- From: Lloyd McKenzie <lloyd@lmckenzie.com>
- Date: Wed, 10 Dec 2014 23:07:23 -0700
- To: Vipul Kashyap <kashyap.vipul@gmail.com>
- Cc: David Booth <david@dbooth.org>, w3c semweb HCLS <public-semweb-lifesci@w3.org>, HL7 ITS <its@lists.hl7.org>
- Message-ID: <CAJ860JLV9PJ6QYnw=rhtr6LBwN8pbvPJgCnGdAbkd0zkxaKkTw@mail.gmail.com>
Hi Vipul, To me, your first two points go together. The only reason to do an RDF representation is to support implementations that want to make use of semantic web technologies for inference purposes. I wouldn't describe either as requirements for the syntax though. A requirement would be a particular type of inference that we wanted to enable (or wanted to optimize for). In terms of your third point, there's two different ways we could interpret this. One would be to say that we'll convert both FHIR structures and FHIR vocabulary into RDF and include the linkage between them as part of the class model. I'm definitely on-side with that. The second way would be to say that we'll be able to easily integrate existing ontologies from other code systems such as SNOMED with the FHIR structure ontology. I think that's a much tougher thing to do, though it may be possible in some cases. I'd like to treat it as a secondary objective, but am ok with having it on the table. (Feel free to add your thoughts to the wiki page.) 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 Wed, Dec 10, 2014 at 2:59 PM, Vipul Kashyap <kashyap.vipul@gmail.com> wrote: > Good list, Lloyd. Would like to suggest some more additions (apologies if > these have already been suggested). > > > > · Clearly articulate the value of the new RDF/RDFS/OWL > representation over the current XML/JSON representation > > · Enablement of OWL/RDFS inference – so we could identify use > cases that cannot be easily done based on the XML/JSON representation > > · A common OWL/RDFS representation for information model elements > *and* medical terminology concepts. > > > > Thoughts. Suggestions? > > > > ---Vipul > > > > *From:* Lloyd McKenzie [mailto:lloyd@lmckenzie.com] > *Sent:* Monday, December 08, 2014 1:36 PM > *To:* David Booth > *Cc:* w3c semweb HCLS; its@lists.hl7.org > *Subject:* Re: Minutes of last week's (Dec 2) HL7 ITS RDF Subgroup / W3C > HCLS COI call -- Review of FHIR ontology approaches (cont.) > > > > I think we need to define our objectives for the RDF representation. Mine > are as follows: > > > > 1. It must be possible to round-trip from XML/JSON through RDF > representation > > * This includes retaining information about order of repeating elements > > * Needs to allow for extensions where-ever they can appear, including > simple types (date, boolean, etc.) > > 2. We want to be able to represent instances as RDF and Profiles as > OWL/RDFS > > 3. Syntax needs to be "safe" when dealing with modifier extensions > > 4. Syntax should support vocabulary bindings to code, Coding and > CodeableConcept - including dealing with extensible value sets and > multi-code system value sets > > 5. Syntax should enforce constraints that are representable in RDF (i.e. > schema constraints, regular expressions, etc.) > > 6. In the RDFS/OWL, should expose at least minimal annotation information > for display > > > > > > 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 Mon, Dec 8, 2014 at 11:11 AM, David Booth <david@dbooth.org> wrote: > > I'm so sorry I forgot to send these out last Tuesday, but here are draft > minutes from our call, with Eric Prud'hommeaux reviewing his FHIR ontology > approach: > http://www.w3.org/2014/12/02-hcls-minutes.html > and below in plain text. > > Also, as a reminder, tomorrow's call (Tuesday) will continue with Claude > Nanjo reviewing his FHIR ontology approach. > > Thanks, > David Booth > -------------------------------------------------------- > [1]W3C > > [1] http://www.w3.org/ > > - DRAFT - > > Semantic Web Health Care and Life Sciences Interest Group Teleconference > > 02 Dec 2014 > > See also: [2]IRC log > > [2] http://www.w3.org/2014/12/02-hcls-irc > > Attendees > > Present > Bryn_Rhodes, Cati, Claude_Nanjo, David_Booth, EricP, > Guoqian, Hans_Cools, Ingeborg, Joshua_Phillips, > Kerstin_Forsberg, Marc_Twagirumukiza, Neda, Paul_Knapp, > TimW, Tony_Mallia, Charlie_Mead, egonw_(IRC_only?), > Scott_Marshall, Patricia, Rob_Hausam, Vassil_(IRC_only?) > > Regrets > Chair > David Booth (and Paul Knapp) > > Scribe > dbooth > > Contents > > * [3]Topics > 1. [4]Approve Minutes of previous meetings > 2. [5]Action Review > 3. [6]FHIR Ontology Review > * [7]Summary of Action Items > __________________________________________________________ > > <trackbot> Date: 02 December 2014 > > <ericP> trackbot, start meeting > > <trackbot> Meeting: Semantic Web Health Care and Life Sciences > Interest Group Teleconference > > <trackbot> Date: 02 December 2014 > > <ericP> oops > > <TimW> TimW is from +1.919.767... > > <RHausam> RHausam is 801.949.1556 > > <Claude> [8]https://global.gotomeeting.com/join/157514853 > > [8] https://global.gotomeeting.com/join/157514853 > > <Claude> Please join our GoToMeeting > > Approve Minutes of previous meetings > > Nov 18: > [9]http://wiki.hl7.org/index.php?title=ITS_RDF_Concall_Minutes_ > 20141118 > > [9] > http://wiki.hl7.org/index.php?title=ITS_RDF_Concall_Minutes_20141118 > > Nov 25: > [10]http://wiki.hl7.org/index.php?title=ITS_RDF_Concall_Minutes > _20141125 > > [10] > http://wiki.hl7.org/index.php?title=ITS_RDF_Concall_Minutes_20141125 > > Nov 18 minutes unanimously approved. > > Nov 25 minutes unanimously approved. > > Action Review > > <scribe> ACTION: ericP to set up tracker [recorded in > [11]http://www.w3.org/2014/11/25-hcls-minutes.html#action01 -- > PENDING > > [11] http://www.w3.org/2014/11/25-hcls-minutes.html#action01 > > <trackbot> Created ACTION-2 - Set up tracker [recorded in > [12]http://www.w3.org/2014/11/25-hcls-minutes.html#action01 -- > pending [on Eric Prud'hommeaux - due 2014-12-09]. > > [12] http://www.w3.org/2014/11/25-hcls-minutes.html#action01 > > <scribe> ACTION: Tony to find out more details about how iCat > handles ICD-11 ont and report back [recorded in > [13]http://www.w3.org/2014/11/18-hcls-minutes.html#action01 -- > PENDING > > [13] http://www.w3.org/2014/11/18-hcls-minutes.html#action01 > > <trackbot> Error finding 'Tony'. You can review and register > nicknames at <[14]http://www.w3.org/2014/HCLS/track/users>. > > [14] http://www.w3.org/2014/HCLS/track/users > > <scribe> ACTION: Guoqian to figure out whether he can share URI > conventions for ICD-11 [recorded in > [15]http://www.w3.org/2014/11/25-hcls-minutes.html#action07 -- > PENDING > > [15] http://www.w3.org/2014/11/25-hcls-minutes.html#action07 > > <trackbot> Created ACTION-3 - Figure out whether he can share > uri conventions for icd-11 [recorded in > [16]http://www.w3.org/2014/11/25-hcls-minutes.html#action07 -- > pending [on Guoqian Jiang - due 2014-12-09]. > > [16] http://www.w3.org/2014/11/25-hcls-minutes.html#action07 > > <Claude> For those who just joined IRC, we also have a > GoToMeeting at: > > <Claude> [17]https://global.gotomeeting.com/join/157514853 > > [17] https://global.gotomeeting.com/join/157514853 > > <scribe> ACTION: Kerstin and Ingeborg to prepare a status and > future state ideas for PhUSE-FDA work [recorded in > [18]http://www.w3.org/2014/11/18-hcls-minutes.html#action05 -- > PENDING > > [18] http://www.w3.org/2014/11/18-hcls-minutes.html#action05 > > <trackbot> Error finding 'Kerstin'. You can review and register > nicknames at <[19]http://www.w3.org/2014/HCLS/track/users>. > > [19] http://www.w3.org/2014/HCLS/track/users > > <scribe> ACTION: Eric to establish/make a wiki page for C-CDA > RDF representations work [recorded in > [20]http://www.w3.org/2014/11/18-hcls-minutes.html#action06 -- > PENDING > > [20] http://www.w3.org/2014/11/18-hcls-minutes.html#action06 > > <trackbot> Created ACTION-4 - Establish/make a wiki page for > c-cda rdf representations work [recorded in > [21]http://www.w3.org/2014/11/18-hcls-minutes.html#action06 -- > pending [on Eric Prud'hommeaux - due 2014-12-09]. > > [21] http://www.w3.org/2014/11/18-hcls-minutes.html#action06 > > <scribe> ACTION: Eric and Joshua to report on C-CDA RDF > representations work plan [recorded in > [22]http://www.w3.org/2014/11/18-hcls-minutes.html#action07 -- > PENDING > > [22] http://www.w3.org/2014/11/18-hcls-minutes.html#action07 > > <trackbot> Created ACTION-5 - And joshua to report on c-cda rdf > representations work plan [recorded in > [23]http://www.w3.org/2014/11/18-hcls-minutes.html#action07 -- > pending [on Eric Prud'hommeaux - due 2014-12-09]. > > [23] http://www.w3.org/2014/11/18-hcls-minutes.html#action07 > > Joshua: Sent email describing a use case. Will add to wiki > page. > > <scribe> ACTION: Tony and Rob to report their plan on > High-level concept mapping to RDF work [recorded in > [24]http://www.w3.org/2014/11/18-hcls-minutes.html#action08 -- > PENDING > > [24] http://www.w3.org/2014/11/18-hcls-minutes.html#action08 > > <trackbot> Error finding 'Tony'. You can review and register > nicknames at <[25]http://www.w3.org/2014/HCLS/track/users>. > > [25] http://www.w3.org/2014/HCLS/track/users > > <scribe> ACTION: Tony and all to decide on a wiki for Term Info > work [recorded in > [26]http://www.w3.org/2014/11/18-hcls-minutes.html#action09] -- > PENDING > > [26] http://www.w3.org/2014/11/18-hcls-minutes.html#action09] > > <trackbot> Error finding 'Tony'. You can review and register > nicknames at <[27]http://www.w3.org/2014/HCLS/track/users>. > > [27] http://www.w3.org/2014/HCLS/track/users > > <scribe> ACTION: Guoqian to figure out whether he can share URI > conventions for ICD-11 [recorded in > [28]http://www.w3.org/2014/11/25-hcls-minutes.html#action07] > > [28] http://www.w3.org/2014/11/25-hcls-minutes.html#action07] > > <trackbot> Created ACTION-6 - 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] > [on Guoqian Jiang - due 2014-12-09]. > > [29] http://www.w3.org/2014/11/25-hcls-minutes.html#action07] > > <scribe> [PENDING] > > FHIR Ontology Review > > <Claude> Please use GoToMeeting only for video > > [30]https://global.gotomeeting.com/join/157514853 > > [30] https://global.gotomeeting.com/join/157514853 > > Access Code: 157-514-853 > > Eric's slides: -> > [31]http://www.w3.org/2014/Talks/1125-fhir-rdf-egp/ FHIR-RDF > > [31] http://www.w3.org/2014/Talks/1125-fhir-rdf-egp/ > > Eric: Our goal was to let anything in FHIR XML be translated > into RDF. > ... We wrote something that read the XML definition files and > produced something that maps the XML to RDF. > ... Python code reads the json definition files and spits out > XML, being the parts that we need of the FHIR spec. > ... "subs" is what is allowed inside a FHIR resource. > ... effectively the attributes of a resource. > ... Then we embedded that in an XSLT script, and hand edited > the foot of it. > ... The stuff we wrote into the footer of the XSLT says that > for a particular construct in the XML instance data, there's > special handling, such as URLs for identifiers. > > David: How does the fact that it is an atom feed affect the > interpretatinon of the XML? > > Eric: It leaves some other graph stuff superimposed on it. > > Marc: Re datatypes, you used FHIR value, but the value itself > looks like it is a string. > ... If it is a string, then reasoners cannot do much with it. > > Eric: Datatype values are showing up as literals. > > Marc: Another is that a date is just a string, not an xsd:date. > ... On slide 2 > > Eric: Ideally it should have the datatype stuck on the end of > it. There's a tension between having the datatype on the > fhir:value and having it on a blank node. > ... The natural RDF-ish way to do it would be using > xsd:datetime. > ... Need to decide which of these ways will be most palatable > to RDF folks versus native FHIR folks. > ... Sometimes these things are not just datetimes in FHIR. Need > to make it as simple as possible and no simpler. > > Guoqian: Is a different URI being used for the namespaces? Will > it cause problems when you use SPARQL across different models? > > Eric: I tested some of this. I stuck a bunch of these > namespaces together, and I believe we've addressed your > concern. > > David: Is the datatype issue due to the fact that datatypes are > extensible in FHIR? > > Eric: Maybe. RDF needs to be monotonic. > > Paul: Modifying extensions can appear only in the roots of > classes (considering the complex type as a class) > > Eric: The XSLT footer has the custom code for extensions. > > Paul: We did that to limit what you need to examine, to find > out if there is a modifying extension. > > Claude: I think you can have modifying extensions on the root > type and anything that is defined from the root type. > > ISSUE: FHIR Modifying extensions and monotonicity > > <trackbot> Created ISSUE-1 - Fhir modifying extensions and > monotonicity. Please complete additional details at > <[32]http://www.w3.org/2014/HCLS/track/issues/1/edit>. > > [32] http://www.w3.org/2014/HCLS/track/issues/1/edit > > Eric: Example here may not be up to date. Anyone know? > > Paul: the dev site has DSTU 2. > > Eric: Another script generates the ShEx definitions from the > FHIR spec. > ... and the ShEx is used to generate FHIR XML back again from > FHIR RDF. > ... Slide 7 is showing how to take C-CDA in RDF and producing > FHIR RDF. > > Guoqian: The result prefix is fhir but should be patient. > > Eric: Yes, you're right. That can be fixed in the ShEx. > > Tony: Sort of verbatim translation. The difference is maybe > target audience style -- a style that is good for the general > tools used in RDF. Only difference is the end style of RDF. > ... Establishing closure between FHIR ontology and SNOMED-CT > would need to happen. Main difference is in the final RDF > style. > > <pknapp> Zakim: Have to leave for another meeting, thx, great > work. > > Eric: Will need to need to be a balance. > ... Once we have transliterated, what we map to our dream > ontology. May want to balance how much is wedged into the XSLT > and how much into the interpretive dance later. > > Claude: Might want a low level FHIR ont and a higher level FHIR > ont both. > > David: I kind of like the auto-generated aspect of this > approach. > > <vassil> чуит > > ADJOURNED > > <vassil> quit > > <ericP> [33]coding mapping example > > [33] > https://www.w3.org/wiki/HCLS/ClinicalObservationsInteroperability/FDATherapeuticAreaOntologies#codeAndSystemToIRI > > <ericP> (for next week) > > <vassil> exit > > Summary of Action Items > > [PENDING] ACTION: Eric and Joshua to report on C-CDA RDF > representations work plan [recorded in > [34]http://www.w3.org/2014/11/18-hcls-minutes.html#action07] > [PENDING] ACTION: Eric to establish/make a wiki page for C-CDA > RDF representations work [recorded in > [35]http://www.w3.org/2014/11/18-hcls-minutes.html#action06] > [PENDING] ACTION: ericP to set up tracker [recorded in > [36]http://www.w3.org/2014/11/25-hcls-minutes.html#action01] > [PENDING] ACTION: Guoqian to figure out whether he can share > URI conventions for ICD-11 [recorded in > [37]http://www.w3.org/2014/11/25-hcls-minutes.html#action07] > [PENDING] ACTION: Kerstin and Ingeborg to prepare a status and > future state ideas for PhUSE-FDA work [recorded in > [38]http://www.w3.org/2014/11/18-hcls-minutes.html#action05] > [PENDING] ACTION: Tony and all to decide on a wiki for Term > Info work [recorded in > [39]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 > [40]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 > [41]http://www.w3.org/2014/11/18-hcls-minutes.html#action01] > > [34] http://www.w3.org/2014/11/18-hcls-minutes.html#action07 > [35] http://www.w3.org/2014/11/18-hcls-minutes.html#action06 > [36] http://www.w3.org/2014/11/25-hcls-minutes.html#action01 > [37] http://www.w3.org/2014/11/25-hcls-minutes.html#action07 > [38] http://www.w3.org/2014/11/18-hcls-minutes.html#action05 > [39] http://www.w3.org/2014/11/18-hcls-minutes.html#action09 > [40] http://www.w3.org/2014/11/18-hcls-minutes.html#action08 > [41] http://www.w3.org/2014/11/18-hcls-minutes.html#action01 > > [End of minutes] > __________________________________________________________ > > > Minutes formatted by David Booth's [42]scribe.perl version > 1.140 ([43]CVS log) > $Date: 2014-12-02 17:30:25 $ > __________________________________________________________ > > [42] http://dev.w3.org/cvsweb/~checkout~/2002/scribe/scribedoc.htm > [43] 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 [44]http://dev.w3.org/cvsweb/~checkout~/2002/ > scribe/ > > [44] http://dev.w3.org/cvsweb/~checkout~/2002/scribe/ > > Guessing input format: RRSAgent_Text_Format (score 1.00) > > No ScribeNick specified. Guessing ScribeNick: dbooth > Inferring Scribes: dbooth > Default Present: DBooth, +1.919.767.aaaa, ericP, rhausam, TimW, Joshua_P > hillips, +1.202.528.aabb, charlie, +1.469.226.aacc, Tony, Neda, patricia > , Mark_Twagirumukiza, Kerstin_Forsberg, Cati, Kerstin, +1.801.368.aadd, > +1.604.250.aaee, Bryn_Rhodes, +31.62.427.aaff, mscottm, Guoqian, +1.608. > 310.aagg, vassil, +41.78.847.aahh, [IPcaller] > > WARNING: Replacing previous Present list. (Old list: Bryn_Rhodes, Cati, > Claude_Nanjo, David_Booth, EricP, Guoqian, Hans_Cools, Ingeborg, Joshua_ > Phillips, Kerstin_Forsberg, Marc_Twagirumukiza, Neda, Paul_Knapp, TimW, > Tony_Mallia, Charlie_Mead, egonw, (IRC, only?), Scott_Marshall, Patricia > , Rob_Hausam, Vassil, (IRC, only?)) > Use 'Present+ ... ' if you meant to add people without replacing the lis > t, > such as: <dbooth> Present+ Bryn_Rhodes, Cati, Claude_Nanjo, David_Booth, > EricP, Guoqian, Hans_Cools, Ingeborg, Joshua_Phillips, Kerstin_Forsberg > , Marc_Twagirumukiza, Neda, Paul_Knapp, TimW, Tony_Mallia, Charlie_Mead, > egonw_(IRC_only?), Scott_Marshall, Patricia, Rob_Hausam, Vassil_(IRC_on > ly?) > > Present: Bryn_Rhodes Cati Claude_Nanjo David_Booth EricP Guoqian Hans_Co > ols Ingeborg Joshua_Phillips Kerstin_Forsberg Marc_Twagirumukiza Neda Pa > ul_Knapp TimW Tony_Mallia Charlie_Mead egonw_(IRC_only?) Scott_Marshall > Patricia Rob_Hausam Vassil_(IRC_only?) > Found Date: 02 Dec 2014 > Guessing minutes URL: [45]http://www.w3.org/2014/12/02-hcls-minutes.html > People with action items: all eric ericp guoqian ingeborg joshua kerstin > rob tony > > [45] http://www.w3.org/2014/12/02-hcls-minutes.html > > > [End of [46]scribe.perl diagnostic output] > > [46] 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 > > >
Received on Thursday, 11 December 2014 06:08:19 UTC