12 Nov 2013

See also: IRC log




Disease Ontology

ericP: Ontology mapping from, for example, SNOMED to LOINC is problematic and it is difficult to reuse the mapping.
... <someone> at Emory wanted to map from SNOMED to other ontologies.

<deborah> 650.433.aaee is Deborah_McGuinness

<deborah> does anyone know who the contact is for the 12 therapeutic areas at ibm?

ericP: FDA has contracted IBM to model 12 therapeutic areas in RDF.

ericP and Charlie: We have been bugging the FDA about that for a while and it seems to have worked.

charlie: IBM has contracted to 2 small companies to do the work, which only started yesterday.

<deborah> Deborah is interested in staying up to date and seeing early versions of the therapeutic models

charlie: in feb, they were talking about using BRIDG and the ISO21090 (Healthcare data types)

<deborah> diabetes, clinical issues, disease ontology (based on snomed), and xx

ericP: Disease ontology that Emory wants to do is based on SNOMED

sivaram: what is the goal?

<ericP> Sivaram: how does it differ from SNOMED disease areas?

<deborah> goal: have summary level data for use in clinical trials

charlie: FDA's goal is to provide summary level data for trials
... summary data in SDTM uses MedDra but the FDA feels that the data isn't granular / specific enough to do the types of analysis that they want to do.

<Sivaram> Like to see some examples of the inadequacy of it

<Sivaram> and what they expect to see from the proposed new model

charlie: they didn't feel that they could handle the volume of data from thousands of studies and patients

<deborah> does someone have a link for that description?

charlie: When they first announced, number of areas was 55, went up too 65 areas, IBM has been contracted for 12 areas.

Deborah: Are there any areas still to be contracted?

<ericP> Sivaram: do they have examples of what they want to do?

Charlie: All the contracts are spoken for and have come through Duke and XXXX.

<ericP> ... on the CDISC site, looking at the TAs you see a data model

<deborah> i see http://www.cdisc.org/therapeutic but i do not see a full list of the 65 areas or the first 12 for modeling in rdf

Sivaram: If you're looking at the disease model, you're looking at many different aspects, such as biochemical aspects, pathways, etc. (doesn't understand motivation for a 'data model' for disease)
... Have to watch out for conflation of the various models.

<Sajjad__INSERM_> If I correctly followed the discussion so far, it is about the summary data model; as compared to medical domain of the therapeutic disease. For example, a data model used to report ICSR forms to FDA is E2B(R2) http://www.ich.org/fileadmin/Public_Web_Site/ICH_Products/Guidelines/Efficacy/E2B/Step4/E2B_R2__Guideline.pdf

Charlie: BRIDG and SNOMED can provide the context for some terms.

Eric: Suspect that many of the elements will connect and it will work out while working in RDF.

Sivaram: Does this fall into the category of ADaM?

Charlie: You would have to ask FDA that. Seems to, yes.

Eric: What are your favorite disease ontologies?

<Sivaram> SNOMED for its coverage

<ericP> SNOMED refsets

Deborah: People who use Epic, like folks at Mt. Sinai, use templates, sort of light-weight ontologies.

<ericP> Intelligent Medical Objects

<Sajjad__INSERM_> http://www.imbi.uni-freiburg.de/~schober/DCO/

<Sajjad__INSERM_> http://www.debugit.eu/

Sajjad: What is the purpose of the disease ontologies?

<ericP> mscottm: used Human Disease Ontology

<ericP> ... now mapping between NCIt and SNOMED

<Sajjad__INSERM_> http://www.imbi.uni-freiburg.de/~schober/dco_owlDoc/

Eric: My guess is that they are used to fill in CRF. (Charlie confirms)

<Sivaram> lol

<ericP> deborah: was going to start with the SNOMED.

<ericP> Sivaram: looking at Phase I,II, SNOMED will cover a lot from a breadth perspective

<ericP> ... RxNORM will give deep coverage, but need ChEbi for small models

<ericP> charlie: recall that the goal is Phase IV clinical trials

<Sivaram> ChEbi for molecules that are not yet released

<deborah> it would be a service if we kept a list of starting points for this. i am interested in participating in this list and also following up

<ericP> ... so unclear if they'll be diving into {gene,prote}omics at this point

Charlie: Initial focus is Phase IV clinical trials

<ericP> deborah: what's unique about Phase IV that will affect the ontology?

Deborah: Why Phase IV?

<ericP> charlie: humans, already passed many hurdles



Eric: FHIR is a web-oriented way to represent EMR data
... Lessons from v3 and RIM is that people don't want to deal with lots of elements and attributes, so FHIR is relatively skinny although there are efforts to map back to RIM.

<ericP> https://github.com/jmandel/fhir-rdf/tree/master/generic/tests

<deborah> make to genomics - deborah is also interested in starting points there. i am pulling in some content from some linked data resources there




<deborah> i looked up fhir Fast Healthcare Interoperability Resources

Eric: Josh created a tool to generate RDF (ttl) from the XML using the FHIR spec. This gives us a way to compare them and decide where we want them to be different.

<Sajjad__INSERM_> Given/If we have OWL version of HL7, what would be the position of FHIR? I mean, in terms of usage. Does OWL version of HL7 would be enough ?

<Sajjad__INSERM_> Sorry, I am disconnected from voice, trying to back on

Eric: (interpreting OWL version of HL7 as ORIM) - not practically. If we derive the RDF of FHIR from ORIM, it will be hilariously complex.
... (Eric was answering Sajjad's question)

<Sajjad__INSERM_> trying to connect the conference bridge, but getting the message that the conference is restricted at this time :(

Eric: (his plea for help) We have unit tests for transforms so we would like help with improving the XML2RDF transforms.

<deborah> i just lost audio

<deborah> i just tried to call back in and i can not get back in - it says "the conference is restricted at this time"

<deborah> i would be interested in hearing the rest of the answre after the nih big data call

Summary of Action Items

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Got date from IRC log name: 12 Nov 2013
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