[Bioperl-l] Extracting Gene Names Genome Ontology (GO) with Perl

Wijaya Edward ewijaya at i2r.a-star.edu.sg
Sun Apr 22 07:59:28 EDT 2007


Hi Chris,
 
I've downloaded GO Database.
Which of these we should install in our MySQL database,
so that it can be used for GO::AppHandle task below?
 
-rw-rw-r--   1 ewijaya ewijaya 1.6G Apr  9 12:23 go_200704-assocdb-data
-rw-rw-r--   1 ewijaya ewijaya 483M Apr  9 12:23 go_200704-assocdb.rdf-xml
-rw-rw-r--   1 ewijaya ewijaya 3.2K Apr  9 12:23 go_200704-assocdb-summary.txt
drwxrwxr-x   2 ewijaya ewijaya 4.0K Apr  7 00:41 go_200704-assocdb-tables
-rw-rw-r--   1 ewijaya ewijaya 3.3K Apr  9 12:23 go_200704-obo-xml.dtd
-rw-rw-r--   1 ewijaya ewijaya 4.5K Apr  9 12:23 go_200704-rdf.dtd
-rw-rw-r--   1 ewijaya ewijaya  29K Apr  9 12:23 go_200704-schema-mysql.sql
-rw-rw-r--   1 ewijaya ewijaya 3.1G Apr  9 12:25 go_200704-seqdb-data
-rw-rw-r--   1 ewijaya ewijaya  93M Apr  9 12:26 go_200704-seqdb.fasta
-rw-rw-r--   1 ewijaya ewijaya 3.2K Apr  9 12:25 go_200704-seqdb-summary.txt
drwxrwxr-x   2 ewijaya ewijaya 4.0K Apr  8 05:38 go_200704-seqdb-tables
-rw-rw-r--   1 ewijaya ewijaya  51M Apr  9 12:26 go_200704-termdb-data
-rw-rw-r--   1 ewijaya ewijaya  18M Apr  9 12:26 go_200704-termdb.obo-xml
-rw-rw-r--   1 ewijaya ewijaya  39M Apr  9 12:26 go_200704-termdb.owl
-rw-rw-r--   1 ewijaya ewijaya  29M Apr  9 12:26 go_200704-termdb.rdf-xml
-rw-rw-r--   1 ewijaya ewijaya  749 Apr  9 12:26 go_200704-termdb-summary.txt
drwxrwxr-x   2 ewijaya ewijaya 4.0K Apr  2 00:31 go_200704-termdb-tables
drwxrwxr-x  22 ewijaya ewijaya 4.0K Apr  1 23:35 go_200704-utilities-src

Or is there a way we can upload all of them automatically to mysql database?
Thanks and hope to hear from you again.
 
--
Edward
 

________________________________

From: Chris Mungall [mailto:cjm at fruitfly.org]
Sent: Tue 4/17/2007 2:49 AM
To: Wijaya Edward
Cc: spiros at lokku.com; bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] Extracting Gene Names Genome Ontology (GO) with Perl




Download:
http://search.cpan.org/~cmungall/go-db-perl

or do:

cpan GO::AppHandle

The API call you want is here:
http://search.cpan.org/~cmungall/go-db-perl/GO/
AppHandle.pm#get_deep_products

Here is an example snippet:

   use GO::AppHandle;
   my $apph=GO::AppHandle->connect(@ARGV);
   my $go_acc = shift @ARGV;
   my $gps = $apph->get_deep_products({term=>{acc=>$go_acc}});
   foreach my $gp (@$gps) {
     printf "%s %s\n", $gp->xref->acc, $gp->symbol;
   }

You will need to download the GO Database.

Cheers
Chris

On Apr 16, 2007, at 8:14 AM, Wijaya Edward wrote:

>
> Hi Spiros,
>
> Thanks for your reply. I am interested to apply it for
> all the kind of organisms related to that particular GO ID.
>
> Do you have a CPAN module for that?
> --
> Edward WIJAYA
> SINGAPORE
>
> ________________________________
>
> From: s.denaxas at gmail.com on behalf of Spiros Denaxas
> Sent: Mon 4/16/2007 11:10 PM
> To: Wijaya Edward
> Cc: bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] Extracting Gene Names Genome Ontology (GO) 
> with Perl
>
>
>
> Hi Edward,
>
> What organism are you interested in? I have some code from my PhD
> based on the Saccharomyces cerevisiae genome. Basically uses the SGD
> flat files and a local MySQL instance of GO. Might be worth turning
> into modules if people are interested in it, although it is pretty
> organism oriented and the lack of abstraction might introduce a number
> of problems.
>
> Spiros
>
> On 4/16/07, Wijaya Edward <ewijaya at i2r.a-star.edu.sg> wrote:
>>
>> Dear all,
>>
>> Given a GO id, is there a way to extract all
>> the related gene names from that id with Perl?
>>
>> Anybody has experience with that?
>> I've looked through GO module in CPAN, but can't seem
>> to find any tool that facilitated that searc
>>
>> Look forward very much for your advice.
>>
>> --
>> Edward WIJAYA
>> SINGAPORE
>>
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