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Re: seeks input on Study Data Exchange Standards

From: M. Scott Marshall <mscottmarshall@gmail.com>
Date: Fri, 17 Aug 2012 15:36:34 +0200
Message-ID: <CACHzV2MrDmELL5sLMGGcS0KHka4uDWyNq616shZ7k=V7J0BwTw@mail.gmail.com>
To: "Deus, Helena" <helena.deus@deri.org>
Cc: "Sahay, Ratnesh" <ratnesh.sahay@deri.org>, 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" <ronan.fox@deri.org>
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<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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Received on Friday, 17 August 2012 13:44:18 GMT

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