RE: seeks input on Study Data Exchange Standards

hi all,



sorry to have missed the discussion.  having been involved with HL7 the
last several years, glad to see some progress is being made on acceptance
of semantic web technologies.  as an ANSI organization, a change such as
moving to a different representation is not a step that is either lightly
or easily taken.



i think the resistance to v3 at HL7 is more on the migration front,
especially since the vendors have already made their investments.  newer
initiatives, i think, are doing better.



cheers,

michael



Michael Miller

Software Engineer

Institute for Systems Biology





*From:* M. Scott Marshall [mailto:mscottmarshall@gmail.com]
*Sent:* Tuesday, August 21, 2012 7:24 AM
*To:* Deus, Helena; Peter.Hendler@kp.org; Sahay, Ratnesh;
kerstin.l.forsberg@gmail.com; LINMD.SIMON@mcrf.mfldclin.edu;
meadch@mail.nih.gov
*Cc:* public-semweb-lifesci@w3.org
*Subject:* Re: seeks input on Study Data Exchange Standards



I took some rough notes at http://www.w3.org/2012/08/21-hcls-minutes.html .



Best,

Scott



On Tue, Aug 21, 2012 at 3:03 PM, Deus, Helena <helena.deus@deri.org> wrote:

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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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 Thank you.



*"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<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 <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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 Thank you.

*"Lin MD, Simon"
<**LINMD.SIMON@mcrf.mfldclin.edu*<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<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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-- 
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