Closed gocentral closed 9 years ago
Original comment by: mah11
Logged In: YES user_id=436423 Originator: NO
The bulk addition is coming along ... slowly. It helps to have these lists to confirm that the synonyms are exact (or whatever scope), but it's not critical.
m
Original comment by: mah11
Original comment by: mah11
Logged In: YES user_id=1473024 Originator: NO
Hello,
I've been meaning to (automatically) align IntEnz and GO and supply some sort of sensible loading table for some time (but have never quite got round to it).
What would be the best thing for me to supply? Or is this process already in motion?
Best wishes, Colin.
Original comment by: batchelorc
Logged In: YES user_id=436423 Originator: NO
Hi Colin,
It would be great to have something from you! I do have a bulk add well under way (and I wish I'd know about your plan -- might've saved me some work over the past few days), and it will help quite a bit to have another source to refer to. I'm seeing a lot of "synonyms" in the Expasy file that clearly shouldn't be "exact"-scope synonyms in GO, and I hope I'm reaching the same conclusions as you would about what scope they should be.
Would you be able to do something, perhaps tab-delimited, with GO ID, synonym text, and synonym scope? The GO term name wouldn't hurt but isn't as essential as the first 3 bits of info.
cheers, midori
Original comment by: mah11
Logged In: YES user_id=436423 Originator: NO
first round of bulk add committed (not least so I don't lose the work!)
further refinement very likely when Colin sends his file
see SF 1195550 for more details
https://sourceforge.net/tracker/?func=detail&atid=440764&aid=1195550&group\_id=36855
Original comment by: mah11
Original comment by: mah11
Hi Midori,
You may not want these, if we're going to collect them automatically...but here are a few more new synonyms I"ve found.
Thanks, Maria
GO term: GO:0004070 aspartate carbamoyltransferase activity
Current synonyms: none
New synonyms: exact: aspartate transcarbamylase exact: ATCase exact: carbamylaspartotranskinase
Reference for new synonyms: http://www.expasy.ch/cgi-bin/nicezyme.pl?2.1.3.2
GO term: GO:0004088 carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity
Current synonyms: exact: carbamoyl-phosphate synthetase (glutamine-hydrolyzing) exact: carbamoyl phosphate synthase (glutamine-hydrolyzing) activity
New synonyms: exact: carbamoyl phosphate synthetase exact: carbamoylphosphate synthetase II exact: carbamyl phosphate synthetase (glutamine) exact: CPS exact: GD-CPSase exact: glutamine-dependent carbamoyl-phosphate synthase exact: glutamine-dependent carbamyl phosphate synthetase
Reference for new synonyms: http://www.expasy.org/enzyme/6.3.5.5
GO term: GO:0004644 phosphoribosylglycinamide formyltransferase activity
Current synonyms: none
New synonyms: exact: 2-amino-N-ribosylacetamide 5'-phosphate transformylase exact: 5'-phosphoribosylglycinamide transformylase exact: 5,10-methenyltetrahydrofolate:2-amino-N-ribosylacetamide ribonucleotide transformylase exact: GAR formyltransferase exact: GAR TFase exact: GAR transformylase exact: GART exact: glycinamide ribonucleotide transformylase
Reference for new synonyms: http://www.expasy.ch/cgi-bin/nicezyme.pl?2.1.2.2
GO term: GO:0004017 adenylate kinase activity
Current synonyms: none
New synonyms: exact: adenylic kinase exact: adenylokinase exact: myokinase
Reference for new synonyms: http://www.expasy.ch/cgi-bin/nicezyme.pl?2.7.4.3
GO term: GO:0003866 3-phosphoshikimate 1-carboxyvinyltransferase activity
Current synonyms: none
New synonyms: exact: 3-enol-pyruvoylshikimate-5-phosphate synthase exact: 5-enolpyruvylshikimate-3-phosphate synthase exact: EPSP synthase
Reference for new synonyms: http://www.expasy.org/enzyme/2.5.1.19
GO term: GO:0004337 geranyltranstransferase activity
Current synonyms: exact: farnesyl pyrophosphate synthetase activity exact: farnesyl-diphosphate synthase activity exact: geranyltransferase
New synonyms: exact: farnesyl diphosphate synthetase exact: FPP synthetase
Reference for new synonyms: http://www.expasy.ch/cgi-bin/nicezyme.pl?2.5.1.10
GO term: GO:0004360 glutamine-fructose-6-phosphate transaminase (isomerizing) activity
Current synonyms: exact: glucosamine-6-phosphate isomerase (glutamine-forming) activity
New synonyms: exact: D-fructose-6-phosphate amidotransferase exact: GlcN6P synthase exact: glucosamine--fructose-6-phosphate aminotransferase (isomerizing) exact: glucosamine-6-phosphate synthase exact: hexosephosphate aminotransferase exact: L-glutamine-D-fructose-6-phosphate amidotransferase
Reference for new synonyms: http://www.expasy.ch/cgi-bin/nicezyme.pl?2.6.1.16
Reported by: mariacostanzo
Original Ticket: "geneontology/ontology-requests/4406":https://sourceforge.net/p/geneontology/ontology-requests/4406