- From: Lloyd McKenzie <lloyd@lmckenzie.com>
- Date: Thu, 27 Nov 2014 13:51:38 +0100
- To: Grahame Grieve <grahame@healthintersections.com.au>
- Cc: David Booth <david@dbooth.org>, w3c semweb HCLS <public-semweb-lifesci@w3.org>, "its@lists.hl7.org" <its@lists.hl7.org>
- Message-ID: <CAJ860JKuf3_8x+DeEHsDVbjy5_pkbUn7mMFE0YTM-dZr1bvYYw@mail.gmail.com>
Hi grahame, I took that as a given. Objects will just have properties. Some of those properties will have a URL base of the resource, some will have a URL of some extension definition. -------------------------------------- Lloyd McKenzie +1-780-993-9501 Note: Unless explicitly stated otherwise, the opinions and positions expressed in this e-mail do not necessarily reflect those of my clients nor those of the organizations with whom I hold governance positions. On Thu, Nov 27, 2014 at 1:38 PM, Grahame Grieve < grahame@healthintersections.com.au> wrote: > there's no reason why a RDF form shouldn't put extensions as siblings, not > children. Does that make any difference? > > Grahame > > > On Wed, Nov 26, 2014 at 6:42 PM, Lloyd McKenzie <lloyd@lmckenzie.com> > wrote: > >> Sorry I missed the call (and I'm likely to miss the next one too). The >> general representation of FHIR in RDF/OWL is pretty straight-forward. FHIR >> has Resources which are structures that can contain sub-structures. The >> structures correspond to classes. The elements within those structures >> correspond to properties. >> >> However, there are several tricky bits we need to deal with: >> >> 1. All elements are extensible, even the simple types. So birthDate >> isn't actually a simple type, but instead a complex type with an optional >> "value" property with type xsd:date, but can have other properties in >> addition/instead >> >> 2. In addition to "regular" extensions, resources can have >> modifierExtensions which change the meaning of at least some other >> properties. That sort of behavior gives reasoners fits, but we need to >> account for it >> >> 3. The terminologies we link to are continuously evolving. FHIR allows >> identifying the version of the code system a code is from - do we have to >> make that matter? I did it in the RIM ontology, but it's painful. >> >> 4. Coded elements can have multiple codings and the meaning of the >> codings won't necessarily be equivalent. The solution will have to work in >> an environment where multiple codings are declared and mappings exist >> between the codes >> >> 5. In FHIR there are defaults and information can sometimes be conveyed >> by the absence of information. E.g. If a patient doesn't declare the >> "animal" element, it's inferred to be a human. This doesn't play that >> nicely with an open-world view where failing to declare "animal" doesn't >> mean that patient isn't an animal. >> >> 6. In FHIR, repeating elements are treated as lists/arrays where order >> matters and must be retained. >> >> 7. Finally, the RDF sytntax needs to be round-trippable with the XML and >> JSON syntaxes. I.e. An instance must be convertable from RDF to JSON to >> XML to RDF without any loss of information and with the conversion process >> not knowing anything other than the FHIR resource and data type >> definitions. (And ideally, the round-tripped version should still be valid >> against any digital signatures.) >> >> The RDF (FHIR instance) and OWL (FHIR profile definition) representations >> will need to take into account the above. (It's possible I've missed a >> couple of "gotchas" too - so feel free to supplement this list.) >> >> >> Lloyd >> >> -------------------------------------- >> Lloyd McKenzie >> >> +1-780-993-9501 >> >> >> >> Note: Unless explicitly stated otherwise, the opinions and positions >> expressed in this e-mail do not necessarily reflect those of my clients nor >> those of the organizations with whom I hold governance positions. >> >> On Tue, Nov 25, 2014 at 7:09 PM, David Booth <david@dbooth.org> wrote: >> >>> Draft minutes from today's call: >>> http://www.w3.org/2014/11/25-hcls-minutes.html >>> and also below in plain text. Thanks to Tony for an excellent intro to >>> his FHIR ontology approach! Tony's slides: >>> http://lists.w3.org/Archives/Public/www-archive/2014Nov/ >>> att-0048/FHIR_OWLv3.pdf >>> >>> Next week will will continue with EricP's and Claude's FHIR ontology >>> approaches. >>> >>> Thanks! >>> David Booth >>> >>> -------------------------------------- >>> >>> [1]W3C >>> >>> [1] http://www.w3.org/ >>> >>> - DRAFT - >>> >>> HCLS with Tony Mallia on FHIR ontology >>> >>> 25 Nov 2014 >>> >>> See also: [2]IRC log >>> >>> [2] http://www.w3.org/2014/11/25-hcls-irc >>> >>> Attendees >>> >>> Present >>> Tony_Mallia, David_Booth, Josh_Mandel, Rob_Hausam, >>> EricP_Joshua_Phillips, Patricia_Grime(sp?), Stan_Huff, >>> Cecil_Lynch, mscottm, Guoqian, Charlie_Mead, >>> Marc_Twagirumukiza, Rafael_Richards_(IRC_only?), >>> Daniel_Karlsson, Cati_Martinez_Costa_(IRC_only?) >>> >>> Regrets >>> Chair >>> DavidBooth >>> >>> Scribe >>> ericP >>> >>> Contents >>> >>> * [3]Topics >>> 1. [4]Role call and agenda >>> 2. [5]Logistics >>> 3. [6]Orphaned action items >>> 4. [7]Review of Work Projects >>> 5. [8]PhUSE-FDA project (formerly CDISC2RDF) >>> 6. [9]C-CDA RDF representations >>> 7. [10]High-level concept mapping to RDF (AR typeCodes, >>> etc.) >>> 8. [11]Comparison of FHIR ontology approaches >>> * [12]Summary of Action Items >>> __________________________________________________________ >>> >>> <JoshM> So should I be dialing into gotomeeting, or the W3C >>> bridge? >>> >>> <dbooth> zakim aadd is PatriciaGrime >>> >>> <Claude_> 1. Please join my meeting. >>> [13]https://global.gotomeeting.com/join/157514853 2. Use your >>> microphone and speakers (VoIP) - a headset is recommended. Or, >>> call in using your telephone. Dial +1 (213) 289-0016 Access >>> Code: 157-514-853 Audio PIN: Shown after joining the meeting >>> Meeting ID: 157-514-853 GoToMeeting® Online Meetings Made Easy® >>> >>> [13] https://global.gotomeeting.com/join/157514853 >>> >>> Role call and agenda >>> >>> <inserted> Postponed approving last week's minutes, because no >>> ITS co-chair is on the call to permit formal approval. >>> >>> <daniel> daniel karlsson here, not identified >>> >>> Logistics >>> >>> <scribe> ACTION: ericP to set up tracker [recorded in >>> [14]http://www.w3.org/2014/11/25-hcls-minutes.html#action01] >>> >>> <dbooth> Orphaned action items >>> >>> Orphaned action items >>> >>> Review of Work Projects >>> >>> <dbooth> ACTION: Tony to find out more details about how iCat >>> handles ICD-11 ont and report back [recorded in >>> [15]http://www.w3.org/2014/11/18-hcls-minutes.html#action01] -- >>> PENDING >>> >>> [15] http://www.w3.org/2014/11/18-hcls-minutes.html#action01] >>> >>> PhUSE-FDA project (formerly CDISC2RDF) >>> >>> <dbooth> ACTION: Kerstin and Ingeborg to prepare a status and >>> future state ideas for PhUSE-FDA work [recorded in >>> [16]http://www.w3.org/2014/11/18-hcls-minutes.html#action05] -- >>> PENDING >>> >>> [16] http://www.w3.org/2014/11/18-hcls-minutes.html#action05] >>> >>> C-CDA RDF representations >>> >>> <dbooth> ACTION: Eric to establish/make a wiki page for C-CDA >>> RDF representations work [recorded in >>> [17]http://www.w3.org/2014/11/18-hcls-minutes.html#action06] >>> >>> [17] http://www.w3.org/2014/11/18-hcls-minutes.html#action06] >>> >>> <dbooth> [PENDING] >>> >>> High-level concept mapping to RDF (AR typeCodes, etc.) >>> >>> <dbooth> ACTION: Tony and Rob to report their plan on >>> High-level concept mapping to RDF work [recorded in >>> [18]http://www.w3.org/2014/11/18-hcls-minutes.html#action08] -- >>> PENDING >>> >>> [18] http://www.w3.org/2014/11/18-hcls-minutes.html#action08] >>> >>> <dbooth> ACTION: Rob and all to decide on a wiki for Term Info >>> work [recorded in >>> [19]http://www.w3.org/2014/11/18-hcls-minutes.html#action09] -- >>> PENDING >>> >>> [19] http://www.w3.org/2014/11/18-hcls-minutes.html#action09] >>> >>> <dbooth> Should be an action for Rob instead of Tony. >>> >>> -> >>> [20]https://www.w3.org/wiki/HCLS/ClinicalObservationsInteropera >>> bility/TermInfo HCLS TermInfo page >>> >>> [20] https://www.w3.org/wiki/HCLS/ClinicalObservationsInteropera >>> bility/TermInfo >>> >>> Comparison of FHIR ontology approaches >>> >>> <dbooth> gotomeeting link: >>> [21]https://global.gotomeeting.com/join/157514853 >>> >>> [21] https://global.gotomeeting.com/join/157514853 >>> >>> <scribe> scribenick: ericP >>> >>> Tony: this is exploratory work to see the issues around an >>> ontology for FHIR >>> ... w3c defines many exchange formats >>> ... RDFXML is widely used >>> ... will present in Turtle 'cause ericP proposed that. i never >>> look at the bits so RDF/XML is fine for me >>> ... in FHIR, you exchange a fragment of an ontology >>> ... but if you're using a SemWeb environment, you can import >>> other ontologies to see the full picture >>> ... the refs to resources are like FHIR resources >>> >>> <dbooth> Tony Mallia's FHIR ontology slides: >>> [22]http://lists.w3.org/Archives/Public/www-archive/2014Nov/att >>> -0048/FHIR_OWLv3.pdf >>> >>> [22] http://lists.w3.org/Archives/Public/www-archive/2014Nov/ >>> att-0048/FHIR_OWLv3.pdf >>> >>> Tony: but in terminologies, you express it as an RDF URI which >>> you have gotten from some other mechanism >>> ... in the exchange, we see that it's a system of ontologies: >>> ... .. exchange >>> ... .. terminology >>> ... .. instance record >>> ... . >>> ... next step: work out the distributed ontology >>> ... fhir types point to terms. you change what is mostly the >>> facts to a recieving system which maps it to pictures >>> ... slide 4: ballot adverse reaction example >>> ... example symptoms is embedded rather than a resource >>> ... exposure has an external link to the substance >>> >>> dbooth: is this an appropriate example? >>> >>> cecil: by "embedded objects", you mean attributes of the >>> resource itself >>> >>> Tony: we have a mixture of patterns which we need to deal with >>> ... , need to figure out how we'd map from one to another >>> ... [slide 6] >>> ... an XML element name points to a type in the schema >>> ... RDF has a direct expression of type >>> ... elements ref'd in object properties can be embedded or >>> external >>> ... example asserts that record:AR123456 is a >>> fhir:AdverseReaction, as well as a SNOMED 241931004 >>> ... protege threw in that it was a named individual >>> ... do we talk about a symptom as an AdverseReaction? >>> ... in RDF, we don't care if a node is local or needs to be >>> resolved via a query >>> >>> dbooth: record: is instance data? >>> >>> Marc_Twagirumukiza: this SNOMED code is a big class. do we >>> expect to have granular codes e.g. skin rash? >>> >>> Tony: snomed equiv need not be expressed in the instance. >>> ... the relationshop between fhir:AdverseReaction and the equiv >>> snomed term would not appear in the instance data >>> ... [slide 7] >>> ... defining constraints about an "Adverse Reaction" >>> ... this is a style for doing a FHIR ontology >>> ... [slide 8] >>> ... this is a slice of a snapshot of the SNOMED ontology >>> ... there are versioned variants (seen at the bottom) >>> >>> Cecil: if you're looking at an individual FHIR resource, why >>> would you carry the subclass? >>> ... could get verbose >>> >>> Tony: payload just has the ref to 241931004 >>> ... the rest is in the SNOMED ontology >>> ... [slide 9] >>> ... in ICD-11, codes are classes, as with SNOMED-CT >>> >>> Guoqian: ICD comes from WHO. WHO has produced an RDF rendering >>> of ICD-11Beta >>> >>> <dbooth> Mistake on Tony's slide: ICD-11 is from WHO, not ISO. >>> >>> Tony: do you have an example of the formation of WHO URLs? >>> >>> Guoqian: will see if i can share >>> >>> Tony: probably similar to IHTSDO's approach >>> >>> <dbooth> ACTION: Guoqian to figure out whether he can share URI >>> conventions for ICD-11 [recorded in >>> [23]http://www.w3.org/2014/11/25-hcls-minutes.html#action07] >>> >>> Tony: [slide 10] >>> ... when you import other ontologies, you see the larger >>> picture >>> ... notation: '?' indicates a value set >>> ... [slide 11 - combined ontology] >>> ... alergy instance in the middle. >>> ... all of this binding occurs with closures in the RDF >>> ... [slide 12 - example with allergy to penicillin] >>> ... when you say "some penicillin", it's idenifying an abstract >>> ... those may be better in the terminology >>> ... but when it's a particular instance, better in the instance >>> >>> Cecil: if you're using owl:someOf, your saying that it's an >>> unknown instance. >>> ... if i wanted to describe this, i'd put it in a >>> SubstanceAdministration resource with a lot ID/batch, etc. >>> >>> JoshM: when we see a FHIR representation, we see an instance. >>> where did that "some" come from >>> ... ? >>> >>> Tony: came from me playing with it, to get it to connect to a >>> SNOMED penicillin >>> ... this is an alergy to something that may happen in the >>> future >>> >>> Cecil: it's implied that it happened at some date or at least >>> that you recorded it on some date. >>> >>> <dbooth> Tony: record:SomePenicillin means a dose of penicillin >>> -- not the OWL notion of "some". >>> >>> Tony: [slide 13] >>> ... view of allergy 1 >>> ... infers that it's an alergic disposition and moderage >>> ... causative agent is inferred >>> ... goal was to represent this in OWL. >>> ... i didn't see any real problems >>> ... working from the UML concept model >>> >>> <dbooth> David: Did you translate the FHIR data manually to >>> RDF? Tony: Yes. >>> >>> Tony: saying "this is an artifact of the ITS XML representation >>> of FHIR, could it be different with RDF?" >>> >>> Marc_Twagirumukiza: can we use the SNOMED predicates outside of >>> SNOMED? >>> >>> <dbooth> Marc: The use of SNOMED as predicates. Can we use them >>> out of SNOMED terminology, in FHIR? >>> >>> dbooth: in theory those SNOMED predicates tie in to the rest of >>> the SNOMED ontology >>> >>> Tony: this was a big discussion in the earlier work >>> ... when do you bring in other stuff and when does it overlap >>> FHIR structure >>> >>> dbooth: have to make sure you don't contradict SNOMED so if you >>> import more SNOMED later, we won't violate anything >>> >>> daniel: this has been explored in CIMI >>> ... consider that any ontology with the ambition of SNOMED-CT >>> will be less expressive than an information structure. >>> ... in an ontology of health care, you'd represent universals >>> ... having laterality in the information model and the term >>> model is good but the terminology model will be less >>> expressive. >>> >>> dbooth: this is a motivation for step 6 in the yosemite project >>> >>> <dbooth> The need for consistency across ontologies is one of >>> the reasons for Step 6 of the [24]http://yosemiteproject.org/ >>> roadmap. >>> >>> [24] http://yosemiteproject.org/ >>> >>> <dbooth> ADJOURNED >>> >>> <dbooth> IRC info: [25]https://www.w3.org/wiki/IRC >>> >>> [25] https://www.w3.org/wiki/IRC >>> >>> <dbooth> meeting notes conventions: >>> [26]http://dev.w3.org/2002/scribe/scribedoc.htm >>> >>> [26] http://dev.w3.org/2002/scribe/scribedoc.htm >>> >>> Summary of Action Items >>> >>> [NEW] ACTION: Eric to establish/make a wiki page for C-CDA RDF >>> representations work [recorded in >>> [27]http://www.w3.org/2014/11/18-hcls-minutes.html#action06] >>> [NEW] ACTION: ericP to set up tracker [recorded in >>> [28]http://www.w3.org/2014/11/25-hcls-minutes.html#action01] >>> [NEW] ACTION: Guoqian to figure out whether he can share URI >>> conventions for ICD-11 [recorded in >>> [29]http://www.w3.org/2014/11/25-hcls-minutes.html#action07] >>> >>> [27] http://www.w3.org/2014/11/18-hcls-minutes.html#action06 >>> >>> [PENDING] ACTION: Kerstin and Ingeborg to prepare a status and >>> future state ideas for PhUSE-FDA work [recorded in >>> [30]http://www.w3.org/2014/11/18-hcls-minutes.html#action05] >>> [PENDING] ACTION: Rob and all to decide on a wiki for Term Info >>> work [recorded in >>> [31]http://www.w3.org/2014/11/18-hcls-minutes.html#action09] >>> [PENDING] ACTION: Tony and Rob to report their plan on >>> High-level concept mapping to RDF work [recorded in >>> [32]http://www.w3.org/2014/11/18-hcls-minutes.html#action08] >>> [PENDING] ACTION: Tony to find out more details about how iCat >>> handles ICD-11 ont and report back [recorded in >>> [33]http://www.w3.org/2014/11/18-hcls-minutes.html#action01] >>> >>> [30] http://www.w3.org/2014/11/18-hcls-minutes.html#action05 >>> [31] http://www.w3.org/2014/11/18-hcls-minutes.html#action09 >>> [32] http://www.w3.org/2014/11/18-hcls-minutes.html#action08 >>> [33] http://www.w3.org/2014/11/18-hcls-minutes.html#action01 >>> >>> [End of minutes] >>> __________________________________________________________ >>> >>> >>> Minutes formatted by David Booth's [34]scribe.perl version >>> 1.140 ([35]CVS log) >>> $Date: 2014-11-25 18:05:13 $ >>> __________________________________________________________ >>> >>> [34] http://dev.w3.org/cvsweb/~checkout~/2002/scribe/scribedoc.htm >>> [35] http://dev.w3.org/cvsweb/2002/scribe/ >>> >>> Scribe.perl diagnostic output >>> >>> [Delete this section before finalizing the minutes.] >>> This is scribe.perl Revision: 1.140 of Date: 2014-11-06 18:16:30 >>> Check for newer version at [36]http://dev.w3.org/cvsweb/~checkout~/2002/ >>> scribe/ >>> >>> [36] http://dev.w3.org/cvsweb/~checkout~/2002/scribe/ >>> >>> Guessing input format: RRSAgent_Text_Format (score 1.00) >>> >>> Succeeded: s/slive/slice/ >>> Succeeded: s/CID-11/ICD-11/ >>> Succeeded: s/some/"some"/ >>> Succeeded: s/___/Marc/ >>> Succeeded: s/Work Projects/Review of Work Projects/ >>> Succeeded: i/zakim, RobHausem is really rhausam/Postponed approving last >>> week's minutes, because no ITS co-chair is on the call to permit formal >>> approval. >>> FAILED: s/<JoshM> So should I be dialing into gotomeeting, or the W3C br >>> idge?// >>> Succeeded: s/<JoshM> The channel topic indicates gotomeeting// >>> Succeeded: s/<JoshM> Ah// >>> Succeeded: s/<JoshM> I would like to suggest that talky.io may not work >>> for this particular group-chat use case.// >>> Succeeded: s/<JoshM> Is there a meeting happening somewhere? I tried bri >>> dge, talky, and gotomeeting// >>> Succeeded: s/<daniel> will audio be on gotomeeting as well?// >>> Succeeded: s/<trackbot> Sorry, but no Tracker is associated with this ch >>> annel.//g >>> Succeeded: s|s/<JoshM> So should I be dialing into gotomeeting, or the W >>> 3C bridge?//|| >>> FAILED: s/So should I be dialing into gotomeeting, or the W3C bridge?// >>> Succeeded: s|s/So should I be dialing into gotomeeting, or the W3C bridg >>> e?//|| >>> FAILED: s/So should I be dialing into gotomeeting, or the W3C bridge// >>> Succeeded: s|s/So should I be dialing into gotomeeting, or the W3C bridg >>> e//|| >>> Succeeded: s/Tony and all to decide/Rob and all to decide/ >>> Succeeded: s/please ignore the next hand to go up// >>> Succeeded: s/embodded/embedded/ >>> Succeeded: s/ht eearlier/the earlier/ >>> Found ScribeNick: ericP >>> Inferring Scribes: ericP >>> Default Present: +1.978.794.aaaa, DBooth, +1.617.500.aabb, +1.801.949.aa >>> cc, +1.202.260.aadd, EricP, +1.410.624.aaee, Joshua_Phillips, [IPcaller] >>> , +1.801.507.aaff, Tony, patricia, +1.415.537.aagg, StanHuff, CecilLynch >>> , rhausam, mscottm, Guoqian, +33.1.73.71.aahh, +1.617.500.aaii >>> Present: Tony_Mallia David_Booth Josh_Mandel Rob_Hausam EricP_Joshua_Phi >>> llips Patricia_Grime(sp?) Stan_Huff Cecil_Lynch mscottm Guoqian Charlie_ >>> Mead Marc_Twagirumukiza Rafael_Richards_(IRC_only?) Daniel_Karlsson Cati >>> _Martinez_Costa_(IRC_only?) >>> Got date from IRC log name: 25 Nov 2014 >>> Guessing minutes URL: [37]http://www.w3.org/2014/11/25-hcls-minutes.html >>> People with action items: all eric ericp guoqian ingeborg kerstin rob to >>> ny >>> >>> [37] http://www.w3.org/2014/11/25-hcls-minutes.html >>> >>> >>> [End of [38]scribe.perl diagnostic output] >>> >>> [38] http://dev.w3.org/cvsweb/~checkout~/2002/scribe/scribedoc.htm >>> >>> >>> >>> ************************************************************ >>> *********************** >>> Manage subscriptions - http://www.HL7.org/listservice >>> View archives - http://lists.HL7.org/read/?forum=its >>> Unsubscribe - http://www.HL7.org/tools/unsubscribe.cfm?email=lloyd@ >>> lmckenzie.com&list=its >>> Terms of use - http://www.HL7.org/myhl7/managelistservs.cfm?ref=nav# >>> listrules >>> >> >> >> *********************************************************************************** >> Manage your subscriptions <http://www.HL7.org/listservice> | View the >> archives <http://lists.HL7.org/read/?forum=its> | Unsubscribe >> <http://www.HL7.org/tools/unsubscribe.cfm?email=grahame@healthintersections.com.au&list=its> >> | Terms of use >> <http://www.HL7.org/myhl7/managelistservs.cfm?ref=nav#listrules> >> > > > > -- > ----- > http://www.healthintersections.com.au / grahame@healthintersections.com.au > / +61 411 867 065 >
Received on Thursday, 27 November 2014 12:52:29 UTC