- From: Marc Twagirumukiza <marc.twagirumukiza@agfa.com>
- Date: Thu, 27 Nov 2014 15:03:44 +0100
- To: lloyd@lmckenzie.com
- Cc: David Booth <david@dbooth.org>, Grahame Grieve <grahame@healthintersections.com.au>, "its@lists.hl7.org" <its@lists.hl7.org>, w3c semweb HCLS <public-semweb-lifesci@w3.org>
- Message-ID: <OFED587746.E317E881-ONC1257D9D.004C9389-C1257D9D.004D3F1A@agfa.com>
Hi again Lloyd
Thanks for a quick feedback.
You raised a nice question here: why fhir:Gender and not fhir:code, It
would be ideal (just for mapping purpose) to have fhir:Gender. In her data
Gender is used from Gender catalog. We can mapp the catalaogs to
fhir:Gender. This may also help to disambiguate from other codeable
objects (so many in fhir!). Of course this is an initial thoughts which
needs to be tested in patient data environment.
Again for just mapping purpose, it would be useful to follow the first
approach...
Kind Regards,
Marc Twagirumukiza | Agfa HealthCare
Senior Clinical Researcher | HE/Advanced Clinical Applications Research
T +32 3444 8188 | M +32 499 713 300
http://www.agfahealthcare.com
http://blog.agfahealthcare.com
Click on link to read important disclaimer:
http://www.agfahealthcare.com/maildisclaimer
From: Lloyd McKenzie <lloyd@lmckenzie.com>
To: Marc Twagirumukiza/AXPZC/AGFA@AGFA
Cc: David Booth <david@dbooth.org>, Grahame Grieve
<grahame@healthintersections.com.au>, "its@lists.hl7.org"
<its@lists.hl7.org>, w3c semweb HCLS <public-semweb-lifesci@w3.org>
Date: 27/11/2014 14:41
Subject: Re: Agenda for Tue Nov 25 HL7 ITS RDF Subgroup / W3C HCLS
COI call -- Review of FHIR ontology approaches
Hi Marc,
Well, if we go the first route, we'd need to have something like
fhir:birthDate_ that was able to contain extensions. It's really a
question of which is going to be more natural. Note that we'd have to do
the same to deceasedBoolean and deceasedDate. Question: why did you use
fhir:Gender instead of fhir:code?
--------------------------------------
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 2:24 PM, Marc Twagirumukiza <
marc.twagirumukiza@agfa.com> wrote:
Hi Lloyd,
The 7 points raised here are really important and I hope we will discuss
them in coming sessions of the task force deeply.
I would like just ask a clarification about the 1st one:
" 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"
What of the 2 options do you see as a possible mapping for instance for
formalizing the patient resource?
<Patient xmlns="http://hl7.org/fhir">
<gender><!-- 0..1 CodeableConcept Gender for administrative purposes § -->
</gender>
<birthDate value="[dateTime]"/><!-- 0..1 The date and time of birth for
the individual § -->
<deceased[x]><!-- 0..1 boolean|dateTime Indicates if the individual is
deceased or not § --></deceased[x]> [....]
1)To something like [sorry to use Turtle format]:
fhir:patient
fhir:gender fhir:Gender;
fhir:birthDate xsd:DateTime;
fhir:deceasedFlag xsd:boolean;
fhir:deceasedDateTime xsd:DateTime.
Or
2)To something like this:
fhir:patient
fhir:gender fhir:Gender;
fhir:birthDate [
fhir:value xsd:DateTime
];
fhir:deceasedFlag xsd:boolean;
fhir:deceasedDateTime xsd:DateTime.
Kind Regards,
Marc Twagirumukiza | Agfa HealthCare
Senior Clinical Researcher | HE/Advanced Clinical Applications Research
T +32 3444 8188 | M +32 499 713 300
http://www.agfahealthcare.com
http://blog.agfahealthcare.com
Click on link to read important disclaimer:
http://www.agfahealthcare.com/maildisclaimer
From: Lloyd McKenzie <lloyd@lmckenzie.com>
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>
Date: 27/11/2014 13:54
Subject: Re: Agenda for Tue Nov 25 HL7 ITS RDF Subgroup / W3C HCLS
COI call -- Review of FHIR ontology approaches
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/ClinicalObservationsInteroperability/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
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Received on Thursday, 27 November 2014 14:04:10 UTC