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geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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EC:4.1.99 xrefs to remove #18149

Closed sjm41 closed 4 years ago

sjm41 commented 4 years ago

4.1.99.- is for all "Other carbon-carbon lyases" in EC: https://enzyme.expasy.org/EC/4.1.99.-

As such, I think it needs to be removed as an xref on these more specific GO terms:

[Term] id: GO:0003913 name: DNA photolyase activity xref: EC:4.1.99

[Term] id: GO:0034579 name: (1-methylpentyl)succinate synthase activity xref: EC:4.1.99

[Term] id: GO:0071771 name: aldehyde decarbonylase activity xref: EC:4.1.99 N.B. see related ticket on this particular term - #18148

hdrabkin commented 4 years ago

GO:0003913; updated to EC:4.1.99.3 and RHEA:10672 GO:0034579; removed GO:0071771; go def does not agree with assigned EC (4.1.99.5) used for def, and the gene mentioned in the publication uses the RHEA def I would get looking up 4.1.99.5 def and not the GO Def. @tberardini , this term was requested by Kate Dreher of Tair; can you trace? I think the def should be A long-chain aldehyde + O(2) + 2 NADPH <=> an alkane + formate + H(2)O + 2 NADP(+) (from EC def, to be changed to RHEA def a long-chain fatty aldehyde + H(+) + 2 NADPH + O2 = a long-chain alkane + formate + H2O + 2 NADP(+)

sjm41 commented 4 years ago

GO:0003913; updated to EC:4.1.99.3 and RHEA:10672

I'm not sure that's right. GO:0003913 is "DNA photolyase activity" EC:4.1.99.3 is "Deoxyribodipyrimidine photo-lyase."

and a child of GO:0003913 is "deoxyribodipyrimidine photo-lyase activity" (GO:0003904) that already has the specific EC:4.1.99.3 xref.

So I think GO:0003913/"DNA photolyase activity" can't have an EC xref.

sjm41 commented 4 years ago

Hi Harold - just checking you saw my last reply on this?

sjm41 commented 4 years ago

@tberardini Hi Tanya - Any thoughts on this, or the related #18148?

hdrabkin commented 4 years ago

I made the assignment based on DNA photolyase as a synonym in EC:4.1.99.3; https://enzyme.expasy.org/EC/4.1.99.3 However, I will move the RHEA

sjm41 commented 4 years ago

Ah, I see. I guess we'll then have two GO terms with the same EC xref - is that OK?

[Term] id: GO:0003913 name: DNA photolyase activity def: "Catalysis of the repair of a photoproduct resulting from ultraviolet irradiation of two adjacent pyrimidine residues in DNA." [GOC:mah, PMID:11124949] xref: EC:4.1.99.3

[Term] id: GO:0003904 name: deoxyribodipyrimidine photo-lyase activity def: "Catalysis of the reaction: cyclobutadipyrimidine (in DNA) = 2 pyrimidine residues (in DNA). This reaction represents the reactivation of irradiated DNA by light." [EC:4.1.99.3] xref: EC:4.1.99.3

hdrabkin commented 4 years ago

Yes absolutely because the EC is more about mechanism whereas RHEA is about the substrates and products. However, you know looking at the def "...two adjacent pyrimidine residues" in one and .. cyclobutadipyrimidine (in DNA); I can't really think of how the two pyrimidines would be anthing other than adjacent. Maybe these should be merged

sjm41 commented 4 years ago

Note that id: GO:0003913 (DNA photolyase activity) is actually a parent of these two child terms, implying there must be some (intended) difference in scope of the 3 of them:

[Term] id: GO:0003904 name: deoxyribodipyrimidine photo-lyase activity def: "Catalysis of the reaction: cyclobutadipyrimidine (in DNA) = 2 pyrimidine residues (in DNA). This reaction represents the reactivation of irradiated DNA by light." [EC:4.1.99.3] xref: EC:4.1.99.3

id: GO:0003914 name: DNA (6-4) photolyase activity def: "Catalysis of the reaction: pyrimidine-pyrimidone (6-4) photoproduct (in DNA) = 2 pyrimidine residues (in DNA). Catalyzes the reactivation of ultraviolet-irradiated DNA." [GOC:mah, PMID:11124949] xref: EC:4.1.99.13

hdrabkin commented 4 years ago

Hm. The 6-4 is a specific reactant apparently occurring 33% of the time https://en.wikipedia.org/wiki/Pyrimidine_dimer

If anything, GO:0003913 and GO:0003904 appear to be the same, but GO:0003904 is more specific. But apparently most people think of the 6,6,5,5 dimer unless otherwise noted. see https://www.researchgate.net/figure/Pyrimidine-dimers-are-the-main-UV-induced-DNA-photoproducts-and-affect-the-phosphodiester_fig1_323371532

mah11 commented 4 years ago

I haven't looked at these in many years, but I did put in some of the definitions back in the day. They are indeed a bit different, as Steven has inferred/guessed. There are (at least) two possible photoproducts that can form when UV hits two adjacent pyrimidines.

I found the introduction to https://doi.org/10.1093/nar/gkz359 helpful to dredge up the memory. There may be room to improve the the text defs, and I really can't help with the ER xrefs, but the ontology structure looks correct.

hdrabkin commented 4 years ago

No wait. I take back the merge. The RHEA that goes with the EC and will go with GO:0003904 and not GO:0003913, specifically uses CHEBI term CHEBI:65263 for the 6,6,5,5

hdrabkin commented 4 years ago

Also requesting a RHEA for the 6-4 product while I"m at it. RHEA ticket 176724

hdrabkin commented 4 years ago

RHEA:62232 thymidine(6-4)thymidine in DNA = thymidine dimer in DNA RHEA:62236 cytidine(6-4)cytidine in DNA = cytosine dimer in DNA + H+ RHEA:62240 thymidine(6-4)cytidine in DNA = thymine-cytidine dinucleotide in DNA RHEA:62244 cytidine(6-4)thymidine in DNA = cytidine-thymine dinucleotide in DNA

They will be linked to EC 4.1.99.13, but the generic reaction will still be a text reaction, as we cannot create "a pyrimidine" in Rhea, for that cytosine and thymine are too different. The reaction should become available in release 2020_02 tentatively scheduled for 26 February 2020.

sjm41 commented 4 years ago

Hi Harold, I'm just catching up on this thread.... I think one conclusion from this (particularly reading Midori's comment of 22nd Nov) is that EC 4.1.99.3 should only be an xref on GO:0003904, right? But I still see it on the parent term (GO:0003913), though it's not in the right format:

id: GO:0003913 name: DNA photolyase activity namespace: molecular_function def: "Catalysis of the repair of a photoproduct resulting from ultraviolet irradiation of two adjacent pyrimidine residues in DNA." [GOC:mah, PMID:11124949] xref: EC:\:4.1.99.3

Maybe you tried to delete it but something went wrong??

hdrabkin commented 4 years ago

apparently something did. I'm surprised that the :: is not picked up in a travis check. I'm going in now to fix

sjm41 commented 4 years ago

Looks like the syntax of the malformed xref got modified when I copied and pasted. It's actually "xref: EC:\:4.1.99.3"

hdrabkin commented 4 years ago

Gone.