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COI meeting record March 11th

From: Eric Prud'hommeaux <eric@w3.org>
Date: Tue, 11 Mar 2008 16:53:44 -0400
To: "Kashyap, Vipul" <VKASHYAP1@PARTNERS.ORG>
Cc: public-hcls-coi@w3.org, public-semweb-lifesci@w3.org
Message-ID: <20080311205344.GA9840@w3.org>
* Kashyap, Vipul <VKASHYAP1@PARTNERS.ORG> [2008-03-07 10:05-0500]
> 11th March Agenda:  
>  
> Telcon Chair: Eric Prud'hommeaux
> 
> 1. Roll Call
> 2. Review Action Items from previous calls.
> 3. ACGT ontology representation of Diabetes Patient Data - Holger
> 5. Mappings if any between ACGT ontology and CDISC/HL7

covered 3 and 5 in meeting

> 4. Discussion on how CDISC/HL7 is reused, if at all
> 6. Discussion on Scope for POC - Labs, Medications, Vital Signs
> 7. Discussion on Logistics for loading and using Patient Data - Parsa/Eric P

4,6,7 postponed

minutes at: http://www.w3.org/2008/03/11-hcls-minutes

included inline:
                                      COI

11 Mar 2008

   See also: [2]IRC log and [3]Vipul's agenda

Attendees

   Present
          EricP, Jennifer, Rachel, Kerstin_Forsberg, Bo, Jyoti,
          holger_stenzhor1, Helen_Chen, CristianCocos

   Regrets
   Chair
          ericP

   Scribe
          Jyoti

Contents

     * [4]Topics
         1. [5]ACGT ontology representation of Diabetes Patient Data
         2. [6]Discussion on Logistics for loading and using Patient Data
         3. [7]Mappings if any between ACGT ontology and CDISC/HL7
         4. [8]overall mapping plan
     * [9]Summary of Action Items
     __________________________________________________________________

ACGT ontology representation of Diabetes Patient Data

   ACGT presentation:
          [10]PDF
          [11]Powerpoint

   Holger: I spoke with Chris this morning and will be presenting the
   slides

   <ericP> => [12]http://www.ifomis.org/acgt/coi-presentation.ppt slides

   Cris: I will give the presentation. ACGT means advanced clinical
   genomic trails.

   ACGT is an OWL-DL ontology. Formally defined relations and other
   restrictions.

   ACGT leverages BFO (Basic Formal Ontology) as the top-level ontology

   <ericP> Chris: adding an OWL anatomy ontology

   As of Oct 2007, there were a total of 1109 classes (primitive: 1028,
   defined: 81)

   Cris: there were a total of 121 restrictions

   <ericP> Cris: constraints extension includes identifying disjoint
   classes

   Cris: important upcoming work is to start adding FMA (anatomy) classes

   <ericP> Helen: will you be able to do classifications with your
   reasoner after adding FMA?

   <ericP> Cris: old slides; we have given up on this because FMA doesn't
   lend itself well to OWL

   <ericP> Helen: try Galen

   <ericP> Cris: Alan Rector suggested we set our sights on something more
   modest

   Cris: we spoke with Alan Rector and he suggested something less complex
   ... "Patient" is a role in ACGT and Jennifer agrees with that
   characterization

   ericP: difference between a role and a object?

   Cris: role is a dependent continuant and object is an independent
   continuant.
   ... dependent continuant depends on something else for its own
   existence. E.g., quality of an "item" depends on the "item" for its own
   existence.
   ... role is a dependent continuant because certain entities can play
   different roles, and so it can attach to independent continuant at
   different times

   <ericP> [slide 26]

   Holger: ACGT contains concepts for clinical trials and genomic research
   ... concepts/relationships encoded in the ontology are represented in
   Trial of Principle (TOP Trial) forms

Discussion on Logistics for loading and using Patient Data

   ericP: we will discuss the last agenda item
   ... we will NOT discuss the last agenda item :-)

   canceled as Parsa isn't present.

Mappings if any between ACGT ontology and CDISC/HL7

   <ericP> holger_stenzhor1: was hoping Christian could address this

   Holger: Cris will probably be able to explain the mapping issue much
   better. ACGT does not directly encode the mappings directly.
   ... ACGT partners (from Greece?) will be addressing the mapping issue

   <ericP> ACTION: Holger to invite Chris to discuss Mappings if any
   between ACGT ontology and CDISC/HL7 or to provide a narrative himself
   [recorded in
   [13]http://www.w3.org/2008/03/11-hcls-minutes.html#action01]

   Helen: is ACGT.owl is the latest file?

   <holger_stenzhor1> www.ifomis.org/acgt/1.0

   Holger: yup its latest

   <ericP> => [14]http://www.ifomis.org/acgt/1.0 ACGT ontology

overall mapping plan

   Helen: we should think how the inclusion/exclusion criteria is not
   buried under the SPARQL query
   ... these criteria are part of the trials protocol itself

   ericP: not sure if there are other ways of encoding the
   inclusion/exclusion apart from it being a part of the query

Summary of Action Items

   [NEW] ACTION: Holger to invite Chris to discuss Mappings if any between
   ACGT ontology and CDISC/HL7 or to provide a narrative himself [recorded
   in [15]http://www.w3.org/2008/03/11-hcls-minutes.html#action01]

   [End of minutes]
     __________________________________________________________________


    Minutes formatted by David Booth's [16]scribe.perl version 1.133
    ([17]CVS log)
    $Date: 2008/03/11 20:46:41 $

References

   1. http://www.w3.org/
   2. http://www.w3.org/2008/03/11-hcls-irc
   3. http://www.w3.org/mid/DBA3C02EAD0DC14BBB667C345EE2D12401E2B3CE@PHSXMB20.partners.org
   4. http://www.w3.org/2008/03/11-hcls-minutes#agenda
   5. http://www.w3.org/2008/03/11-hcls-minutes#item01
   6. http://www.w3.org/2008/03/11-hcls-minutes#item02
   7. http://www.w3.org/2008/03/11-hcls-minutes#item03
   8. http://www.w3.org/2008/03/11-hcls-minutes#item04
   9. http://www.w3.org/2008/03/11-hcls-minutes#ActionSummary
  10. http://www.ifomis.org/acgt/coi-presentation.pdf
  11. http://www.ifomis.org/acgt/coi-presentation.ppt
  12. http://www.ifomis.org/acgt/coi-presentation.ppt
  13. http://www.w3.org/2008/03/11-hcls-minutes.html#action01
  14. http://www.ifomis.org/acgt/1.0
  15. http://www.w3.org/2008/03/11-hcls-minutes.html#action01
  16. http://dev.w3.org/cvsweb/~checkout~/2002/scribe/scribedoc.htm
  17. http://dev.w3.org/cvsweb/2002/scribe/

-- 
-eric

office: +1.617.258.5741 32-G528, MIT, Cambridge, MA 02144 USA
mobile: +1.617.599.3509

(eric@w3.org)
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Received on Tuesday, 11 March 2008 21:34:35 GMT

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