David,
Thank you for the minutes and sorry I could not attend this week.
I am a member of one of the PhUSE working groups mentioned by
Kerstin. This is our somewhat outdated Wiki page:
http://www.phusewiki.org/wiki/index.php?title=Analysis_Results_Model
We recently adopted the RDF Data Cube as our model and are working on
an R package for data conversion. We are already using the SDTM as
RDF to form code lists for our cube. Our current focus is on
conversion of Demographics and AE data, then expanding to other
domains. It was a member of our group that recently presented to
CDISC.
I am also a member of the newly-formed PhUSE working group that is
coordinating the end-to-end connectivity for the outputs from our
various PhUSE Semantic Web Technology efforts.
The PhUSE CSS conference will take place in March in Silver Spring
Maryland where there is an increasing focus on SW tech.
http://www.phuse.eu/css.aspx
All of this is just for an FYI. I am on vacation next week and may
not be able to make the next meeting, though I look forward to
future participation
Best Regards,
Tim
-----Original Message----- From: David Booth
[mailto:[email protected]] Sent: Tuesday, November 18, 2014 2:52 PM
To: [email protected]; w3c semweb HCLS Cc: Claude Nanjo; Eric
Prud'hommeaux Subject: Re: Proposed agenda for Nov 18 HL7 ITS RDF /
W3C HCLS COI call
Draft minutes are at http://www.w3.org/2014/11/18-hcls-minutes.html
and in plain text below.
--------------------------------------------------------- [1]W3C
[1] http://www.w3.org/
- DRAFT -
HL7 ITS RDF Subgroup / W3C HCLS
18 Nov 2014
See also: [2]IRC log
[2] http://www.w3.org/2014/11/18-hcls-irc
Attendees
Present Brian_Pech, Bryn_Rhodes, David_Booth, EricPrud'hommeaux,
Ingeborg, Joshua_Phillips, Kerstin_Forsberg, Marc_Twagirumukiza,
Paul_Knapp, Rob_Hausam, Tony_Mallia, Daniel_Karlsson, Vassil
Regrets Chair David Booth (and Paul Knapp)
Scribe ericP
Contents
* [3]Topics 1. [4]Minutes 2. [5]previous minutes 3. [6]Logistics 4.
[7]Followup on last week's discussion with Mark Musen 5. [8]Proposed
work items 6. [9]FHIR ontology 7. [10]ICD-11 and SNOMED 8.
[11]Bridging VA, Intermountain and other models 9. [12]Issue
tracking 10. [13]Use Cases 11. [14]PhUSE-FDA project (formerly
CDISC2RDF) 12. [15]C-CDA RDF representations 13. [16]High-level
concept mapping to RDF (AR typeCodes, etc.) 14. [17]Other work
proposed work items * [18]Summary of Action Items
__________________________________________________________
<Marc_Twagirumukiza> Hi every one this is Marc Twagirumukiza from
Agfa Healthcare
Minutes
<dbooth>
[19]http://wiki.hl7.org/index.php?title=ITS_RDF_ConCall_Agenda#
Agenda
[19]
http://wiki.hl7.org/index.php?title=ITS_RDF_ConCall_Agenda#Agenda
<dbooth> ITS page: [20]http://wiki.hl7.org/index.php?title=ITS_WG
[20] http://wiki.hl7.org/index.php?title=ITS_WG
<dbooth> RDF subgroup:
[21]http://wiki.hl7.org/index.php?title=ITS_RDF_ConCall_Agenda#
Agenda
[21]
http://wiki.hl7.org/index.php?title=ITS_RDF_ConCall_Agenda#Agenda
<dbooth> Meeting minutes:
[22]http://www.w3.org/2014/11/04-hcls-minutes
[22] http://www.w3.org/2014/11/04-hcls-minutes
previous minutes
<scribe> scribenick: ericP
pknapp: PROPOSED to accept
[23]http://www.w3.org/2014/11/04-hcls-minutes as a record of the last
meeting
[23] http://www.w3.org/2014/11/04-hcls-minutes
Logistics
APPROVED: accept [24]http://www.w3.org/2014/11/04-hcls-minutes as a
record of the last meeting
[24] http://www.w3.org/2014/11/04-hcls-minutes
(unanimous)
dbooth: two wiki choices or this HL7/W3C joint work ... which shall
we use for administative stuff? ... other work, e.g. FHIR ontology,
can be on another wiki
<Marc_Twagirumukiza> I support HL7 wiki as well
dbooth: but for the admin stuff i propose that HL7 host the
adminstrative wiki
PROPOSED use the HL7 wiki as the administrative wiki
APPROVED: use the HL7 wiki as the administrative wiki
(unanimous)
-> [25]https://www.w3.org/wiki/HCLS/ClinicalObservationsInteropera
bility COI Task Force
[25]
https://www.w3.org/wiki/HCLS/ClinicalObservationsInteroperability
ericP
Followup on last week's discussion with Mark Musen
ericP: note the tech topics, e.g. FDA therapeutic areas, terminfo,
etc.
<dbooth> The recording:
[26]https://www.dropbox.com/sh/d7a9bb6ppqgo9xn/AAApWheLsxRSyEKF
a0Kr4qNna?dl=0
[26]
https://www.dropbox.com/sh/d7a9bb6ppqgo9xn/AAApWheLsxRSyEKFa0Kr4qNna?dl=0
dbooth: any followup on Mark's presentation?
<dbooth> Rough notes: [27]http://www.w3.org/2014/11/11-hcls-minutes
[27] http://www.w3.org/2014/11/11-hcls-minutes
Tony: following up with MarkM on the details hidden by the ICAT
interface.
<dbooth> ACTION: Tony to find out more details about how iCat handles
ICD-11 ont and report back [recorded in
[28]http://www.w3.org/2014/11/18-hcls-minutes.html#action01]
<Zakim> ericP, you wanted to point out the snomed examples in the FDA
TA work
-> [29]https://www.w3.org/wiki/File:Snomedct_extract_descriptive.t tl
SNOMED example
[29] https://www.w3.org/wiki/File:Snomedct_extract_descriptive.ttl
<dbooth> Eric: If you're digging into this, here's an example of
SNOMED that I took, and found all of the examples of everything that
they said about it -- level in the cell, test results, in range, out
of range. All the entities that SNOMED teases apart. It would be
great to take the same slice of ICD-11
<daniel> There is a new way of representing lab in SNOMED CT as of
recently
<dbooth> ... Not a legit SNOMED extraction though, because I changed
the nubmers to human readable URLs.
Tony: i've got the 110M SNOMED snapshot from earlier this year.
<dbooth> David: Might be a good use case!
ericP: you shouldn't have to dig back into the 110M 'cause i already
did that
Tony: still waiting for access details from MarcM ... I've been
looking at the bits that i've already dug into, e.g. allergies to bee
stings
<daniel> Here's an alpha version of new lab content
<Marc_Twagirumukiza> ...just to disambiguate it's Mark
<daniel> Daniel Karlsson
<daniel> [30]https://csfe.aceworkspace.net/sf/go/doc10215?nav=1
[30] https://csfe.aceworkspace.net/sf/go/doc10215?nav=1
daniel: there's a new style for SNOMED
Tony: is there a style guide you can point to? ... once we dig down
into the details of the ontologies, you're sucked in for 2 years
<daniel> [email protected]
Proposed work items
dbooth: we have lots of potential work items and limited resources
... we can persue multiple things but it will depend on the
individual champions.
FHIR ontology
<Marc_Twagirumukiza> I would volunteer in the FHIR ontology, --- just
as related work to what we did for SALUS project
<Marc_Twagirumukiza>
[31]http://www.srdc.com.tr/projects/salus/blog/?p=342
[31] http://www.srdc.com.tr/projects/salus/blog/?p=342
dbooth: claude nanjo and ericP have worked on this. we should
schedule reviews
Tony: we discussed this in the HCLS COI call ... the issues were what
models for what use cases and how to build the ontology
dbooth: on one end of the spectrum there's "what ontology facilitates
machine transformation" ... on the other, "what ontology facilitates
humen understanding"
Tony: there's also which supports SemWeb inference ... we may want to
bring these together or maybe not
Marc_Twagirumukiza: reusable graphs need to be human-readable,
machine-readable, etc. ... we did this for SALUS, "entities" were RDF
graphs at the domain level. we could map it to other data. ... so
hoping to contribute to this task
<dbooth> Eric: I can present what Josh and I did.
dbooth: so you're stressing the convergence
<dbooth> Claude's work attempted to be more human friendly.
ericP: i can present the stuff that Josh and I did
<Marc_Twagirumukiza> Actually what can help there is not to 'just'
ontologyze FHIR but to build up a partitioned reusable domain RDF
graphs from the complexe information model
<Marc_Twagirumukiza> those will be a key for converging and mapping
as well
dbooth: claude did an ontology as well
Tony: i can present what i did at VA
<dbooth> ACTION: Tony and Eric to work with each other and Claude to
prepare comparison of FHIR ontology approaches [recorded in
[32]http://www.w3.org/2014/11/18-hcls-minutes.html#action02]
<dbooth> My view is that the *most* important is an ontology that
works well for machine processing -- instance data translation,
inference, etc. That needs to be the basis. Then making it more human
friendly -- or conceptually understandable -- would be nice to have.
dbooth: priority should be machine processing
Tony: agree. "reasoner-friendly" ... something we can use with
existing tools
ICD-11 and SNOMED
dbooth: we discussed this earlier.
Bridging VA, Intermountain and other models
Tony: depends on what MarkM can give me. i have no access to the
bits.
<dbooth> David: Not a current work project. Create a wiki page for
project ideas backlog?
dbooth: maybe we should create a backlog page
Tony: rep from VA would be rafael (not on this call)
Marc_Twagirumukiza: sometimes the backlog becomes a brainstorming
place with no followup.
<dbooth> ACTION: David to create a wiki page for backlog [recorded
in [33]http://www.w3.org/2014/11/18-hcls-minutes.html#action03]
Marc_Twagirumukiza: but very necessary, also needs an issue tracker
Issue tracking
<dbooth> Eric: W3C Tracker is integrated with IRC
ericP: we can start with tracker, which will work with IRC and
public-semweb-lifesci
Use Cases
<dbooth> ACTION: ericP to send pointers to existing wiki pages
[recorded in
[34]http://www.w3.org/2014/11/04-hcls-minutes.html#action01] [DONE]
[34] http://www.w3.org/2014/11/04-hcls-minutes.html#action01]
<dbooth> (Eric already pointed to the W3C COI page)
dbooth: what use cases with what goals?
<dbooth> Eric: Migration of CCDA to FHIR
<dbooth> Eric: Utility on FHIR RDF that would motivate mapping of
FHIR XML to FHIR RDF
dbooth: need different levels of use cases ... need one simple enough
for a slide, e.g. BP ... it would be nice if they could be used
across different purposes.
PhUSE-FDA project (formerly CDISC2RDF)
Kerstin_Forsberg: know the CDISC2RDF. can work on this.
Ingeborg: i know SDTM quite well
<Kerstin_Forsberg> [email protected]
<Ingeborg> [email protected]
<dbooth> ACTION: Kerstin and Ingeborg to prepare a status and future
state ideas for PhUSE-FDA work [recorded in
[35]http://www.w3.org/2014/11/18-hcls-minutes.html#action05]
<dbooth> Kerstin and Ingeborg have volunteered to champion the
PhUSE-FDA work.
ericP: our use cases for FDA-TA were to: ... .. make different
studies in the same therapeutic area compatible for safety and
efficacy analysis ... .. make e.g. drugs in differnt TAs comparable
for safety signals
C-CDA RDF representations
<dbooth> ACTION: Eric to establish/make a wiki page for C-CDA RDF
representations work [recorded in
[36]http://www.w3.org/2014/11/18-hcls-minutes.html#action06]
dbooth: ericP is champion
Joshua_Phillips: i'd like to work on this.
<dbooth> ACTION: Eric and Joshua to report on C-CDA RDF
representations work plan [recorded in
[37]http://www.w3.org/2014/11/18-hcls-minutes.html#action07]
High-level concept mapping to RDF (AR typeCodes, etc.)
Tony: this is kind of light-weight. ... "how do you represent the
terminology?" ... from the top down, identify topics, e.g. transport
mechanisms
<Kerstin_Forsberg> FDA/PhUSE Semantic technology project's first
delivery was "just" to represenet existing CDISC foundational
standards in RDF. Not representing the actual clinical trial data
(e.g. blood pressure). Hwoever, they are moving beyond that and I
know there was a presentation from FRDA at CDISC Interchannge
conference last week on representing CDASH (raw data such as blood
pressure) in RDF.
Tony: it's a style guide. a set of patterns.
-> [38]https://www.w3.org/wiki/HCLS/ClinicalObservationsInteropera
bility/TerminologyExpressivity high-level terminology approaches
[38]
https://www.w3.org/wiki/HCLS/ClinicalObservationsInteroperability/TerminologyExpressivity
<Kerstin_Forsberg> There is also a FDA/PhUSE subproject to
reperesent analysis results data, e.g. avg. blood pressure for
propulation reported in a study report
dbooth: if there's already a wiki, use it.
<dbooth> David: I would caution that there can be so many different
views on high level models, adoption/use would have to be voluntary.
I would worry about being perceived as telling people how that they
MUST do things. But best practices recommendations sound great.
-> [39]https://www.w3.org/wiki/HCLS/ClinicalObservationsInteropera
bility/FDATherapeuticAreaOntologies#Coding_specificity terminology
coding example
[39]
https://www.w3.org/wiki/HCLS/ClinicalObservationsInteroperability/FDATherapeuticAreaOntologies#Coding_specificity
Tony: i'll list the topics. some may be black holes
RobHausam_: i'm interested.
<dbooth> Rob Hausam
<dbooth> 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]
Other work proposed work items
RobHausam_: want to look at the interface between terminology and
infor model
<dbooth> Rob: Propose Term info work
<dbooth> Eric: Charlie Mead and I created a wiki page on that
<daniel> I'm in
<dbooth> ACTION: Tony and all to decide on a wiki for Term Info work
[recorded in
[41]http://www.w3.org/2014/11/18-hcls-minutes.html#action09]
<dbooth> ADJOURNED
Summary of Action Items
[NEW] ACTION: David to create a wiki page for backlog [recorded in
[42]http://www.w3.org/2014/11/18-hcls-minutes.html#action03] [NEW]
ACTION: Eric and Joshua to report on C-CDA RDF representations work
plan [recorded in
[43]http://www.w3.org/2014/11/18-hcls-minutes.html#action07] [NEW]
ACTION: Eric to establish/make a wiki page for C-CDA RDF
representations work [recorded in
[44]http://www.w3.org/2014/11/18-hcls-minutes.html#action06] [NEW]
ACTION: Kerstin and Ingeborg to prepare a status and future state
ideas for PhUSE-FDA work [recorded in
[45]http://www.w3.org/2014/11/18-hcls-minutes.html#action05] [NEW]
ACTION: Tony and all to decide on a wiki for Term Info work [recorded
in [46]http://www.w3.org/2014/11/18-hcls-minutes.html#action09] [NEW]
ACTION: Tony and Eric to work with each other and Claude to prepare
comparison of FHIR ontology approaches [recorded in
[47]http://www.w3.org/2014/11/18-hcls-minutes.html#action02] [NEW]
ACTION: Tony and Rob to report their plan on High-level concept
mapping to RDF work [recorded in
[48]http://www.w3.org/2014/11/18-hcls-minutes.html#action08] [NEW]
ACTION: Tony to find out more details about how iCat handles ICD-11
ont and report back [recorded in
[49]http://www.w3.org/2014/11/18-hcls-minutes.html#action01]
[DONE] ACTION: ericP to send pointers to existing wiki pages
[recorded in
[50]http://www.w3.org/2014/11/04-hcls-minutes.html#action01]
[50] http://www.w3.org/2014/11/04-hcls-minutes.html#action01
[End of minutes]
__________________________________________________________
Minutes formatted by David Booth's [51]scribe.perl version 1.140
([52]CVS log) $Date: 2014-11-18 17:10:56 $
__________________________________________________________
[51] http://dev.w3.org/cvsweb/~checkout~/2002/scribe/scribedoc.htm
[52] http://dev.w3.org/cvsweb/2002/scribe/
Scribe.perl diagnostic output
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scribe.perl Revision: 1.140 of Date: 2014-11-06 18:16:30 Check for
newer version at [53]http://dev.w3.org/cvsweb/~checkout~/2002/
scribe/
[53] http://dev.w3.org/cvsweb/~checkout~/2002/scribe/
Guessing input format: RRSAgent_Text_Format (score 1.00)
Succeeded: s/inference/transformation/ Succeeded: s/issue track/issue
tracker/ Found ScribeNick: ericP Inferring Scribes: ericP Default
Present: DBooth, EricP, +1.604.250.aaaa, +1.678.999.aabb, +1.202
.528.aadd, PaulKnapp, +1.703.983.aaee, Marc_Twagirumukiza, BrianPech,
Jo shua_Phillips, +1.801.368.aaff, BrynRhodes, +1.978.794.aagg,
+1.608.310. aahh, Tony, Vassil, +1.801.949.aaii, Kerstin_Forsberg
Present: Brian_Pech Bryn_Rhodes David_Booth EricPrud'hommeaux
Ingeborg J oshua_Phillips Kerstin_Forsberg Marc_Twagirumukiza
Paul_Knapp Rob_Hausam Tony_Mallia Daniel_Karlsson Vassil Got date
from IRC log name: 18 Nov 2014 Guessing minutes URL:
[54]http://www.w3.org/2014/11/18-hcls-minutes.html People with action
items: all david eric ingeborg joshua kerstin rob ton y
[54] http://www.w3.org/2014/11/18-hcls-minutes.html
[End of [55]scribe.perl diagnostic output]
[55] http://dev.w3.org/cvsweb/~checkout~/2002/scribe/scribedoc.htm
On 11/17/2014 06:12 PM, David Booth wrote:
Proposed agenda for tomorrow (Tuesday):
http://wiki.hl7.org/index.php?title=ITS_RDF_ConCall_Agenda
Logistics: Tuesdays, 11:00am Eastern US (Boston) time zone Zakim
(W3C teleconference bridge). Dial-In #: +1.617.761.6200 (Cambridge,
MA) VoIP address: sip:[email protected] Participant Access Code:
4257 ("HCLS") IRC: irc.w3.org port 6665 channel #HCLS
Thanks, David Booth
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