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RE: seeks input on Study Data Exchange Standards

From: <Peter.Hendler@kp.org>
Date: Tue, 21 Aug 2012 15:24:54 -0700
To: meadch@mail.nih.gov
Cc: kerstin.l.forsberg@gmail.com, public-semweb-lifesci@w3.org
Message-ID: <OF9CC26A02.C8A218C0-ON88257A61.0079F8F4-88257A61.007B20BE@kp.org>
At Kaiser we use SNOMED subsumption to automatically generate preference 
lists for different specialties, and to pre populate (only after humans 
edit the list) work flow for chemo therapy.

But for outcomes research or quality reporting it has real value too. 

Using both SQL and subsumption you can automatically find things like 

"find all disorders that are a kind of adverse drug reaction where drug is 
a subtype of antibiotic and was given for a kind of gram negative 
bacterial infection of the digestive system".

Try that with only SQL.

Just an idea but..  Wouldn't it be helpful if HL7 models would have the 
ability to label certain nodes as intensional (for example you can bind 
any kind of SNOMED organism to this node)? 

You can use a SNOMED reasoner or an OWL reasoner on this node to find all 
the kinds of infectious agents that are a subtype of gram negative 

Which would be one of the individual subsumption queries needed in the 
above example.

A given node might have the following.

It's meta tags would be:

intensional = "true"
ontology = "SNOMED-CT"
logic = "EL+"
hierarchies= "Organism"
post_coordination_allowed = "false"

The users of the model wouldn't have to talk to the creator of the model, 
they'd already know they can use the reasoner on the "causative agent" 

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"Mead, Charlie (NIH/NCI) [C]" <meadch@mail.nih.gov> 
08/21/2012 02:54 PM

Kerstin Forsberg <kerstin.l.forsberg@gmail.com>, 
"public-semweb-lifesci@w3.org" <public-semweb-lifesci@w3.org>

RE: seeks input on Study Data Exchange Standards

Totally agree.  The more we can show people the advantages of SW 
representations, the better.  Eric and I are trying to come up with a 
"message and explanation" with a couple of really concrete examples to 
address the question of "isn't this just another silver bullet?" Hopefully 
we can make some progress on that in the next few weeks.  Also, I (and any 
others who happen to be at the upcoming HL7 meeting should a) try and have 
an organizational meeting, and b) sit down with Wayne (now CDISC CTO) and 
talk through some of this with him.  I know from talking with him at my 
last CDISC BoD meeting (Sept 2011) and the more recent BRIDG BoD meeting 
(June 2012) that is interested in the subject.

From: Kerstin Forsberg [kerstin.l.forsberg@gmail.com]
Sent: Tuesday, August 21, 2012 4:34 PM
To: public-semweb-lifesci@w3.org
Subject: Re: seeks input on Study Data Exchange Standards

Great discussion in the meeting today and on the email list:  BRIDG/OWL, 
FHIR/SW, Extensional and Intensional /" design-time" and "run-time" 
models, ... a lot of interesting things seems to converge for how to model 
patient data.

At the same time I think it would be useful to explore a RDF 
implementation of today's CDISC SDTM domains (and Supplement Qualifier) 
data structures. That is,RDF triples and as an alt. to ODM/XML for data 

So far my focus has been on pushing CDISC, and NCI, towards "Linked 
Clinical Data Standards", see 
as a prereq. to be able to get to "Linked Clinical Data"

Kind Regards
Received on Tuesday, 21 August 2012 22:25:42 UTC

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