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.d...@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.d...@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:mscottmarsh...@gmail.com] > Sent: 17 August 2012 13:33 > To: Deus, Helena > Cc: Sahay, Ratnesh; peter.hend...@kp.org; linmd.si...@mcrf.mfldclin.edu; > kerstin.l.forsb...@gmail.com; mea...@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.d...@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.d...@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.hend...@kp.org [mailto:peter.hend...@kp.org] > Sent: 15 August 2012 16:18 > To: linmd.si...@mcrf.mfldclin.edu > Cc: kerstin.l.forsb...@gmail.com; mea...@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 > > > > > NOTICE TO RECIPIENT: If you are not the intended recipient of this e-mail, > you are prohibited from sharing, copying, or otherwise using or disclosing > its contents. If you have received this e-mail in error, please notify the > sender immediately by reply e-mail and permanently delete this e-mail and any > attachments without reading, forwarding or saving them. Thank you. > > > "Lin MD, Simon" <linmd.si...@mcrf.mfldclin.edu> > > 08/15/2012 08:11 AM > > To > > "Mead, Charlie (NIH/NCI) [C]" <mea...@mail.nih.gov>, Kerstin Forsberg > <kerstin.l.forsb...@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.si...@mcrf.mfldclin.edu > www.marshfieldclinic.org/birc > > For scheduling assistance, please contact > Crystal Gumz, Administrative Secretary > gumz.crys...@mcrf.mfldclin.edu > 715-221-6403 > > > -----Original Message----- > From: Mead, Charlie (NIH/NCI) [C] [mailto:mea...@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.forsb...@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 > > ______________________________________________________________________ > The contents of this message may contain private, protected and/or privileged > information. If you received this message in error, you should destroy the > e-mail message and any attachments or copies, and you are prohibited from > retaining, distributing, disclosing or using any information contained > within. Please contact the sender and advise of the erroneous delivery by > return e-mail or telephone. Thank you for your cooperation. >
