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Re: HCLS Scientific Discourse Call Monday, 11 April 2011 10 am EST, 3 PM BST: talk by Jodi Schneider

From: Waard, Anita de A (ELS-AMS) <A.dewaard@elsevier.com>
Date: Sat, 30 Apr 2011 14:48:44 -0400
Message-ID: <07626332-468C-49A5-8C68-F68778A48CBF@elsevier.com>
To: "Waard, Anita de A (ELS-AMS)" <A.dewaard@elsevier.com>
Cc: "Alexander Garcia Castro" <alexgarciac@gmail.com>, "Jodi Schneider" <jodi.schneider@deri.org>, "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 don't have a speaker for Monday but I propose whoever is interested does dail in to discuss:
1) timeframe and names for ideas below
2) how close are we to fulfilling our original use cases?
3) overlap with other HCLS subgroups
4) in summary: next steps.
Time & nrs as per usual - will update when I'm on a real computer (now on mobile). 

Best,

Anita de Waard


On Apr 17, 2011, at 5:02 PM, "Waard, Anita de A (ELS-AMS)" <A.dewaard@elsevier.com> wrote:

> 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
> Universit├Ąt 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 Saturday, 30 April 2011 18:51:37 GMT

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