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.rai...@eurac.edu] Sent: Wednesday, September 13, 2017 8:49 AM To: Aditya Bhagwat; bioc-devel@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 > > > > Disclaimer: This email and its attachments may be confidential and are > intended solely for the use of the individual to whom it is addressed. If you > are not the intended recipient, any reading, printing, storage, disclosure, > copying or any other action taken in respect of this e-mail is prohibited and > may be unlawful. If you are not the intended recipient, please notify the > sender immediately by using the reply function and then permanently delete > what you have received.. > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > Disclaimer: This email and its attachments may be confidential and are intended solely for the use of the individual to whom it is addressed. If you are not the intended recipient, any reading, printing, storage, disclosure, copying or any other action taken in respect of this e-mail is prohibited and may be unlawful. If you are not the intended recipient, please notify the sender immediately by using the reply function and then permanently delete what you have received.. _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
