That would be fantastic, thanks very much. :)
2009/1/26 Jie Luo <[email protected]> > Hi Allyson, > > > > We will have beta release on Uniprot biomart soon (a week or so). I will > let you know in due course. > > > > Regards > > > > Jie > > > > > > *From:* [email protected] [mailto: > [email protected]] *On Behalf Of *Allyson Lister > *Sent:* 26 January 2009 09:19 > *To:* Syed Haider > *Cc:* [email protected]; Jie Luo > *Subject:* Re: Fwd: interpreting GO IDs > > > > Hi Syed, Jie, > > I will try Ensembl, but I would be very interested in the new Uniprot mart > - I had no way of knowing that the prototype was so out of date, as it is > the one on the biomart.org martview, and therefore I assumed it was the > one to use. > > Jie, could you please let me know how to connect to the new Uniprot mart, > and if/when it is available from the biomart.org martview application? > > Thanks :) > > 2009/1/24 Syed Haider <[email protected]> > > Hi Allyson, > > looking at your query, seems you are using UNIPROT PROTOTYPE which is quite > out of date and so is GO data in UNIPROT PROTOTYPE. The new and > comprehensive version of UNIPROT is about to be released (Jie cc'ed here can > point you to the test site too). Also, I guess the attributes you are > interested in can be retrieved from Ensembl too, please try that. > > Thanks > Syed > > > Allyson Lister wrote: > > Hi Syed, > > I guess I'm still not following. I select "All" rows, and I do get a longer > list, but still *every cell* in the GO ID column says "GO:0007049". Now, > this ID is for "cell cycle" (see > http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0007049&session_id=6322amigo1232721760< > http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0007049&session_id=6322amigo1232721760>). > This implies to me that there is a problem in the display of the martview, > and that it is displaying this one GO ID for all go terms that fit the > query. Or, there could be a problem in the results of the query, which would > be more of a problem. > > > > The display as shown below when the GO Description is included is wrong, > I'm sorry to say. It should have different go ids for each row. > > Does this explain what I'm getting at a little better? > > Thanks for being so quick to reply! > > :) > > 2009/1/23 Syed Haider <[email protected] <mailto:[email protected]>> > > Hi Allyson, > > I guess its just because that you are looking at the snapshot of > data. If you retrieve the complete results set, that will be the > same in terms of first three columns. Please try that and let me > know if that explains... > > Cheers > Syed > > > Allyson Lister wrote: > > Hi Syed, > > I'm not sure that is the reason, because even though the GO > IDs *seem* identical, the GO Descriptions, as seen in the > image, are all different. Indeed, when I add the unique > results only flag, I get the exact same result. > > Seeing as the image didn't seem to have been passed, here is a > bad cut-and-paste of the table (irrespective of the unique > results flag): > > P32797 GO:0007049 CDC13 cell cycle > P32797 GO:0007049 CDC13 physiological process > P32797 GO:0007049 CDC13 cellular process > P32797 GO:0007049 CDC13 cellular physiological process > P32797 GO:0007049 CDC13 intracellular > P32797 GO:0007049 CDC13 cell > P32797 GO:0007049 CDC13 chromosome > P32797 GO:0007049 CDC13 intracellular > non-membrane-bound organelle > P32797 GO:0007049 CDC13 non-membrane-bound organelle > P32797 GO:0007049 CDC13 intracellular organelle* > > *Weirdly, when I remove the "GO Description" attribute, as I > said in my first email, I get a result where the GO IDs seem > to be properly displayed. > > P32797 GO:0007049 CDC13 > P32797 GO:0007582 CDC13 > P32797 GO:0009987 CDC13 > P32797 GO:0050875 CDC13 > P32797 GO:0005622 CDC13 > P32797 GO:0005623 CDC13 > P32797 GO:0005694 CDC13 > P32797 GO:0043232 CDC13 > P32797 GO:0043228 CDC13 > P32797 GO:0043229 CDC13 > > So, what do you think is going on here? > > Thanks! :) > > 2009/1/23 Syed Haider <[email protected] <mailto:[email protected]> > > <mailto:[email protected] <mailto:[email protected]>>> > > > > > Hi Allyson, > I am not sure why it dint reach mart-dev earlier on. The > history > is available here: > > > http://listserver.ebi.ac.uk/mailing-lists-archives/mart-dev/threads.html > > May be it never made it to the list because you were sending an > attachment, and its not possible to send attachments to the > list :) > > Anyways, I guess the reason you see many GO IDs when you select > Description attribute is because of redundant rows against > several > Gene IDs and associated GO IDs. The best is to try > UniqueRows flag > and see if that removes the irrrelevant rows. > > Cheers > Syed > > > > > ---------- Forwarded message ---------- > From: *Allyson Lister* <[email protected] > <mailto:[email protected]> > <mailto:[email protected] > <mailto:[email protected]>> > <mailto:[email protected] > <mailto:[email protected]> > <mailto:[email protected] > <mailto:[email protected]>>>> > Date: 2009/1/16 > Subject: interpreting GO IDs > To: "[email protected] <mailto:[email protected]> > <mailto:[email protected] <mailto:[email protected]>> > <mailto:[email protected] <mailto:[email protected]> > <mailto:[email protected] <mailto:[email protected]>>>" > <[email protected] <mailto:[email protected]> > <mailto:[email protected] <mailto:[email protected]>> > <mailto:[email protected] <mailto:[email protected]> > > <mailto:[email protected] <mailto:[email protected]>>>> > > > > Not sure if this made it to the mailing list the first > time, > so sending again. Apologies if you get it twice! > > > > > Hi all, > > I've just run this query on the biomart.org > <http://biomart.org> > <http://biomart.org> <http://biomart.org> martview > application: > > > > <?xml version="1.0" encoding="UTF-8"?> > <!DOCTYPE Query> > > <Query virtualSchemaName = "default" formatter = "TSV" > header > = "0" uniqueRows = "0" count = "" datasetConfigVersion > = "0.5" > > <Dataset name = > "uniprot" interface = "default" > > > > > <Filter name = "gene_name" value = "cdc13"/> > <Attribute name = "sptr_ac" /> > <Attribute name = "go_id" /> > <Attribute name = "gene_name" /> > > > > <Attribute name = "go_name" /> > </Dataset> > </Query> > > And I get the attached result (screenshot). I may be > extremely > dense here, but why are all of the GO IDs the same for the > first few GO descriptions? When I just choose GO ID > (and not > also GO description in the Attributes section, I get a > variety > of GO IDs. > > Anyone know what I'm doing wrong in querying or > interpreting? > > Many thanks! > > -- > Allyson Lister > http://lurena.vox.com > > CISBAN, http://www.cisban.ac.uk > Newcastle University > > > > -- > Allyson Lister > http://lurena.vox.com > > CISBAN, http://www.cisban.ac.uk > Newcastle University > > > > -- > Allyson Lister > http://lurena.vox.com > > CISBAN, http://www.cisban.ac.uk > Newcastle University > > > ------------------------------------------------------------------------ > > > > > -- > Allyson Lister > http://lurena.vox.com > > CISBAN, http://www.cisban.ac.uk > Newcastle University > > > > > -- > > Allyson Lister > http://lurena.vox.com > > CISBAN, http://www.cisban.ac.uk > Newcastle University > > > > > -- > > Allyson Lister > http://lurena.vox.com > > CISBAN, http://www.cisban.ac.uk > Newcastle University > -- Allyson Lister http://lurena.vox.com CISBAN, http://www.cisban.ac.uk Newcastle University
