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try Ensembl, but I would be very interested in the new Uniprot mart - I had no way of knowing that the prototype was so out of date, as it is the one on the biomart.org martview, and therefore I assumed it was the one to use.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 out of date and so is GO data in UNIPROT PROTOTYPE.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
