IRC log of hcls on 2013-12-17

Timestamps are in UTC.

15:22:05 [RRSAgent]
RRSAgent has joined #hcls
15:22:05 [RRSAgent]
logging to
15:22:09 [ericP]
Zakim, this will be hcls
15:22:09 [Zakim]
ok, ericP; I see SW_HCLS()11:00AM scheduled to start in 38 minutes
15:59:02 [Zakim]
SW_HCLS()11:00AM has now started
15:59:09 [Zakim]
+ +1.919.681.aaaa
15:59:55 [Zakim]
16:00:11 [Zakim]
16:00:36 [agray]
agray has joined #hcls
16:00:47 [Zakim]
16:00:53 [Zakim]
16:01:57 [Zakim]
16:02:22 [MikeDenny]
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16:03:28 [ericP]
agenda+ FDA Therapeutic Areas progress
16:03:36 [Zakim]
16:03:47 [ericP]
agenda+ Disease ontology [Emory, Neda, Claude]
16:04:00 [ericP]
agenda+ Terminology Mapping chat
16:04:55 [ericP]
Zakim, take up agendum 1
16:04:55 [Zakim]
agendum 1. "FDA Therapeutic Areas progress" taken up [from ericP]
16:05:46 [ericP]
scribenick: MikeDenny
16:05:50 [Zakim]
16:06:06 [ericP]
ericP: blah blah blah
16:06:15 [ericP]
... and still more blah blah blah
16:06:22 [Zakim]
16:06:29 [kerstin_]
kerstin_ has joined #HCLS
16:06:46 [MikeDenny]
16:06:59 [Sajjad_INSERM]
Sajjad_INSERM has joined #hcls
16:07:12 [kerstin]
kerstin has joined #hcls
16:07:25 [Zakim]
16:07:35 [eafry]
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16:07:36 [ericP]
-> FDA TA MetaModel
16:08:12 [ericP]
Zakim, who's speaking?
16:08:20 [kerstin]
kerstin has joined #hcls
16:08:22 [Zakim]
ericP, listening for 10 seconds I heard sound from the following: ??P2 (10%)
16:09:01 [ericP]
Zakim, please mute ??P2
16:09:01 [Zakim]
??P2 should now be muted
16:09:16 [ericP]
Zakim, please unmute ??P2
16:09:16 [Zakim]
??P2 should no longer be muted
16:09:19 [ericP]
Zakim, please mute ??P2
16:09:19 [Zakim]
??P2 should now be muted
16:10:13 [kerstin]
16:10:19 [ericP]
-> FDA TA MetaModel
16:12:11 [ericP]
-> Protege
16:13:03 [MikeDenny]
<ericP> FDA Therapeutic Areas modeling effort underway to describe disease effects -- being supported by HCLS with OWL modeling.
16:13:33 [ericP]
-> bottom-most ontology for use in Protege
16:14:18 [Zakim]
16:14:44 [matthias_samwald]
matthias_samwald has joined #hcls
16:15:00 [matthias_samwald]
just dialed in.
16:15:15 [ericP]
-> FDA TA MetaModel
16:15:35 [matthias_samwald]
16:15:37 [MikeDenny]
<ericP> May be helpful for efficacy assessment with notion of 'therapeutic intervention' class.
16:16:26 [Sajjad_INSERM]
You mentioned that you facing some errors: are they parsing errors or modelling errors?
16:16:36 [MikeDenny]
<emory> speaking in above where attributed to ericP
16:18:12 [Zakim]
16:18:46 [Zakim]
16:19:01 [MikeDenny]
<emory> Answers question about lack of fine granularity in model by referring to it as a metamodel that will drive specific therapeuic areas.
16:19:59 [kerstin]
I can see some future alignment opportunties with some of the mid-level OBO ontologies e.g. Ontology for General Medical Science (OGMS) and Ontology for Biomedical Investigations (OBI)
16:20:18 [MikeDenny]
<emory> Answers question about kinds of observations supported like composite observations by asking for suggestions.
16:21:26 [MikeDenny]
< ??> Suggests nested panels etc.
16:22:28 [MikeDenny]
<emory> Question of level of detail needed in this modeling is still being discussed with FDA.
16:25:33 [MikeDenny]
<emory> IIn response to question about clinical trial submission using OWL specification instead of FHIR, for example, this is taken as a consideration.
16:26:15 [kerstin]
If for example neurological TA is one of the 12 FDA TAs it could be interesting to look into some alignement opportunties with the NeuroPsychological Testing Ontology
16:26:31 [MikeDenny]
<??> How do you handle disease where you do not know underlying physiological process?
16:27:52 [MikeDenny]
<emory> The metamodel is now a pragmatic approach.
16:28:22 [kerstin]
MikeDenny: Good question - check out my references above and also the reference articla behind OGMS, check out
16:30:42 [MikeDenny]
<emory> Ansers question of how do you link this metamodel with other standards by referring to C-CDA and FHIR mapping being a goal of the project.
16:31:22 [kerstin]
quick question - How are behind folks behind MikeDenny and TallTed alias (behind kerstin in Kerstin Forsberg, AstraZenenca)?
16:33:25 [ericP]
Zakim, take up next agendum
16:33:25 [Zakim]
agendum 2. "Disease ontology" taken up [from Emory, Neda, Claude]
16:33:31 [kerstin]
16:33:36 [MikeDenny]
<emory> Calls for volunteers to continue on this work to demonstrate to FDA the value of RDF and OWL modeling.
16:33:47 [eafry]
16:34:02 [Zakim]
- +1.919.681.aaaa
16:36:32 [ericP]
eafry: neda took the UMLS data and created a script to dump the hierarchy in the current SNOMED disease tree
16:37:18 [ericP]
... there may be other relevant branches but to start, she grabbed the disease tree
16:37:36 [ericP]
... she exposed the preferred label as the node label
16:37:58 [ericP]
... her next pass will expose the UMLS CUI and the SNOMED code
16:38:19 [ericP]
... the purpose of the tree is to make available the majority of the disease concepts in SNOMED
16:38:28 [MikeDenny]
<eafry> The login for the site above showing a couple of public ontologies will need username + password of 'test'.
16:38:35 [ericP]
... it's very disorganized
16:39:18 [Claude]
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16:40:01 [ericP]
... a goal is to find a smaller set of terms which can be post-coordinated to submsume current pre-coordinated terms
16:40:35 [ericP]
... once we get the extracts with the UMLS codes, we can start extend into other ontologies
16:40:50 [ericP]
... so we've been thinking about axes needed for post-coordination
16:41:25 [MikeDenny]
<eafry> Show relation between pre-coordination and post-coordination SNOMED coding to express diseases using an OWL model.
16:41:30 [ericP]
... age, etiology (which could go into the TA metamodel), signs and symptoms, ...
16:42:17 [ericP]
... enable q's like "what are the diseases which produce hives and shortness of breath?"
16:42:36 [ericP]
... there's a discussion area, as well as notes and viersion history
16:43:14 [ericP]
... this will ideally allow us to collaboratively move to post-coordinated
16:43:48 [ericP]
neda: when we have these concepts as classes, we'll be able to attach more rules and use them for e.g. clinical decision support
16:43:55 [MikeDenny]
<eafry> The site includes a Disease Ontology and a FHIR Ontology.
16:44:57 [ericP]
Sajjad_INSERM: what branches of SNOMED do you have?
16:45:13 [ericP]
eafry: |clinical observations| |disease|
16:45:23 [ericP]
... we'll need more stuff, but that's our start
16:46:43 [MikeDenny]
<eafry> The Disease Ontology is the branch of SNOMED starting at Clinical Obervations - Disease.
16:47:10 [ericP]
Zakim, take up next agendum
16:47:10 [Zakim]
agendum 3. "Terminology Mapping chat" taken up [from ericP]
16:49:46 [ericP]
1 Document different ways that terminology mappings led to inappropriate assertions, potentially because of transitive inference as in Hong Sun's examples.
16:49:49 [ericP]
2 Examine successful/valid uses of termmaps for sensitivity to use context. Does your use of the termmap imply that it's useful to someone else?
16:49:52 [ericP]
3 Describe how to fix the failures, e.g. the lenses from EHR4CR.
16:49:54 [ericP]
4 Codify the context associated with the fixes to enable someone else with the same context to employ them.
16:49:57 [ericP]
5 Once we have a good story, ask the owners of the terminologies to own the mappings.
16:51:49 [Zakim]
16:52:08 [kerstin]
Lenses are from OpenPHACTS
16:53:17 [ericP]
alister: the idea of a Lense is you turn on or off mapping because e.g. two chemicals share stereochemistry or INCHI key
16:53:47 [kerstin]
Some examples of Justifuications sitting behind the Open PHACTS Lenses are described in my blog post on applying the same thinking on terminiligy mappings
16:53:58 [ericP]
... the tool captures the mappings and justifications
16:54:19 [MikeDenny]
<Alister> Lens used in Terminology Mapping to turn on and off mappings based on their context.
16:56:24 [agray]
Here is the paper where we outline the original idea behind lenses. This was done in the context of linking data instances rather than terminologies, but the approach could easily be ported across.
16:57:11 [MikeDenny]
<ericP> Call for volunteers to continue work on this Terminology Mapping project.
16:57:35 [agray]
I'm happy to be involved.
16:58:26 [MikeDenny]
<allister> In response to request, will try to dig up a demo that works.
17:00:05 [kerstin]
Here's a nice blog post from Hong et al in the SALUS project
17:00:19 [agray]
I will email details of a working example for the use of lenses in the Open PHACTS project. (It needs some explanations to make it work.)
17:00:54 [Zakim]
17:01:23 [Zakim]
17:01:24 [Sajjad_INSERM]
Paper Link on Terminology Mapping from Hong:
17:01:59 [Zakim]
17:02:05 [Zakim]
17:02:07 [Zakim]
17:02:12 [ericP]
next meeting 7 Jan
17:02:12 [MikeDenny]
Good Bye!
17:02:21 [ericP]
RRSAgent, please draft minutes
17:02:21 [RRSAgent]
I have made the request to generate ericP
17:02:29 [ericP]
RRSAgent, please make log world-readable
17:02:34 [Zakim]
17:02:41 [Zakim]
17:02:44 [eafry]
eafry has left #hcls
17:03:16 [Zakim]
17:08:16 [Zakim]
disconnecting the lone participant, ??P14, in SW_HCLS()11:00AM
17:08:17 [Zakim]
SW_HCLS()11:00AM has ended
17:08:17 [Zakim]
Attendees were +1.919.681.aaaa, neda, ericP, Mike_Denny, Kerstin_Forsberg, [IPcaller], EmoryFry