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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> Topic: HCLS standards - Helena
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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?
>
>
>
>
>
>
>
>
> *NOTICE TO RECIPIENT:*  If you are not the intended recipient of this
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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<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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>
> *"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
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>
>
> -----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