[Bioc-devel] Creating an org.Hs.uniprot.db package

[Aditya Bhagwat]

Hi Johannes,

Thanks for your feedback!

I tried ensembl based maps earlier, but I loose many features.

In LCMS proteomics the unit of identification and quantification is a uniprot accession, so annotation mappings would benefit from a uniprot-centric database object.

Cheers,

Aditya



________________________________________
From: Rainer Johannes [Johannes.Rainer at eurac.edu]
Sent: Wednesday, September 13, 2017 8:49 AM
To: Aditya Bhagwat; bioc-devel at r-project.org
Subject: Re: [Bioc-devel] Creating an org.Hs.uniprot.db package

Hi Aditya,

you could check the more recent ensembldb EnsDb databases to see if
there is something in them you might need/want.
I've added protein annotations to them (as provided by Ensembl). They
contain the Ensembl protein domains, the AA sequence, all protein domain
families (as defined/linked in Ensembl) and the mapping from Ensembl
protein IDs to Uniprot (which is unfortunately not always 1:1) - and you
get the mapping to the encoding transcripts for free ;)

To play around with it I suggest you get one of the EnsDb databases from
AnnotationHub:

library(AnnotationHub)
query(AnnotationHub(), "EnsDb.Hsapiens")

and fetch one of those. Have also a look at the ensembldb vignette(s)
for starters.

cheers, jo

On 09/13/2017 07:02 AM, Aditya Bhagwat wrote:
> Hey guys,
>
> I love the org.Hs.eg.db package (and similar others for other organisms).
>
> I work a lot with LCMSMS proteomics data, and I have always missed a similar org.Hs.uniprot.db package, so I am thinking of creating that (and then sharing it on BioC, to benefit fellow proteomics R users).
>
> Would you agree that this is of general interest? (Or does this in some form already exist and have I overlooked it?)
>
> Thanks for your feedback!
>
> Cheers,
>
> Aditya
>
>
>
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