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). 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]> > 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]>> >> >> 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]>>> >> Date: 2009/1/16 >> Subject: interpreting GO IDs >> To: "[email protected] <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>>" >> <[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> 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
