- From: David Booth <david@dbooth.org>
- Date: Thu, 11 Dec 2014 14:56:02 -0500
- To: Vipul Kashyap <kashyap.vipul@gmail.com>, 'Lloyd McKenzie' <lloyd@lmckenzie.com>
- CC: 'w3c semweb HCLS' <public-semweb-lifesci@w3.org>, its@lists.hl7.org
Thanks Vipul, I've added them to the wiki for consideration: http://wiki.hl7.org/index.php?title=FHIR_Ontology_Requirements David On 12/10/2014 04:59 PM, Vipul Kashyap 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 > <mailto: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 <tel: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 19:56:32 UTC