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

Tue, Sep 12, 2017 11:00 PM

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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Thread (7 messages)

Aditya Bhagwat Creating an org.Hs.uniprot.db package Sep 12 Rainer Johannes Creating an org.Hs.uniprot.db package Sep 12 Aditya Bhagwat Creating an org.Hs.uniprot.db package Sep 12 Vincent Carey Creating an org.Hs.uniprot.db package Sep 13 Karim Mezhoud Creating an org.Hs.uniprot.db package Sep 13 Aditya Bhagwat Creating an org.Hs.uniprot.db package Sep 13 Karim Mezhoud Creating an org.Hs.uniprot.db package Sep 13