RE: seeks input on Study Data Exchange Standards

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] 
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] 
Sent: 18 August 2012 21:05
To: M. Scott Marshall
Cc: Sahay, Ratnesh; 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
 
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
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:mscottmarshall@gmail.com] 
Sent: 17 August 2012 13:33
To: Deus, Helena
Cc: Sahay, Ratnesh; Peter.Hendler@kp.org; LINMD.SIMON@mcrf.mfldclin.edu; 
kerstin.l.forsberg@gmail.com; meadch@mail.nih.gov; 
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
helena.deus@deri.org
+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: Peter.Hendler@kp.org [mailto:Peter.Hendler@kp.org] 
Sent: 15 August 2012 16:18
To: LINMD.SIMON@mcrf.mfldclin.edu
Cc: kerstin.l.forsberg@gmail.com; meadch@mail.nih.gov; 
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" <LINMD.SIMON@mcrf.mfldclin.edu>
08/15/2012 08:11 AM


To
"Mead, Charlie (NIH/NCI) [C]" <meadch@mail.nih.gov>, Kerstin Forsberg <
kerstin.l.forsberg@gmail.com>, HCLS hcls <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 
Lin.Simon@mcrf.mfldclin.edu 
www.marshfieldclinic.org/birc

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


-----Original Message-----
From: Mead, Charlie (NIH/NCI) [C] [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 [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/regulatory-new-drug-review-solutions-for-study-data-exchange-standards-notice-of-meeting-request-for



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