[BioC] How updated is hom.Hs.inp.db? (to get homologous mapping between mouse and human symbol)?

[Marc Carlson]

Hi Peng,

Yes it's a fact of life that inparanoid has not updated their data for a 
while.  It's pretty likely however that a lot of what you care about 
will not have changed appreciably.  Especially if you are comparing gene 
to gene mappings between human and mouse.  Another resource that you can 
look at for mouse to human gene to gene mappings is homologene.  There 
is not currently an annotation package for homologene although I have 
almost made one on several occasions.

Also, I think that the ensembl biomaRts also have homology information, 
so you could also use the biomaRt package if you are not a fan of 
inparanoid.


   Marc



On 07/26/2012 03:14 PM, Peng Yu wrote:
> Hi,
>
> I'm wondering to how updated hom.Hs.inp.db is.
>
> "Title:         Homology information for Homo Sapiens from Inparanoid"
>
> According to the title of the package, the data is from Inparanoid.
> However, when I check http://inparanoid.sbc.su.se/cgi-bin/index.cgi,
> it says "Version 7.0, Updated June 2009 (release notes)". It seems to
> me that the data in Inparanoid is not very updated? In this case, if I
> want to get the reasonably updated symbol mapping between human and
> mouse, is it better to just to go ncbi, or is there a more convenient
> alternative? (BTW, I also see something in the vignette of
> annotationTools, not sure if this is the best way.)
>
> Thanks!
>
> --
> Regards,
> Peng
>
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