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ebi-chebi / ChEBI

Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds.
https://www.ebi.ac.uk/chebi
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Misuse of xref labels in CHEBI #3370

Open cmungall opened 7 years ago

cmungall commented 7 years ago

Example:

[Term]
id: CHEBI:51990
name: tetrabutylammonium fluoride
subset: 3_STAR
synonym: "N,N,N-tributylbutan-1-aminium fluoride" EXACT IUPAC_NAME [IUPAC]
synonym: "261.283" RELATED MONOISOTOPIC_MASS [ChEBI]
synonym: "C16H36FN" RELATED FORMULA [ChEBI]
synonym: "261.46210" RELATED MASS [ChEBI]
synonym: "0" RELATED CHARGE [ChEBI]
synonym: "[F-].CCCC[N+](CCCC)(CCCC)CCCC" RELATED SMILES [ChEBI]
synonym: "FPGGTKZVZWFYPV-UHFFFAOYSA-M" RELATED InChIKey [ChEBI]
synonym: "InChI=1S/C16H36N.FH/c1-5-9-13-17(14-10-6-2,15-11-7-3)16-12-8-4;/h5-16H2,1-4H3;1H/q+1;/p-1" RELATED InChI [ChEBI]
xref: Reaxys:3570522 "Reaxys"
xref: Beilstein:3570522 "Beilstein"
xref: CAS:429-41-4 "ChemIDplus"
xref: PMID:21142041 "Europe PMC"
xref: PMID:21517057 "Europe PMC"
xref: PMID:22229781 "Europe PMC"
xref: PMID:15074950 "Europe PMC"
is_a: CHEBI:24060
is_a: CHEBI:51992
relationship: has_role CHEBI:63060

E.g.

xref: Beilstein:3570522 "Beilstein"

The intent for the xref label in obo format is to assign a typically unique name to the specific entity, e.g Beilstein:3570522.

You seem to be using this field as a source of provenance. Provenance can instead be stated with:

xref: Beilstein:3570522 {source="Beilstein"}

But this may cause issues for your users who have written ad-hoc obo parsers.

cthoyt commented 4 years ago

Hi, I would also like to see this addressed

muthuvenkat commented 4 years ago

@cmungall , @cthoyt its done now. Please check the nightly files. We also have been using alt_id for secondary identifier, which robot is complaining about the duplicate. what is the right way to add this information ?