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Re: Reminder: Scientific Discourse Concall May 3, 10am EDT

From: David R Newman <drn05r@ecs.soton.ac.uk>
Date: Tue, 04 May 2010 18:08:49 +0100
To: Tim Clark <tim_clark@harvard.edu>
Cc: Susanna-Assunta Sansone <sansone@ebi.ac.uk>, Michael Miller <mmiller@teranode.com>, HCLS IG <public-semweb-lifesci@w3.org>, "Anita de A (ELS-AMS) Waard" <A.dewaard@elsevier.com>, Annamaria Carusi <annamaria.carusi@oerc.ox.ac.uk>, David Shotton <david.shotton@zoo.ox.ac.uk>, Carole Goble <carole.goble@manchester.ac.uk>, Matthew Gamble <matthew.gamble@gmail.com>, Satya Sahoo <satya_sanket@hotmail.com>, Jun Zhao <jun.zhao@zoo.ox.ac.uk>, David DeRoure <dder@ecs.soton.ac.uk>, Michel Dumontier <michel.dumontier@gmail.com>, Ted Liefeld <liefeld@broadinstitute.org>, Alexander Pico <apico@gladstone.ucsf.edu>
Message-ID: <EMEW3|cc3619f162a9133fa4306c9260aca591m43I8s06drn05r|ecs.soton.ac.uk|1272992929.28925.97.camel@clearway.ecs.soton.ac.uk>
Hi All,

During yesterday's concall I was asked to flesh out some detail
surrounding the myExperiment classes defined in
http://esw.w3.org/File:SWAN-myExp-v4.jpg that are to be aligned with the
SWAN Ontology.  

I mentioned how one of the modules of the myExperiment Ontology
(http://rdf.myexperiment.org/ontologies/components/) allows the inner
workings of a workflow to be defined,  including which processors (e.g.
web services) it uses and how these are arranged.
http://rdf.myexperiment.org/img/components.png is a basic diagram
summarizing how these inner workings are organised.  The metadata to
describe these processors is fairly basic, limited to what can be
extracted from the workflow specification itself.

It is the goal of myExperiment to integrate with a similar project
called BioCatalogue (http://www.biocatalogue.org/).  This project
provides a web-based system to allow users to submit, annotate, monitor,
curate and discover web services, particularly those in the life
sciences domain.  At present this project is in the process producing an
ontology so that it can provide RDF for representing both the services
and metadata gathered from the community about these services.  This
will contain a lot more information about the actually biological
entities involved with a web service. I had a brief chat with one of the
people working on this and he said that he was hoping to use the myGrid
(http://www.mygrid.org.uk/tools/service-management/mygrid-ontology/) and
EDAM (http://edamontology.sourceforge.net/) ontologies as a basis for
defining the service and biological aspects of the ontology.

The intention is to use a Linked Data approach to facilitate this
integration, so that a web service described as part of a workflow on
myExperiment can be associated with one that is described by
BioCatalogue through an owl:sameAs relationship.  This would allow
myExperiment to take advantage of this extra information.  This
information could be used in a scientific discourse context to better
understand in a biologicial sense what is being analysed when a workflow
is enacted.  The community annotation of these services may also be
useful.

I hope this information clarifies some of the questions raised by the
discussion yesterday.

Regards

David R Newman 



On Mon, 2010-05-03 at 20:34 -0400, Tim Clark wrote:
> Hi Susanna,
> 
> Important for us to know the time frame of this replacement - I don't mind if we use - for example - MO short term and OBI long term, but I do want to assure that we can link properly to data we retrieve from ArrayExpress and GEO and / or other legacy resources.   Or for that matter, current resources.  
> 
> Would you and Michael possibly be able to participate in the next "Synthesis" call on May 17 to discuss?  It would be very helpful.
> 
> Best
> 
> Tim
> 
> On May 3, 2010, at 6:01 PM, Susanna-Assunta Sansone wrote:
> 
> > Hi Tim and all,
> > 
> > note that OBI replaces MO (terms from the latter are being decomposed/defined  -where relevant-and enclosed in the fomer).
> > You'd better use OBI directly to avoid confusion.
> > 
> > Susanna
> > 
> > Tim Clark wrote:
> >> I stand corrected and will use that terminology in future.  Thanks Michael.
> >> 
> >> Tim
> >> 
> >> On May 3, 2010, at 11:00 AM, Michael Miller wrote:
> >> 
> >>> hi all,
> >>> 
> >>> 
> >>> it's the MGED Ontology, or MO.  MGED is a non-profit organization with many initiatives in the standards area, particularly MIAME, MAGE-OM (MAGE-ML, MAGE-TAB), in next gene sequencing, and MO.  we also have our upcoming yearly meeting in conjunction with ISMB in july.
> >>> 
> >>> 
> >>> cheers,
> >>> michael
> >>> 
> >>> 
> >>> Michael Miller
> >>> Principal Software Developer
> >>> www.teranode.com <http://www.teranode.com>
> >>> 
> >>> 
> >>> 
> >>> *From:* public-semweb-lifesci-request@w3.org <mailto:public-semweb-lifesci-request@w3.org> [mailto:public-semweb-lifesci-request@w3.org <mailto:public-semweb-lifesci-request@w3.org>] *On Behalf Of *Tim Clark
> >>> *Sent:* Sunday, May 02, 2010 4:25 AM
> >>> *To:* HCLS IG
> >>> *Cc:* Anita de A (ELS-AMS) Waard; Annamaria Carusi; David Shotton; Carole Goble; David R Newman; Matthew Gamble; Satya Sahoo; Jun Zhao; David DeRoure; Michel Dumontier; Ted Liefeld; Alexander Pico
> >>> *Subject:* Reminder: Scientific Discourse Concall May 3, 10am EDT
> >>> 
> >>> 
> >>> Reminder: Scientific Discourse Concall May 3, 10am EDT
> >>> 
> >>> 
> >>> This call will be led by Sudeshna Das and will focus on the _Discourse + Data + Experiment subtask_ - - integrating SWAN, myExperiment, MGED and OBI 
> >>> 
> >>> §  Dial-In #: +1.617.761.6200 (Cambridge, MA)
> >>> 
> >>> §  Dial-In #: +33.4.89.06.34.99 (Nice, France)
> >>> 
> >>> §  Dial-In #: +44.117.370.6152 (Bristol, UK)
> >>> 
> >>> §  Participant Access Code: 42572 ("HCLS2")
> >>> 
> >>> §  IRC Channel: irc.w3.org <http://irc.w3.org> port 6665 channel #HCLS2 (see W3C IRC page <http://www.w3.org/Project/IRC/> for details, or see Web IRC <http://cgi.w3.org/member-bin/irc/irc.cgi>)
> >>> 
> >>> 
> >>> See http://esw.w3.org/HCLSIG/SWANSIOC/Actions/SWANmyExpArray for details and background.
> >>> 
> >>> 
> >>> Best
> >>> 
> >>> 
> >>> Tim 
> >>> 
> >>> 
> >>> 
> >> 
> > 
> > 
> 
> 
Received on Wednesday, 5 May 2010 13:12:05 GMT

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