EC cross references in definition, not in general cross references

[pgaudet]

• [x] GO:0103040 aldose sugar dehydrogenase activity EC:1.1.5.- >> replaced EC def xref by MetaCyc, add PMID for e. Eoli paper since the UniProt entry P75804 has no EC or RHEA.
• [x] GO:0102910 dirigent protein activity EC:1.10.3.- >> META&id=G-15194 states:

  Dirigent protein is a coupling agent that lacks a catalytically active oxidative center, but can confer stereospecificity in both lignin and lignan formation. It is able to bind and orientate coniferyl alcohol-derived free radicals which can then undergo stereoselective coupling.

• removed partial EC, add MetaCyc as def xref, moved under molecular_function, since there is no catalytic activity
• [x] GO:0102818 lycopene cleavage oxygenase activity EC:1.13.12.-
• Changed the def xref for MetaCyc:RXN-8236, as MetaCyc associates this activity to https://www.uniprot.org/uniprotkb/Q70YP8/entry, which has no EC or RHEA.
• [x] GO:0102433 phenylalanine 4-hydroxylase (N10-formyl-tetrahydrofolate dependent) activity EC:1.14.16.1
• Obsolete & replace by : MetaCyc RXN-13907 is linked to https://www.uniprot.org/uniprotkb/A8HQD7/entry, which is already associated with the correct EC, that corresponds to GO phenylalanine 4-monooxygenase activity (No annotations)
• [x] GO:0051342 regulation of cyclic-nucleotide phosphodiesterase activity EC:3.1.4.17
• BP: removed
• [x] GO:0102208 2-polyprenyl-6-hydroxyphenol methylase activity EC:2.1.1.222 >> added EC as a general xref
• [x] GO:0033832 alpha,alpha-trehalose phosphorylase (configuration-retaining) activity EC:2.4.1.231 >> added EC as a general xref
• [x] GO:0102089 dehydroscoulerine synthase activity EC:1.21.3.- : obsolete & replace by reticuline oxidase activity since this is mapped to EC:1.21.3.3 and this reaction is also described in EC:1.21.3.3 (No annotations)
• [x] GO:1990107 thiazole synthase activity EC:2.8.1.10 >> added EC as a general xref
• [ ] GO:0102310 dTDP-(2R,6S)-6-hydroxy-2-methyl-3-oxo-3,6-dihydro-2H-pyran-4-olate 3-ketoreductase (dTDP-4-dehydro-2,6-dideoxy-alpha-D-allose-forming) activity EC:1.17.1.-
• [ ] GO:0102544 ornaline synthase activity EC:1.5.1.-
• [ ] GO:0047288 beta-D-galactosyl-(1->3)-N-acetyl-beta-D-galactosaminide alpha-2,3- sialyltransferase EC:2.4.3.2
• [ ] GO:0103041 thiosulfate-thioredoxin sulfurtransferase activity EC:2.8.1.-
• [ ] GO:0102140 heparan sulfate N-deacetylase activity EC:3.1.1.-
• [ ] GO:1990043 5' deoxyribonuclease (pyrimidine dimer) activity EC:3.1.25.-
• [ ] GO:0033942 4-alpha-D-(1->4)-alpha-D-glucanotrehalose trehalohydrolase activity EC:3.2.1.141
• [ ] GO:0102274 glutathione S-conjugate carboxypeptidase activity EC:3.4.17.-
• [ ] GO:0033966 N-substituted formamide deformylase activity EC:3.5.1.91
• [ ] GO:0103072 straight chain (R)-2-hydroxy fatty acyl-CoA lyase activity EC:4.1.-.-
• [ ] GO:0103028 murein hydrolase activity EC:4.2.2.-
• [ ] GO:0103031 L-Ala-D/L-Glu epimerase activity EC:5.1.1.-
• [ ] GO:0103033 beta-galactosidase activity (lactose isomerization) EC:5.4.1.-
• [ ] GO:0018824 (hydroxyamino)benzene mutase activity EC:5.4.4.1
• [ ] GO:0102115 peptidoglycan asparagine synthase activity EC:6.3.1.-
• [ ] GO:0042961 ATPase-coupled antimonite transmembrane transporter activity EC:7.3.2.7
• [ ] GO:0015437 lipopolysaccharide floppase activity EC:7.5.2.5

[pgaudet]

Note sure what to do - @sjm41 what do you think ?

• [ ] GO:0015930 glutamate synthase activity EC:1.4.-.- : removed partial EC, as this was not right, but this is a grouping class for 'glutamate synthase (NADPH) activity' 'glutamate synthase (ferredoxin) activity' 'glutamate synthase (NADH) activity'

It seems useful to keep. Should I add the 3 ECs as narrowMatches on the parent?

[sjm41]

I agree this seems a useful grouping term, so would be good to keep. As for its general xref, I guess the choice is either what you suggest or else adding EC:1.4.-.- as broadMatch.

Of those choices, your suggestion seems better. Unless doing that would have undesired consequences for the EC2GO annotation pipeline?

[pgaudet]

GOA filters most specific annotations based on the same pipeline, so the solution I propose would work and not produce redundant annotations.