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RE: HCLS Scientific Discourse conference call - Use Case Review - Mon October 10, 10am-11am EDT / 14:00-15:00 UTC

From: Waard, Anita de A (ELS-AMS) <A.dewaard@elsevier.com>
Date: Mon, 10 Oct 2011 17:33:52 +0200
Message-ID: <994C62F4D342094CB0A2A3431B8ED8500A9D62CC@ELSAMSEXCP02VA.science.regn.net>
To: "Waard, Anita de A (ELS-AMS)" <A.dewaard@elsevier.com>, "Tim Clark" <tim.clark@rcn.com>, "HCLS IG" <public-semweb-lifesci@w3.org>, <scidiscourse@googlegroups.com>
Cc: "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 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>, "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>, "Jun Zhao" <jun.zhao@zoo.ox.ac.uk>
Dear all,

Thanks for a very productive call today! Notes/action items:

We discussed the tentative use cases for the group, http://www.w3.org/wiki/HCLSIG/SWANSIOC/Actions/RhetoricalStructure/meetings/20111010 

Use case # 1: Enhancing Drug-mechanism Knowledge in Drug Product Labels:
https://docs.google.com/document/d/1QpW-axtGL7Tuhd_Zcaf30a4-s4S_lveIJtpKL5QBLfQ/edit?hl=en_US:

- Richard Boyce of Pittsburgh discussed his work, all agreed this was a perfect fit for the Scientific Discourse group. 
- Jodi and Anita said they would prefer to work on this use cases over their own (#2); Joanne is also interested in collaborating on this. All: agree to update and rework this use case before the next call (planned for October 31st). 

Use case # 2: https://docs.google.com/document/d/15MIVtMoznrd7kVkCVYGVcil4Jg2oc3SaHFnd1vXMi6o/edit?hl=en_US

- Jodi and Anita are going to merge this with # 1.

Use case # 3: MIBBI Core: defining minimal information requirements for biomedical investigations defined and mapped to RDF: 

- David Shotton and Tim Clark will prepare a version of this before the next call. 

Use case # 4: Structuring computer science publications during authoring

- Tim Clark and/or Tudor Groza to rework the old use case: http://www.w3.org/wiki/HCLSIG/SWANSIOC/Actions/RhetoricalStructure/UseCases/2 to the new HCLS template: http://www.w3.org/wiki/HCLSIG/UCT

Use case # 5: Mining Treatment Outcomes 

Anita and Joanne will write up this use before the next meeting; Joanne will try to involve the RPI students in this use case. Might be interesting to involve SMA patient and/or depression. 

Use case # 6: Linking patient data to clinical recommendations, and recommendations to clinical evidence 
Shelve for now - might be used at a later stage. 

Please let me know if you have any further questions, edits, or additions to these items.

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-AMS)
Sent: Sun 10/9/2011 19:28
To: Waard, Anita de A (ELS-AMS); Tim Clark; HCLS IG; scidiscourse@googlegroups.com
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
Subject: HCLS Scientific Discourse conference call - Use Case Review- Mon October 10,  10am-11am EDT / 14:00-15:00 UTC 
 
Dear all,

Tomorrow is the next Scientific Discourse Meeting. We will discuss the use cases we are currently working on. Richard Boyce is joining our group and will expand on his use case pertaining to drug package inserts. 

All use cases, to the extent that they are available, and the agenda and dialup details can be found on our wiki:
http://www.w3.org/wiki/HCLSIG/SWANSIOC/Actions/RhetoricalStructure/meetings/20111010. An unlinked version is given below.

Best, 

Anita 

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

Agenda:

1. Discuss tentative Use Cases
2. Next steps
3. AOB


[edit] Tentative use cases as per 06 Oct 2011

1. Enhance Drug-mechanism Knowledge in Drug Product Labels

    * Lead: Richard Boyce
    * Partners - possibly merge with next use case? 

2. Annotating Truth Values: Helping Knowledge Discovery Through Hypothesis-Based Epistemic Markup

    * Leads: Jodi Schneider, Anita de Waard
    * Partners: DERI, Elsevier – still need pharma partner 

3. MIBBI Core: defining minimal information requirements for biomedical investigations defined and mapped to RDF

    * Leads: David Shotton, Tim Clark, Philippe Rocca-Serra 

4. Structuring computer science publications during authoring - rewrite of this use case

    * Leads: Tim Clark, Tudor Groza
    * Partners: MGH/Harvard, Macquarie, Elsevier 

5. Mining Treatment Outcomes: Develop a generic, anonymised, multi-EHS compliant format and an information architecture that allows access to symptom/treatment data as a Linked Data source that can be made freely available and used for drug efficacy/outcome (meta)studies

    * Leads: Anita de Waard, Joanne Luciano
    * Partners: RPI, Elsevier, - need clinical/patient forum and/or pharma partner 

6. Linking patient data to clinical recommendations, and recommendations to clinical evidence

    * Leads: Paul Groth, Anita de Waard
    * Partners: VU, Philips, Elsevier 

[edit] Dial-in & IRC Information:

    * Time: 10:00 EDT
    * 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 

-----Original Message-----
From: Waard, Anita de A (ELS-AMS)
Sent: Mon 9/26/2011 9:15
To: Tim Clark; HCLS IG; scidiscourse@googlegroups.com
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
Subject: RE: Reminder: HCLS Sci Disc call - ISA-RDF & Use Case Review- Mon 26 Sept 10am-11am EDT / 14:00-15:00 UTC 
 
Dear all,

Further to the first agenda point, use cases, for our call in 42 minutes, I'd like to review:

a) The new HCLS Use Case template which can be found here: https://docs.google.com/document/d/1DRnwXw7xIOLTjZ4TUiDtT80ouSQYfUqM9KWKXVgr60s/edit?hl=en_US 

b) Our current three use cases: http://www.w3.org/wiki/HCLSIG/SWANSIOC/Actions/RhetoricalStructure#Use_Cases

and ask ourselves and each other:

1) Are these use cases still valid, or have they been addressed by our work so far? 
2) If they are valid, how can we get them to be compliant with the new format: can someone take on each use cases?
3) If there's time: brainstorm about other use cases, or otherwise make a plan to gather more use cases before the next meeting. 

Talk in a bit! Best,

- Anita.  

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



-----Original Message-----
From: Tim Clark [mailto:tim.clark@rcn.com]
Sent: Fri 9/23/2011 11:04
To: HCLS IG; scidiscourse@googlegroups.com
Cc: Alberto Accomazzi; Allen, Bradley P (ELS-SDG); Sophia Ananiadou; Philip Bourne; Gully Burns; Daniel, Ronald (ELS-SDG); Rahul Dave; Waard, Anita de A (ELS-AMS); 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
Subject: Reminder: HCLS Sci Disc call - ISA-RDF & Use Case Review- Mon 26 Sept 10am-11am EDT / 14:00-15:00 UTC 
 
Colleagues:

This is a reminder for the biweekly HCLS Scientific Discourse concall scheduled for Monday, 26 Sept 10am-11am EDT / 14:00-15:00 UTC.

As discussed in the previous call, we'll be focusing on defined tasks and use cases for the coming year. 

- we will begin a review and update of our use cases

- ISA-RDF will be discussed as a potential shared task for 2011-12 (see underlying ISA-TAB project here:  http://isa-tools.org/  for some background)
 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
Best

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

Received on Monday, 10 October 2011 15:35:06 GMT

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