GO Help query (from website)

[Pankaj Jaiswal]

Hi Emily,

Its great to know about the efforts going on at EBI. I will be 
interested to know more on this, so will be Will Spooner at EBI. He is 
our Ensembl and Gramene Mart developer. In the meantime we are working 
on mapping such objects for cereals as well and provide the querying 
capability via the GrameneMart (a BioMart face of Gramene). Several 
datasets are already present [http://www.gramene.org/Multi/martview].

Pankaj

Emily Dimmer wrote:
> Hi Pankaj,
> 
> The GOA group does often help with queries regarding identifier mapping 
> - there are a number of methods, some of which we supply via our close 
> links with UniProt, some of which are provided by other tools with which 
> we are familiar (e.g. BioMart, SRS, IPI ). The proteomics group at the 
> EBI is working towards having one application that can provide mappings 
> for a range of sequence identifiers. I think that both the QuickGO and 
> AmiGO browsers are interested in using this application, or something 
> similar, to improve the ability of users to search for GO annotations.
> 
> cheers,
> Emily
> 
> Pankaj Jaiswal wrote:
> 
>> Hi Eurie,
>>
>> Thanks for the help. I have replied the the person off the GO list 
>> with some more tips on querying the same at Gramene database.
>>
>> BTW one aspect that I find from this query is that, more and more 
>> people want to know GO annotations using their source sequences from 
>> ESTs, GSS, cDNAs, UniGenes etc. Using the BLAST is a very effective 
>> way of doing this, but certainly not a good practice to ask everyone 
>> to perform BLAST. The solution, I see lies in mapping the  ESTs, GSS, 
>> cDNAs, UniGenes to the object we have in our Association files. This 
>> will give them a straight forward answer. I also agree that it is 
>> beyond the scope of GO, but is there a way the source dbs can provide 
>> the data (I am sure many of the have this kind of mapping), that can 
>> be used by GO to facilitate this query.
>>
>> Pankaj
>>
>> Eurie Hong wrote:
>>
>>> Hello,
>>>
>>> It appears that the cDNA clone with the GenBank accession AK110615 is 
>>> currently not annotated.   You can BLAST the sequence of AK110615 
>>> against the sequences available in AmiGO to identify if the gene that 
>>> encodes this cDNA has been annotated:
>>>
>>> http://amigo.geneontology.org/cgi-bin/gost/gost.cgi
>>>
>>> A BLASTX using the cDNA sequence hits the Oryza sativa (japonica 
>>> cultivar-group) gene Os11g0255500:
>>>
>>> http://amigo.geneontology.org/cgi-bin/amigo/go.cgi?search_constraint=gp&view=details&session_id=3361b1172551729&gp=Q53LC7 
>>>
>>>
>>> I am cc'ing the staff at Gramene (http://www.gramene.org/) who 
>>> provide GO annotations for Oryza sativa (japonica cultivar-group) so 
>>> that they can answer any further questions you might have.
>>>
>>> Cheers,
>>> Eurie
>>>
>>> *******************************************
>>> Eurie L. Hong, Ph.D.
>>> Scientific Curator
>>> Saccharomyces Genome Database: http://www.yeastgenome.org/
>>> Gene Ontology: http://www.geneontology.org/
>>> *******************************************
>>>
>>>
>>> On Feb 25, 2007, at 5:33 AM, noreply at genome.stanford.edu wrote:
>>>
>>>> contactName: psrao
>>>> contactEmail: psrao at ccmb.res.in
>>>> contactText: Please ley me know how can I get GO terms(Go:7275) from 
>>>> NCBI Gene Accession numbers(AK110615)
>>>>
>>>
>>>
>>
> 
> 

-- 
Pankaj Jaiswal
G-15, Bradfield Hall
Dept. of Plant Breeding and Genetics
Cornell University
Ithaca, NY-14853, USA

Ph. +1-607-255-3103 / 4199
fax: +1-607-255-6683