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HCLS Scientific Discourse Call Monday, 18 April 2011: Next steps:a demo, a paper and a meeting.

From: Waard, Anita de A (ELS-AMS) <A.dewaard@elsevier.com>
Date: Mon, 18 Apr 2011 21:08:06 +0200
Message-ID: <994C62F4D342094CB0A2A3431B8ED8500A9D5AB1@ELSAMSEXCP02VA.science.regn.net>
To: "Waard, Anita de A (ELS-AMS)" <A.dewaard@elsevier.com>, "Alexander Garcia Castro" <alexgarciac@gmail.com>, "Jodi Schneider" <jodi.schneider@deri.org>
Cc: "barend mons" <barend.mons@nbic.nl>, "M. Scott Marshall" <mscottmarshall@gmail.com>, "Tim Clark" <tim_clark@harvard.edu>, "HCLS IG" <public-semweb-lifesci@w3.org>, "Alberto Accomazzi" <aaccomazzi@cfa.harvard.edu>, "Sophia Ananiadou" <Sophia.Ananiadou@manchester.ac.uk>, "Philip Bourne" <bourne@sdsc.edu>, "Gully Burns" <gully@usc.edu>, "Daniel, Ronald (ELS-SDG)" <R.Daniel@elsevier.com>, "Rahul Dave" <rahuldave@gmail.com>, "Alf Eaton" <A.Eaton@nature.com>, "Matthew Gamble" <matthew.gamble@gmail.com>, "Yolanda Gil" <gil@isi.edu>, "Alyssa Goodman" <agoodman@cfa.harvard.edu>, "Paul Groth" <pgroth@gmail.com>, "Tudor Groza" <tudor.groza@deri.org>, "Hays, Ellen (ELS-BUR)" <E.Hays@elsevier.com>, "Maryann Martone" <maryann@ncmir.ucsd.edu>, "David R Newman" <drn05r@ecs.soton.ac.uk>, "Scerri, Antony (ELS-CAM)" <A.scerri@elsevier.com>, "Jack Park" <jackpark@gmail.com>, "Silvio Peroni" <speroni@cs.unibo.it>, "Steve Pettifer" <steve.pettifer@manchester.ac.uk>, "Philippe Rocca-Serra" <proccaserra@googlemail.com>, "Cartic Ramakrishnan" <cartic@isi.edu>, "RebholzSchuhmann" <d.rebholz.schuhmann@gmail.com>, "David Shotton" <david.shotton@zoo.ox.ac.uk>, "Kaitlin Thaney" <k.thaney@digital-science.com>, "Karin Verspoor" <Karin.Verspoor@ucdenver.edu>, "Lynette Hirschman" <lynette@mitre.org>, "Susanna-Assunta Sansone" <sa.sansone@gmail.com>, "Kees van Bochove" <business@keesvanbochove.nl>, "Katy Wolstencroft" <katy@cs.man.ac.uk>, "Jun Zhao" <jun.zhao@zoo.ox.ac.uk>, "Paul Groth" <pgroth@few.vu.nl>
Dear all,

We had a very productive call this morning, and are planning three things:

1) Joint work on annotation a corpus of documents with links to workflow components and data. 
This will allow a concrete instantiation of the medium-grained ontology, and offer a discussion point for describing the experiment/paper link which we are approaching from many different sides. 
Alex Garcia will jumpstart this process by making a collection of full-text Elsevier documents available which he has annotated with RDF; after seeing these, we will select a subcorpus to mark up 
a) Data
b) Experimental model
c) Key discourse components
from, and work to make a demonstrator.

2) A paper. 
Discussing our various models, and ways to integrate; include discussion re. overlap/difference between (explicit, personal) knowledge in discourse and (implicit, shared) knowledge that underlies experimental models. Could be possible outcome of demo. 

3) A face-to-face meeting. 
Kees van Bochove has kindly agreed to organise this. Possible venues: ISMB in Vienna, ICBO in Buffalo, or a one-off workshop in hte Netherlands. Topic: Experiment/discourse integration: models, examples, and next steps. Specifically, Kees wants to discuss with whoever might be interested in co-organising this face to face:
-- work plan: what do we want to achieve --> which outcome would we like from the symposium: when are we happy?
-- (candidate) attendee list
-- options for date/time/place

If you are interested in participating in any of these parts, can you please either share to the people on this list, or indicate this at or before the next meeting? Any other comments are most welcome, as well.

With thanks to everyone on the call today, 
best,

- Anita.  

Anita de Waard
Disruptive Technologies Director, Elsevier Labs
http://elsatglabs.com/labs/anita/
a.dewaard@elsevier.com



-----Original Message-----
From: public-semweb-lifesci-request@w3.org on behalf of Waard, Anita de A (ELS-AMS)
Sent: Sun 4/17/2011 16:57
To: Alexander Garcia Castro; Jodi Schneider
Cc: barend mons; M. Scott Marshall; Tim Clark; HCLS IG; Alberto Accomazzi; Sophia Ananiadou; Philip Bourne; Gully Burns; Daniel, Ronald (ELS-SDG); Rahul Dave; Alf Eaton; Matthew Gamble; Yolanda Gil; Alyssa Goodman; Paul Groth; Tudor Groza; Hays, Ellen (ELS-BUR); Maryann Martone; David R Newman; Scerri, Antony (ELS-CAM); Jack Park; Silvio Peroni; Steve Pettifer; Philippe Rocca-Serra; Cartic Ramakrishnan; RebholzSchuhmann; David Shotton; Kaitlin Thaney; Karin Verspoor; Lynette Hirschman; Susanna-Assunta Sansone; Kees van Bochove; Katy Wolstencroft; Jun Zhao; Paul Groth
Subject: RE: HCLS Scientific Discourse Call Monday, 11 April 2011 10 am EST, 3  PM BST: talk by Jodi Schneider
 
Dear all,

Jodi's talk last week seemed to spur on a great amount of discussion, and this week, as we don't have a speaker, I would like to spend our time about the issues Jodi's talk brought up. These include:
- Alex's points below - links between the paper and workflow and experimental ontologies;
- The connection (and if there is one) between nanopublications/triples/research highlights (will explain on the call) and medium-grained structure
- Uses for medium-grained structure mark up: what would be a good set of use cases? Can we find some concrete projects to work on?
- An issue that has been discussed on a few calls now which we can also discuss is the difference between data, author's intent, persuasive structure and nanopublication-type summaries.
- A point that Joanne raised: can we plan a meeting to discuss this stuff in person?

I am sure much more will come up, once we start talking. Feel free to send around more questions before the call, so we have a list of them to consider before we start. 

Thanks, and look forward to talking to you tomorrow, 

Best, 

- Anita.  

Anita de Waard
Disruptive Technologies Director, Elsevier Labs
http://elsatglabs.com/labs/anita/
a.dewaard@elsevier.com



-----Original Message-----
From: public-semweb-lifesci-request@w3.org on behalf of Alexander Garcia Castro
Sent: Mon 4/11/2011 11:25
To: Jodi Schneider
Cc:...
 
Hi Jodi, nice talk.

As a general question, shouldn't the description of  experiments be
something to be described by domain specific ontologies? Also, there are
repositories for experiments, e.g  Array express for microarrays; there are
also minimal standards for reporting several experimental
procedures, shouldn't the sections in the document make use of, pointing to,
these resources? if ORB and other document related ontologies go into
describing experimental information I am afraid it may be difficult
to maintain and not very practical to implement.

fine-graining ORB should, in my opinion, make use of other ontologies for
addressing domain specific issues. for instance, if a researcher wants to go
deeper into materials and methods most likely the information that will
allow him/her to "replicate" the experiment will be living somewhere else in
the web; also, most likely there will be an ontology for specific
experimental procedures, measures, etc involved.

Once the structure of the document is solved it is easy to use resources
such as bio2rdf to resolve it against existing resources in the web. if not,
then authors can easily point to these external resources -AO can easily
deal with such a use case. my point is, experimental information is highly
domain specific and there are now ontologies (OBI) and repositories for
experimental information as well as efforts
for standardizing minimal amounts of information (http://www.mibbi.org/index.php/Main_Page) for reporting specific
experimental procedures, shouldn't the fine grained structure of ORB  seek
to make use of these resources?

On Mon, Apr 11, 2011 at 8:09 AM, Jodi Schneider <jodi.schneider@deri.org>wrote:

> Looking forward to talking with you in about an hour.
>
> Here are slides for discussion -- about the overall goal of bridging
> between ORB and the fine-grained ontology with a middle-grained ontology.
>
> The other two PDFs show
> (1) the relationship between ORB and Anita's middle-grained ontology and
> (2) a first attempt to bridge between DExI (top-level) and Anita's
> middle-grained ontology.
>
> -Jodi
>
>
>
>
>
>
>
> On 10 Apr 2011, at 19:38, Waard, Anita de A (ELS-AMS) wrote:
>
> > Dear all,
> >
> > Monday's scientific discourse call will focus on an update of the
> medium-grained ontology alignment by Jodi Schneider: see agenda and call
> details below, or at
> http://www.w3.org/wiki/HCLSIG/SWANSIOC/Actions/RhetoricalStructure/meetings/20110411
> >
> > Kind regards,
> >
> > Anita
> > Anita de Waard
> > Disruptive Technologies Director, Elsevier Labs
> > http://elsatglabs.com/labs/anita/
> > a.dewaard@elsevier.com
> >
> > Meeting April 11, 2011, 10 am EST, 3 pm BST, 4 pm CET
> > [edit] Agenda:
> >
> >    * Jodi Schneider: 'Medium-grained ontology and alignment'
> >    * Status of ontology development
> >    * AOB
> >
> > [edit] Dial-in & IRC Information
> >
> >    * Dial-In #: +1.617.761.6200 (Cambridge, MA)
> >    * Dial-In #: +33.4.26.46.79.03 (Paris, France)
> >    * Dial-In #: +44.203.318.0479 (London, UK)
> >    * Participant Access Code: 42572 ("HCLS2")
> >    * IRC Channel: irc.w3.org port 6665 channel #HCLS2 use IRC direct
> link or (see W3C IRC page for details, or see Web IRC)
> >    * Mibbit quick start: Click on mibbit for instant IRC access
> >    * Duration: 1hr
> > Elsevier B.V. Registered Office: Radarweg 29, 1043 NX Amsterdam, The
> Netherlands, Registration No. 33156677 (The Netherlands)
> >
>
>
>


-- 
Alexander Garcia
http://www.alexandergarcia.name/
http://www.usefilm.com/photographer/75943.html
http://www.linkedin.com/in/alexgarciac
Postal address:
Alexander Garcia, Tel.: +49 421 218 64211
Universitšt Bremen
Enrique-Schmidt-Str. 5
D-28359 Bremen

Elsevier B.V. Registered Office: Radarweg 29, 1043 NX Amsterdam, The Netherlands, Registration No. 33156677 (The Netherlands)





Elsevier B.V. Registered Office: Radarweg 29, 1043 NX Amsterdam, The Netherlands, Registration No. 33156677 (The Netherlands)

Received on Monday, 18 April 2011 19:10:09 GMT

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