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.
library(AnnotationHub)
ah = AnnotationHub()
hs8 = ah$inparanoid8.Orthologs.hom.Homo_sapiens.inp8.sqlite
hs8
columns(hs8)
k = head(keys(hs8, 'TOXOPLASMA_GONDII'))
select(hs8, k, 'HOMO_SAPIENS', '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 it?
Thanks in advance for your opinions,
Marc
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