26 Nov 2013

See also: IRC log


Kerstin_Forsberg, +, +, ericP, charlie, +1.617.500.aacc, Josh, EmoryFry, +1.469.226.aadd, claud_nanjo, neda, [IPcaller], Mike_Denny


<scribe> scribenick: ericP


charlie: FDA has 5 Therapeutic Areas in SemWeb
... we're working on 12 more
... a DO would be helpful WRT TAs
... FDA doesn't use SNOMED
... if the semantics suffice, we could bind it to MeDRA as well

emory: the goal is to use current anatomic concepts current organized by anatomic location
... the disease manifestation of e.g. lung and kidney disease would be related to anatomy but the concepts would be broader

charlie: FDA is describing TA work in terms of efficacy points, which are related to underlying pathophysiological attributes
... FDA is committed to reusing existing ontologies. expect that they have had to confront some disease issues already

emory: within our group, charlie and ericP can resolve the ontology against the TAs and avoid duplication.

charlie: i think FDA really does want to share [which we need for deduplication]

emory: i'm currently polling ihsedo to see if anyone's already doing this.
... i want to make sure we don't get bogged down in @@1

<Josh> (IHDSDO)

charlie: it's not clear yet what drug models they'll develop

<Josh> er, IHTSDO

emory: we can start the modeling work and let ericP and charlie alert if there are conflicts

charlie: i expect they are modeling the intersection between a pathophysiological process and a objective assessment of the efficacy of a treatment modality

claud: SNOMED seems to becoming the standard for expressing clinical findings.
... is it possible that our effort be done as an extension to SNOMED?

emory: i discussed with keith campbell (VA rep at IHTSDO).
... keith is first checking to see that anyone else is working on a disease ontology (reduce risk of duplication).
... second, providing an update on the SNOMED naming and extension process because he encourages us to model using the @@3 workbench, and create an extension, modeled using SNOMED conventions and rules, and submit it to SNOMED.
... there needs to be alignment with SNOMED process, ideally following their conventions.
... sites and symptoms should all be pre-existing
... [re: winnowing down SNOMED], is see use cases for "the one"
... re: what is the purpose of doing a pathophysiological hierarchy, i want to do diagnostic reasoning over clinical observations
... e.g. if i see signs and symptoms in different organs, i should be able to generate a differential diagnosis

<Kerstin> Disease and diseare areas, such as Infectius diseases, models using on the Ontology for General Medical Science (OGMS) http://code.google.com/p/ogms/ - See this central illustration http://kerfors.blogspot.se/2011/09/icbo2011-disease-terminologies-and.html

emory: focusing on pathophysiology instead of sites
... others may have other use cases

<Kerstin> The OGMS based disease ontologies are not (yet) connected to SNOMED sign/symptoms, nor to LOINC measurements, of my knowledge.

ericP: i suspect that the attributes for research are considerably wider than what will eventually be used e.g. in the bodies of CDS rules

emory: does this seem too-far-fetched?
... we need broad enough interest to engage subject matter experts
... I can reach out the Bob at ASU (and his PhD students). Neda has ties to UCSD.
... Josh and charlie, do you know of communities where folks might be interested in providing commentary on our efforts?

charlie: i may be working on implementation guides, which would be me well in SNOMED. i did emergency med so i'm not an authority.

Josh: rafael richards is certainly excited about having RDF representations

neda: we extracted UMLS terms to index DBGAP
... they're waiting for funding, but they'd be a good use case
... (at UCSD)
... Niggam Shah (Stanford) was working on a disease ontology as well

emory: I can call Samson Tu to see if there's interest within the protege group.
... i'd like to get one of my engineers to extract the relevent branches of SNOMED and load them into WebProtege.
... i've never used V2, but i've heard good things about it from a collaborative perspective

neda: i have the ontology that we used for DBGAP

emory: whether we pull the concepts from SNOMED or from an existing model, we'll load them into webprotege.
... ericP and I talked about who's best to manage the project

ericP: who's funding niggam's work?

neda: NIH was supposed to fund DBGAP work (closed for a bit 'cause of shutdown...)
... this was joint work to do NLP to integrate patient data
... part of this was a disease ontology.
... original PI was wendy chapman

emory: let's create a mission statement and ask neda to approach the above for ideas and engagement.

ericP: what's the related HL7 WG?

charlie: about a year ago, that would have been patient care

Josh: and we should ping lloyd

emory: could ericP or Josh catch Neda and Claud with the FDA work?

<Kerstin> Let us all know when you do that FHIR2RDF intro - I need a recap to get all of thsi great work

Summary of Action Items

[End of minutes]

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$Date: 2013-12-02 23:57:22 $