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

From: Joanne Luciano (gmail) <jluciano@gmail.com>
Date: Mon, 2 May 2011 08:40:25 -0400
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>
Message-Id: <51743DB0-5FD2-4B38-AB83-9422DAF436D8@gmail.com>
To: "Waard, Anita de A (ELS-AMS)" <A.dewaard@elsevier.com>
Hi,
Regrets - I can't make the call today.  Will be at Nano 2011: Medicine, Science, and Engineering (at RPI).

On Apr 30, 2011, at 2:48 PM, Waard, Anita de A (ELS-AMS) wrote:

> 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
>> 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, 2 May 2011 12:41:03 GMT

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