[Go] Announcement:Change in dictybase gene association file

[Suzanna Lewis]

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
> _______________________________________________
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>