That would be fantastic, thanks very much.
:)
2009/1/26 Jie Luo <[email protected] <mailto:[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]>
[mailto:[email protected]
<mailto:[email protected]>] *On Behalf Of *Allyson Lister
*Sent:* 26 January 2009 09:19
*To:* Syed Haider
*Cc:* [email protected] <mailto:[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out of date, as it is the one on the biomart.org
<http://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
<http://biomart.org> martview application?
Thanks :)
2009/1/24 Syed Haider <[email protected] <mailto:[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is quite out of date and so is GO data in UNIPROT PROTOTYPE.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>
<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]>
<mailto:[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]>>
<mailto:[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]>>>
<mailto:[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]>>>
<mailto:[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]>>>
<mailto:[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> <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
