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Re: HCLS SciDiscourse call Monday April 2, 2012, 11am EDT: Matt Gamble on MIMV, the Minimum Information Model Vocabulary

From: Susanna Sansone <sa.sansone@gmail.com>
Date: Sun, 25 Mar 2012 12:52:45 -0400
Message-ID: <4F6F4D5D.405@gmail.com>
To: Bob Futrelle <bob.futrelle@gmail.com>
CC: Tim Clark <tim_clark@harvard.edu>, HCLS IG <public-semweb-lifesci@w3.org>, Joanne Luciano <jluciano@cs.rpi.edu>, "Waard, Anita de A (ELS-NYC)" <A.dewaard@elsevier.com>, "<scidiscourse@googlegroups.com>" <scidiscourse@googlegroups.com>, "<mal@aber.ac.uk>" <mal@aber.ac.uk>, Alberto Accomazzi <aaccomazzi@cfa.harvard.edu>, "Allen, Bradley P(ELS-SDG)" <B.Allen@elsevier.com>, Sophia Ananiadou <Sophia.Ananiadou@manchester.ac.uk>, Philip Bourne <bourne@sdsc.edu>, Gully Burns <gully@usc.edu>, "Ronald (ELS-SDG) Daniel" <R.Daniel@elsevier.com>, Rahul Dave <rahuldave@gmail.com>, Alf Eaton <A.Eaton@nature.com>, Alexander Garcia Castro <alexgarciac@gmail.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 RNewman <drn05r@ecs.soton.ac.uk>, "Antony (ELS-CAM) Scerri" <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>, Jodi Schneider <jodi.schneider@deri.org>, 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>, Kees van Bochove <business@keesvanbochove.nl>, Katy Wolstencroft <katy@cs.man.ac.uk>, JunZhao Zhao <jun.zhao@zoo.ox.ac.uk>, "Taylor, Michael (ELS-OXF)" <Mi.Taylor@elsevier.com>
Dear Bob,
to be precise, the reference you mention to our Science piece is just to 
the BioSharing effort (biosharing.org); we launched its site in that paper.
Look forward to the talk.
Regards,
Susanna


-- 
Susanna-Assunta Sansone, PhD
Principal Investigator,
Team Leader

Projects: www.isa-tools.org|www.mibbi.org|www.biosharing.org

University of Oxford		Tel: +44(0)1865 610622
Oxford e-Research Centre	Fax: +44(0)1865 610612
7 Keble Road, Oxford		skype: susanna-a.sansone
OX1 3QG, UK			uk.linkedin.com/in/sasansone



On 24/03/2012 15:28, Bob Futrelle wrote:
> This is in reference to,
>
> "Please join us on Monday April 2, 2012, 10am EDT / 14:00 UTC, to 
> hear Matt Gamble of the University of Manchester School of Computer 
> Science, present on MIMV, the Minimum Information Model Vocabulary. "
>
> For background on MMIV-related work, see Matt's paper, with Carole Goble:
>
> (2011) /Quality, Trust, and Utility of Scientific Data on the Web: 
> Towards a Joint Model/
> Matthew Gamble, Carole Goble, Proceedings of the International 
> Conference on Web Science 2011 (WebSci11)
>
> A link to the paper can be found on this page:
>
> http://sierra-nevada.cs.man.ac.uk/
>
> In the paper they mention "minimum information model", with a 
> reference to,
>
> D. Field, S.-A. Sansone, A. Collis, T. Booth, P. Dukes,
> S. K. Gregurick, K. Kennedy, P. Kolar, E. Kolker,
> M. Maxon, S. Millard, A.-M. Mugabushaka, N. Perrin, J. E. Remacle, K. 
> Remington, P. Rocca-Serra, C. F. Taylor, M. Thorley, B. Tiwari, and J. 
> Wilbanks. /Megascience/. /’Omics data sharing/. Science (New York, 
> N.Y.), 326(5950):234–6, Oct. 2009.
>
> Which can be found at,
>
> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2770171/?tool=pubmed
>
>  - Bob Futrelle
>    BioNLP.org
>
>
>
> On Sat, Mar 24, 2012 at 12:00 PM, Tim Clark <tim_clark@harvard.edu 
> <mailto:tim_clark@harvard.edu>> wrote:
>
>     Dear Colleagues:
>
>     Please join us on Monday April 2, 2012, 10am EDT / 14:00 UTC, to
>     hear Matt Gamble of the University of Manchester School of
>     Computer Science, present on MIMV, the Minimum Information Model
>     Vocabulary.
>
>     Monday April 2, 2012, 10am EDT / 14:00 UTC
>
>   #  Dial-In #: +1.617.761.6200 <tel:%2B1.617.761.6200> (Cambridge, MA)
>   # Dial-In #: +33.4.26.46.79.03 <tel:%2B33.4.26.46.79.03> (Paris,
>     France)
>   # Dial-In #: +44.203.318.0479 <tel:%2B44.203.318.0479> (London, UK)
>   # Participant Access Code: 42572 ("HCLS2")
>   # IRC Channel: irc.w3.org <http://irc.w3.org> port 6665 channel
>     #HCLS2 use IRC direct link
>     <http://www.mibbit.com/chat/?server=irc.w3.org:6665&channel=%23hcls2>
>     or (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>)
>   # Mibbit quick start: Click on mibbit for instant IRC access
>   # Duration: 1hr
>
>     Tim Clark
>     Director of Informatics, MassGeneral Institute
>     for Neurodegenerative Disease
>     Instructor in Neurology, Harvard Medical School
>     65 Landsdowne St, 2nd floor
>     Cambridge MA 02139 USA
>
>
>
>     Begin forwarded message:
>
>>     *Resent-From: *public-semweb-lifesci@w3.org
>>     <mailto:public-semweb-lifesci@w3.org>
>>     *From: *Tim Clark <tim.clark@rcn.com <mailto:tim.clark@rcn.com>>
>>     *Subject: **Re: HCLS SciDiscourse call Monday January 23, 2012,
>>     Use Case overview; Talk on DOMEO planned for January 30*
>>     *Date: *January 30, 2012 1:34:14 PM EST
>>     *To: *Joanne Luciano <jluciano@gmail.com <mailto:jluciano@gmail.com>>
>>     *Cc: *"Waard, Anita de A (ELS-NYC)" <A.dewaard@elsevier.com
>>     <mailto:A.dewaard@elsevier.com>>, HCLS IG
>>     <public-semweb-lifesci@w3.org
>>     <mailto:public-semweb-lifesci@w3.org>>,
>>     "<scidiscourse@googlegroups.com
>>     <mailto:scidiscourse@googlegroups.com>>"
>>     <scidiscourse@googlegroups.com
>>     <mailto:scidiscourse@googlegroups.com>>, "<mal@aber.ac.uk
>>     <mailto:mal@aber.ac.uk>>" <mal@aber.ac.uk
>>     <mailto:mal@aber.ac.uk>>, Alberto Accomazzi
>>     <aaccomazzi@cfa.harvard.edu <mailto:aaccomazzi@cfa.harvard.edu>>,
>>     "Allen, Bradley P(ELS-SDG)" <B.Allen@elsevier.com
>>     <mailto:B.Allen@elsevier.com>>, Sophia Ananiadou
>>     <Sophia.Ananiadou@manchester.ac.uk
>>     <mailto:Sophia.Ananiadou@manchester.ac.uk>>, Philip Bourne
>>     <bourne@sdsc.edu <mailto:bourne@sdsc.edu>>, Gully Burns
>>     <gully@usc.edu <mailto:gully@usc.edu>>, "Daniel, Ronald
>>     (ELS-SDG)" <R.Daniel@elsevier.com
>>     <mailto:R.Daniel@elsevier.com>>, Rahul Dave <rahuldave@gmail.com
>>     <mailto:rahuldave@gmail.com>>, Alf Eaton <A.Eaton@nature.com
>>     <mailto:A.Eaton@nature.com>>, Alexander Garcia Castro
>>     <alexgarciac@gmail.com <mailto:alexgarciac@gmail.com>>, Matthew
>>     Gamble <matthew.gamble@gmail.com
>>     <mailto:matthew.gamble@gmail.com>>, Yolanda Gil <gil@isi.edu
>>     <mailto:gil@isi.edu>>, Alyssa Goodman <agoodman@cfa.harvard.edu
>>     <mailto:agoodman@cfa.harvard.edu>>, Paul Groth <pgroth@gmail.com
>>     <mailto:pgroth@gmail.com>>, Tudor Groza <tudor.groza@deri.org
>>     <mailto:tudor.groza@deri.org>>, "Hays, Ellen (ELS-BUR)"
>>     <E.Hays@elsevier.com <mailto:E.Hays@elsevier.com>>, Maryann
>>     Martone <maryann@ncmir.ucsd.edu <mailto:maryann@ncmir.ucsd.edu>>,
>>     David RNewman <drn05r@ecs.soton.ac.uk
>>     <mailto:drn05r@ecs.soton.ac.uk>>, "Scerri, Antony (ELS-CAM)"
>>     <A.scerri@elsevier.com <mailto:A.scerri@elsevier.com>>, Jack Park
>>     <jackpark@gmail.com <mailto:jackpark@gmail.com>>, Silvio Peroni
>>     <speroni@cs.unibo.it <mailto:speroni@cs.unibo.it>>, Steve
>>     Pettifer <steve.pettifer@manchester.ac.uk
>>     <mailto:steve.pettifer@manchester.ac.uk>>, Philippe Rocca-Serra
>>     <proccaserra@googlemail.com <mailto:proccaserra@googlemail.com>>,
>>     Cartic Ramakrishnan <cartic@isi.edu <mailto:cartic@isi.edu>>,
>>     Jodi Schneider <jodi.schneider@deri.org
>>     <mailto:jodi.schneider@deri.org>>, David Shotton
>>     <david.shotton@zoo.ox.ac.uk <mailto:david.shotton@zoo.ox.ac.uk>>,
>>     Kaitlin Thaney <k.thaney@digital-science.com
>>     <mailto:k.thaney@digital-science.com>>, Karin Verspoor
>>     <Karin.Verspoor@ucdenver.edu
>>     <mailto:Karin.Verspoor@ucdenver.edu>>, Lynette Hirschman
>>     <lynette@mitre.org <mailto:lynette@mitre.org>>, Susanna-Assunta
>>     Sansone <sa.sansone@gmail.com <mailto:sa.sansone@gmail.com>>,
>>     Kees van Bochove <business@keesvanbochove.nl
>>     <mailto:business@keesvanbochove.nl>>, Katy Wolstencroft
>>     <katy@cs.man.ac.uk <mailto:katy@cs.man.ac.uk>>, JunZhao
>>     <jun.zhao@zoo.ox.ac.uk <mailto:jun.zhao@zoo.ox.ac.uk>>, "Taylor,
>>     Michael (ELS-OXF)" <Mi.Taylor@elsevier.com
>>     <mailto:Mi.Taylor@elsevier.com>>
>>
>>     For those of you who could not make today's very interesting Sci
>>     Discourse call, I am attaching a link to the slides.
>>
>>     http://www.slideshare.net/paolociccarese/domeo-and-text-mining
>>
>>     Best
>>
>>     Tim
>>
>>
>>     On Jan 30, 2012, at 9:53 AM, Joanne Luciano wrote:
>>
>>>     Hi,
>>>
>>>     We have been on winter break here, so nothing to report at the
>>>     moment. I have been working on other projects (including CSHALS
>>>     from the chairing and tutorial side). I look forward to updating
>>>     next time. Unfortunately I cannot make the call today.
>>>
>>>     Happy New Year!
>>>
>>>     Kind regards,
>>>
>>>     Joanne
>>>
>>>     Sent from my iPhone
>>>
>>>     On Jan 23, 2012, at 11:23 AM, "Waard, Anita de A (ELS-NYC)"
>>>     <A.dewaard@elsevier.com <mailto:A.dewaard@elsevier.com>> wrote:
>>>
>>>>     Please find enclosed the notes to our call. For a hyperlinked
>>>>     version, see
>>>>     http://www.w3.org/wiki/HCLSIG/SWANSIOC/Actions/RhetoricalStructure/meetings/20120103
>>>>
>>>>>
>>>>     Notes:
>>>>
>>>>     1. Use case 1 status, Rich Boyce:
>>>>
>>>>      * gearing up for the C-SHALS presentation
>>>>      * in abstract we talked about a conceptual prototype for 2
>>>>     packages, this is now available
>>>>      * Now going through the process of building a linked data set
>>>>     and revamping prototype in Linked Data standard
>>>>      * Current prototype: what does Package Insert enhanced with
>>>>     scientific literature look like? Now, want to mark up a paper,
>>>>     take annotations and bring into Linked Data graph and link to
>>>>     section in Package insert for two drugs
>>>>      * code will be posted here
>>>>      * Project page for the code here
>>>>      * Road map with milestones, are dividing among themselves
>>>>      * Now have all the structured product labels in the code
>>>>     repository and scientific articles for 2 drugs at C-SHALS
>>>>      * Met with Pieder Caduff to discuss XPharm/Pharmapendium to
>>>>     discuss details; figuring out protocol for this
>>>>      * Should talk to Provenance group; as Elsevier opens up
>>>>     Pharmapendium we should bring in some provenance markup to
>>>>     identify where data comes from - is Satellite standard
>>>>     compliant with new provenance standard?
>>>>
>>>>     Anita to do: look at Satellite and PROV overlap Rich: at noon I
>>>>     will have a few full-text annotated with Sapienta will send it
>>>>     around
>>>>
>>>>     2. Use case 2 , David Shotton -
>>>>
>>>>      * Stripped out information re. infectious disease - diagram
>>>>     mibio.png (sent around earlier)
>>>>      * Form to fill in is here can generate a report in the middi
>>>>     format in XML; recently at a hackathon people repurposed this
>>>>     format to describe cancer research papers
>>>>      * Now want to share with rest of the team and see what next
>>>>     steps are
>>>>
>>>>     Q Anita how can this be used? A: david: can accompany article
>>>>     as a supplementary file; can be published separately e.g. as a
>>>>     pointer to the article or as a submission to e.g. Dryad or
>>>>     other data repository
>>>>
>>>>      * Questions: 1) Are these the right things you want to add 2)
>>>>     How/where is it added?
>>>>      * Anita: suggest also looking at Rutgers research data metadata
>>>>
>>>>     3. Use case 3
>>>>
>>>>      * No news, ask Joanne Luciano for update next general meeting
>>>>
>>>>     4. Next calls:
>>>>
>>>>      * We'll keep 4-week general call schedule
>>>>      * Next general call February 20: Anita will invite someone
>>>>     from the PROV group to present [1]
>>>>      * Next week (January 30, 2012): Paolo Ciccarese will present
>>>>     re. DOMEO
>>>>>
>>>>
>>>>     Best,
>>>>
>>>>     - Anita.
>>>>
>>>>     Anita de Waard
>>>>     Disruptive Technologies Director, Elsevier Labs
>>>>     http://elsatglabs.com/labs/anita/
>>>>     a.dewaard@elsevier.com <mailto:a.dewaard@elsevier.com>
>>>>
>>>>
>>>>
>>>>     -----Original Message-----
>>>>     From: Waard, Anita de A (ELS-NYC)
>>>>     Sent: Fri 1/20/2012 16:30
>>>>     To: Waard, Anita de A (ELS-NYC); Tim Clark; HCLS IG;
>>>>     scidiscourse@googlegroups.com
>>>>     <mailto:scidiscourse@googlegroups.com>; mal@aber.ac.uk
>>>>     <mailto:mal@aber.ac.uk>
>>>>     Cc: Alberto Accomazzi; Allen, Bradley P (ELS-SDG); Sophia
>>>>     Ananiadou; Philip Bourne; Gully Burns; Daniel, Ronald
>>>>     (ELS-SDG); Rahul Dave; Alf Eaton; Alexander Garcia Castro;
>>>>     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; Jodi
>>>>     Schneider; David Shotton; Kaitlin Thaney; Karin Verspoor;
>>>>     Lynette Hirschman; Susanna-Assunta Sansone; Kees van Bochove;
>>>>     Katy Wolstencroft; Jun Zhao; Taylor, Michael  (ELS-OXF)
>>>>     Subject: HCLS SciDiscourse call Monday January 23, 2012, Use
>>>>     Case overview; Talk on DOMEO planned for January 30
>>>>
>>>>     Dear all,
>>>>
>>>>     I cordially invite you to Monday's scientific discourse call,
>>>>     where we will do a status update on the three use cases we are
>>>>     working on.
>>>>
>>>>     For links, more details and dial-in info see the wiki, and below:
>>>>     http://www.w3.org/wiki/HCLSIG/SWANSIOC/Actions/RhetoricalStructure/meetings/20120103
>>>>
>>>>     Dial-in & IRC Information:
>>>>
>>>>     Dial-In #: +1.617.761.6200 <tel:%2B1.617.761.6200> (Cambridge, MA)
>>>>     Dial-In #: +33.4.26.46.79.03 <tel:%2B33.4.26.46.79.03> (Paris,
>>>>     France)
>>>>     Dial-In #: +44.203.318.0479 <tel:%2B44.203.318.0479> (London, UK)
>>>>     Participant Access Code: 42572 ("HCLS2")
>>>>     IRC Channel: irc.w3.org <http://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
>>>>
>>>>     Next week, on January 30, Paolo Ciccarese will present his work
>>>>     on the DOMEO web annotation toolkit. The Domeo Web Annotation
>>>>     Toolkit provides several important items of common
>>>>     infrastructure that can help support the textmining community
>>>>     by offering:
>>>>     - Shared results repository with selective sharing (personal,
>>>>     group, public)
>>>>     - Standardized serialization and export of results in
>>>>     Annotation Ontology RDF/XML
>>>>     - Results injection and contextualization on any web page
>>>>     - Common curation, annotation and comparison user interface
>>>>     - Web service interfaces
>>>>
>>>>     His talk and demo will discuss current facilities and future
>>>>     plans for Domeo relating to specifically to textmining use
>>>>     cases. Also, Paolo and a representative from the
>>>>     Apache/Clerezza community will discuss DOMEO's integration with
>>>>     the Apache framework.
>>>>
>>>>     Best,
>>>>
>>>>     - Anita.
>>>>
>>>>     Anita de Waard
>>>>     Disruptive Technologies Director, Elsevier Labs
>>>>     http://elsatglabs.com/labs/anita/
>>>>     a.dewaard@elsevier.com <mailto:a.dewaard@elsevier.com>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>     Elsevier B.V. Registered Office: Radarweg 29, 1043 NX
>>>>     Amsterdam, The Netherlands, Registration No. 33156677 (The
>>>>     Netherlands)
>>>>
>>>>
>>
>>
>>
>>
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Received on Sunday, 25 March 2012 15:52:16 GMT

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