15:00:34 <RRSAgent> RRSAgent has joined #hcls
15:00:34 <RRSAgent> logging to http://www.w3.org/2016/06/28-hcls-irc
15:00:36 <trackbot> RRSAgent, make logs world
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15:00:38 <trackbot> Zakim, this will be HCLS
15:00:38 <Zakim> ok, trackbot
15:00:39 <trackbot> Meeting: Semantic Web Health Care and Life Sciences Interest Group Teleconference
15:00:39 <trackbot> Date: 28 June 2016
15:00:42 <dbooth> Chair: David Booth
15:03:07 <dbooth> Present: David Booth, Amol, Shahram, EricP
15:03:18 <dbooth> Topic: ShEx validator
15:03:40 <dbooth> eric: people are using them.  There are two, mine and Jose's.
15:04:41 <dbooth> ... Harold is using the Fancy ShEx demo interactively to validate, then uses the service to run all examples.
15:04:51 <dbooth> ... Is there  a public service available?
15:05:02 <dbooth> s/... Is/dbooth: Is/
15:06:05 <dbooth> eric: There is a service running somewhere, that has harnesses for certain functions.  Jose set one up on that.
15:07:08 <dbooth> eric: There are three implementations of ShEx FHIR validators.  Harold is working on a fourth.
15:07:31 <dbooth> ... Someone at INRIA is working on a fifth.
15:07:41 <dbooth> s/FHIR validators/validators/
15:08:42 <dbooth> dbooth: Should we still set up a FHIR shex validator on yosemiteproject.org site?
15:09:09 <dbooth> eric: sure.
15:09:25 <dbooth> dbooth: we should discuss details offline about how to set it up.
15:10:25 <dbooth> Topic: Issues List
15:10:26 <dbooth> https://github.com/w3c/hcls-fhir-rdf/issues
15:11:58 <dbooth> https://www.w3.org/2016/06/14-hcls-minutes.html#item03
15:12:41 <ericP> -> http://shexjs.herokuapp.com/ generic shex.js server
15:14:25 <dbooth> Topic: Issue 30: What should the type of fhir:link target be in the ShEx?
15:14:32 <dbooth> https://www.w3.org/2016/06/14-hcls-minutes.html#item03
15:16:43 <dbooth> Examples provided by Eric:
15:16:45 <dbooth> # Option 1:
15:16:45 <dbooth> <Obs1> a fhir:Observation;
15:16:45 <dbooth>   fhir: Observation.performer [
15:16:45 <dbooth>     link <http://hl7.org/fhir/Practitioner/f005>;
15:16:46 <dbooth>     Reference.reference [
15:16:46 <dbooth>       fhir:value "Practitioner/f005" ] ];
15:16:48 <dbooth> # Option 2:
15:16:50 <dbooth> <Obs1> a fhir:Observation;
15:16:52 <dbooth>   fhir: Observation.performer [
15:16:54 <dbooth>   link <http://hl7.org/fhir/Practitioner/f005>;
15:16:56 <dbooth>   Reference.reference [
15:17:00 <dbooth>   fhir:value "Practitioner/f005" ] ];
15:17:02 <dbooth> <http://hl7.org/fhir/Practitioner/f005> a fhir:Practitioner .
15:17:04 <dbooth> # Option 3:
15:17:06 <dbooth> <Obs1> a fhir:Observation;
15:17:08 <dbooth>   fhir: Observation.performer [
15:17:10 <dbooth>   link <http://hl7.org/fhir/Practitioner/f005>;
15:17:12 <dbooth>   Reference.reference [
15:17:14 <dbooth>     fhir:value "Practitioner/f005" ] ;
15:17:16 <dbooth>   a fhir:PractitionerReference . ];
15:18:38 <dbooth> Here they are again, with typos corrected:
15:18:39 <dbooth> # Option 1:
15:18:39 <dbooth> <Obs1> a fhir:Observation;
15:18:39 <dbooth>   fhir:Observation.performer [
15:18:39 <dbooth>     fhir:link <http://hl7.org/fhir/Practitioner/f005>;
15:18:39 <dbooth>     fhir:Reference.reference [
15:18:41 <dbooth>       fhir:value "Practitioner/f005" ] ];
15:18:43 <dbooth> # Option 2:
15:18:45 <dbooth> <Obs1> a fhir:Observation;
15:18:47 <dbooth>   fhir:Observation.performer [
15:18:49 <dbooth>   fhir:link <http://hl7.org/fhir/Practitioner/f005>;
15:18:51 <dbooth>   fhir:Reference.reference [
15:18:53 <dbooth>   fhir:value "Practitioner/f005" ] ];
15:18:55 <dbooth> <http://hl7.org/fhir/Practitioner/f005> a fhir:Practitioner .
15:18:57 <dbooth> # Option 3:
15:19:01 <dbooth> <Obs1> a fhir:Observation;
15:19:03 <dbooth>   fhir:Observation.performer [
15:19:05 <dbooth>   fhir:link <http://hl7.org/fhir/Practitioner/f005>;
15:19:07 <dbooth>   fhir:Reference.reference [
15:19:09 <dbooth>     fhir:value "Practitioner/f005" ] ;
15:19:11 <dbooth>   a fhir:PractitionerReference . ];
15:25:38 <dbooth> MEETING CANCELED -- not enough key people could make it today.
15:25:52 <dbooth> However, the 5pm call will go ahead.
15:25:57 <dbooth> ADJOURNED
15:26:20 <dbooth> Topic: =================== 5pm Call =======================
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20:59:15 <hsolbrig> present+ hsolbrig
21:00:34 <dbooth> present+ David Booth, EricP
21:05:09 <dbooth> present+ Marc T
21:05:44 <dbooth> Topic: FHIR on schema.org
21:06:21 <dbooth> harold: in a proposal that Dr Chute and Dr Chang wrote to the BD2K people, it was suggested to publish metadata elements on schema.org .
21:06:41 <dbooth> ... There are a couple of different models for publishing there.  One is to publish an entirely separate context.
21:07:39 <dbooth> ... Marc has been doing an extension to schema.org , and that's an ontology of components of medicine that would be used to mark up a Mayo site or others.
21:08:19 <dbooth> ... We concluded that since we said we would do it, we would publish.
21:08:51 <dbooth> ... It had been proposed to use by some of the google people, that there could be value in putting it on schema.org.
21:09:23 <dbooth> ... There was also opposition, folks didn't think it would work.  But we decided to do a trial baloon, and then open it to the community and evaluate it.
21:09:58 <dbooth> ... in order to make it work with the schema.org site, i had to put in schema.org URIs.
21:10:09 <hsolbrig>  http://fhir.fhir-schema-org.appspot.com/
21:10:13 <dbooth> ... One thing we can do is put the related FHIR URIs into the model itself.
21:11:10 <hsolbrig> http://fhir.fhir-schema-org.appspot.com/docs/full.html
21:12:12 <dbooth> harold: If you click "Extension fhir" on that page, and scroll down, you'll see the FHIR organization of the resources.
21:12:49 <dbooth> ... Some of the complex datatypes don't work, because i wasn't sure what to do about them.
21:13:18 <dbooth> ... There are a number of schema types in schema.org, json, used to mark up HTML pages.
21:13:46 <dbooth> ... For example, Cleveland Clinic currently marks up their pages with the info that Marc put together.
21:13:57 <dbooth> ... First question: Should this be here at all?  Does it have value?
21:14:22 <dbooth> ... Renato said that FHIR is for marking up clinical records and they have no business on the web anyway.
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21:14:57 <dbooth> Marc: As background, when we started this initiative in 2011 the intention of schema.org was to mark up web resources, so that the big engines can retrieve data.
21:15:25 <hsolbrig> http://my.clevelandclinic.org/health/diseases_conditions/hic_anemia
21:15:33 <dbooth> ... in 2012 when we started exchanging electronic health records, when I was working for Agfa, we saw that everyone was using their own resource names.
21:15:56 <hsolbrig> If you view source on the above link, you can see the schema.org medical terms in use
21:16:02 <dbooth> ... We said, why not use a public vocabulary?  We hijacked the schema.org medical terms, not only in web pages, but to formalize EHR data.
21:16:18 <ericP> SALUS
21:16:29 <dbooth> ... When we started doing that it was within SALUS
21:16:52 <dbooth> ... At that time, we saw that the vocab was incomplete, and the terms that we wanted to use were not those given.
21:17:26 <dbooth> ... So we took an initiative to fine tune that vocabulary, but google and others were very resistant at first.  They wanted to see the use case.
21:17:49 <dbooth> ... WE showed them, 7 universities were exchanging data this way.
21:18:16 <hsolbrig> http://schema.org/docs/meddocs.html   --- this is the work Mark T is talking about
21:18:21 <dbooth> ... Using it in a consortium, but eventually exposing the vocabulary on the web.
21:18:29 <dbooth> ... Not the private data, but the vocabulary.
21:19:06 <dbooth> ... We then got an additional initiative, BioSchemas, in connection with BD2K, and also led by Michel Dumontier at Stanford and others.
21:19:12 <hsolbrig> http://bioschemas.org/
21:20:13 <dbooth> marc: This increased the use of the vocab.  But last year we decided with google to first extract the existing vocab, fine tune it, make an extension.
21:20:53 <dbooth> ... Next step will be extension, guided by use cases.  First is clinicaltrials.gov . They want to publish the trials using the schema.  Stanford folks are also involved.
21:21:08 <dbooth> ... BioSchema is also suggesting a wide range.
21:21:50 <dbooth> ... Health insurance plans also want to use it internally.  They have already submitted a patch.
21:22:18 <ericP> q+ to say that the common factor is that all of these leverage schema.org for some combination of govornance and popularity
21:22:27 <dbooth> http://pending.schema.org/
21:22:40 <dbooth> http://pending.schema.org/HealthInsurancePlan
21:23:00 <dbooth> marc: The want to use it not only internally, but between health plans in the US.
21:23:41 <dbooth> ... When you have a term in schema.org or extension, we put already equivalent class in SNOMED CT.
21:23:56 <dbooth> ack ericP
21:24:54 <ericP> ack ack ericP
21:25:01 <dbooth> trackbot, start meeting
21:25:03 <trackbot> RRSAgent, make logs world
21:25:04 <Zakim> Zakim has joined #hcls
21:25:05 <trackbot> Zakim, this will be HCLS
21:25:06 <Zakim> ok, trackbot
21:25:07 <trackbot> Meeting: Semantic Web Health Care and Life Sciences Interest Group Teleconference
21:25:07 <trackbot> Date: 28 June 2016
21:25:58 <Marc_Twagirumukiza> Marc_Twagirumukiza has joined #hcls
21:26:16 <dbooth> eric: The common thread here, in SALUS, the common factor ... schema.org gives us some governance and popularity.
21:26:35 <dbooth> ... That is fundamentally in tension with organizations owning their own schema.
21:26:53 <dbooth> ... For example, the schema that you get from Spackman's SNOMED ont gives you some URIs.
21:27:09 <dbooth> ... But if you put it in schema.org you would have to put a bunch of slashes after it.
21:27:38 <dbooth> ... On one hand I'm opposed to a single central schema, because it goes against distributed extensibility of semantic web.
21:28:22 <dbooth> ... But schema.org provided an extension mechanism that was not available for the SNOMED ont.
21:28:52 <hsolbrig> q+
21:29:09 <Marc_Twagirumukiza> +q
21:29:10 <dbooth> ... Ultimately there is a cost to having a centralization of schemas, that your distributed extensibility atrophies, and you cannot address the long tail
21:29:44 <dbooth> ... It does not hurt to have schema.org owning more stuff, but I worry what we're learning about the value of distributed extensibility.
21:29:50 <dbooth> ack hsolbrig
21:30:08 <dbooth> harold: I don't think schema.org is intended to be an ontology publiching org per se.
21:30:31 <dbooth> ... But to the extent that they recognize markup in web pages and do intelligent this with them.
21:31:04 <dbooth> ... As a primary publishjing mechanism for ont I don't think you should use schema.org.
21:31:29 <dbooth> ... But the community can take advantage of some of these big aggregators and write interesting tools.
21:31:55 <dbooth> ... But the question Renato raises is whehter we should encourage EHR to be published.
21:31:59 <dbooth> q+ grahame
21:32:02 <dbooth> ack Marc
21:32:33 <dbooth> marc: Agree.  If you see the way schema was working, my intention from the beginning was to make a branch from schema.org, an extension.
21:33:15 <dbooth> ... The core vocab is very hard to put a single term inside.  But when you are in an extension it is easy to suggestion something, but the policy of extending terms is that if we do not have a use case we do not add a term.
21:33:31 <dbooth> ... To align with vocabs.  The intention is to make a kind of hub of vocabs.
21:33:50 <dbooth> ... It does not display the SNOMED link, but it is there, and reasoners can use it.
21:34:10 <dbooth> ... You can extract all SNOMED equivalent classes.
21:34:34 <dbooth> ... The intention is not to create yet another vocab.
21:34:37 <dbooth> ack grahame
21:35:03 <dbooth> grahame: First, i disagree with renato about policy.  It is not our business to impose our policy preferences on everyone else.
21:35:19 <dbooth> ... If people want to share their healthcare data, they should be allowed to do so.
21:35:30 <ericP> to grahame's point, CDC mines tons of information from tweets
21:35:52 <dbooth> ... Regarding fhir on schema.org, I want to understand why the URLs are a problem, and whether it should or sholdn't be the same URLs for identifiers.
21:36:37 <dbooth> ... There's a change in perspective between healthcare processes and biomed ontologies.  They're veryu diofferent languages.  hard to map.
21:36:54 <dbooth> ... That seems at the heart of what you would do with schema.org -- exploring those boundaries.
21:37:13 <ericP> q+ to say that health care processes and biomed ontologies connect, but are pretty different use cases on their own
21:37:23 <dbooth> ... Use case: medical providers want to hook into patient portal and link from patient healtchare records and knowledge relevant to their conditions.
21:37:55 <dbooth> ... info buttons allow them to be linked, but it is not semantic and not clever.  There is potential overlap, synergy.
21:37:59 <dbooth> ack ericp
21:37:59 <Zakim> ericP, you wanted to say that health care processes and biomed ontologies connect, but are pretty different use cases on their own
21:38:44 <dbooth> eric: The use cases for writing what is useful care after a heart attack is different from the ont you use to say that "bob had chest pains and our diagnosis was heart attack".
21:39:19 <Marc_Twagirumukiza> +q
21:39:37 <dbooth> ... They do connect.  If you dig into the clinical model, you find out that it is a heart attack.  That's the same heart attack that shows up in the biomed ont.  But the things that are said about it are different.
21:39:47 <dbooth> grahame: Its the bridging that concerns up most.
21:39:54 <dbooth> ack marc
21:40:15 <hsolbrig> q+
21:40:30 <dbooth> marc: Agree.  When you look at the use cases, how to formalize healthcare data, but clinical data is different.
21:40:49 <dbooth> ... When we started to extend schema.org the intention was to bridge the gap between them.
21:41:10 <dbooth> ... For exmaple, how FHIR formalizes medical condition, we can easily use schema.org to put predicates on it.
21:41:43 <dbooth> ... Currently not yet done, but in the pipeline, to be published.  Started experimenting with equivalentClass.
21:41:59 <dbooth> ... Use case is to allow reasoning engine to generate new knowledge.
21:42:09 <dbooth> ... Next is to add equivalentProperty.
21:42:30 <dbooth> ... Big step is to extend this vocabulary.  They are not yet fine enough for clinical use.
21:42:44 <dbooth> ack hsolbrig
21:42:56 <dbooth> harold: There are a couple of additional use cases that came to mind.
21:43:38 <dbooth> ... One is the annotation here could be used to mark information that is derived from a FHIR record.  Don't know how useful that would be, but FHIR requires an HTML rendering as part of the record.  This could add traceability.
21:44:28 <dbooth> ... Another place for added value, with personal devices for steps, glucose, heart rate etc., if we had a markup that we could convince the makers to generate, we might get some interesting benefits without necessarily requiring them to use a formal FHIR resource.
21:44:49 <dbooth> q?
21:45:53 <dbooth> marc: I jumped on the work that harold did.  Very good info.   Mobile devices need things like this.  Such use cases would convince these people.
21:46:09 <dbooth> ... How to make FHIR on schema.org?  First is to discuss if it is useful, worthwhile.
21:46:23 <dbooth> ... i am convinced that it is.  Need it to converge.  How?  Need to discuss.
21:46:44 <dbooth> ... Could either take the work that harold did already.
21:47:02 <dbooth> ... We could do mappings like we did to SNOMED.
21:47:06 <ericP> q+ to say that there have been projects where CDC grepped tweets for indications of epidemic
21:47:12 <dbooth> ... Good to collect information from everyone.  Useful?
21:47:48 <dbooth> eric: If we're looking for use cases, the CDC has done projects where they have grepped tweets to get evidence of epidemic.
21:48:03 <dbooth> ... if we gave them a nice structured model, they might do better.
21:48:44 <dbooth> dbooth: There was also the well-known google example of predicting the flu before the CDC could.
21:49:09 <dbooth> harold: I owe grahame an explanation and a schema.org expert to tell me where to use schema.org URIs.
21:49:16 <dbooth> ... I'll contact marc about that.
21:49:28 <dbooth> ... And Dan Brickley.  I'll cc folks on that.
21:49:33 <Marc_Twagirumukiza> also post request here: https://www.w3.org/community/schemed/
21:49:53 <dbooth> ... We can put together a few examples, JSON-LD feeds and other things are kind of interesting.
21:50:07 <dbooth> ... Propose in the next week or two to get trial examples put together.
21:50:33 <dbooth> ... We're using a github site.
21:50:46 <hsolbrig> https://github.com/crDDI/schemaorg
21:51:10 <dbooth> ... I'll find the parser to show how I assembled it.
21:51:27 <dbooth> ACTION: Harold to put together examples of FHIR on schema.org
21:51:27 <trackbot> Created ACTION-64 - Put together examples of fhir on schema.org [on Harold Solbrig - due 2016-07-05].
21:52:34 <dbooth> harold: One question: do we need FHIR as it exists now on schema.org?   Or should the HCLS references on schema.org include FHIR references?
21:52:55 <dbooth> grahame: We can modify the FHIR publication infrastructure to make it more suitable for that if necessary.
21:53:17 <dbooth> harold: the publication is a simple RDF model.  Basically just subclass/superclass-type stuff.
21:54:38 <dbooth> Topic: Meeting time
21:55:25 <dbooth> eric: Could do one hour later?
21:55:37 <dbooth> grahame: renato mentioned childcare duties at 7am
21:57:07 <dbooth> harold: I'm willing to do 4am or 5am if needed.
21:58:11 <dbooth> dbooth: What about 7am or 8am Eastern US?
21:58:31 <dbooth> grahame: That would be 9pm or 10pm.
22:01:13 <dbooth> ACTION: Dbooth to ask renato about scheduling a special teleconference time when he could join, 7am or 8am ET or 6pm ET
22:01:14 <trackbot> Created ACTION-65 - Ask renato about scheduling a special teleconference time when he could join, 7am or 8am et or 6pm et [on David Booth - due 2016-07-05].
22:02:06 <dbooth> present+ Rob Hausam, Grahame Grieve
22:02:51 <dbooth> ADJOURNED
22:02:57 <dbooth> rrsagent, draft minutes
22:02:57 <RRSAgent> I have made the request to generate http://www.w3.org/2016/06/28-hcls-minutes.html dbooth
22:05:22 <dbooth> i/Could do one hour later/dbooth: Tried unsuccessfully to get Renato to join this call.  Would like to get him on a teleconference to discuss.  Can we schedule a special teleconference to accommodate his timezone need?
22:05:40 <dbooth> rrsagent, draft minutes
22:05:40 <RRSAgent> I have made the request to generate http://www.w3.org/2016/06/28-hcls-minutes.html dbooth
22:17:20 <dbooth> i/5pm Call/Topic: ========================= CALL CANCELED ======================
22:17:45 <dbooth> s/CALL CANCELED/11am ET CALL CANCELED/
22:17:54 <dbooth> rrsagent, draft minutes
22:17:54 <RRSAgent> I have made the request to generate http://www.w3.org/2016/06/28-hcls-minutes.html dbooth
22:19:57 <dbooth> Present: 11AM: David_Booth, Amol, Shahram, EricP, 5PM: David_Booth, EricP, hsolbrig, Marc_T, Rob_Hausam, Grahame_Grieve
22:20:01 <dbooth> rrsagent, draft minutes
22:20:01 <RRSAgent> I have made the request to generate http://www.w3.org/2016/06/28-hcls-minutes.html dbooth