IRC log of hcls on 2013-11-12

Timestamps are in UTC.

16:01:53 [RRSAgent]
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16:01:53 [RRSAgent]
logging to http://www.w3.org/2013/11/12-hcls-irc
16:02:01 [ericP]
Zakim, this is COI
16:02:01 [Zakim]
sorry, ericP, I do not see a conference named 'COI' in progress or scheduled at this time
16:02:07 [ericP]
Zakim, this is hcls
16:02:07 [Zakim]
ok, ericP; that matches SW_HCLS()11:00AM
16:02:13 [ericP]
Zakim, who is here?
16:02:13 [Zakim]
On the phone I see Kerstin_Forsberg, stevebattle7, +1.413.442.aaaa, +1.832.726.aabb
16:02:15 [Zakim]
On IRC I see RRSAgent, Zakim, Josh, achille_zappa, deborah, TallTed, egonw__, ericP
16:02:42 [Sajjad__INSERM_]
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16:03:04 [Zakim]
+ +33.1.73.71.aacc
16:03:17 [Zakim]
+??P9
16:03:33 [Sivaram]
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16:03:46 [ericP]
Zakim, ??P9 is Sajjad
16:03:46 [Zakim]
+Sajjad; got it
16:03:55 [Zakim]
+ +31.62.427.aadd
16:03:59 [charlie]
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16:04:21 [ericP]
Zakim, aadd is mscottm
16:04:21 [Zakim]
+mscottm; got it
16:04:29 [ericP]
Zakim, who is here?
16:04:29 [Zakim]
On the phone I see Kerstin_Forsberg, stevebattle7, +1.413.442.aaaa, +1.832.726.aabb, +33.1.73.71.aacc, Sajjad, mscottm
16:04:31 [Zakim]
On IRC I see charlie, Sivaram, Sajjad__INSERM_, RRSAgent, Zakim, Josh, achille_zappa, deborah, TallTed, egonw__, ericP
16:04:36 [mscottm]
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16:04:48 [ericP]
Zakim, aaaa is Josh
16:04:48 [Zakim]
+Josh; got it
16:05:06 [mscottm]
Zakim, who is on the phone?
16:05:06 [Zakim]
On the phone I see Kerstin_Forsberg, stevebattle7, Josh, +1.832.726.aabb, +33.1.73.71.aacc, Sajjad, mscottm
16:05:35 [Deborah_]
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16:06:09 [ericP]
topic: Disease Ontology
16:07:21 [mscottm]
ericP: Ontology mapping from, for example, SNOMED to LOINC is problematic and it is difficult to reuse the mapping.
16:07:59 [Zakim]
+ +1.650.433.aaee
16:08:14 [mscottm]
..<someone> at Emory wanted to map from SNOMED to other ontologies.
16:08:15 [Zakim]
+Mike_Denny
16:09:15 [deborah]
650.433.aaee is Deborah_McGuinness
16:10:24 [deborah]
does anyone know who the contact is for the 12 therapeutic areas at ibm?
16:10:32 [mscottm]
..FDA has contracted IBM to model 12 therapeutic areas in RDF.
16:11:22 [mscottm]
ericP and Charlie: We have been bugging the FDA about that for a while and it seems to have worked.
16:13:15 [mscottm]
charlie: IBM has contracted to 2 small companies to do the work, which only started yesterday.
16:14:16 [deborah]
Deborah is interested in staying up to date and seeing early versions of the therapeutic models
16:15:41 [mscottm]
charlie: in feb, they were talking about using BRIDG and the ISO21090 (Healthcare data types)
16:16:18 [deborah]
diabetes, clinical issues, disease ontology (based on snomed), and xx
16:16:39 [mscottm]
ericP: Disease ontology that Emory wants to do is based on SNOMED
16:17:04 [mscottm]
sivaram: what is the goal?
16:17:24 [ericP]
Sivaram: how does it differ from SNOMED disease areas?
16:17:29 [deborah]
goal: have summary level data for use in clinical trials
16:17:50 [mscottm]
charlie: FDA's goal is to provide summary level data for trials
16:19:42 [mscottm]
charlie: 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.
16:20:27 [Sivaram]
Like to see some examples of the inadequacy of it
16:20:54 [Sivaram]
and what they expect to see from the proposed new model
16:20:59 [mscottm]
charlie: they didn't feel that they could handle the volume of data from thousands of studies and patients
16:22:13 [deborah]
does someone have a link for that description?
16:24:00 [mscottm]
..When they first announced, number of areas was 55, went up too 65 areas, IBM has been contracted for 12 areas.
16:24:07 [Kerstin]
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16:25:29 [mscottm]
Deborah: Are there any areas still to be contracted?
16:25:48 [ericP]
Sivaram: do they have examples of what they want to do?
16:26:04 [mscottm]
Charlie: All the contracts are spoken for and have come through Duke and XXXX.
16:26:27 [ericP]
... on the CDISC site, looking at the TAs you see a data model
16:27:07 [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
16:29:13 [mscottm]
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)
16:30:20 [mscottm]
Sivaram: Have to watch out for conflation of the various models.
16:31:24 [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
16:32:04 [mscottm]
Charlie: BRIDG and SNOMED can provide the context for some terms.
16:33:45 [mscottm]
Eric: Suspect that many of the elements will connect and it will work out while working in RDF.
16:37:29 [mscottm]
Sivaram: Does this fall into the category of ADAM?
16:38:44 [mscottm]
Charlie: You would have to ask FDA that. Seems to, yes.
16:41:02 [mscottm]
Eric: What are your favorite disease ontologies?
16:41:18 [Sivaram]
SNOMED for its coverage
16:42:46 [ericP]
SNOMED refsets
16:43:04 [mscottm]
Deborah: People who use Epic, like folks at Mt. Sinai, use templates, sort of light-weight ontologies.
16:43:41 [ericP]
Intelligent Medical Objects
16:43:54 [mscottm]
s/ADAM/ADaM/g
16:44:32 [Zakim]
-Kerstin_Forsberg
16:45:26 [Zakim]
-Josh
16:45:41 [Sajjad__INSERM_]
http://www.imbi.uni-freiburg.de/~schober/DCO/
16:45:54 [Sajjad__INSERM_]
http://www.debugit.eu/
16:45:58 [mscottm]
Sajjad: What is the purpose of the disease ontologies?
16:46:00 [Zakim]
+Josh
16:46:33 [ericP]
mscottm: used Human Disease Ontology
16:46:53 [ericP]
... now mapping between NCIt and SNOMED
16:47:08 [Sajjad__INSERM_]
http://www.imbi.uni-freiburg.de/~schober/dco_owlDoc/
16:47:15 [mscottm]
Eric: My guess is that they are used to fill in CRF. (Charlie confirms)
16:47:35 [Sivaram]
lol
16:47:42 [ericP]
deborah: was going to start with the SNOMED.
16:48:32 [ericP]
Sivaram: looking at Phase I,II, SNOMED will cover a lot from a breadth perspective
16:49:27 [ericP]
... RxNORM will give deep coverage, but need ChEbi for small models
16:49:47 [ericP]
charlie: recall that the goal is Phase III clinical trials
16:50:04 [Sivaram]
ChEbi for molecules that are not yet released
16:50:08 [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
16:50:10 [ericP]
... so unclear if they'll be diving into {gene,prote}omics at this point
16:50:25 [ericP]
s/goal is Phase III/goal is Phase IV/
16:51:06 [mscottm]
Charlie: Initial focus is Phase IV clinical trials
16:51:18 [ericP]
deborah: what's unique about Phase IV that will affect the ontology?
16:51:23 [mscottm]
Deborah: Why Phase IV?
16:51:31 [ericP]
charlie: humans, already passed many hurdles
16:54:47 [mscottm]
lol
16:54:52 [ericP]
topic: FHIR
16:56:07 [mscottm]
Eric: FHIR is a web-oriented way to represent EMR data
16:57:29 [mscottm]
..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.
16:58:03 [ericP]
https://github.com/jmandel/fhir-rdf/tree/master/generic/tests
16:58:13 [deborah]
make to genomics - deborah is also interested in starting points there. i am pulling in some content from some linked data resources there
16:58:38 [Mike]
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16:58:57 [mscottm]
https://github.com/jmandel/fhir-rdf/blob/master/generated/patient-example-a.ttl
16:59:10 [mscottm]
http://www.hl7.org/implement/standards/fhir/resources.html
17:01:26 [mscottm]
https://github.com/jmandel/fhir-rdf/tree/master/generated
17:02:59 [Zakim]
-Sajjad
17:03:30 [deborah]
i looked up fhir Fast Healthcare Interoperability Resources
17:05:08 [mscottm]
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.
17:05:48 [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 ?
17:06:13 [Sajjad__INSERM_]
Sorry, I am disconnected from voice, trying to back on
17:08:50 [Zakim]
-Mike_Denny
17:09:36 [mscottm]
Eric: (interpreting OWL version of HL7 as ORIM) - not practically. If we derive the RDF of FHIR from ORIM, it will be hilariously complex.
17:10:04 [mscottm]
.. (Eric was answering Sajjad's question)
17:12:54 [Sajjad__INSERM_]
trying to connect the conference bridge, but getting the message that the conference is restricted at this time :(
17:13:50 [mscottm]
Eric: (his plea for help) We have unit tests for transforms so we would like help with improving the XML2RDF transforms.
17:14:59 [deborah]
i just lost audio
17:16:16 [Zakim]
-mscottm
17:16:17 [Zakim]
- +1.832.726.aabb
17:16:17 [Zakim]
- +33.1.73.71.aacc
17:16:18 [Zakim]
-Josh
17:16:18 [Zakim]
-stevebattle7
17:16:23 [deborah]
i just tried to call back in and i can not get back in - it says "the conference is restricted at this time"
17:16:36 [deborah]
i would be interested in hearing the rest of the answre after the nih big data call
17:16:38 [ericP]
RRSAgent, please draft minutes
17:16:38 [RRSAgent]
I have made the request to generate http://www.w3.org/2013/11/12-hcls-minutes.html ericP
17:17:00 [ericP]
deborah, i'll scribe it here:
17:17:12 [ericP]
i dunno
17:17:52 [ericP]
in slightly more detail, it'd be practical to go after smallish grants with short review cycles for that work but i don't know where to find them
17:18:31 [Sajjad__INSERM_]
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17:21:18 [Zakim]
disconnecting the lone participant, +1.650.433.aaee, in SW_HCLS()11:00AM
17:21:21 [Zakim]
SW_HCLS()11:00AM has ended
17:21:21 [Zakim]
Attendees were Kerstin_Forsberg, stevebattle7, +1.413.442.aaaa, +1.832.726.aabb, +33.1.73.71.aacc, Sajjad, +31.62.427.aadd, mscottm, Josh, +1.650.433.aaee, Mike_Denny
17:33:46 [egonw__]
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