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Re: semantic web for EHRs

From: Susie Stephens <susie.stephens@gmail.com>
Date: Fri, 12 Mar 2010 14:24:50 -0500
Message-ID: <fcc499201003121124h793f6c17p1352883f6ed53d2@mail.gmail.com>
To: Kingsley Idehen <kidehen@openlinksw.com>
Cc: dirk.colaert@agfa.com, conor dowling <conor-dowling@caregraf.com>, public-semweb-lifesci@w3.org, public-semweb-lifesci-request@w3.org
The Translational Medicine Ontology (TMO) task has created some fake patient
data in RDF. We are working to create an interface to that data and other
data that we have in RDF, e.g. pharmacogenomics, side effects, diagnostics,
formulary. We are basing the interface on the Open Vista system. Information
is on the task's wiki page (http://esw.w3.org/topic/HCLSIG/PharmaOntology).

Susie



On Fri, Mar 12, 2010 at 2:14 PM, Kingsley Idehen <kidehen@openlinksw.com>wrote:

> dirk.colaert@agfa.com wrote:
>
>>
>> We (Agfa HealthCare) are doing a project on European level around
>> infectious diseases. We collect data in different hospitals (with different
>> CIS systems), we data mine the retrieved results sets , store the results in
>> a knowledge repository and use this knowledge for decision support.
>> The data collection, mentioned above is using sparql and a domain ontology
>> we created. Having the results of the different hospitals in the same
>> formalism and using the same ontologies ensure semantic interoperability and
>> makes the merging of the results sets very easy.
>> The whole thing creates what we call a " virtual clinical data repository"
>> because we don't have to centrally store clinical data. Each clinical site
>> implemented a sparql endpoint, hiding the intrinsics of the specific site
>> We use D2R to convert from sparql to sql..
>>
>> The site of our project is www.debugit.eu
>> Unfortunately there is no much technical detail on that site.
>>
>
> Do you have links for to data?
>
> Kingsley
>
>
>>
>>
>> Kind Regards,
>> *
>> Dirk Colaert | **Agfa HealthCare*
>> Advanced Clinical Application Manager | HE/Advanced Clinical Applications
>> Research
>> T  +32 3444 8408 | F  +32 3 444 8401 | M  +32 497 47 08 71
>>
>> Quadrat NV, Kortrijksesteenweg 157, 9830 Sint-Martens-Latem, Belgium
>> http://www.agfa.com/healthcare/
>> ------------------------------------------------------------------------
>> Click on link to read important disclaimer:
>> http://www.agfa.com/healthcare/maildisclaimer
>>
>>
>> *Kingsley Idehen <kidehen@openlinksw.com>*
>> Sent by: public-semweb-lifesci-request@w3.org
>>
>> 12/03/2010 14:40
>>
>>
>> To
>>        conor dowling <conor-dowling@caregraf.com>
>> cc
>>        public-semweb-lifesci@w3.org
>> Subject
>>        Re: semantic web for EHRs
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> conor dowling wrote:
>> >
>> >     > U.S.? (There's little here from what I can see - the
>> >     interoperability push is around SOAP).
>> >
>> >     In my view, SOAP is the wrong direction.  It is just adds
>> >     complexity and
>> >     contributes to "babelization":
>> >     http://www.w3.org/2003/Talks/0717-semweb-dbooth/slide10-0.html
>> >
>> >
>> > you're right but here's the rub - there's $'s in babel. Bad IT -
>> > translation layers and their maintenance - is good business, sometimes.
>> >
>> > Take the U.S. NHIN CONNECT project whose laudable goal is to allow
>> > patient record exchange between institutions big and small. It tackles
>> > what's need - security, credentials, opt-in etc - and then ... well,
>> > it gets all SOAP'y. Gateways, adapters, layers, all those layers. What
>> > about a "web of interlinked data", just add security policy ...??
>> >
>> > It's annoying because think how easy linking is - in reality and now,
>> > not just conceptually, some time away. (I know I'm preaching to the
>> > choir here but ...)
>> >
>> > Take a patient vital - http://vista.caregraf.org/rambler/120.5/716
>> > (Christopher's blood pressure at a date). This record is typed by the
>> > VA vital type, http://vista.caregraf.org/rambler/120.51/1 (blood
>> > pressure), one of 19 that the system records (
>> > http://vista.caregraf.org/rambler/120.51 ). Vital type is a "locked
>> > file" ( http://vista.caregraf.org/rambler/schema/120.51 ), one of many
>> > terminology files in VistA.
>> >
>> > Now, on the face of it, such data is meaningless outside this VistA.
>> > We need a "mapping layer", an "RPC". A "type-mapper". A reformatter.
>> > Layers ...
>> >
>> > BUT WE KNOW (on this group) that it is trival to do something like ...
>> >                         :120.51/1 ---- same as -----> SNOMED:392570002
>> > and heh presto, your vitals are "linked". Were Christopher lucky
>> > enough to end up in the Cleveland Clinic then this and his other data
>> > would be trivial to query - no longer site or even VA-specific.
>> >
>> > And this isn't an isolated case. It's true in general. (I'm working on
>> > an "linked patient browser" - needs very little code - and this
>> > principle holds true for procedures, medicines, vaccines ...).
>> >
>> > The train is leaving the station on health records (in the U.S.
>> > 'meaningful use' is about to get nailed down) and they're made for the
>> > web of data but all we have are soap bubbles, all a drift ...
>> Is there going to be an RDF model based Linked Data View over this data?
>> Or are you looking for help re. Linked Data publishing etc?
>>
>> --
>>
>> Regards,
>>
>> Kingsley Idehen                      President & CEO
>> OpenLink Software    Web: http://www.openlinksw.com
>> Weblog: http://www.openlinksw.com/blog/~kidehen
>> Twitter/Identi.ca: kidehen
>>
>>
>>
>>
>>
>>
>>
>>
>
> --
>
> Regards,
>
> Kingsley Idehen       President & CEO OpenLink Software     Web:
> http://www.openlinksw.com
> Weblog: http://www.openlinksw.com/blog/~kidehen
> Twitter/Identi.ca: kidehen
>
>
>
>
>
>
Received on Friday, 12 March 2010 19:25:24 GMT

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