a few more new synonyms

[gocentral]

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

[gocentral]

• assigned_to: nobody --> gomidori

Original comment by: mah11

[gocentral]

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

[gocentral]

• assigned_to: gomidori --> nobody

Original comment by: mah11

[gocentral]

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

[gocentral]

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

[gocentral]

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

[gocentral]

• assigned_to: nobody --> gomidori
• status: open --> closed-accepted

Original comment by: mah11