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RE: Expression RDF note

From: Michael Miller <Michael.Miller@systemsbiology.org>
Date: Mon, 17 Sep 2012 08:00:39 -0700
Message-ID: <4435f3e727ac60a1d439637eb2f9516f@mail.gmail.com>
To: Suzanna Lewis <suzi@berkeleybop.org>
Cc: HCLS <public-semweb-lifesci@w3.org>, expressionrdf@googlegroups.com, ilpuccio.febo@gmail.com
hi all,

my further take on this.  others who've been working on this, please pipe
in if you have a different take or i've gotten something wrong.

gene expression (the microarray and NGS version of it) was chosen
originally because the group had expertise in it and there was a desire to
pick one (yes, one) -omics as an example of how to translate an experiment
in that -omic into RDF.  not surprisingly, with the popularity of gene
expression through out the noughties, there were actually already a few
efforts for creating the RDF so the paper that the note is based on became
focused on how three of these variants could be reconciled with each
other, choosing one of them to be canonical.

obviously it is an excellent idea to start RDFizing various different
-omics but i think we should let that be future work and wrap up this
note.  i think that the focus on producing RDF for a  single -omic that is
very familiar and ubiquitous is great and that it shows that multiple RDF
representations can be resolved with each other makes an excellent example
how future work can extend converting multiple -omics into RDF.  let's not
extend the scope of an already focused piece, let's finish up what we have
then move on to newer and brighter -omics to come.

cheers,
michael

Michael Miller
Software Engineer
Institute for Systems Biology

> -----Original Message-----
> From: Suzanna Lewis [mailto:selewis@lbl.gov] On Behalf Of Suzanna Lewis
> Sent: Saturday, September 15, 2012 2:32 PM
> To: Chisato Yamasaki
> Cc: Michel Dumontier; Michael Miller; HCLS;
> expressionrdf@googlegroups.com; ilpuccio.febo@gmail.com
> Subject: Re: Expression RDF note
>
> Perhaps the oldest use of 'gene expression' refers to in-situ imaging
> experiments of whole organisms, embryos, tissues, stages etc (pre-dates
> both chip and RNAseq experiments). In situs are still extremely common
in
> the lab. And the name 'gene expression' for these is accurately
descriptive.
>
> Will the note encompass these types of experiments as well?
>
> On Sep 10, 2012, at 11:16 PM, Chisato Yamasaki <chisato-
> yamasaki@aist.go.jp> wrote:
>
> > # I am sending the previous email again as I met some messages;
> > Hi,
> > I am working on human gene expression database, H-ANGEL.
> > e.g.)
> > http://www.h-invitational.jp/hinv/h-
> angel/wge_server.cgi?gpid=HIX0005064
> > where we have rather classical gene expression data, such as
micorarray,
> DNA
> > chips, ESTs, BodyMaps, etc.
> > We are planning to make this data into RDFs, and interested in to know
> what
> > kind of and how to share the information with the other databases, so
that
> I
> > am intereted to join this discussion.
> >
> > About the teleco, I am also a member of ISB bord which is also having
> > international teleco from UK, US and Asia,
> > and we had recent skype meeting at time below;
> > 10pm Tokyo
> > 2pm UK
> > 3pm Europe
> > 6am Bay Area, USA
> >
> > For me it is OK to have meeting at 10 - 12pm, so we may set the teleco
at
> > those times.
> > Looking forward to see you !!
> >
> > Best regards,
> > Chisato Yamasaki
> >
> > Integrated Database and Systems Biology Team
> > Biomedicinal Information Research Center (BIRC)
> > National Institute of Advanced Industrial Science and Technology
(AIST)
> >
> > Waterfront Bio-IT Research Building, 2-4-7 Aomi,
> > Koto-ku, Tokyo 135-0064, Japan.
> > Tel: +81-3-3599-8800, Fax: +81-3-3599-8801
> > E-mail: chisato-yamasaki@aist.go.jp
> > Skype: jbirc_cyamasak
> > Linkedin: http://www.linkedin.com/in/chisatoyamasaki
> > H-InvDB: http://www.h-invitational.jp
> > MEDALS: http://medals.jp/etop
> > ==========================================
> > ----- Original Message -----
> > From: "Michel Dumontier" <michel.dumontier@gmail.com>
> > To: "Michael Miller" <Michael.Miller@systemsbiology.org>
> > Cc: "HCLS" <public-semweb-lifesci@w3.org>;
> <expressionrdf@googlegroups.com>;
> > <ilpuccio.febo@gmail.com>; <chisato-yamasaki@aist.go.jp>
> > Sent: Tuesday, September 11, 2012 12:56 AM
> > 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
> >>
> >
Received on Monday, 17 September 2012 15:01:05 GMT

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