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RE: Expression RDF note

From: Michael Miller <Michael.Miller@systemsbiology.org>
Date: Mon, 10 Sep 2012 11:20:18 -0700
Message-ID: <fef40dec7195727116b876369d44a73b@mail.gmail.com>
To: Helena Deus <helenadeus@gmail.com>, Michel Dumontier <michel.dumontier@gmail.com>
Cc: "Lin MD, Simon" <LINMD.SIMON@mcrf.mfldclin.edu>, ilpuccio.febo@gmail.com, expressionrdf@googlegroups.com, HCLS <public-semweb-lifesci@w3.org>, chisato-yamasaki@aist.go.jp
hi all,



'“genome profiling” can also include the work of SNP identification etc.'



i think looking at SNP identification is not a bad idea but even tho the
same technology is used, in the end, the analysis is very different for
both microarray and NGS snp identification than gene expression.  just
because the initial processing is similar, from a systems biology
perspective, i don't really see a difference between 'genome profiling' and
any -omics technology, where as using either microarrays or NGS to do gene
expression studies is a distinct -omics as is SNP identification.



'both the term "gene expression" and the note itself are still associated
with microarrays'



this is not the case that i've seen, particularly in the context of a gene
expression study.  in TCGA, microarray based studies are slowly but surely
being replaced by NGS gene expression studies and there has been no
confusion.



so for the note i think it will be much clearer to stay with gene
expression and, as part of the systems biology working group, begin to move
into these other -omics and how they can be used together to form a model.



my 2˘,

michael



Michael Miller

Software Engineer

Institute for Systems Biology



*From:* Helena Deus [mailto:helenadeus@gmail.com]
*Sent:* Monday, September 10, 2012 10:01 AM
*To:* Michel Dumontier
*Cc:* Lin MD, Simon; ilpuccio.febo@gmail.com; expressionrdf@googlegroups.com;
Michael Miller; HCLS; chisato-yamasaki@aist.go.jp
*Subject:* Re: Expression RDF note



thumbs up for "genome profiling" :)



Helena F. Deus, PhD

Unit Leader, Bioinformatics and Computational Biology

Digital Enterprise Research Institute

helena.deus@deri.org

+353 91 495 270



On Sep 10, 2012, at 5:48 PM, Michel Dumontier wrote:



Lin et al, expanding the scope to genomic profiling is an excellent and
most welcome idea :)



Scott - ok, then let's plan asia-europe and europe-americas calls.



m.

On Tue, Sep 11, 2012 at 1:37 AM, Lin MD, Simon <
LINMD.SIMON@mcrf.mfldclin.edu> wrote:

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/ibif 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> 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

+353 91 495 270



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 |
www.marshfieldclinic.org/birc



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







*From:* Michel Dumontier [mailto:michel.dumontier@gmail.com]
*Sent:* Monday, September 10, 2012 10:56 AM
*To:* Michael Miller
*Cc:* HCLS; expressionrdf@googlegroups.com; ilpuccio.febo@gmail.com;
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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-- 

Michel Dumontier

Associate Professor of Bioinformatics, Carleton University

Chair, W3C Semantic Web for Health Care and the Life Sciences Interest Group

http://dumontierlab.com
Received on Monday, 10 September 2012 18:26:44 GMT

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