[Bioperl-l] Entrez Gene and bioperl-db

Sean Davis sdavis2 at mail.nih.gov
Tue Dec 14 11:41:04 EST 2004


I have heard rumors that the gene ontology and cdd stuff are going to  
be in the refseq entries rather than a "gene2go" file, but I haven't  
seen direct confirmation of this.  If you look in the CDS section of  
some of the refseq entries  
db=nucleotide&val=56550106 as an example), you will see the gene  
ontology information there.  I honestly don't know how this is handled  
by bioperl-db....  Also, I wish I could say I KNEW what NCBI was doing  
here so that we could all plan, but I don't.


On Dec 14, 2004, at 10:39 AM, Law, Annie wrote:

> Hey Sean,
> As always good to hear from you.  Which particular file are you  
> referring to
> in the
> Ftp folders? Basically, there is the gene2unigene file but no  
> equivalent of
> loc2go.
> I wrote to NCBI and they said there will be more files to come but no
> mention specifically about an equivalent of
> Loc2go.
> Have a wonderful Christmas and a happy new year,
> Annie.
> -----Original Message-----
> From: Sean Davis [mailto:sdavis2 at mail.nih.gov]
> Sent: Tuesday, December 14, 2004 5:55 AM
> To: Law, Annie
> Cc: 'bioperl-l at portal.open-bio.org'
> Subject: Re: [Bioperl-l] Entrez Gene and bioperl-db
> The information from Entrez Gene is in the form of tab-delimited text
> files, so parsing and loading should be pretty straightforward?  Of
> course, there is no sequence information loaded.  In fact, given what
> is available in Gene right now, is it sufficient to load RefSeq?  The
> Gene Reference Into Function is not included with refseq, nor is the
> omim (for human) mapping, but the gene ontology, function, and summary
> function, as well as mapping to Gene ID are included, so will that do
> it?
> Sean
> On Dec 13, 2004, at 11:03 AM, Law, Annie wrote:
>> Hi,
>> I was wondering with regards to bioperl-db the scripts and schema and
>> load_seqdatabase.pl has there been preparation for integration of
>> Entrez gene information when locuslink is phased out?  Or if it has
>> already been
>> changed could somebody point
>> me to the documentation or changed code?
>> Thanks,
>> Annie.
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at portal.open-bio.org
>> http://portal.open-bio.org/mailman/listinfo/bioperl-l

More information about the Bioperl-l mailing list