ureidopropionate measurement	HMDB0000026||KEGG COMPOUND:C02642	EFO:0010641 (3-ureidopropionate measurement; exact synonym)
hydroxylysine measurement	HMDB0000450||KEGG COMPOUND:C16741	EFO:0800002 (5-hydroxylysine measurement; exact synonym)
mercuric chloride measurement	KEGG COMPOUND:C13377	EFO:0022068 (mercuric chloride measurement)

[earlEBI]

@ar-ibrahim Hi Arwa - Thank you! Zooma doesn't pick up these things! 🙏

[ar-ibrahim]

Hi James @udp. There are 28 lipid terms in this metabolites request. Will you add them as part of the swisslipids terms in OBA or should they go in EFO?

Term requested	Database x-ref
25-hydroxycholesterol measurement	HMDB0006247||KEGG COMPOUND:C15519
(5z7e)-(3s)-262626-trifluoro-27-nor-910-seco-5710(19)-cholestatriene-325-diol measurement	lipidmaps:LMST03020024
(5z7e)-(3s)-262626272727-hexafluoro-910-seco-5710(19)16-cholestatetraen-23-yne-325-diol measurement	lipidmaps:LMST03020077
1-(10z13z16z-nonadecatrienoyl)-sn-glycero-3-phosphocholine measurement	lipidmaps:LMGP01050003
1-(1z-eicosenyl)-glycero-3-phospho-(1-myo-inositol) measurement	lipidmaps:LMGP06070001
1-(5z8z11z14z17z-eicosapentaenoyl)-glycero-3-phospho-(1-myo-inositol) measurement	lipidmaps:LMGP06050026
1-(8-3-ladderane-octanoyl-2-(8-3-ladderane-octanyl)-sn-glycerol measurement	lipidmaps:LMGL02070009
1-(8-5-ladderane-octanyl)-2-(8-3-ladderane-octanyl)-sn-glycerol measurement	lipidmaps:LMGL02030030
1-(9z-octadecenoyl)-sn-glycero-3-phosphoserine measurement	lipidmaps:LMGP03050001
1-eicosyl-2-(4z7z10z13z16z19z-docosahexaenoyl)-glycero-3-phosphoserine measurement	lipidmaps:LMGP03020093
1-eicosyl-2-(7z10z13z16z-docosatetraenoyl)-glycero-3-phosphoserine measurement	lipidmaps:LMGP03020068
1-o-alpha-d-glucopyranosyl-12-nonadecandiol measurement	lipidmaps:LMFA13010006
12-aminolauramide measurement	lipidmaps:LMFA08010015
2s-amino-3r4r5s14r-tetrahydroxyeicos-6e-enoic acid measurement	lipidmaps:LMSP01080062
3-o-(beta-d-glucopyranosyl)-campest-5-en-3beta-ol measurement	lipidmaps:LMST01031126
(E)-isoheptadec-2-enoyl-CoA measurement	lipidmaps:LMFA07050145
311-dihydroxy-tetradecanoic acid measurement	lipidmaps:LMFA01050081
5-hydroperoxy-7-35-epidioxy-2-(2-octenyl)-cyclopentyl-6-heptenoic acid measurement	lipidmaps:LMFA01040028
9z-hexadecenamide measurement	lipidmaps:LMFA08010010
cyanidin 35-diglucoside (66-malyl diester) measurement	lipidmaps:LMPK12010207
n-(11z-eicosaenoyl)-ethanolamine measurement	lipidmaps:LMFA08040010
n-(15z-tetracosenoyl)-1-deoxysphing-4-enine measurement	lipidmaps:LMSP00000010
n-(2-hydroxy-docosanoyl)-pentadecasphing-4-enine-1-phosphoethanolamine measurement	lipidmaps:LMSP03020075
n-(3e-hexadecenoyl)-deoxysphing-4-enine-1-sulfonate measurement	lipidmaps:LMSP00000003
n-(9z12z15z-octadecatrienoyl)-glutamine measurement	lipidmaps:LMFA00000004
N-(heptadecanoyl)-ethanolamine measurement	lipidmaps:LMFA08040049
n-octadecanoyl-taurine measurement	lipidmaps:LMFA08020078
sphinga-4e8e10e-trienine measurement	lipidmaps:LMSP01080013

[ar-ibrahim]

Hey Lizzy @earlEBI. I added the new EFO metabolite terms which will be available after the June (15th) release. Will keep you updated about the lipid terms.

[jamesamcl]

@ar-ibrahim Hmmm! They should probably go into OBA yes - but it looks like only 6 of them map to SwissLipids:

https://www.swisslipids.org/#/mapper?from=LipidMaps&to=SwissLipids&ids=LMST03020024,LMST03020077,LMGP01050003,LMGP06070001,LMGP06050026,LMGL02070009,LMGL02030030,LMGP03050001,LMGP03020093,LMGP03020068,LMFA13010006,LMFA08010015,LMSP01080062,LMST01031126,LMFA07050145,LMFA01050081,LMFA01040028,LMFA08010010,LMPK12010207,LMFA08040010,LMSP00000010,LMSP03020075,LMSP00000003,LMFA00000004,LMFA08040049,LMFA08020078,LMSP01080013

I haven't tried to map them to ChEBI (the mapping tool didn't work) so maybe we will get some results there. But maybe we will need an import for lipidmaps into OBA as well as swisslipids (unless these are in swisslipids and it's just the mapping from lipidmaps that's missing).

Tagging https://github.com/obophenotype/bio-attribute-ontology/issues/242

[earlEBI]

Hi, could I just check if these lipid terms are still in progress? Please let me know when I can add to the GWAS Catalog.

[rays22]

I have updated the gsheet so that the OBA trait IDs can be looked up for the lipid-related EFO terms requested in this ticket. @ar-ibrahim , could you kindly check if these OBA trait terms have been imported into EFO.

ID	LABEL	REQUESTED LABEL
OBA:2045054	level of 25-hydroxycholesterol in blood serum	25-hydroxycholesterol measurement
OBA:2045037	level of (5Z,7E)-(3S)-26,26,26-trifluoro-27-nor-9,10-seco-5,7,10(19)-cholestatriene-3,25-diol in blood serum	(5z7e)-(3s)-262626-trifluoro-27-nor-910-seco-5710(19)-cholestatriene-325-diol measurement
OBA:1000312	vitamin D metabolic process quality	(5z7e)-(3s)-262626272727-hexafluoro-910-seco-5710(19)16-cholestatetraen-23-yne-325-diol measurement
OBA:2045046	level of PC(19:3(10Z,13Z,16Z)/0:0) in blood serum	1-(10z13z16z-nonadecatrienoyl)-sn-glycero-3-phosphocholine measurement
OBA:2045060	level of 1-O-(1Z-eicosenyl)-sn-glycero-3-phospho-1D-myo-inositol in blood serum	1-(1z-eicosenyl)-glycero-3-phospho-(1-myo-inositol) measurement
OBA:2045059	level of 1-(5Z,8Z,11Z,14Z,17Z-eicosapentaenoyl)-sn-glycero-3-phospho-1D-myo-inositol in blood serum	1-(5z8z11z14z17z-eicosapentaenoyl)-glycero-3-phospho-(1-myo-inositol) measurement
OBA:2045038	level of 1-(8-[3]-ladderane-octanoyl)-2-(8-[3]-ladderane-octanyl)-sn-glycerol in blood serum	1-(8-3-ladderane-octanoyl-2-(8-3-ladderane-octanyl)-sn-glycerol measurement
OBA:2045052	level of dialkylglycerol in blood serum	1-(8-5-ladderane-octanyl)-2-(8-3-ladderane-octanyl)-sn-glycerol measurement
OBA:2045055	level of 1-O-oleoyl-sn-glycero-3-phosphoserine in blood serum	1-(9z-octadecenoyl)-sn-glycero-3-phosphoserine measurement
OBA:2045047	level of PS(O-20:0/22:6(4Z,7Z,10Z,13Z,16Z,19Z)) in blood serum	1-eicosyl-2-(4z7z10z13z16z19z-docosahexaenoyl)-glycero-3-phosphoserine measurement
OBA:2045045	level of PS(O-20:0/22:4(7Z,10Z,13Z,16Z)) in blood serum	1-eicosyl-2-(7z10z13z16z-docosatetraenoyl)-glycero-3-phosphoserine measurement
OBA:2045041	level of 1-O-alpha-D-Glucopyranosyl-1,2-nonadecandiol in blood serum	1-o-alpha-d-glucopyranosyl-12-nonadecandiol measurement
OBA:2045053	level of 12-aminododecanoic acid in blood serum	12-aminolauramide measurement
OBA:2045049	level of Sphingofungin B in blood serum	2s-amino-3r4r5s14r-tetrahydroxyeicos-6e-enoic acid measurement
OBA:2045039	level of campesterol 3-beta-D-glucoside in blood serum	3-o-(beta-d-glucopyranosyl)-campest-5-en-3beta-ol measurement
OBA:2045056	level of (E)-isoheptadec-2-enoyl-CoA in blood serum	(E)-isoheptadec-2-enoyl-CoA measurement
OBA:2045051	level of Ipurolic acid in blood serum	311-dihydroxy-tetradecanoic acid measurement
OBA:2045048	level of 5-hydroperoxy-7-[3,5-epidioxy-2-(2-octenyl)-cyclopentyl]-6-heptenoic acid in blood serum	5-hydroperoxy-7-35-epidioxy-2-(2-octenyl)-cyclopentyl-6-heptenoic acid measurement
OBA:2045040	level of palmitoleamide in blood serum	9z-hexadecenamide measurement
OBA:VT0010487	response to xenobiotic stimulus trait	cyanidin 35-diglucoside (66-malyl diester) measurement
OBA:2045058	level of N-gondoylethanolamine in blood serum	n-(11z-eicosaenoyl)-ethanolamine measurement
OBA:2045029	level of ceramide in blood serum	n-(15z-tetracosenoyl)-1-deoxysphing-4-enine measurement
OBA:2045057	level of ceramide phosphoethanolamine in blood serum	n-(2-hydroxy-docosanoyl)-pentadecasphing-4-enine-1-phosphoethanolamine measurement
OBA:2045043	level of N-(3E-hexadecenoyl)-deoxysphing-4-enine-1-sulfonate in blood serum	n-(3e-hexadecenoyl)-deoxysphing-4-enine-1-sulfonate measurement
OBA:2045050	level of N-linolenoyl glutamine in blood serum	n-(9z12z15z-octadecatrienoyl)-glutamine measurement
OBA:2045042	level of Margaroyl-EA in blood serum	N-(heptadecanoyl)-ethanolamine measurement
OBA:2045036	level of N-stearoyltaurine in blood serum	n-octadecanoyl-taurine measurement
OBA:2045044	level of (4E,8E,10E-d18:3)sphingosine in blood serum	sphinga-4e8e10e-trienine measurement