MetaCyc:4-NITROPHENYLPHOSPHATASE-RXN xref

[sjm41]

MetaCyc:4-NITROPHENYLPHOSPHATASE-RXN is currently an xref on:

id: GO:0016791 name: phosphatase activity def: "Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate." [GOC:curators, GOC:pg] synonym: "4-nitrophenylphosphatase activity" NARROW [] synonym: "4-nitrophenylphosphate phosphohydrolase activity" NARROW [] synonym: "ecto-p-nitrophenyl phosphatase activity" NARROW [] synonym: "K-pNPPase activity" NARROW [] synonym: "nitrophenyl phosphatase activity" NARROW [] synonym: "NPPase activity" NARROW [] synonym: "p-nitrophenylphosphatase activity" NARROW [] synonym: "p-nitrophenylphosphate phosphohydrolase activity" NARROW [] synonym: "para-nitrophenyl phosphatase activity" NARROW [] synonym: "phosphatase" RELATED [] synonym: "phosphoric monoester hydrolase activity" EXACT [] synonym: "PNPPase activity" NARROW []xref: EC:3.1.3.- xref: MetaCyc:4-NITROPHENYLPHOSPHATASE-RXN is_a: GO:0042578 ! phosphoric ester hydrolase activity

It should either be removed or at least made a narrow xref. It corresponds to 4-nitrophenylphosphatase (https://enzyme.expasy.org/EC/3.1.3.41), but we don't have a GO term for that - though I see similar terms are listed as narrow synonyms on GO:0016791 (so maybe it was merged at some point).

[ValWood]

This might be OK. We can make narrow synonyms but not narrow x-refs and this is an x-ref. This would be the correct place for MetaCyc:4-NITROPHENYLPHOSPHATASE-RXN to land.

@pgaudet reopen if this is incorrect.

[sjm41]

Other narrow xrefs look like this:

id: GO:0016805 name: dipeptidase activity def: "Catalysis of the hydrolysis of a dipeptide." [https://www.ebi.ac.uk/merops/about/glossary.shtml#DIPEPTIDASE, PMID:19879002] synonym: "cytosolic dipeptidase activity" NARROW [] xref: EC:3.4.13.- xref: EC:3.4.13.18 {source="skos:narrowMatch"} xref: EC:3.4.13.21 {source="skos:narrowMatch"} xref: MetaCyc:3.4.13.18-RXN {source="skos:narrowMatch"} xref: MetaCyc:3.4.13.18-RXN xref: MetaCyc:3.4.13.21-RXN {source="skos:narrowMatch"} is_a: GO:0008238 ! exopeptidase activity

[ValWood]

OK I have no idea how to do that. This one will need to wait until next week!

[sjm41]

Sure, no problem! The issue with the current situation is that the BioCyc 'Pathway Tools' software sees this MetaCyc xref on the GO:0016791 term, and then maps any gene annotated with "phosphatase activity" (which is a lot) to that very specific MetaCyc:4-NITROPHENYLPHOSPHATASE-RXN reaction. That's obviously wrong and leads to many false positive reaction/pathway associations at BioCyc.

Actually, I'm not sure if flagging this xref as ' {source="skos:narrowMatch"}' will solve that issue....

Would be cleaner to (re)instate the "4-nitrophenylphosphatase activity (EC:3.1.3.41)" term - I see there are 1,700 UniProt entries annotated to EC:3.1.3.41. I'll have a look to see if there's a old ticket about that term to say if/why it was obsoleted.

[sjm41]

I see they are a few previous tickets relating to this. Here's a summary (in chronological order):

10647

Long discussion (Antonia, Val, Pascale, Peter, Tanya) about whether 4-nitrophenylphosphatase activity (GO:0003869)/EC:3.1.3.41 represents a physiological activity or is just used as a general assay for phosphatase activity. Final decision was to merge '4-nitrophenylphosphatase' with 'phosphatase activity'.

10730

Mapping of 4-nitrophenylphosphatase activity IEA: with IUBMB:3.1.3.41, queried by Val. "We believe that based on the fact that this reaction is not expected to occur in vivo, but is rather an in vitro assay, we should not have this mapping in GO." David OS confirms merge from #10647 has happened, and feels 4-nitrophenylphosphatase synonyms should be kept on 'phosphatase activity'

14306 / #16819

Steven requests that EC:3.1.3.41 is removed as an xref of 'GO:0016791 phosphatase activity' - Harold agrees and removes it. Steven later notices that the RHEA and MetaCyc xrefs (equivalent to EC:3.1.3.41) were not removed - Harold says that these have also be removed - but it now looks like the RHEA was removed, but the MetaCyc was not.

So, there was a merge of '4-nitrophenylphosphatase activity' with 'phosphatase activity', and the EC and RHEA xrefs for '4-nitrophenylphosphatase activity' were removed from 'phosphatase activity', but the corresponding MetaCyc xref was forgotten about and still remains.

So I think 'MetaCyc:4-NITROPHENYLPHOSPHATASE-RXN' should just be removed from 'phosphatase activity'.

[ValWood]

Not sure why this didn't autoclose (check I didn't close something else by mistake)

[sjm41]

Hi @ValWood So, did you remove the MetaCyc xref in the end? (There's no pull request linked above, so I can't easily check myself!)

[ValWood]

It was supposed to be in here https://github.com/geneontology/go-ontology/pull/25764 but I can't see it. I will check tomorrow.

[pgaudet]

The bad xref was removed.

I removed extra synonyms, added the link to this ticket.

[pgaudet]

Thanks for the archeology @sjm41 !

[sjm41]

Great, thanks both!