15:00:48 RRSAgent has joined #hcls 15:00:48 logging to http://www.w3.org/2014/05/27-hcls-irc 15:00:55 zakim, this is hcls 15:00:55 ok, dbooth; that matches SW_HCLS()11:00AM 15:01:07 zakim, code? 15:01:07 the conference code is 4257 (tel:+1.617.761.6200 sip:zakim@voip.w3.org), dbooth 15:01:24 +DBooth 15:01:28 +Ingeborg 15:01:54 Claude has joined #hcls 15:02:15 Ingeborg has joined #hcls 15:02:23 +Tony 15:02:40 zakim, who is here? 15:02:40 On the phone I see Mike_Denny, [GVoice], [IPcaller], DBooth, Ingeborg, Tony 15:02:42 On IRC I see Ingeborg, Claude, RRSAgent, Zakim, dbooth, Mehmet, egonw, ericP 15:02:57 Mike has joined #HCLS 15:03:19 zakim, [GVoice] is Mehmet 15:03:19 +Mehmet; got it 15:03:46 Tony_ has joined #HCLS 15:04:12 zakim, [IPcaller] is Claude 15:04:12 +Claude; got it 15:04:34 agenda+ claude: An approach to Modifying Extensions in FHIR ont 15:05:17 agenda+ Movement toward RDF-based electronic health records 15:06:19 agenda+ Salus 15:07:05 agenda+ Current problems of HL7, and whether RDF can help 15:08:05 zakim, take up agenda 3 15:08:05 agendum 3. "Salus" taken up [from dbooth] 15:08:11 Topic: Salus 15:08:56 Ingeborg: Looked at bioportal and UMLS and could not find any work on OMOP, but found SALUS. 15:09:06 +EricP 15:09:21 ... Looks like a project for defining common data elements for post-market surveillance 15:09:43 ... Building semantic metadata repository. Downloaded a paper on it. Anyone familiar with their work? 15:10:18 Eric: i know them well. They participated for a little well. 15:11:31 ... They'ave been doing post-market surveillance. their work involved a lot of term mapping. they were trying to figure out the right way to write that "x is the same as y" , "and if x is the same as y, and y is the same as z, are x and z the same? maybe optimistic". 15:12:23 Mike: You spoke about Salus in July 15, 2013 15:12:35 http://www.w3.org/2013/07/12-hcls-minutes 15:13:00 https://www.w3.org/wiki/HCLS/ClinicalObservationsInteroperability 15:13:38 tony: Might this have moved to ITSDU? 15:14:19 eric: I don't think so. They had some EU grants. I don't think their work woudl have coincided with the terminology work. 15:14:53 +Neda 15:15:42 David: They reported the ICD-11 work using web protege as successful. 15:16:24 ingeborg: Jan 2014 paper on Salus talked about Salus common information model, and seems to have an RDF representatino. 15:17:20 ingeborg: Not sure how to determine whether someone else's semantic work will work for my needs. 15:19:07 zakim, take up agendum 2 15:19:07 agendum 2. "Movement toward RDF-based electronic health records" taken up [from dbooth] 15:19:10 Neda has joined #hcls 15:19:45 tony: curious whether there's movement toward using RDF-based EHRs. Triplestore might be a nice way to handle an EHR. 15:20:05 eric: There's stuff close with the FDA now. Submitting clinical trial data in RDF. 15:20:36 ... I don't know if the backing store can be RDF yet, for triplestore performance. 15:20:47 tony: federated stores also. 15:23:19 eric: we could use MIMIC2 database from MIT and Harvard, to see what happens if you use an RDF EHR and try to do useful queries? Or only use RDF for an interface? We don't have to say to use RDF under the covers, but to use it for interchange. 15:24:08 tony: wondering how many ont and how the importing works. you can define an ont for the structure with some governance, and ont for the instances also. how do you manage them? 15:24:26 eric: Or they overlap. 15:25:12 tony: Tbox gives the types, both structural and semantic. Interested to see how individual data would be organized. separate ontologies? 15:25:56 eric: would be equiv to SPARQL endpoint for a corpus of patients. tbox axioms in the patient data? 15:26:44 tony: An instance of Observation related to this named patient. Do you declare this instance to be a member of an ont, so it has a prefix? How do you organize your prefixes, and therefore your ontologies? 15:27:08 ... Your instance ontologies need to import the type ontologies. THinking about the strucutres about how these ont may work. 15:29:48 eric: EHR for CR (Clinical Records), and EU project, is looking at using RDF for this. 15:30:00 ... FHIR could be viewed as RDF. 15:31:41 david: some small-scale projects are experimenting with it. also the work that claude, neda and I are doing for the DoD is taking instance data from 30-year old MUMPS based system and representing in RDF for use in as-yet undertermined future systems. 15:32:02 tony: I was thinkg more of native storage of RDF. 15:32:35 eric: Also cecil lynch's work forthe CDC doing outbreak detection, using OWL rules. 15:33:16 zakim, take up agendum 1 15:33:16 agendum 1. "claude: An approach to Modifying Extensions in FHIR ont" taken up [from dbooth] 15:33:52 claude: moving to the next step of FHIR ont. how to represent Modifying Extensions? 15:34:35 ... had some discussions. An idea: currently in the OFHIR ont there are extension points, extension super property, and then on Disease you might have modifying and non-modifying extensions (disjoint). 15:35:15 ... So when you want to write an extension you do it in your own namespace, but you also make the ext a subproperty of either ModifyingExtension or NonModifyingExtension. 15:35:50 ... A ModifyingExtension is one that may change the semantics of its container. E.e., saying that a medical condition is absent. 15:36:29 ... You'd attach this and use a restriction that defines a new concept that is the set of all things that have that extension. 15:36:52 Mike: The ModifyingExtension would a subclass of that resource class? 15:37:33 claude: the set of all conditions that have a modifying extension of a particular type. e.g., Absence would have the negation indicator of True. 15:40:41 david: maybe the modified class coudl be RELATED to the original class. 15:41:12 claude: you have a concept that containsnn info about a condition, and it can be partitioned into those that are affirmative about it, and those that are negations of that condition. 15:41:31 ... FHIR does not have an notion of clinical statement. 15:42:15 ... So when you have a condition class it is a statement of a condition. Two possibilities: 1 the patient has a condition. 2. the patient does not have a condition. A third possibility: the patient has an unknown probability of having that condition. 15:42:35 ... Those three are subclasses of statemetns i can make about that patient's possible condition. 15:43:22 ... The negative statement is the intersection of all statements of denial intersecting all statements about conditions. 15:44:01 ... Asthma versus not-Asthma. 15:45:08 david: Hard to follow in the abstract, but intriguing. Bring an exmple to discuss? 15:46:32 claude: Negation is easier if you make clinical statements explicit, so that you can negate the statement instead of negating the disease. I can bring an example next week. 15:47:02 tony: interesting conflict in how FHIR develops things. Allergy and tolerance has Confirmed, Refuted or Resolved. That's another way to handle negation. 15:48:44 eric: Value of ModifyingExtension will be useful in a small space, but semantic reuse will come when they become popular. E.g., for negation, or for a restricting date range. FHIR tries not to chase all use cases right now, and push subtleties into SemanticExtension. 15:49:23 ... Status Indicator is an exmplae of where they'll end up. Considering putting it into the core. Values other than Confirmed, Refuted Unknown (e.g., Mild) would still be extensions. 15:49:34 ... Parties would know to look for particular extensions. 15:50:28 zakim, take up agendum 3 15:50:28 agendum 3. "Salus" taken up [from dbooth] 15:50:32 oops 15:50:38 zakim, take up agendum 2 15:50:38 agendum 2. "Movement toward RDF-based electronic health records" taken up [from dbooth] 15:50:42 damn 15:51:01 zakim, take up agendum 4 15:51:01 agendum 4. "Current problems of HL7, and whether RDF can help" taken up [from dbooth] 15:51:03 :) 15:52:03 claude: semantic cleanliness, e.g., criticality or severity -- attribute of condition. But Refuted is not an attribute of the condition, it is about the statement about the condition. 15:52:20 ... This is where the benefits of RDF come into play. 15:52:37 ... But the fact that things are not well defined semantically in many models is a problem. 15:53:10 tony: higher levels of what thesee different concepts are -- orthogonal? -- accuracy of the recording, etc. orthogonal different things. 15:53:27 claude: semantic overloading 15:53:56 eric: The ones that can change independently would be non-modifying extensions. 15:55:13 claude: I suspect that many of the modifying ext are really about the statemnts rather than about the medical condition. 15:55:42 eric: We'll have to manage that in RDF. 15:56:48 tony: Just ran across a presentation by Charlie Mead on this. 15:57:46 Topic: Next week 15:57:57 David: I'll be busy with Healthcare Datapalooza conference 15:58:06 Claude: I can chair that week. 15:58:16 Eric: I'll be busy with child care, but call in from the park. 15:58:40 http://dbooth.org/2013/semtech/slides/02-Mead-RDFWorkshop-2.pdf 15:58:46 Claude: if we move to a world where everything is represented in RDF, could it scale to handle the job? 15:59:12 -Ingeborg 15:59:14 -Tony 15:59:17 ADJOURNED 15:59:26 -Neda 15:59:27 -DBooth 15:59:28 -Claude 15:59:39 -Mike_Denny 15:59:41 -EricP 16:00:01 -Mehmet 16:00:02 SW_HCLS()11:00AM has ended 16:00:02 Attendees were Mike_Denny, DBooth, Ingeborg, Tony, Mehmet, Claude, EricP, Neda 16:32:01 egonw has joined #HCLS 18:04:23 rrsagent, make logs public 18:04:31 Meeting: HCLS 18:04:32 Chair: DBooth 18:04:41 zakim, who was here? 18:04:41 I don't understand your question, dbooth. 19:39:07 egonw has joined #HCLS 19:43:20 egonw_ has joined #HCLS