- From: <Tim.Williams@ucb.com>
- Date: Wed, 19 Nov 2014 13:07:36 +0000
- To: <david@dbooth.org>, <its@lists.HL7.org>, <public-semweb-lifesci@w3.org>
- CC: <cnanjo@cognitivemedicine.com>, <eric@w3.org>, <Tim.Williams@ucb.com>
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 This is our somewhat outdated Wiki page: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:david@dbooth.org]
Sent: Tuesday, November 18, 2014 2:52 PM
To: its@lists.hl7.org; 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> daniel.karlsson@liu.se
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> kerstin.l.forsberg@astrazeneca.com
<Ingeborg> ingeborgholt@gmail.com
<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
[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 [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:zakim@voip.w3.org Participant Access Code: 4257 ("HCLS")
> IRC: irc.w3.org port 6665 channel #HCLS
>
> Thanks,
> David Booth
________________________________
UCB BIOSCIENCES, Inc.
Mail P.O. Box 110167 - Research Triangle Park - NC 27709 - USA
Via Courier 8010 Arco Corporate Drive - Suite 100 - Raleigh - NC 27617 - USA
Phone +1 919 767 2555 - Fax +1 919 767 2570
(Ref: #*UBI0111) [Ref-UBI0111]
________________________________
Legal Notice: This electronic mail and its attachments are intended solely for the person(s) to whom they are addressed and contain information which is confidential or otherwise protected from disclosure, except for the purpose for which they are intended. Dissemination, distribution, or reproduction by anyone other than the intended recipients is prohibited and may be illegal. If you are not an intended recipient, please immediately inform the sender and return the electronic mail and its attachments and destroy any copies which may be in your possession. UCB screens electronic mails for viruses but does not warrant that this electronic mail is free of any viruses. UCB accepts no liability for any damage caused by any virus transmitted by this electronic mail. (Ref: #*UG1107) [Ref-UG1107]
________________________________
Received on Wednesday, 19 November 2014 13:08:09 UTC