[Go] Announcement:Change in dictybase gene association file

[Siddhartha Basu]

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