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RE: seeks input on Study Data Exchange Standards

From: Deus, Helena <helena.deus@deri.org>
Date: Tue, 21 Aug 2012 14:03:45 +0100
Message-ID: <316ADBDBFE4F4D4AA4FEEF7496ECAEF908644B11@EVS1.ac.nuigalway.ie>
To: <Peter.Hendler@kp.org>, "Sahay, Ratnesh" <ratnesh.sahay@deri.org>
Cc: <kerstin.l.forsberg@gmail.com>, <LINMD.SIMON@mcrf.mfldclin.edu>, <meadch@mail.nih.gov>, <mscottmarshall@gmail.com>, <public-semweb-lifesci@w3.org>, "Sahay, Ratnesh" <ratnesh.sahay@deri.org>
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From: Peter.Hendler@kp.org [mailto:Peter.Hendler@kp.org] 
Sent: 19 August 2012 20:09
To: Sahay, Ratnesh
Cc: Deus, Helena; kerstin.l.forsberg@gmail.com; LINMD.SIMON@mcrf.mfldclin.edu; meadch@mail.nih.gov; mscottmarshall@gmail.com; public-semweb-lifesci@w3.org; Sahay, Ratnesh
Subject: 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 <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; Peter.Hendler@kp.org <mailto:Peter.Hendler@kp.org> ; LINMD.SIMON@mcrf.mfldclin.edu <mailto:LINMD.SIMON@mcrf.mfldclin.edu> ; Kerstin Forsberg; meadch@mail.nih.gov <mailto: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 <mailto: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 <mailto:mscottmarshall@gmail.com> ] 
Sent: 17 August 2012 13:33
To: Deus, Helena
Cc: Sahay, Ratnesh; Peter.Hendler@kp.org <mailto:Peter.Hendler@kp.org> ; LINMD.SIMON@mcrf.mfldclin.edu <mailto:LINMD.SIMON@mcrf.mfldclin.edu> ; kerstin.l.forsberg@gmail.com <mailto:kerstin.l.forsberg@gmail.com> ; meadch@mail.nih.gov <mailto:meadch@mail.nih.gov> ; public-semweb-lifesci@w3.org <mailto: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 <mailto:helena.deus@deri.org>  
+353 91 495 270 <tel:%2B353%2091%20495%20270>  
  
  
  
  
  
  
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>  [mailto:Peter.Hendler@kp.org <mailto:Peter.Hendler@kp.org> ] 
Sent: 15 August 2012 16:18
To: LINMD.SIMON@mcrf.mfldclin.edu <mailto:LINMD.SIMON@mcrf.mfldclin.edu> 
Cc: kerstin.l.forsberg@gmail.com <mailto:kerstin.l.forsberg@gmail.com> ; meadch@mail.nih.gov <mailto:meadch@mail.nih.gov> ; public-semweb-lifesci@w3.org <mailto: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 <mailto:LINMD.SIMON@mcrf.mfldclin.edu> > 

08/15/2012 08:11 AM 

 

To

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

For scheduling assistance, please contact
    Crystal Gumz, Administrative Secretary
    gumz.crystal@mcrf.mfldclin.edu <mailto: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 [kerstin.l.forsberg@gmail.com <mailto: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 <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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