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

[Aditya Bhagwat]

Hey guys,

Thanks for your responses!
Exactly the kind of feedback I wanted, to ensure that what is being intended makes sense.

Resource to be used is UniprotKB.  Preview the first 10 entries:
http://www.uniprot.org/uniprot/?sort=&desc=&compress=no&query=&fil=organism:%22Homo%20sapiens%20(Human)%20[9606]%22&limit=10&force=no&preview=true&format=txt<http://www.uniprot.org/uniprot/?sort=&desc=&compress=no&query=&fil=organism:%22Homo%20sapiens%20(Human)%20%5b9606%5d%22&limit=10&force=no&preview=true&format=txt>

How it will look like? Similar to org.Hs.eg.db, using the AnnotationDbi::select interface etc.

Why not org.Hs.eg.db?

·         Many uniprot accessions are simply not present in org.Hs.eg.db. Take non-canonical isoforms. They are badly represented in org.Hs.eg.db, but are essential in LCMS proteomics.

·         org.Hs.eg.db does not offer an easy way to map uniprot accessions to uniprot summary. I would include that in the org.Hs.uniprot.db package

·         In LCMS proteomics, protein identification is performed by comparing the observed MS spectra to those you would expect from an organism-specific protein sequence database. Using the same protein sequence database for annotation as is being used for identification would provide a one-to-one mapping between analysis and annotation..

Why not biomaRt

·         A reasonably deep LCMS proteomics experiment quantifies 7000 proteins. Retrieving annotation for these through biomaRt would be slow (an overnight activity). I want something that works instantaneously.

·         From what I remember you can actually not access the uniprot summary (which gives a paragraph on current known knowledge for a protein) field from within biomaRt.

What do you guys think?
Thanks for your feedback!

Cheers,

Aditya


From: Karim Mezhoud [mailto:kmezhoud at gmail.com]
Sent: Wednesday, September 13, 2017 1:35 PM
To: Vincent Carey
Cc: Aditya Bhagwat; bioc-devel at r-project.org
Subject: Re: [Bioc-devel] Creating an org.Hs.uniprot.db package

Hi,
I general LCMSMS generate mass/charge data of Amino Acid or peptides.
The goal in to identify which  protein belong the peptides.
The Software used with LCMSMS can match the peptides to Uniprot database , and ranks putative proteins by scores.
Could the tell us what is the interest of org.Hs.uniprot.db versus default UniprotKB?
Thanks,
Karim


On Wed, Sep 13, 2017 at 11:19 AM, Vincent Carey <stvjc at channing.harvard.edu<mailto:stvjc at channing.harvard.edu>> wrote:
can you say a little more about what resource will be tapped and what it
will look like?  you can
already use uniprot identifiers as keys into org.Hs.eg.db

On Tue, Sep 12, 2017 at 9:05 AM, Aditya Bhagwat <
adb2018 at qatar-med.cornell.edu<mailto:adb2018 at qatar-med.cornell.edu>> 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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