[Go] [Fwd: Re: Announcement:Change in dictybase gene association file]

[Siddhartha Basu]

Hi,
The gp2protein file and corresponding script are  updated to reflect the
chagnes. The new version of gp2protein file is also commited in the cvs. 

thanks,
-siddhartha

> 
>    -------- Original Message --------
> 
>       Subject: Re: [Go] Announcement:Change in dictybase gene association     
>                file                                                           
>          Date: Wed, 10 Dec 2008 08:42:43 -0800                                
>          From: Suzanna Lewis <suzi at berkeleybop.org>                           
>            To: dbarrell at ebi.ac.uk                                             
>            CC: go at genome.stanford.edu                                         
>    References: <492dd261.86c3f10a.1854.7cdd at mx.google.com>                    
>                <493FB36A.2050900 at ebi.ac.uk>                                   
> 
>  I hope so, it will be impossible otherwise for the downstream software 
>  to work.
> 
>  On Dec 10, 2008, at 4:17 AM, Daniel Barrell wrote:
> 
>  > Hi Siddhartha,
>  >
>  > Will you also update your gp2protein file to match these changes?
>  >
>  > Cheers
>  >
>  > Dan
>  >
>  > Siddhartha Basu wrote:
>  >> Hello everybody,
>  >> Some dictyBase users have commented on the difficulties that 
>  >> result  because the primary
>  >> identifier for genes occasionally changes. This occurs whenever, 
>  >> for  example, the gene
>  >> model changes or when a computationally predicted gene gets 
>  >> upgraded  to a manually
>  >> curated gene. To provide an identifier that will more reliably 
>  >> point to a  gene, while
>  >> maintaining the principle that changes in gene models or curation 
>  >> status will be
>  >> reflected by updated IDs for those sequences, dictyBase is 
>  >> introducing a new Gene
>  >> Identifier. This Gene ID has the format DDB_G####### (for example, 
>  >> DDB_G1234567) and is
>  >> stable  regardless of curation status of the gene. The identifier 
>  >> is tied to each of its
>  >> associated  features in the genome (transcripts, ESTs, proteins, 
>  >> their annotations and
>  >> sequences) and therefore serves as a major entry point for 
>  >> searching, retrieving and
>  >> displaying  every piece of information from dictyBase. This ID is 
>  >> also tied to the
>  >> chromosomal segment that  contains the gene of interest, rather 
>  >> than the sequence itself.
>  >> For more information  please look at the Sept.  11th release 
>  >> announcement on our front
>  >> page (http:// www.dictybase.org).
>  >> To  be consistent with the use of this new gene identifier, we are  
>  >> incorporating the
>  >> dictyBase Gene ID in our gene association (GA) file. As a result,  
>  >> the Gene ID will
>  >> permenantly replace the existing DDB ID in column two of our GA  
>  >> file. The remainder of
>  >> the file, its format and the url at which this id will get  
>  >> resolved will be unaffected.
>  >> If you have any feedback, questions, concerns, or need  help with 
>  >> software migrations
>  >> please feel free to contact us.
>  >> The new version of this gene association file (GA) will be 
>  >> available  starting next
>  >> Thursday,  Dec 4th, from the download section of our web site, and  
>  >> the week after at the
>  >> main gene ontology web site (http://geneontology.org/GO.current.annotations.shtml
>  >> ).
>  >> Thanks,
>  >> -siddhartha
>  >> Siddhartha Basu
>  >> Software developer, dictybase
>  >> www.dictybase.org
>  >> _______________________________________________
>  >> Go mailing list
>  >> Go at geneontology.org
>  >> http://fafner.stanford.edu/mailman/listinfo/go
>  >
>  > --
>  >
>  > Daniel Barrell
>  > EMBL - The EBI
>  > Wellcome Trust Genome Campus
>  > Hinxton, Cambridge CB10 1SD
>  > Phone: +44 (0)1223 492551
>  > Email: dbarrell at ebi.ac.uk
>  > _______________________________________________
>  > Go mailing list
>  > Go at geneontology.org
>  > http://fafner.stanford.edu/mailman/listinfo/go
>  >
> 
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