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Meeting record: COI call Tue 17 Dec

From: Eric Prud'hommeaux <eric@w3.org>
Date: Tue, 17 Dec 2013 12:35:55 -0500
To: public-semweb-lifesci@w3.org, Charlie Mead <charlie.mead@yahoo.com>, Claude Nanjo <cnanjo@gmail.com>, Josh Mandel <jmandel@gmail.com>, Hans Constandt <hans@ontoforce.com>, Christel Daniel <christel.daniel@crc.jussieu.fr>, 'Sajjad Hussain' <sajjad.hussain@crc.jussieu.fr>, Mustafa Yuksel <mustafa@srdc.com.tr>, Gokce Banu Laleci Erturkmen <gokce@srdc.com.tr>, Erick Von Schweber <erick@surveyorhealth.com>, "Solbrig, Harold R." <Solbrig.Harold@mayo.edu>, Stan Huff <Stan.Huff@imail.org>, "Jiang, Guoqian, M.D., Ph.D." <Jiang.Guoqian@mayo.edu>, "Emory Fry (Google Drive)" <eafry@gmx.com>, Conor Dowling <conor-dowling@caregraf.com>, David Booth <david@dbooth.org>, Arash Shaban-Nejad <arash.shaban-nejad@mail.mcgill.ca>, Michael Denny <msdenny@mitre.org>, Kerstin Forsberg <kerstin.l.forsberg@gmail.com>, hong.sun@agfa.com, jakub.kozak@collite.cz, suat@srdc.com.tr, a.j.g.gray@hw.ac.uk, Frank.van.Harmelen@cs.vu.nl, annette@cs.vu.nl
Message-ID: <20131217173553.GF7149@w3.org>
* Eric Prud'hommeaux <eric@w3.org> [2013-12-17 09:02-0500]
>   Agenda:
>     Disease ontology (Emory, Neda, Claude)  
> 
>     Terminology Mapping chat at SWAT4LS (ericP)
>       see <http://www.w3.org/mid/20131210163614.GA16733@w3.org>

This was a bad link. Contents are in
  <http://www.w3.org/2013/12/17-hcls-minutes#item03>

> +   FDA Therapeutic Areas progress
> +     see <http://www.w3.org/2013/12/FDA-TA/>

Meeting record at <http://www.w3.org/2013/12/17-hcls-minutes>
or as text below:

17 Dec 2013

Contents

     * [3]Topics
         1. [4]FDA Therapeutic Areas progress
         2. [5]Disease ontology
         3. [6]Terminology Mapping chat
     * [7]Summary of Action Items
     __________________________________________________________________

FDA Therapeutic Areas progress

   <ericP> scribenick: MikeDenny

   <ericP> ericP: blah blah blah

   <ericP> ... and still more blah blah blah

   test

   <ericP> [8]FDA TA MetaModel

   <kerstin> URL?

   <ericP> [9]FDA TA MetaModel

   <ericP> [10]Protege

   <ericP> FDA Therapeutic Areas modeling effort underway to describe
   disease effects -- being supported by HCLS with OWL modeling.

   <ericP> [11]bottom-most ontology for use in Protege

   <matthias_samwald> just dialed in.

   <ericP> [12]FDA TA MetaModel

   <matthias_samwald> thanks.

   <ericP> May be helpful for efficacy assessment with notion of
   'therapeutic intervention' class.

   <Sajjad_INSERM> You mentioned that you facing some errors: are they
   parsing errors or modelling errors?

   <emory> speaking in above where attributed to ericP

   <emory> Answers question about lack of fine granularity in model by
   referring to it as a metamodel that will drive specific therapeuic
   areas.

   <kerstin> I can see some future alignment opportunties with some of the
   mid-level OBO ontologies e.g. Ontology for General Medical Science
   (OGMS) and Ontology for Biomedical Investigations (OBI)

   <emory> Answers question about kinds of observations supported like
   composite observations by asking for suggestions.

   < ??> Suggests nested panels etc.

   <emory> Question of level of detail needed in this modeling is still
   being discussed with FDA.

   <emory> IIn response to question about clinical trial submission using
   OWL specification instead of FHIR, for example, this is taken as a
   consideration.

   <kerstin> If for example neurological TA is one of the 12 FDA TAs it
   could be interesting to look into some alignement opportunties with the
   NeuroPsychological Testing Ontology
   [13]https://code.google.com/p/neuropsychological-testing-ontology/

   <??> How do you handle disease where you do not know underlying
   physiological process?

   <emory> The metamodel is now a pragmatic approach.

   <kerstin> MikeDenny: Good question - check out my references above and
   also the reference articla behind OGMS, check out
   [14]http://code.google.com/p/ogms/

   <emory> Ansers question of how do you link this metamodel with other
   standards by referring to C-CDA and FHIR mapping being a goal of the
   project.

   <kerstin> quick question - How are behind folks behind MikeDenny and
   TallTed alias (behind kerstin in Kerstin Forsberg, AstraZenenca)?

Disease ontology

   <kerstin> thx

   <emory> Calls for volunteers to continue on this work to demonstrate to
   FDA the value of RDF and OWL modeling.

   <eafry> [15]http://64.87.15.66:8888/webprotege

   <ericP> eafry: neda took the UMLS data and created a script to dump the
   hierarchy in the current SNOMED disease tree

   <ericP> ... there may be other relevant branches but to start, she
   grabbed the disease tree

   <ericP> ... she exposed the preferred label as the node label

   <ericP> ... her next pass will expose the UMLS CUI and the SNOMED code

   <ericP> ... the purpose of the tree is to make available the majority
   of the disease concepts in SNOMED

   <eafry> The login for the site above showing a couple of public
   ontologies will need username + password of 'test'.

   <ericP> ... it's very disorganized

   <ericP> ... a goal is to find a smaller set of terms which can be
   post-coordinated to submsume current pre-coordinated terms

   <ericP> ... once we get the extracts with the UMLS codes, we can start
   extend into other ontologies

   <ericP> ... so we've been thinking about axes needed for
   post-coordination

   <eafry> Show relation between pre-coordination and post-coordination
   SNOMED coding to express diseases using an OWL model.

   <ericP> ... age, etiology (which could go into the TA metamodel), signs
   and symptoms, ...

   <ericP> ... enable q's like "what are the diseases which produce hives
   and shortness of breath?"

   <ericP> ... there's a discussion area, as well as notes and viersion
   history

   <ericP> ... this will ideally allow us to collaboratively move to
   post-coordinated

   <ericP> neda: when we have these concepts as classes, we'll be able to
   attach more rules and use them for e.g. clinical decision support

   <eafry> The site includes a Disease Ontology and a FHIR Ontology.

   <ericP> Sajjad_INSERM: what branches of SNOMED do you have?

   <ericP> eafry: |clinical observations| |disease|

   <ericP> ... we'll need more stuff, but that's our start

   <eafry> The Disease Ontology is the branch of SNOMED starting at
   Clinical Obervations - Disease.

Terminology Mapping chat

   <ericP> 1 Document different ways that terminology mappings led to
   inappropriate assertions, potentially because of transitive inference
   as in Hong Sun's examples.

   <ericP> 2 Examine successful/valid uses of termmaps for sensitivity to
   use context. Does your use of the termmap imply that it's useful to
   someone else?

   <ericP> 3 Describe how to fix the failures, e.g. the lenses from
   EHR4CR.

   <ericP> 4 Codify the context associated with the fixes to enable
   someone else with the same context to employ them.

   <ericP> 5 Once we have a good story, ask the owners of the
   terminologies to own the mappings.

   <kerstin> Lenses are from OpenPHACTS

   <ericP> alister: the idea of a Lense is you turn on or off mapping
   because e.g. two chemicals share stereochemistry or INCHI key

   <kerstin> Some examples of Justifuications sitting behind the Open
   PHACTS Lenses are described in my blog post on applying the same
   thinking on terminiligy mappings
   [16]http://kerfors.blogspot.se/2013/09/justifications-of-mappings.html

   <ericP> ... the tool captures the mappings and justifications

   <Alister> Lens used in Terminology Mapping to turn on and off mappings
   based on their context.

   <agray> Here is the paper where we outline the original idea behind
   lenses. This was done in the context of linking data instances rather
   than terminologies, but the approach could easily be ported across.
   [17]http://ceur-ws.org/Vol-951/paper5.pdf

   <ericP> Call for volunteers to continue work on this Terminology
   Mapping project.

   <agray> I'm happy to be involved.

   <allister> In response to request, will try to dig up a demo that
   works.

   <kerstin> Here's a nice blog post from Hong et al in the SALUS project
   [18]http://www.srdc.com.tr/projects/salus/blog/?p=241

   <agray> I will email details of a working example for the use of lenses
   in the Open PHACTS project. (It needs some explanations to make it
   work.)

   <Sajjad_INSERM> Paper Link on Terminology Mapping from Hong:
   [19]http://arxiv.org/ftp/arxiv/papers/1310/1310.4156.pdf

   <ericP> next meeting 7 Jan

   Good Bye!

Summary of Action Items

   [End of minutes]
     __________________________________________________________________


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Found ScribeNick: MikeDenny
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WARNING: No "Present: ... " found!
Possibly Present: Claude EmoryFry IPcaller Kerstin_Forsberg MikeDenny Mike_Denny
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n_ matthias_samwald neda scribenick
You can indicate people for the Present list like this:
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<dbooth> Meeting: Weekly Baking Club Meeting


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Got date from IRC log name: 17 Dec 2013
Guessing minutes URL: [23]http://www.w3.org/2013/12/17-hcls-minutes.html
People with action items:

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References

   1. http://www.w3.org/
   2. http://www.w3.org/2013/12/17-hcls-irc
   3. http://www.w3.org/2013/12/17-hcls-minutes#agenda
   4. http://www.w3.org/2013/12/17-hcls-minutes#item01
   5. http://www.w3.org/2013/12/17-hcls-minutes#item02
   6. http://www.w3.org/2013/12/17-hcls-minutes#item03
   7. http://www.w3.org/2013/12/17-hcls-minutes#ActionSummary
   8. http://www.w3.org/2013/12/FDA-TA/
   9. http://www.w3.org/2013/12/FDA-TA/
  10. http://www.w3.org/2013/12/FDA-TA/FDA-TA-renalRejection-Classes-tab.png
  11. http://www.w3.org/2013/12/FDA-TA/subjects.ttl
  12. http://www.w3.org/2013/12/FDA-TA/
  13. https://code.google.com/p/neuropsychological-testing-ontology/
  14. http://code.google.com/p/ogms/
  15. http://64.87.15.66:8888/webprotege
  16. http://kerfors.blogspot.se/2013/09/justifications-of-mappings.html
  17. http://ceur-ws.org/Vol-951/paper5.pdf
  18. http://www.srdc.com.tr/projects/salus/blog/?p=241
  19. http://arxiv.org/ftp/arxiv/papers/1310/1310.4156.pdf
  20. http://dev.w3.org/cvsweb/~checkout~/2002/scribe/scribedoc.htm
  21. http://dev.w3.org/cvsweb/2002/scribe/
  22. http://dev.w3.org/cvsweb/~checkout~/2002/scribe/
  23. http://www.w3.org/2013/12/17-hcls-minutes.html
  24. http://dev.w3.org/cvsweb/~checkout~/2002/scribe/scribedoc.htm

-- 
-ericP

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