New term request for Chen PMID:36635386 (WC_20230126)

[Santhi1901]

415 metabolite terms:

https://docs.google.com/spreadsheets/d/1otj6b535EM7O-K8G2C1N3UUWQDlIT0DC/edit#gid=1187117326

[dosumis]

Please see comments on #1882

Note - as for that request - these are all blood metabolite measurements

[Santhi1901]

I have now added the CAS ID/KEGG ID/PubChem ID if provided in the paper. Removed those terms which don't have any IDs. 28 terms. Please let me know if there is anything else that needs to be updated.

[zoependlington]

@udp There is one lipid term in this request to be added into OBA when you have the Swiss Lipids import sorted, I found a Lipid Map ref (LMFA01030407):

measurement	Child of	CAS	KEGG	PUBCHEM	Synonyms	Definition	PMID reference	editor
Blood docosatrienoate measurement	lipid measurement	59708-86-0	C16534	5312556		The determination of the amount of docosatrienoate in a blood sample	36635386	Santhi Ramachandran

The following have been added to EFO and will be available after the June release:

ID	LABEL
EFO:0022197	Blood 3-hydroxymyristate measurement
EFO:0022198	Blood citramalate measurement
EFO:0022199	Blood 2,3-dihydroxypyridine measurement
EFO:0022200	Blood Glutaconic acid measurement
EFO:0022201	Blood Citraconic acid measurement
EFO:0022202	Blood N-acetyl-2-aminoadipate measurement
EFO:0022203	Blood N-carbamoylalanine measurement
EFO:0022204	Blood N(1)-acetylspermidine measurement
EFO:0022205	Blood N(8)-acetylspermidine measurement
EFO:0022206	Blood N-acetylasparagine measurement
EFO:0022207	Blood N-acetylproline measurement
EFO:0022208	Blood 2,2'-Methylenebis(6-tert-butyl-p-cresol) measurement
EFO:0022209	Blood ethylparaben sulfate measurement
EFO:0022210	Blood pantoate measurement
EFO:0022211	Blood succinimide measurement
EFO:0022212	Blood dibutyl sulfosuccinate measurement
EFO:0022213	Blood cytosine measurement
EFO:0022214	Blood vanillic alcohol sulfate measurement
EFO:0022215	Blood 3,4-dihydroxybutyrate measurement
EFO:0022216	Blood 4-oxo-retinoic acid measurement
EFO:0022217	Blood N-acetylcarnosine measurement
EFO:0022218	Blood 1H-indole-7-acetic acid measurement
EFO:0022219	Blood 2,3-dihydroxy-2-methylbutyrate measurement
EFO:0022220	Blood 3-hydroxyoctanoylcarnitine
EFO:0022221	Blood 2,4-di-tert-butylphenol measurement
EFO:0022222	Blood pyridoxal measurement
EFO:0022223	metabolite ratio

[dosumis]

@Santhi1901 - 28 terms sees like a pretty poor hit rate compared to 415 you initially requested. I'm wondering about what counted as an ID for choosing terms.

Sheet 2 in this supplementary material table from the paper maps metabolites to a very rich set of IDs that can be used in mapping (e.g. inchkey, SMILES) https://static-content.springer.com/esm/art%3A10.1038%2Fs41588-022-01270-1/MediaObjects/41588_2022_1270_MOESM4_ESM.xls

Metabolites	Compound ID (Metabolon)	CHRO_LIB_ENTRY_ID	COMP_ID	LIB_ID	SUPER_PATHWAY	SUB_PATHWAY	PATHWAY_SORTORDER	TYPE	INCHIKEY	SMILES	CAS	CHEMSPIDER	HMDB	HMDB_curated	KEGG	PUBCHEM	PUBCHEM_curated
S-1-pyrroline-5-carboxylate	X35	166164	42370	400	Amino Acid	Glutamate Metabolism	62	NAMED	DWAKNKKXGALPNW-REWHXWOFAV	OC(C1CCC=N1)=O	2906-39-0	10140206	HMDB0001301	HMDB0001301	C04322	11966181	11966181
spermidine	X50	157851	485	402	Amino Acid	Polyamine Metabolism	545	NAMED	ATHGHQPFGPMSJY-UHFFFAOYAK	NCCCCNCCCN	124-20-9	1071	HMDB0001257	HMDB0001257	C00315	1102	1102
1-methylnicotinamide	X55	155829	27665	400	Cofactors and Vitamins	Nicotinate and Nicotinamide Metabolism	4316	NAMED	LDHMAVIPBRSVRG-UHFFFAOYAE	C[N+]1=CC(C([NH-])=O)=CC=C1	1005-24-9	8305504	HMDB0000699	HMDB0000699	C02918	457	457

[Santhi1901]

@dosumis I am not able to open the Excel mentioned above.

Out of the 415 terms, for 34 terms, I was able to find some broader EFO terms 308 terms were metabolite ratios; I had requested 'metabolite ratio' as a new term and mapped those to metabolite ratio 46 terms I couldn't find any ID or any existing terms in EFO so have mapped to metabolite measurement.

[rays22]

There is one lipid term in this request to be added into OBA when you have the Swiss Lipids import sorted, I found a Lipid Map ref (LMFA01030407):

@ar-ibrahim , When you add the new term to OBA trait term entity_attribute_location.tsv, please use CHEBI:80549 - 13,16,19-Docosatrienoic acid as the lipid component instead of LMFA01030407 13,16,19-docosatrienoic acid. The reason for this is that ChEBI (as an OBO ontology) provides broader structural taxonomy context and better links to biological properties than the specialist Lipidmaps database.

[rays22]

@ar-ibrahim , When you add the new term to OBA trait term entity_attribute_location.tsv, please use CHEBI:80549 - 13,16,19-Docosatrienoic acid as the lipid component instead of LMFA01030407 13,16,19-docosatrienoic acid. The reason for this is that ChEBI (as an OBO ontology) provides broader structural taxonomy context and better links to biological properties than the specialist Lipidmaps database.

@ar-ibrahim , You may need to update chebi slim and add CHEBI:80549 to it, then refresh OBA imports.

[ar-ibrahim]

Lipid term added to OBA as OBA:2050329(blood 13,16,19-Docosatrienoic acid amount) and will be made available following the upcoming OBA release and EFO patch release 3.57.1.

[zoependlington]

@ar-ibrahim Has this also been added to the EFO oba_terms.txt file?