[Bioc-devel] Question about which new organism resources to create

Luo Weijun luo_weijun at yahoo.com
Tue May 6 21:01:37 CEST 2014

This sounds like a great resource, and could help make Bioconductor more useful!
As for what species to include, I would suggest to check the full list of KEGG species:
these are all complete genomes, hence should be generally more relevant species compare to those without complete genomes. Hopefully, many of them are well annotated. At least, the pathway annotations are easily available.
Just my 2 cents,

On Tue, 5/6/14, Marc Carlson <mcarlson at fhcrc.org> wrote:

 Subject: [Bioc-devel] Question about which new organism resources to create
 To: "bioc-devel at r-project.org" <bioc-devel at r-project.org>
 Date: Tuesday, May 6, 2014, 1:14 PM

 Hi everyone,

 As many of you already know we have long provided organism
 annnotation packages that give gene based annotations for
 selected organisms.  And we intend to keep doing
 that.  But these days there is also a lot of other data
 at NCBI that could be used to make gene based databases for
 other organisms.  And at the same time, there is also
 greater and greater demand for annotations from other
 organisms too.  So I aim to make organism based gene
 databases for a wider range of organisms.  However
 instead of just making more packages, I intend to put these
 DBs into the AnnotationHub.  You can get an idea about
 what access will be like by looking at the inparanoid8
 objects that were put in for the last release.

 ah = AnnotationHub()
 hs8 = ah$inparanoid8.Orthologs.hom.Homo_sapiens.inp8.sqlite
 k = head(keys(hs8, 'TOXOPLASMA_GONDII'))
 ## etc.

 Anyhow my reason for posting is that I am now looking at all
 the NCBI data that could be used for annotation packages and
 trying to decide what to include.  About half of the 14
 thousand potential critters in the NCBI dataset only have
 about one gene annotated.  I am guessing that it is not
 worth anyone's time to pre-process those organisms that have
 only one gene.  Or is it?  If you think it might
 be, now would probably be a good time to speak up.

 How many annotations do you guys want/expect in an organism
 package before it becomes annoying that you even downloaded

 Thanks in advance for your opinions,


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