[Go] Announcement:Change in dictybase gene association file

[Daniel Barrell]

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
> 
> 
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-- 

Daniel Barrell
EMBL - The EBI
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD
Phone: +44 (0)1223 492551
Email: dbarrell at ebi.ac.uk