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
