W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > August 2012

RE: seeks input on Study Data Exchange Standards

From: Erich Gombocz <egombocz@io-informatics.com>
Date: Mon, 20 Aug 2012 07:56:56 -0700
Message-ID: <08AE3015BD5DF149951910A5E851F010D40FCC@MAIL-02.io-informatics.com>
To: "Helena Deus" <helena.deus@deri.org>, <Peter.Hendler@kp.org>
Cc: <ratnesh.sahay@deri.org>, <kerstin.l.forsberg@gmail.com>, <LINMD.SIMON@mcrf.mfldclin.edu>, <meadch@mail.nih.gov>, <mscottmarshall@gmail.com>, <public-semweb-lifesci@w3.org>
Dear Helena,

 

Thank you for organizing this - I'll be attending the early morning
meeting tomorrow at 6:00 AM PDT, and am looking forward to it!

 

Cordially, as always,

 

Erich

 

From: Helena Deus [mailto:helena.deus@deri.org] 
Sent: Monday, August 20, 2012 12:16 AM
To: Peter.Hendler@kp.org
Cc: ratnesh.sahay@deri.org; kerstin.l.forsberg@gmail.com;
LINMD.SIMON@mcrf.mfldclin.edu; meadch@mail.nih.gov;
mscottmarshall@gmail.com; public-semweb-lifesci@w3.org
Subject: Re: seeks input on Study Data Exchange Standards

 

Dear all, 

 

The best time for the telco appears to be tomorrow (Tue 21st) at 1PM
GMT/3PM CET/9AM EDT.

 

I've scheduled  a webex meeting for us, information as follows: 

 

Call-in toll-free number (UK): 0800-051-3810

Call-in toll number (UK): +44-20-310-64804

Backup call-in toll number (US/Canada): 1-408-792-6300

Attendee access code: 30282094

 

 

We should also log the meeting minutes using W3C IRC system:
http://irc.w3.org/, channel #hcls

 

Kind Regards,

 

Helena F. Deus, PhD

Unit Leader, Bioinformatics and Computational Biology

Digital Enterprise Research Institute

helena.deus@deri.org

+353 91 495 270

 

 

 

 

 

 

On Aug 19, 2012, at 8:08 PM, Peter.Hendler@kp.org wrote:





I have just proposed an explicit way to address the problem and sent it
out internally for comments.  I hope to be able to discuss it.  Did we
ever finalize a date time and phone number for the discussion? 




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"Sahay, Ratnesh" <ratnesh.sahay@deri.org> 

08/18/2012 02:13 PM 


To

"Sahay, Ratnesh" <ratnesh.sahay@deri.org>, "Deus, Helena"
<helena.deus@deri.org>, "M. Scott Marshall" <mscottmarshall@gmail.com> 


cc

Peter Hendler/CA/KAIPERM@KAIPERM, <LINMD.SIMON@mcrf.mfldclin.edu>,
"Kerstin Forsberg" <kerstin.l.forsberg@gmail.com>,
<meadch@mail.nih.gov>, "HCLS hcls" <public-semweb-lifesci@w3.org> 


Subject

RE: seeks input on Study Data Exchange Standards

 

		




Regarding Peter's concern (a very important one) on the extensional
(closed-world) and Intensional logics in context of HL7+ Semantic Web,
one of my publication (attached)  discuses this in details. 
  
Regards, 
Ratnesh 
  
From: Sahay, Ratnesh [ <mailto:ratnesh.sahay@deri.org>
mailto:ratnesh.sahay@deri.org] 
Sent: 18 August 2012 21:08
To: Deus, Helena; M. Scott Marshall
Cc: Peter.Hendler@kp.org; LINMD.SIMON@mcrf.mfldclin.edu; Kerstin
Forsberg; meadch@mail.nih.gov; HCLS hcls
Subject: RE: seeks input on Study Data Exchange Standards 
  
Good pointer, Lena. 
  
Regards, 
Ratnesh 
  
From: Helena Deus [ <mailto:helena.deus@deri.org>
mailto:helena.deus@deri.org] 
Sent: 18 August 2012 21:05
To: M. Scott Marshall
Cc: Sahay, Ratnesh;  <mailto:Peter.Hendler@kp.org> Peter.Hendler@kp.org;
<mailto:LINMD.SIMON@mcrf.mfldclin.edu> LINMD.SIMON@mcrf.mfldclin.edu;
Kerstin Forsberg;  <mailto:meadch@mail.nih.gov> meadch@mail.nih.gov;
HCLS hcls
Subject: Re: seeks input on Study Data Exchange Standards 
  
A few papers in this special issue in the Journal of Biomedical
Informatics (translating standards into practice) may be relevant for
this discussion: 
http://www.sciencedirect.com/science/article/pii/S1532046412000962 
  
Kind regards, 
Lena 
  
Helena F. Deus, PhD 
Unit Leader, Bioinformatics and Computational Biology 
Digital Enterprise Research Institute 
 <mailto:helena.deus@deri.org> helena.deus@deri.org 
+353 91 495 270 
  
  
  
  
  
  
On Aug 17, 2012, at 2:36 PM, M. Scott Marshall wrote: 
  
I have made a new poll with timezone-support enabled: 
http://doodle.com/kx7vrbhamd3s2wmd 
  
Helena, Kirsten, and Ratnesh - please fill the above poll in to avoid
misunderstanding about times. 
  
BTW, I also submitted a feature request to Doodle to make
timezone-support default enabled (opt out instead of opt in). 
  
Cheers, 
Scott

-- 
M. Scott Marshall, PhD
MAASTRO clinic, http://www.maastro.nl/en/1/
http://eurecaproject.eu/
https://plus.google.com/u/0/114642613065018821852/posts
http://www.linkedin.com/pub/m-scott-marshall/5/464/a22 
  
On Fri, Aug 17, 2012 at 3:19 PM, Deus, Helena <helena.deus@deri.org>
wrote: 
Ups, I must have missed the "enable time zone support", could you create
a new poll with time zone enabled, please, Scott? 
  
So far, only me and Kerstin responded to the doodle poll so not too much
harm done. 
(@Kerstin, the default time zone was irish, by the way) 
  
Best, 
Lena 
  
From: M. Scott Marshall [mailto: <mailto:mscottmarshall@gmail.com>
mscottmarshall@gmail.com] 
Sent: 17 August 2012 13:33
To: Deus, Helena
Cc: Sahay, Ratnesh;  <mailto:Peter.Hendler@kp.org> Peter.Hendler@kp.org;
<mailto:LINMD.SIMON@mcrf.mfldclin.edu> LINMD.SIMON@mcrf.mfldclin.edu;
<mailto:kerstin.l.forsberg@gmail.com> kerstin.l.forsberg@gmail.com;
<mailto:meadch@mail.nih.gov> meadch@mail.nih.gov;
<mailto:public-semweb-lifesci@w3.org> public-semweb-lifesci@w3.org; Fox,
Ronan
Subject: Re: seeks input on Study Data Exchange Standards 
  
Hi Helena, 
  
Good initiative all. 
  
Would you please create a doodle with the timezone option (it's easy to
miss unfortunately)? 
  
Also unfortunate that, last I checked, Doodle doesn't let you edit that
config option in but requires you to create an entirely new doodle. 
  
Cheers, 
Scott 
  
n.b. Doodle should make timezones the default! The current design has
caused a lot of confusion and wasted time with international
collaborators. 
  
-- 
M. Scott Marshall, PhD
MAASTRO clinic, http://www.maastro.nl/en/1/
http://eurecaproject.eu/
https://plus.google.com/u/0/114642613065018821852/posts
http://www.linkedin.com/pub/m-scott-marshall/5/464/a22 
On Fri, Aug 17, 2012 at 2:17 PM, Helena Deus <helena.deus@deri.org>
wrote: 
Hi All, 
  
There seems to be a lot of interest in brainstorming about this. 
How about doing an ad hoc call for this? 
  
I've set up a doodle pole so that we can try to agree on a date next
week: http://doodle.com/g5vimt6gyshv77fd 
  
We can use W3C systems, I presume, right, Eric? 
Kind Regards , 
Helena 
  
Helena F. Deus, PhD 
Unit Leader, Bioinformatics and Computational Biology 
Digital Enterprise Research Institute 
 <mailto:helena.deus@deri.org> helena.deus@deri.org 
 <tel:%2B353%2091%20495%20270> +353 91 495 270 
  
  
  
  
  
  
On Aug 15, 2012, at 5:16 PM, Sahay, Ratnesh wrote: 
  
Hi Peter and All, 
  
I think entities that are part of Version 3 XML coreSchemas (e.g,
Vocabulary ) can be represented in OWL or DL, however problem is with
local models (e.g., RMIM) that are context-specific (i.e., time, place,
event dependent information).  One observation in the article below:
"One major characteristic of this Extensional logic is that "classes
must be extended by the authors of the model.".  It is also the case
with the Intensional logic. For example, class-subclass relation needs
to be explicitly stated here as well, with a feature of inference that
may entail  additional relations. I think one of the main differences
between closed-world UML/object-oriented paradigm and open-world
(ontologies) is use of properties.   An ontology property appears, at a
first glance, to be the same as the UML association or attribute.
However, properties in an ontology are first-class modelling elements,
while the UML association or attribute is attached to UML classes where
they are described. This means the UML association or attribute cannot
exist in isolation or as a self-describing entity defining relationships
such as inheritance. More precisely, in an ontology a relation can exist
without specifying any classes to which it might relate.  Some key
benefits that I see of using Semantic Web for the HL7 standard:   
  
(1 ) Semantic Web technologies as a "common medium" where the upper
layer (Information Model or terminologies in OWL) and lower layer (data
in RDF) can be engaged with each other during the 
integration process. Without the need of transformation (or mediation)
between them, as is the case with UML-XML based systems. 
(2)  The mutual use of Semantic Web technologies as a "common medium"
between upper and lower layers provide computable semantics of the
information models (as ontologies), improving 
the reuse and overall data integration. 
  
There are other benefits (and limitations as well) but that require long
discussion. 
  
Regards, 
Ratnesh   
  
From:  <mailto:Peter.Hendler@kp.org> Peter.Hendler@kp.org [mailto:
<mailto:Peter.Hendler@kp.org> Peter.Hendler@kp.org] 
Sent: 15 August 2012 16:18
To:  <mailto:LINMD.SIMON@mcrf.mfldclin.edu>
LINMD.SIMON@mcrf.mfldclin.edu
Cc:  <mailto:kerstin.l.forsberg@gmail.com> kerstin.l.forsberg@gmail.com;
<mailto:meadch@mail.nih.gov> meadch@mail.nih.gov;
<mailto:public-semweb-lifesci@w3.org> public-semweb-lifesci@w3.org
Subject: RE: seeks input on Study Data Exchange Standards 
  
Just did a white paper on it.  I don't think it's a good idea in general
to put clinical models all in OWL or DL at all. 
That part is best left to the SNOMED vocabulary part. 

Here is a very recent paper on how to mix the Extensional and
Intensional parts of the models according to how HL7 V3 does it and how
Kaiser does it. 

http://www.ringholm.com/docs/05000_Clinical_Models_and_SNOMED.htm 




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"Lin MD, Simon" < <mailto:LINMD.SIMON@mcrf.mfldclin.edu>
LINMD.SIMON@mcrf.mfldclin.edu> 

08/15/2012 08:11 AM 

 


To

"Mead, Charlie (NIH/NCI) [C]" < <mailto:meadch@mail.nih.gov>
meadch@mail.nih.gov>, Kerstin Forsberg <
<mailto:kerstin.l.forsberg@gmail.com> kerstin.l.forsberg@gmail.com>,
HCLS hcls < <mailto:public-semweb-lifesci@w3.org>
public-semweb-lifesci@w3.org> 


cc

	

Subject

RE: seeks input on Study Data Exchange Standards


  

 

		





Great topic! I can imagine a potential white paper from this group. 

Besides technology, factors to consider might include: flexibility,
implementation cost, return on investments, path to migration etc.

Best regards,

Simon

==================================================
Simon Lin, MD
Director, Biomedical Informatics Research Center 
Marshfield Clinic Research Foundation 
1000 N Oak Ave, Marshfield, WI 54449 
Office 715-221-7299 
 <mailto:Lin.Simon@mcrf.mfldclin.edu> Lin.Simon@mcrf.mfldclin.edu 
 <http://www.marshfieldclinic.org/birc> www.marshfieldclinic.org/birc

For scheduling assistance, please contact
    Crystal Gumz, Administrative Secretary
     <mailto:gumz.crystal@mcrf.mfldclin.edu>
gumz.crystal@mcrf.mfldclin.edu
    715-221-6403


-----Original Message-----
From: Mead, Charlie (NIH/NCI) [C] [ <mailto:meadch@mail.nih.gov>
mailto:meadch@mail.nih.gov] 
Sent: Wednesday, August 15, 2012 1:02 AM
To: Kerstin Forsberg; HCLS hcls
Subject: RE: seeks input on Study Data Exchange Standards

I would say Yes -- particularly since there is now an effort to
represent some of newest HL7 standards -- FHIR resource definitions in
particular -- using SW approaches...and the BRIDG OWL representation
will almost certainly benefit from this effort.

charlie
________________________________________
From: Kerstin Forsberg [ <mailto:kerstin.l.forsberg@gmail.com>
kerstin.l.forsberg@gmail.com]
Sent: Wednesday, August 15, 2012 1:57 AM
To: HCLS hcls
Subject: FDA: seeks input on Study Data Exchange Standards

FDA seeks "input from industry, technology vendors, and other members of
the public regarding the advantages and disadvantages of current and
emerging open, consensus-based standards for the exchange of regulated
study data. "

In the annoncement for a meeting 5 November FDA ask for responses,
before 5 October, on questions such as "- What are the advantages and
disadvantages of HL7 v3 and CDISC ODM?"

And, interestingly, they also ask: "- Are there other open data exchange
standards that should be evaluated?"

Is this an opportunity for a semantic web based proposal?

Kind Regards

Kerstin Forsberg

AstraZeneca



 
<https://www.federalregister.gov/articles/2012/08/14/2012-19748/regulato
ry-new-drug-review-solutions-for-study-data-exchange-standards-notice-of
-meeting-request-for>
https://www.federalregister.gov/articles/2012/08/14/2012-19748/regulator
y-new-drug-review-solutions-for-study-data-exchange-standards-notice-of-
meeting-request-for

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