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

From: Bob Futrelle <bob.futrelle@gmail.com>
Date: Sat, 24 Mar 2012 15:28:57 -0400
Message-ID: <CAOsWdXrwYPHnGdaGRm8zA_e-i6T3op9n=rM3jvSAQ7jUZ79i7Q@mail.gmail.com>
To: Tim Clark <tim_clark@harvard.edu>
Cc: 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>, Susanna-Assunta Sansone <sa.sansone@gmail.com>, 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>
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> 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 (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<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
> *From: *Tim Clark <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>
> *Cc: *"Waard, Anita de A (ELS-NYC)" <A.dewaard@elsevier.com>, HCLS IG <
> public-semweb-lifesci@w3.org>, "<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>, "Daniel, Ronald (ELS-SDG)" <
> 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>, "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>, 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>, Susanna-Assunta Sansone <sa.sansone@gmail.com>, Kees
> van Bochove <business@keesvanbochove.nl>, Katy Wolstencroft <
> katy@cs.man.ac.uk>, JunZhao <jun.zhao@zoo.ox.ac.uk>, "Taylor, Michael
> (ELS-OXF)" <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> 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
>
>
>
>
> -----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; 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 (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
>
>
> 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
>
>
>
>
>
>
>
>
>
>
>
> Elsevier B.V. Registered Office: Radarweg 29, 1043 NX Amsterdam, The
> Netherlands, Registration No. 33156677 (The Netherlands)
>
>
>
>
>
>
>
>
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Received on Saturday, 24 March 2012 19:29:29 GMT

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