W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > December 2013

no COI call Tue 3 Dec

From: Eric Prud'hommeaux <eric@w3.org>
Date: Mon, 2 Dec 2013 18:59:30 -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>
Message-ID: <20131202235928.GC6440@w3.org>
Hi all, I don't have an agenda lined up so let's cancel this week's call.

last meeting minutes are at:


26 Nov 2013


          Kerstin_Forsberg, +, +, ericP,
          charlie, +1.617.500.aacc, Josh, EmoryFry, +1.469.226.aadd,
          claud_nanjo, neda, [IPcaller], Mike_Denny





     * [3]Topics
         1. [4]FDA DO
     * [5]Summary of Action Items

   <scribe> scribenick: ericP


   charlie: FDA has 5 Therapeutic Areas in SemWeb
   ... we're working on 12 more
   ... a DO would be helpful WRT TAs
   ... FDA doesn't use SNOMED
   ... if the semantics suffice, we could bind it to MeDRA as well

   emory: the goal is to use current anatomic concepts current organized
   by anatomic location
   ... the disease manifestation of e.g. lung and kidney disease would be
   related to anatomy but the concepts would be broader

   charlie: FDA is describing TA work in terms of efficacy points, which
   are related to underlying pathophysiological attributes
   ... FDA is committed to reusing existing ontologies. expect that they
   have had to confront some disease issues already

   emory: within our group, charlie and ericP can resolve the ontology
   against the TAs and avoid duplication.

   charlie: i think FDA really does want to share [which we need for

   emory: i'm currently polling ihsedo to see if anyone's already doing
   ... i want to make sure we don't get bogged down in @@1

   <Josh> (IHDSDO)

   charlie: it's not clear yet what drug models they'll develop

   <Josh> er, IHTSDO

   emory: we can start the modeling work and let ericP and charlie alert
   if there are conflicts

   charlie: i expect they are modeling the intersection between a
   pathophysiological process and a objective assessment of the efficacy
   of a treatment modality

   claud: SNOMED seems to becoming the standard for expressing clinical
   ... is it possible that our effort be done as an extension to SNOMED?

   emory: i discussed with keith campbell (VA rep at IHTSDO).
   ... keith is first checking to see that anyone else is working on a
   disease ontology (reduce risk of duplication).
   ... second, providing an update on the SNOMED naming and extension
   process because he encourages us to model using the @@3 workbench, and
   create an extension, modeled using SNOMED conventions and rules, and
   submit it to SNOMED.
   ... there needs to be alignment with SNOMED process, ideally following
   their conventions.
   ... sites and symptoms should all be pre-existing
   ... [re: winnowing down SNOMED], is see use cases for "the one"
   ... re: what is the purpose of doing a pathophysiological hierarchy, i
   want to do diagnostic reasoning over clinical observations
   ... e.g. if i see signs and symptoms in different organs, i should be
   able to generate a differential diagnosis

   <Kerstin> Disease and diseare areas, such as Infectius diseases, models
   using on the Ontology for General Medical Science (OGMS)
   [6]http://code.google.com/p/ogms/ - See this central illustration

   emory: focusing on pathophysiology instead of sites
   ... others may have other use cases

   <Kerstin> The OGMS based disease ontologies are not (yet) connected to
   SNOMED sign/symptoms, nor to LOINC measurements, of my knowledge.

   ericP: i suspect that the attributes for research are considerably
   wider than what will eventually be used e.g. in the bodies of CDS rules

   emory: does this seem too-far-fetched?
   ... we need broad enough interest to engage subject matter experts
   ... I can reach out the Bob at ASU (and his PhD students). Neda has
   ties to UCSD.
   ... Josh and charlie, do you know of communities where folks might be
   interested in providing commentary on our efforts?

   charlie: i may be working on implementation guides, which would be me
   well in SNOMED. i did emergency med so i'm not an authority.

   Josh: rafael richards is certainly excited about having RDF

   neda: we extracted UMLS terms to index DBGAP
   ... they're waiting for funding, but they'd be a good use case
   ... (at UCSD)
   ... Niggam Shah (Stanford) was working on a disease ontology as well

   emory: I can call Samson Tu to see if there's interest within the
   protege group.
   ... i'd like to get one of my engineers to extract the relevent
   branches of SNOMED and load them into WebProtege.
   ... i've never used V2, but i've heard good things about it from a
   collaborative perspective

   neda: i have the ontology that we used for DBGAP

   emory: whether we pull the concepts from SNOMED or from an existing
   model, we'll load them into webprotege.
   ... ericP and I talked about who's best to manage the project

   ericP: who's funding niggam's work?

   neda: NIH was supposed to fund DBGAP work (closed for a bit 'cause of
   ... this was joint work to do NLP to integrate patient data
   ... part of this was a disease ontology.
   ... original PI was wendy chapman

   emory: let's create a mission statement and ask neda to approach the
   above for ideas and engagement.

   ericP: what's the related HL7 WG?

   charlie: about a year ago, that would have been patient care

   Josh: and we should ping lloyd

   emory: could ericP or Josh catch Neda and Claud with the FDA work?

   <Kerstin> Let us all know when you do that FHIR2RDF intro - I need a
   recap to get all of thsi great work

Summary of Action Items

   [End of minutes]

    Minutes formatted by David Booth's [8]scribe.perl version 1.138
    ([9]CVS log)
    $Date: 2013-12-02 23:57:22 $


   1. http://www.w3.org/
   2. http://www.w3.org/2013/11/26-hcls-irc
   3. http://www.w3.org/2013/11/26-hcls-minutes#agenda
   4. http://www.w3.org/2013/11/26-hcls-minutes#item01
   5. http://www.w3.org/2013/11/26-hcls-minutes#ActionSummary
   6. http://code.google.com/p/ogms/
   7. http://kerfors.blogspot.se/2011/09/icbo2011-disease-terminologies-and.html
   8. http://dev.w3.org/cvsweb/~checkout~/2002/scribe/scribedoc.htm
   9. http://dev.w3.org/cvsweb/2002/scribe/


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Received on Tuesday, 3 December 2013 00:00:04 UTC

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