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RE: Expression RDF note

From: Lin MD, Simon <LINMD.SIMON@mcrf.mfldclin.edu>
Date: Mon, 10 Sep 2012 16:37:49 +0000
To: "ilpuccio.febo@gmail.com" <ilpuccio.febo@gmail.com>, Helena Deus <helenadeus@gmail.com>
CC: Michel Dumontier <michel.dumontier@gmail.com>, "expressionrdf@googlegroups.com" <expressionrdf@googlegroups.com>, "Michael Miller" <Michael.Miller@systemsbiology.org>, HCLS <public-semweb-lifesci@w3.org>, "chisato-yamasaki@aist.go.jp" <chisato-yamasaki@aist.go.jp>
Message-ID: <A5BD550FC766564987DA2A59779890303DFEA3FD@MCL-EXMB02.mfldclin.org>
In light of NGS, shall we call it "genome profiling" to expand the work from 'gene expression'? "genome profiling" can also include the work of SNP identification etc. -Simon

From: Ra [mailto:ilpuccio.febo@gmail.com]
Sent: Monday, September 10, 2012 11:35 AM
To: Helena Deus
Cc: Michel Dumontier; expressionrdf@googlegroups.com; Michael Miller; HCLS; chisato-yamasaki@aist.go.jp; Lin MD, Simon
Subject: Re: Expression RDF note


I can provide support for ngs. Currently I'm working on RnaSeq  and our lab start from raw samples so I have the chance, I'm sure you too,  to have an overview of the compete production of the data. To better understand my topics the page of the lab http://www.ingm.org/research/researchprojects/ib if you have any question please feel free to drop an email.
I also worked on bacteria assembly SNP and ancient DNA. Chip seq is in plan.
Il giorno 10/set/2012 18:24, "Helena Deus" <helenadeus@gmail.com<mailto:helenadeus@gmail.com>> ha scritto:
All,

we discussed, at some point, that NGS data should be supported by the note.

should we call it transcriptomic representation note instead? both the term "gene expression" and the note itself are still associated with microarrays, a completelly different strategy from NGS. but both are related to transcriptomics.

Best
Lena


Helena F. Deus, PhD
Unit Leader, Bioinformatics and Computational Biology
Digital Enterprise Research Institute
helena.deus@deri.org<mailto:helena.deus@deri.org>
+353 91 495 270<tel:%2B353%2091%20495%20270>

On Sep 10, 2012, at 5:13 PM, Lin MD, Simon wrote:


The W3C gene expression note is also of interest to me. I would be happy to contribute a use case of Gene Screening from Next Generation Sequencing. What is the time line of this project? I might not be able to work on it much till the end of Sept. With regard to meetings, I am open and flexible. Thanks! -Simon

==================================================
Simon Lin, MD | Director, Biomedical Informatics Research Center | Marshfield Clinic Research Foundation | 1000 N Oak Ave, Marshfield, WI 54449 | 715-221-7299 | Lin.Simon@mcrf.mfldclin.edu<mailto:Lin.Simon@mcrf.mfldclin.edu> |www.marshfieldclinic.org/birc<http://www.marshfieldclinic.org/birc>

For scheduling assistance, please contact Crystal Gumz, Administrative Secretary | 715-221-6403 |gumz.crystal@mcrf.mfldclin.edu<mailto:gumz.crystal@mcrf.mfldclin.edu>



From: Michel Dumontier [mailto:michel.dumontier@gmail.com<mailto:michel.dumontier@gmail.com>]
Sent: Monday, September 10, 2012 10:56 AM
To: Michael Miller
Cc: HCLS; expressionrdf@googlegroups.com<mailto:expressionrdf@googlegroups.com>; ilpuccio.febo@gmail.com<mailto:ilpuccio.febo@gmail.com>; chisato-yamasaki@aist.go.jp<mailto:chisato-yamasaki@aist.go.jp>
Subject: Expression RDF note

Hi,
 While I was at a very productive BioHackathon, Raoul and Chisato (cc'd) expressed interest in the W3C gene expression note.

https://docs.google.com/document/d/1A5-3tOsifPWPpETBKU-ZA9d7O7wK_nBzTFUBEe-0Bzo/edit?authkey=CK-y8Y8C&authkey=CK-y8Y8C

I'm now teaching every Monday between 10am and 11:30am EDT, so I would prefer that the time be changed for me to participate. However, with participants in North America, Europe and Japan, our scheduling may become significantly more challenging.  Suggestions?

m.

--
Michel Dumontier
Associate Professor of Bioinformatics, Carleton University
Chair, W3C Semantic Web for Health Care and the Life Sciences Interest Group
http://dumontierlab.com

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Received on Monday, 10 September 2012 16:38:29 GMT

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