16:02:33 <RRSAgent> RRSAgent has joined #hcls
16:02:33 <RRSAgent> logging to http://www.w3.org/2015/11/10-hcls-irc
16:02:35 <trackbot> RRSAgent, make logs world
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16:02:37 <trackbot> Zakim, this will be HCLS
16:02:37 <Zakim> I do not see a conference matching that name scheduled within the next hour, trackbot
16:02:38 <trackbot> Meeting: Semantic Web Health Care and Life Sciences Interest Group Teleconference
16:02:38 <trackbot> Date: 10 November 2015
16:03:33 <dbooth> Chair: David Booth
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16:03:49 <dbooth> Topic: ValueSet
16:04:22 <dbooth> http://wiki.hl7.org/images/f/ff/ValueSet_approach.pdf
16:10:08 <dbooth> tony: Representing coding.system as an owl individual directly is a convenience that I'm using.
16:10:19 <dbooth> lloyd: It should have a value property.
16:13:42 <dbooth> (tony showed inference though bridging ont and snomed ont)
16:16:19 <dbooth> tony's owl: http://wiki.hl7.org/index.php?title=RDF_for_Semantic_Interoperability#High-level_concept_mapping_to_RDF_.28AR_typeCodes.2C_etc..29
16:16:36 <dbooth> The OWL links: http://wiki.hl7.org/index.php?title=File:FHIROntology.txt
16:16:43 <dbooth> http://wiki.hl7.org/index.php?title=File:FHIR_SNOMEDCT_Bridge.txt
16:16:49 <dbooth> http://wiki.hl7.org/index.php?title=File:FragmentOWLSNOMEDCT.txt
16:20:01 <ericP> -> http://wiki.hl7.org/images/1/16/FHIROntology.txt FHIR Ont (open from URL in Protege)
16:22:41 <rhausam> rhausam has joined #HCLS
16:23:16 <rhausam> can you send the link again, Eric?
16:23:41 <hsolbrig> No idea what is going on
16:23:58 <hsolbrig> with respect to audio, but I'm no longer seeing the screen share
16:24:25 <dbooth> -> http://wiki.hl7.org/images/1/16/FHIROntology.txt FHIR Ont (open from URL in Protege)
16:25:11 <hsolbrig> I'll just listen... apologies
16:29:12 <dbooth> lloyd: Would be good to start splitting the ontology into what will be generated by HL7 versus what will be in the bridging ontology.
16:31:36 <dbooth> eric: I see this being used as having a FHIR RDF deliverable, then use cases that motivate the design, and that includes SNOMED and bridging ont, maybe DL query, to give us tools to test to know if we broke something.
16:32:00 <dbooth> ... So that when we're working on the XSLT implementation, we can hit the button, see the query and see if we get results.
16:32:33 <dbooth> ... Make progress having a bunch of tests.
16:32:55 <dbooth> ... Don't know how to run Protege or SNAP SPARQL queries from the command line.
16:33:35 <dbooth> ... Could probably do it with OWL API and a reasoner.
16:33:51 <dbooth> rob: I have scripted the reasoner before.
16:35:40 <dbooth> eric: Need to get this in github first.
16:40:47 <dbooth> tony discussing lines 342-372
16:45:58 <hsolbrig> I intend to do this (audio compromised)
16:47:03 <dbooth> dbooth: We're at the point where it would be helpful if at least a couple of other people got your ont and tried it themselves.
16:47:38 <dbooth> ACTION: Harold and Rob to try tony's FHIR ontology and provide feedback
16:47:38 <trackbot> Created ACTION-34 - And rob to try tony's fhir ontology and provide feedback [on Harold Solbrig - due 2015-11-17].
16:49:06 <dbooth> Topic: How ORIM testing was done
16:49:52 <dbooth> eric: talked with lloyd about how validation was done with the ORIM.  Easy to apply it to this situation.
16:51:02 <dbooth> <dbooth> Option A: owl-validation: the owl reasoner barfs if instance data specifies a code does not match the valueset.
16:51:02 <dbooth> <dbooth> Option B: external valueset validator: Owl reasoner does not barf. Instead, an extra closed world inference step is use (perhaps using SWRL or other) to detect the problem.
16:51:44 <dbooth> <dbooth> Proposal: We should do both, but separate the base FHIR ontology (which would NOT cause the reasoner to barf if a wrong code is used) from an additional validation ontology (which WOULD cause the reasoner to barf if a wrong code is used).
16:53:38 <dbooth> dbooth: Is it viable to do both?
16:54:02 <dbooth> eric: Yes, you just need to move certain assertions out.
16:55:31 <dbooth> lloyd: Remove the triple that asserts the binding to the element.  E.g., administrative gender, a valueSet defines what it can be.  The statement to withhold is the assertion that one of the codings for gender must come from this valueSet.  If you yank that triple then you will no longer have a contradiction if the code is not from that VS.
16:56:01 <dbooth> rob: In the OWA, I dont' think that is enough to achieve option A validation.
16:56:19 <dbooth> dbooth: Remember that they're strings, not named individuals.
16:56:24 <dbooth> lloyd: It works.
16:57:08 <dbooth> lloyd: Need to decide which things you do not want OWL to choke on, for example illegal combinations of code and system.
16:57:50 <dbooth> eric: Do we want to use things like cd:administrativeGender?
16:58:02 <dbooth> lloyd: use the fhir: namespace.
16:58:13 <ericP> lloyd: nope, fhir:Observation.administrativeGender
16:58:33 <ericP> ... the RIM used 21090 where possible. FHIR has its own.
16:58:58 <ericP> ... in V3 we had attribute -> concept domain -> value set
16:59:20 <dbooth> lloyd: but we've simplified that in FHIR.
17:00:09 <dbooth> Present: Tony Mallia, Thomas Lukasik, Rob Hausam, Lloyd McKenzie, Harold Solbrig, EricP, David Booth
17:02:52 <hsolbrig> Let me know as soon as the directory is ready to go.
17:04:01 <dbooth> dbooth: the option A add-on ont will be the valueset-validation ontology
17:04:57 <dbooth> ADJOURNED
17:06:38 <ericP> git clone git@github.com:w3c/hcls-fhir-rdf.git
17:07:08 <hsolbrig> The github page presents othert options
17:07:15 <hsolbrig> He can clone directly from the web page...
17:07:19 <dbooth> rrsagent, draft minutes
17:07:19 <RRSAgent> I have made the request to generate http://www.w3.org/2015/11/10-hcls-minutes.html dbooth
17:07:40 <hsolbrig> Note "Clond in Desktop"
17:07:58 <hsolbrig> A way to clone!
17:08:37 <hsolbrig> Oops - forgot that you had to have the desktop available
17:08:58 <hsolbrig> Maybe the "git clone" would be easier...
17:09:09 <hsolbrig> Gotta sign off.
17:46:09 <ericP> http://www.w3.org/2013/12/FDA-TA/
17:50:42 <ericP> orange just hung up my call
17:50:45 <ericP> just a sec...
17:50:49 <Tony> OK
17:52:05 <Tony> Don't hear you yet
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23:34:59 <RRSAgent> logging to http://www.w3.org/2015/11/10-hcls-irc
23:35:12 <dbooth> Meeting: HL7/W3C FHIR Task Force
23:35:23 <dbooth> Topic: FHIR RDF ontology
23:35:23 <dbooth> * Tony (~Tony@public.cloak) has joined #HCLS
23:35:23 <dbooth> https://github.com/w3c/hcls-fhir-rdf
23:35:23 <dbooth> https://github.com/w3c/hcls-fhir-rdf/tree/master/ontology
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23:35:24 <dbooth> Added readme: https://github.com/w3c/hcls-fhir-rdf/tree/master/ontology
23:35:26 <dbooth> dbooth: Please try the ontology!
23:35:28 <dbooth> eric: We should also think about test cases.
23:35:30 <dbooth> davide: Still uneasy about property names.
23:35:32 <dbooth> tony: also, I've been looking at round tripping of the schema, and I don't think we have a requirement for round-tripping the schema.
23:35:35 <dbooth> chris: I'd like to hear how this is intended to fit in with other ontologies.  That's why I'm on the call. :) E.g., OBO Foundry.  Want to avoid FHIR creating yet another ont that will need to be mapped to others.
23:35:38 <dbooth> tony: Still need to look at the gaps between this and OBO.
23:35:40 <dbooth> chris: The relations ont has objects and properties.  Should see how these correspond.
23:35:42 <dbooth> davide: Still trying to figure out: is this an ont of the FHIR resources, or the things that FHIR models, i.e., patients, diseases, etc.
23:35:47 <dbooth> davide: for example, a SubstanceAdministration and an Immunization are disjoint: something cannot be a member of both.
23:35:50 <dbooth> lloyd: correct.
23:35:52 <dbooth> ... the concept that represents the Immunization record and the SubstanceAdministration record are disjoint, but they can reference the same ont when they talk about the med being adminstered.
23:35:55 <dbooth> davide: To bridge into an upper I don't think we can do it directly.
23:35:57 <dbooth> lloyd: Right, FHIR is fundamentally about records -- not knowledge.
23:35:59 <dbooth> chris: Maybe a bridging ont can go from FHIR ont being about records and SNOMED and OBO being about real world things.
23:36:02 <dbooth> dbooth: I think that's correct.
23:36:04 <dbooth> dbooth: What is the best way for us to support that bridge between FHIR's record-oriented ont and real world ontologies?
23:36:07 <dbooth> chris: Would be good to do it in a way that causes minimal work for users.  Barry Smith just published a book on OBO that is one recommended reading.
23:36:10 <dbooth> ... There's also an older paper on OBO foundry.
23:36:12 <dbooth> http://www.amazon.com/Building-Ontologies-Basic-Formal-Ontol
23:36:21 <dbooth> http://www.amazon.com/Building-Ontologies-Basic-Formal-Ontology/dp/0262527812/ref=sr_1_1?ie=UTF8&qid=1447195449&sr=8-1&keywords=barry+smith
23:36:21 <dbooth> Present: EricP, David Booth, Tony mallia, Chris Stoeckert, Davide Sottara, Lloyd McKenzie
23:36:23 <dbooth> http://www.nature.com/nbt/journal/v25/n11/full/nbt1346.html
23:36:25 <dbooth> dbooth: What's the best way forward on this?
23:36:27 <dbooth> eric: What are the use cases?  i worked hard to bridge FDA therapeutic ont to other stuff.  But I didn't justify my time because I did not find any really motivating use cases.  e.g., if we have ont X, we could answer clinical question Y.
23:36:31 <dbooth> I have a biobanking use case. Find cohorts of specimens across institutions. Need to know about specimens but also consent associated with those specimens and the medical record of the donor
23:36:34 <dbooth> davide: This is a discussion we had at Mayo.  Thousands of local systems with their local semantics that we want to normalize, and FHIR is a candidate.  Syntactic normalization is impossible.  Want broader scope of meaning that relates them to other ont.
23:36:38 <dbooth> Guoqian Jiang championed use cases: http://wiki.hl7.org/index.php?title=RDF_for_Semantic_Interoperability#Use_Cases
23:36:41 <dbooth> davide: Not hard to identify use cases, but more work to document them.
23:36:45 <dbooth> chris: If we have some stake in some use cases, we can take them back to our folks to say "we can do this"
23:36:47 <dbooth> davide: If we assume that we will have that bridge ont (or mediation process) then that takes pressure off of the FHIR ont to fill that need.
23:36:50 <dbooth> ACTION: Chris Stoeckert to provide additional resources about how to get into BFO, OBO, etc.
23:36:50 <trackbot> Created ACTION-37 - Stoeckert to provide additional resources about how to get into bfo, obo, etc. [on Chris Pierce - due 2015-11-17].
23:37:00 <dbooth> Created ACTION-35 - Stoeckert to provide additional resources about how to get into bfo, obo, etc. [on Chris Pierce - due 2015-11-17].
23:37:00 <dbooth> tony: record of medical action, versus why it was done.
23:37:00 <dbooth> Ontology for Biomedical Investigations: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2903726/
23:37:00 <dbooth> Topic: Next topics
23:37:01 <dbooth> <dbooth> eric: We should also think about test cases.
23:37:03 <dbooth> <dbooth> davide: Still uneasy about property names.
23:37:05 <dbooth> <dbooth> tony: also, I've been looking at round tripping of the schema, and I don't think we have a requirement for round-tripping the schema.
23:37:08 <dbooth> <dbooth> eric: What are the use cases?
23:37:10 <dbooth> Topic: Use Cases
23:37:12 <dbooth> <ChrisS> I have a biobanking use case. Find cohorts of specimens across institutions. Need to know about specimens but also consent associated with those specimens and the medical record of the donor
23:37:17 <dbooth> https://www.w3.org/wiki/HCLS/ClinicalObservationsInteroperability#Use_Cases
23:37:19 <dbooth> eric: Goal is to see how we would make use of other ontologies with the FHIR RDF ont.
23:37:21 <dbooth> ... Use cases should be written up that way.
23:37:23 <dbooth> ... Need to show how it would be use: the FHIR data, the query to execute, the bits of the ont that enable the query, etc.
23:37:26 <dbooth> ACTION: Chris Stoeckert to show SPARQL queries used in biobanking and show our use case
23:37:26 <trackbot> Created ACTION-38 - Stoeckert to show sparql queries used in biobanking and show our use case [on Chris Pierce - due 2015-11-17].
23:37:28 <dbooth> * trackbot is creating a new ACTION.
23:37:30 <dbooth> Created ACTION-36 - Stoeckert to show sparql queries used in biobanking and show our use case [on Chris Pierce - due 2015-11-17].
23:37:33 <dbooth> ACTION: Davide to get uses cases from Mayo
23:37:33 <trackbot> Error finding 'Davide'. You can review and register nicknames at <http://www.w3.org/2014/HCLS/track/users>.
23:37:35 <dbooth> * trackbot is creating a new ACTION.
23:37:37 <dbooth> Error finding 'Davide'. You can review and register nicknames at <http://www.w3.org/2014/HCLS/track/users>.
23:37:43 <dbooth> Topic: Round tripping of FHIR schema
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23:37:47 <dbooth> lloyd: We'll put whatever we find useful into the OWL from the XML schema, but it does not need to be round trippable.
23:37:50 <dbooth> ... We need to round trip the instances -- not the schema.
23:37:52 <dbooth> * ChrisS (~ChrisS@public.cloak) has left #hcls
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23:37:56 <dbooth> dbooth: agreed.
23:37:58 <dbooth> Chair: David Booth
23:38:03 <dbooth> rrsagent, draft minutes
23:38:03 <RRSAgent> I have made the request to generate http://www.w3.org/2015/11/10-hcls-minutes.html dbooth
23:38:10 <dbooth> rrsagent, make logs public