[Bioperl-l] getting proteins matching GO

[Stefan A Kirov]

Sean,
Please correct me if I am wrong, but GOA is still very limited project,
just the human data is in it (at least this was the case the last time I
saw it last month). And except or the manual annotation there is little
you can do with GOA that you can't through EnsMART. Maybe I am missing
something...
Stefan

On Fri, 5 Nov 2004, Davis, Sean (NIH/NHGRI) wrote:

>
>If I'm not mistaken, the GO database contains mappings from GOA
>(http://www.ebi.ac.uk/GOA/).
>
>Sean
>
>-----Original Message-----
>From: Stefan Kirov
>To: Pedro Antonio Reche
>Cc: Bioperl
>Sent: 11/5/2004 8:29 PM
>Subject: Re: [Bioperl-l] getting proteins matching GO
>
>Pedro,
>You may want to check Bio::Ontology and especially Bio::OntologyIO.
>These are pretty cool modules, but you will have to install bioperl-live
>
>or wait for bioperl 1.5 (which as I understand should be released soon).
>
>You will have to download the GO DB locally and parse it with
>Bio::OntologyIO, I am not sure if somebody is working on remote access
>(not familiar if it is possible at the moment). By the way if you are
>not familiar with mysql and you are OK with perl, Bio::OntologyIO might
>be easiest for you. It will also include anything you are able to get
>from GO website. But you will have to keep local database (or flat
>file). Hope this helps.
>Stefan
>
>
>Pedro Antonio Reche wrote:
>
>> Dear Stefan, thanks a lot  for your e-mail. Actually, I am interested
>> in getting all proteins from all organisms that are tagged with let
>> say the go_process cell signaling. I will try the sites that you
>> indicate to see if they can do the job. Do you know if Bioperl can
>> also do this?
>> Regards,
>>
>> pdro
>> On Nov 5, 2004, at 12:27 PM, Stefan Kirov wrote:
>>
>>> What organism? You can use either EnsMart (for example for human
>>> there is a table called hsapiens_gene_ensembl__xref_go__dm) or you
>>> can use GeneKeyDB if you install it locally (genereg.ornl.gov/gkdb),
>>> there is a table called ll_go, which you can search for the gene
>>> identifier(locuslink), associated with a particular GO term and then
>>> get the protein accession from another table  (something like :
>>> "select r.np_accn from ll_go g, ll_refseq_nm r where r.ll_id=g.ll_id
>>> and g.go_term=?") and fetch the seq from RefSeq, etc. Both Ensembl
>>> and GeneKeyDB are restricted to certain eukaryotes. So it all depends
>
>>> on what kind of organisms you are expected to work with.
>>> Stefan
>>>
>>> Pedro Antonio Reche wrote:
>>>
>>>> Hi,
>>>> I am interested in getting all the protein sequences  matching a
>>>> specific GO term and I wonder if someone would know how to do this.
>>>> Thanks in advance for any help.
>>>> Cheers
>>>>
>>>> pdro
>>>>
>>>> _______________________________________________
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>>>
>>>
>>>
>>> --
>>> Stefan Kirov, Ph.D.
>>> University of Tennessee/Oak Ridge National Laboratory
>>> 5700 bldg, PO BOX 2008 MS6164
>>> Oak Ridge TN 37831-6164
>>> USA
>>> tel +865 576 5120
>>> fax +865-576-5332
>>> e-mail: skirov at utk.edu
>>> sao at ornl.gov
>>>
>>> "And the wars go on with brainwashed pride
>>> For the love of God and our human rights
>>> And all these things are swept aside"
>>>
>>
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>
>
>--
>Stefan Kirov, Ph.D.
>University of Tennessee/Oak Ridge National Laboratory
>5700 bldg, PO BOX 2008 MS6164
>Oak Ridge TN 37831-6164
>USA
>tel +865 576 5120
>fax +865-576-5332
>e-mail: skirov at utk.edu
>sao at ornl.gov
>
>"And the wars go on with brainwashed pride
>For the love of God and our human rights
>And all these things are swept aside"
>
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