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RE: Notes last HCLS Sci Disc call and plan for the next one

From: Michael Miller <Michael.Miller@systemsbiology.org>
Date: Wed, 5 Oct 2011 11:42:04 -0700
Message-ID: <e3160be90f69e75743a268474f77b1bb@mail.gmail.com>
To: David Shotton <david.shotton@zoo.ox.ac.uk>, "Waard, Anita de A (ELS-AMS)" <A.dewaard@elsevier.com>
Cc: Tim Clark <tim.clark@rcn.com>, HCLS IG <public-semweb-lifesci@w3.org>, scidiscourse@googlegroups.com, samwald@gmx.at, gil@isi.edu, 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>, 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>, Kaitlin Thaney <k.thaney@digital-science.com>, Karin Verspoor <Karin.Verspoor@ucdenver.edu>, Lynette Hirschman <lynette@mitre.org>, 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>
hi david,



i'd be interested in this effort.  as you probably know, the bioRDF group
has been working with the gene expression atlas folks on RDF for micro array
experiments that's been based on MAGE-TAB. for a paper and a W3C note.  we
found that there were already 3 versions.



cheers,

michael



Michael Miller

Software Engineer

Institute for Systems Biology





*From:* public-semweb-lifesci-request@w3.org [mailto:
public-semweb-lifesci-request@w3.org] *On Behalf Of *David Shotton
*Sent:* Wednesday, October 05, 2011 9:46 AM
*To:* Waard, Anita de A (ELS-AMS)
*Cc:* Tim Clark; HCLS IG; scidiscourse@googlegroups.com; samwald@gmx.at;
gil@isi.edu; 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; 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; Kaitlin Thaney; Karin
Verspoor; Lynette Hirschman; sa.sansone@gmail.com; Kees van Bochove; Katy
Wolstencroft; Jun Zhao
*Subject:* Re: Notes last HCLS Sci Disc call and plan for the next one



Dear Anita,

re the ISATAB collaboration (your point 2 below): Tim, Philippe and I agreed
to work on this, to take forward the ISA-RDF proposal and combine it with
the generic elements from our MIIDI minimum information standard, the ideas
for MIBBI Core, and other attempts at defining minimal information
requirements for biomedical investigations that Tim knows about.  We will
attempt to come up with an agreed set of terms - that we could call MIBBI
Core for want of a better name - that are defined and mapped to RDF.  I plan
to start work on this tomorrow, with a view to circulating a draft to Tim
and Philippe for amendment, then submission to all the task force in advance
of our next conference call on October 10th.

Kind regards,

David


On 04/10/2011 21:55, Waard, Anita de A (ELS-AMS) wrote:

Dear all,



I think we never put up notes for last week's meeting, oops! The
conclusions were, as far as I can recall:



1 - Re. our old use cases: we will revisit use case 1 (Jodi
Schneider/Anita de Waard) and 2 (Tim will ask Tudor Groza's input).
Use case 3 has been addressed by ORB and is dropped.



2 - Re. ISATAB collaboration: this will also be written up as a use
case according to the new template (see links below)



3 - Before the next call, all use cases will be circulated in draft
and comments invited



4 - Also before the next call, we will all circulate use case ideas we
would like to work on.



In this light, I hereby enclose the draft document Jodi and I have
been working on: Use Case 1, but following the new template.



I would like to solicit collaboration on two other use cases:



1) Linking patient data to clinical recommendations and then to
clinical evidence



2) Mining treatment outcomes as a way to provide an anonymous
'clinical trial' type of data source that can be made freely available
and used for drug efficacy/outcome studies.



If anyone is interested in working on either of these, please drop me a line.



The proposal is that we discuss all submitted and proposed use cases
at the call next week.

All suggestions most welcome!



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: Mon 9/26/2011 9:15

To: Tim Clark; HCLS IG

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 <tim.clark@rcn.com>]

Sent: Fri 9/23/2011 11:04

To: HCLS IG

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)













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





-- 

Dr David Shotton
Image Bioinformatics Research Group, Department of Zoology, University of
Oxford
South Parks Road, Oxford OX1 3PS, UK.   Phone: +44 (0)1865-271193   Skype:
davidshotton
Received on Wednesday, 5 October 2011 18:42:37 GMT

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