Good, up-to-date tutorial on OWL 2 and Protege for Biomedical domain?

[Matthias Samwald]

Dear all,

I'm about to teach a course to medical informatics students that have 
never used OWL before. Are there any good, up-to-date tutorials or even 
course materials on OWL 2, biomedical ontology building and Protege that 
you could recommend? I was surprised to find that most publicly 
available resources have gathered quite a bit of dust (focused on OWL 1, 
old versions of Protege), or are not very accessible. I'd be especially 
interested in materials that avoid using the Pizza ontology ;)


Thanks,
Matthias

--
Assistant Professor
Center for Medical Statistics, Informatics, and Intelligent Systems
Medical University of Vienna
http://samwald.info/

Re: Minutes of last week's (Dec 2) HL7 ITS RDF Subgroup / W3C HCLS COI call -- Review of FHIR ontology approaches (cont.)

[Matthias Samwald]

Dear all,

I have hardly participated in any of the calls lately and am coming at 
this as a bit of an outsider. From my reading it indeed seems that any 
officially accepted RDF version of FHIR data would use a code + code 
system representation of 'concepts' from controlled vocabularies / 
ontologies. In this case, however, I doubt that the added benefit of 
having an RDF version  is rather minimal and does not outweigh the added 
complexity of an additional representation besides XML and JSON.


The potential benefit of FHIR over other existing approaches (such as 
some previous HL7 standards) is simplicity and accessibility through 
standard tooling.


The potential benefits of an RDF/OWL representation of health data are 
bridging the data model-terminology gap, an intuitive representation of 
medical information and easy querying and interlinking of the resulting 
data via intuitive SPARQL queries.


I hope I'm wrong, but my impression is that a simple, mostly syntactic 
mapping of FHIR in RDF might end up having neither of these qualities, 
combining the worst rather than the best of both worlds. A more 
sophisticated mapping, on the other hand, might not allow round-tripping 
the data and would probably not be accepted as part of the official FHIR 
project.


Am I overly sceptical here?

With kind regards,
Matthias Samwald


Am 21.12.2014 00:15, schrieb Lloyd McKenzie:
Well, for FHIR at a minimum, you must be able to round-trip 
instances.  And what will appear in the JSON and XML instances is the 
code + code system (and often multiple code-code system pairs).   
Often, the code + code system won't even link to an ontology that's 
known by the receiver.  And if we want to be able to convert v2 or v3 
instances, what appears over the wire there is the code + code system 
too.  All knowledge of what the binding is for an element is carried 
outside the instance.


--
Lloyd McKenzie

+1-780-993-9501


--
Assistant Professor
Center for Medical Statistics, Informatics, and Intelligent Systems
Medical University of Vienna
http://samwald.info/

Re: hcls-ACTION-12: Figure out whether he can share uri conventions for icd-11 [recorded in http://www.w3.org/2014/11/25-hcls-minutes.html#action07] -- pending

[Matthias Samwald]

Dear all,

It seems like this mailing list is now automatically receiving updates 
from an issue tracker. Will this remain in place for the forseeable 
future? I think in that case some subscribers might want to change how 
the e-mails from this list are handled in their clients (or, possibly, 
choose to unsubscribe -- which might not be intended by the 
administrators!).


Thanks,
Matthias


Am 16.12.2014 17:08, schrieb Semantic Web Health Care and Life Sciences 
Interest Group Issue Tracker:

hcls-ACTION-12: Figure out whether he can share uri conventions for icd-11 
[recorded in http://www.w3.org/2014/11/25-hcls-minutes.html#action07]  -- 
pending

http://www.w3.org/2014/HCLS/track/actions/12

Assigned to: Guoqian Jiang












--
Assistant Professor
Center for Medical Statistics, Informatics, and Intelligent Systems
Medical University of Vienna
http://samwald.info/

Open half-time post-doc postion on 'artificial intelligence in medicine' at the Medical University of Vienna

[Matthias Samwald]

Dear all,

There is an opening for a half-time post-doctoral staff postion on the 
topic of 'artificial intelligence in medicine' at the Medical University 
of Vienna, Austria. Approaches for using IT for personalized medicine 
are of special interest. The current position is half-time and limited 
to 5 years, but there might be possibilities to extend it to full-time 
and to move to a tenure-track position (but this is certainly not 
guaranteed).


The official announcement is only available in German at the moment 
(page 12, bottom):

http://www.meduniwien.ac.at/homepage/fileadmin/HP-Relaunch/pdforganisation/personalabteilung/Bewerbung_Stellenausschreibungen/Personalmitteilungsblatt45-051114.pdf

Please let me know if you have questions.

Best,
Matthias Samwald

--
Assistant Professor
Center for Medical Statistics, Informatics, and Intelligent Systems
Medical University of Vienna
http://samwald.info/

Re: Problem with classifying the Human Phenotype Ontology

[Matthias Samwald]

> TrOWL I have tried, but I have the impression it doesn't really make 
a classification upfront, but rather incrementally on demand. It's just 
an impression, but it classified HP in no time ;)


It is supposed to classify everything. Maybe you don't have a problem at 
all. ;)


 - Matthias


Am 04.08.2014 14:16, schrieb Andrea Splendiani:

Hi,
I didn't see the BioHackathon ML message. I have just realised my mail 
setup is a bit messed up...
TrOWL I have tried, but I have the impression it doesn't really make a 
classification upfront, but rather incrementally on demand. It's just 
an impression, but it classified HP in no time ;)


I will give a try to ELK and Konclude.
What I am bit puzzled with is: this is a largely used ontology. The 
issue of unfeasible classification should have come up already. Either 
I am doing something wrong, or nobody uses the OWL version (or I'm not 
good at googling).


best,
Andrea



On Mon, Aug 4, 2014 at 2:03 PM, Matthias Samwald 
<mailto:matthias.samw...@meduniwien.ac.at>> wrote:


Hi Andrea,

I remember you got the recommendation to try ELK on the
Biohackathon mailing list. Is ELK not working for you?
You might also want to give TrOWL a try if ELK is not working for
you for some reason. Konclude might also be an option as it seems
to outperform most other reasoners, but it does not have a Protege
plugin (don't know if this matters to you). You can also have a
look at the recent results of the OWL reasoner evaluation here:
http://vip.cs.man.ac.uk:8080/live.html

I have not worked with HPO yet, so those are just some general
recommendations.

Best,
Matthias



Am 04.08.2014 13:53, schrieb Andrea Splendiani:

Hi all,

I have stumbled onto a problem for which I would like to hear
from your experience.

In a project, I am using the Human Phenotype Ontology
(http://www.human-phenotype-ontology.org/).
For the sake of the project, I really only need the is_a
structure of the ontology, but as an OWL version was existing,
and as we have anyway an RDF framework to integrate data, I
was thinking of using this version.
The OWL version is not a simple representation of the is_a
structure, as it is including axioms to map phenotypes to,
from a quick inspection, anatomical parts and "qualities".

Now, as with any ontology, I was at first trying to classify
it. This is an ontology (with imports) of around 20k classes
(<200k axioms, ~60k logical axioms). It is big, but not huge.
I simply cannot classify it in any reasonable time.
I have tried a variety of reasoners and, in my longest wait, I
have waited for days but we are under 1%).

Does anybody have experience in classifying it ?

If classification is unfeasible, than which use cases does the
OWL representation cater to?

best,
Andrea Splendiani

Re: Problem with classifying the Human Phenotype Ontology

[Matthias Samwald]

Hi Andrea,

I remember you got the recommendation to try ELK on the Biohackathon 
mailing list. Is ELK not working for you?
You might also want to give TrOWL a try if ELK is not working for you 
for some reason. Konclude might also be an option as it seems to 
outperform most other reasoners, but it does not have a Protege plugin 
(don't know if this matters to you). You can also have a look at the 
recent results of the OWL reasoner evaluation here:

http://vip.cs.man.ac.uk:8080/live.html

I have not worked with HPO yet, so those are just some general 
recommendations.


Best,
Matthias



Am 04.08.2014 13:53, schrieb Andrea Splendiani:

Hi all,

I have stumbled onto a problem for which I would like to hear from 
your experience.


In a project, I am using the Human Phenotype Ontology 
(http://www.human-phenotype-ontology.org/).
For the sake of the project, I really only need the is_a structure of 
the ontology, but as an OWL version was existing, and as we have 
anyway an RDF framework to integrate data, I was thinking of using 
this version.
The OWL version is not a simple representation of the is_a structure, 
as it is including axioms to map phenotypes to, from a quick 
inspection, anatomical parts and "qualities".


Now, as with any ontology, I was at first trying to classify it. This 
is an ontology (with imports) of around 20k classes (<200k axioms, 
~60k logical axioms). It is big, but not huge.

I simply cannot classify it in any reasonable time.
I have tried a variety of reasoners and, in my longest wait, I have 
waited for days but we are under 1%).


Does anybody have experience in classifying it ?

If classification is unfeasible, than which use cases does the OWL 
representation cater to?


best,
Andrea Splendiani

Outcome of clinical pharmacogenomics task force: "An Ontology-Based, Mobile-Optimized System for Pharmacogenomic Decision Support at the Point-of-Care"

[Matthias Samwald]

Dear all,

Just a quick update on an outcome of work done in the context of the 
Clinical Pharmacogenomics task force [1]. The following article on using 
OWL ontologies and reasoning for clinical decision support in 
pharmacogenomics has now been published in PLoS ONE:


*An Ontology-Based, Mobile-Optimized System for Pharmacogenomic Decision 
Support at the Point-of-Care*
Jose Antonio Miñarro-Giménez,  Kathrin Blagec,  Richard D. Boyce, 
Klaus-Peter Adlassnig,  Matthias Samwald

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0093769

With kind regards,
Matthias

[1] https://www.w3.org/wiki/HCLSIG/Pharmacogenomics

Cancelled: Clinical Pharmacogenomics teleconference on Wednesday

[Matthias Samwald]

Unfortunately, it turned out that some key participants have a conflict 
for the proposed time slot, so we have to cancel the teleconference 
today. I will work out another schedule with these participants. Sorry 
for the noise on the mailing list!


Best,
Matthias


Am 22.04.2014 16:56, schrieb Matthias Samwald:
This is a reminder of the Clinical Pharmacogenomics teleconference 
this Wednesday.
Please note that the meeting will start later than usual (12:00 
Eastern time) to make it easier for participants on the westcoast of 
the US to join. We will also use GoToMeeting instead of the usual 
teleconference setup -- instructions for dialing in can be found below.

Thanks to Richard Boyce for setting up the teleconference system.

Cheers,
Matthias

Meeting:  Clinical Pharmacogenomics
Date: April 23, 2014
*Time: 12:00 Eastern Time (9:00 Pacific Time, 18:00 Central European 
Time)*
Conveners:Michel Dumontier, Matthias Samwald
https://www.w3.org/wiki/HCLSIG/Pharmacogenomics/Meetings/2014-04-22_Conference_Call


1.  Please join my meeting.
https://global.gotomeeting.com/join/360351677

2.  Use your microphone and speakers (VoIP) - a headset is 
recommended.  Or, call in using your telephone.


Dial +1 (267) 507-0007
Access Code: 360-351-677
Audio PIN: Shown after joining the meeting

Meeting ID: 360-351-677

GoToMeeting®
Online Meetings Made Easy®

Not at your computer? Click the link to join this meeting from your 
iPhone®, iPad®, Android® or Windows Phone® device via the GoToMeeting app.
--- 

Reminder: Clinical Pharmacogenomics teleconference on Wednesday

[Matthias Samwald]

This is a reminder of the Clinical Pharmacogenomics teleconference this 
Wednesday.
Please note that the meeting will start later than usual (12:00 Eastern 
time) to make it easier for participants on the westcoast of the US to 
join. We will also use GoToMeeting instead of the usual teleconference 
setup -- instructions for dialing in can be found below.

Thanks to Richard Boyce for setting up the teleconference system.

Cheers,
Matthias

Meeting:  Clinical Pharmacogenomics
Date: April 23, 2014
*Time: 12:00 Eastern Time (9:00 Pacific Time, 18:00 Central European 
Time)*
Conveners:Michel Dumontier, Matthias Samwald

https://www.w3.org/wiki/HCLSIG/Pharmacogenomics/Meetings/2014-04-22_Conference_Call


1.  Please join my meeting.
https://global.gotomeeting.com/join/360351677

2.  Use your microphone and speakers (VoIP) - a headset is recommended.  
Or, call in using your telephone.


Dial +1 (267) 507-0007
Access Code: 360-351-677
Audio PIN: Shown after joining the meeting

Meeting ID: 360-351-677

GoToMeeting®
Online Meetings Made Easy®

Not at your computer? Click the link to join this meeting from your 
iPhone®, iPad®, Android® or Windows Phone® device via the GoToMeeting app.

---

Re: Resource Shape 2.0 - W3C Member Submission

[Matthias Samwald]

How does this relate to / overlap with Shape Expressions?
http://www.w3.org/2013/ShEx/Primer

 - Matthias


Am 14.04.2014 18:21, schrieb Michel Dumontier:

Folks,
  The W3C has received a member submission from IBM to specify the 
shape of RDF resources [1]. The shape of an RDF resource is a 
description of the set of triples it is expected to contain and the 
integrity constraints those triples are required to satisfy. Shapes 
can be used to validate RDF data, document RDF APIs, and provide 
metadata to tools, such as form and query builders, that handle RDF data.


[1] http://www.w3.org/Submission/shapes/

m.

Michel Dumontier
Associate Professor of Medicine (Biomedical Informatics), Stanford 
University
Chair, W3C Semantic Web for Health Care and the Life Sciences Interest 
Group

http://dumontierlab.com 

Re: Reminder: Pharmacogenomics teleconference this Wednesday

[Matthias Samwald]

Sorry, Bob!

We ended up not scheduling a meeting for today, unfortunatley I did not 
think about sending out a message to this effect!


 - Matthias



Am 05.02.2014 16:21, schrieb Freimuth, Robert R., Ph.D.:


Hi all,

Are we meeting today?  I seem to be the only one on the call.

Thanks,

Bob

*From:*public-semweb-lifesci-requ...@listhub.w3.org 
[mailto:public-semweb-lifesci-requ...@listhub.w3.org] *On Behalf Of 
*Matthias Samwald

*Sent:* Wednesday, January 15, 2014 9:43 AM
*To:* public-semweb-lifesci@w3.org
*Subject:* Re: Reminder: Pharmacogenomics teleconference this Wednesday

We had to cancel the call today because several people could not dial 
in because of conflicting schedules.*
*The next official telecon slot would be *February 5*. Could you 
please let me (through a private reply) if this date would work for you?


Thanks,
Matthias



Am 14.01.2014 16:28, schrieb Matthias Samwald:

This is a reminder of the Pharmacogenomics teleconference this
Wednesday, the first of this year.

Cheers,
Matthias

Meeting:  Clinical Pharmacogenomics

Date: Janury 15, 2014

Time: 10:15 Eastern Time (16:15 Central European Time)

Conveners:Michel Dumontier, Matthias Samwald

Dial-In #:+1.617.761.6200 (Cambridge, MA)

VoIP address:sip:za...@voip.w3.org

Participant   Access Code: 4257 ("HCLS")

IRC Channel:  irc.w3.org port 6665 channel #HCLS

http://www.w3.org/wiki/HCLSIG/Pharmacogenomics/Meetings/2014-01-15_Conference_Call   


*Suggested Agenda*

  * Recent advances on converting datasets
  * Discussion of schedule -
http://www.w3.org/wiki/HCLSIG/Pharmacogenomics#Schedule - Are
we making progress as planned? Add new milestones for 2014.
  * Discussion about required steps for transitioning from
academic research / proof-of-concept towards real clinical /
industrial applications. Developing strategies for networking
with stakeholders, generating a public profile, evaluation in
realistic clinical settings. Redesign of
http://safety-code.org/ <http://safety-code.org/>
  * Funding opportunities (e.g.

http://ec.europa.eu/research/participants/portal/desktop/en/opportunities/h2020/topics/2282-phc-24-2015.html
)
  * Other topics (please add to wiki page)

Re: Reminder: Pharmacogenomics teleconference this Wednesday

[Matthias Samwald]

We had to cancel the call today because several people could not dial in 
because of conflicting schedules.*
*The next official telecon slot would be *February 5*. Could you please 
let me (through a private reply) if this date would work for you?


Thanks,
Matthias



Am 14.01.2014 16:28, schrieb Matthias Samwald:


This is a reminder of the Pharmacogenomics teleconference this 
Wednesday, the first of this year.


Cheers,
Matthias

Meeting:  Clinical Pharmacogenomics
Date: Janury 15, 2014
Time: 10:15 Eastern Time (16:15 Central European Time)
Conveners:Michel Dumontier, Matthias Samwald
Dial-In #:+1.617.761.6200 (Cambridge, MA)
VoIP address:sip:za...@voip.w3.org
Participant   Access Code: 4257 ("HCLS")
IRC Channel:  irc.w3.org port 6665 channel #HCLS
http://www.w3.org/wiki/HCLSIG/Pharmacogenomics/Meetings/2014-01-15_Conference_Call   


*Suggested Agenda*

  * Recent advances on converting datasets
  * Discussion of schedule -
http://www.w3.org/wiki/HCLSIG/Pharmacogenomics#Schedule - Are we
making progress as planned? Add new milestones for 2014.
  * Discussion about required steps for transitioning from academic
research / proof-of-concept towards real clinical / industrial
applications. Developing strategies for networking with
stakeholders, generating a public profile, evaluation in realistic
clinical settings. Redesign of http://safety-code.org/
  * Funding opportunities (e.g.

http://ec.europa.eu/research/participants/portal/desktop/en/opportunities/h2020/topics/2282-phc-24-2015.html
)
  * Other topics (please add to wiki page)

Reminder: Pharmacogenomics teleconference this Wednesday

[Matthias Samwald]

This is a reminder of the Pharmacogenomics teleconference this 
Wednesday, the first of this year.


Cheers,
Matthias

Meeting:  Clinical Pharmacogenomics
Date: Janury 15, 2014
Time: 10:15 Eastern Time (16:15 Central European Time)
Conveners:Michel Dumontier, Matthias Samwald
Dial-In #:+1.617.761.6200 (Cambridge, MA)
VoIP address:sip:za...@voip.w3.org
Participant   Access Code: 4257 ("HCLS")
IRC Channel:  irc.w3.org port 6665 channel #HCLS
http://www.w3.org/wiki/HCLSIG/Pharmacogenomics/Meetings/2014-01-15_Conference_Call

*Suggested Agenda*

 * Recent advances on converting datasets
 * Discussion of schedule -
   http://www.w3.org/wiki/HCLSIG/Pharmacogenomics#Schedule - Are we
   making progress as planned? Add new milestones for 2014.
 * Discussion about required steps for transitioning from academic
   research / proof-of-concept towards real clinical / industrial
   applications. Developing strategies for networking with
   stakeholders, generating a public profile, evaluation in realistic
   clinical settings. Redesign of http://safety-code.org/
 * Funding opportunities (e.g.
   
http://ec.europa.eu/research/participants/portal/desktop/en/opportunities/h2020/topics/2282-phc-24-2015.html
   )
 * Other topics (please add to wiki page)

Meeting minutes: Pharmacogenomics teleconference this Wednesday

[Matthias Samwald]

The meeting minutes of the teleconference today can be found at
http://www.w3.org/wiki/HCLSIG/Pharmacogenomics/Meetings/2013-11-27_Conference_Call

Cheers,
Matthias

Reminder: Pharmacogenomics teleconference this Wednesday

[Matthias Samwald]

This is a reminder of the Pharmacogenomics teleconference this 
Wednesday. It will be the first after an extended summer hiatus.


Cheers,
Matthias

Meeting:  Clinical Pharmacogenomics
Date: November 27, 2013
Time: 10:15 Eastern Time (16:15 Central European Time)
Conveners:Michel Dumontier, Matthias Samwald
Dial-In #:+1.617.761.6200 (Cambridge, MA)
VoIP address:sip:za...@voip.w3.org
Participant   Access Code: 4257 ("HCLS")
IRC Channel:  irc.w3.org port 6665 channel #HCLS
URL: 
http://www.w3.org/wiki/HCLSIG/Pharmacogenomics/Meetings/2013-11-27_Conference_Call

*Suggested Agenda*

 * Report on progress and insights over the few last months
 * Discussion about required steps for transitioning from academic
   research / proof-of-concept towards real clinical / industrial
   applications. Developing strategies for networking with
   stakeholders, generating a public profile, evaluation in realistic
   clinical settings.
 * Discussion of schedule -
   http://www.w3.org/wiki/HCLSIG/Pharmacogenomics#Schedule - Are we
   making progress as planned? Add new milestones for 2014.

Re: Our paper won the distinguished paper/talk award at Medinfo2013

[Matthias Samwald]

Dear Remzi,

Sorry if this was a bit misleading: In our work we just did a conversion of a 
very selective subset of dbSNP entries (those we identified as essential 
pharmacogenetic markers), and for those we only converted basic information 
(variants for each SNP/indel).

Bio2RDF also does not have dbSNP in its entirety (Michel can correct me if this 
has changed recently). However, some dbSNP entries are represented in a very 
rudimentary way, such as those mentioned in PharmGKB. An example is:
http://bio2rdf.org/dbsnp:rs1042713

These entities do not contain much information from dbSNP, but at least they 
serve as an entry point to other datasets in Bio2RDF (such as PharmGKB). We 
mapped to these identifiers.

Cheers,
Matthias



From: Remzi Celebi 
Sent: Sunday, September 01, 2013 1:05 PM
To: Matthias Samwald 
Cc: Tom Morris ; Joanne Luciano ; Robert, Ph.D. Freimuth ; Joanne Luciano ; 
Simon Lin MD ; Robert Powers ; M. Scott Marshall ; michel.dumont...@gmail.com ; 
Richard Boyce ; public-semweb-lifesci hcls 
Subject: Re: Our paper won the distinguished paper/talk award at Medinfo2013


Hi Matthias,
Congratulation. Good work.
In the paper,  you have mentioned about the conversion of dbSNP to RDF. I 
haven't seen dbSNP on the list of the converted datasets under Bio2RDF project. 
I am also struggling to convert dbSNP to RDF. Could you tell me where can I 
find the RDF verison of dbSNP or Can I access to the script written for 
conversion if there is any? 
Thanks in advance,


Remzi



2013/8/26 Matthias Samwald 


  I have to correct myself. The link on rpi.edu (probably uploaded by Joanne) 
points to a draft of the paper. I uploaded the final version of the paper to
  http://samwald.info/res/samwald_medinfo2013_final.pdf

  Sorry,
  Matthias



   
  Tom Morris wrote:

  > Any links to the paper/presentation?  Are these them? 

  > http://tw.rpi.edu/media/2013/03/14/2b0f/Medinfo2013_JSL.pdf







-- 
Remzi Çelebi

Re: Our paper won the distinguished paper/talk award at Medinfo2013

[Matthias Samwald]

I have to correct myself. The link on rpi.edu (probably uploaded by Joanne) 
points to a draft of the paper. I uploaded the final version of the paper to
http://samwald.info/res/samwald_medinfo2013_final.pdf

Sorry,
Matthias



 
Tom Morris wrote:

> Any links to the paper/presentation?  Are these them? 

> http://tw.rpi.edu/media/2013/03/14/2b0f/Medinfo2013_JSL.pdf

Re: Our paper won the distinguished paper/talk award at Medinfo2013

[Matthias Samwald]

Tom Morris wrote:

> Any links to the paper/presentation?  Are these them? 

> http://tw.rpi.edu/media/2013/03/14/2b0f/Medinfo2013_JSL.pdf

> http://www.slideshare.net/matthiassamwald/samwald-medinfo-2013-presentation-25478857

Yes! 

Cheers,
Matthias

Re: [ANN] MORe reasoner version 0.1.5

[Matthias Samwald]

Michel,

There seems to be a Protege plugin available for download at 
http://code.google.com/p/more-reasoner/downloads/list

I will try running MORe with the Genomic CDS ontology to see how it compares 
with TrOWL. Looking forward to meet you all and discuss these exciting new 
developments in the OWL world at http://ore2013.cs.manchester.ac.uk/ next week, 
by the way!

 - Matthias




From: Michel Dumontier 
Sent: Monday, July 15, 2013 7:24 PM
To: Ernesto Jimenez-Ruiz 
Cc: HCLS 
Subject: Re: [ANN] MORe reasoner version 0.1.5


Ernesto, 
  Have you made your reasoner available for download as a Protege plugin?


m.



On Mon, Jul 15, 2013 at 12:31 PM, Ernesto Jimenez-Ruiz 
 wrote:

  [Apologies for cross-posting]

  Dear all,

  We are happy to announce the new version 0.1.5 of MORe reasoner [1]. MORe is 
open-source and released under GNU Lesser GPL [5].

  MORe is still under active development. The current distribution of MORe 
integrates HermiT [2] and JFact [3], as fully-fledged OWL 2 reasoners, with ELK 
[4] (a reasoner for the OWL 2 EL profile) in a modular way. In particular, MORe 
exploits module extraction techniques to identify a subset of the ontology that 
can be completely classified using ELK.

  MORe is designed in such a way that the fully-fledged (and slower) reasoner 
(i.e., HermiT or JFact) performs as few computations as possible, and the bulk 
of the computation is delegated to the more efficient, profile specific, ELK 
reasoner.

  MORe, with the standalone distribution, can be used from the command line or 
integrated in other OWL API based applications. Additionally, MORe is also 
distributed as a Protege plugin. Snow Owl also includes MORe as a reasoner 
option. See [1] for details.

  The new release added new functionalities and contains several bug fixes (see 
readme file for more details [6]).

  The MORe users' discussion group [7] is available for discussion, questions, 
comments, and bug reports.

  Best regards,
  MORe Team


  [1] http://code.google.com/p/more-reasoner/
  [2] http://www.hermit-reasoner.com/
  [3] http://jfact.sourceforge.net/
  [4] http://code.google.com/p/elk-reasoner/
  [5] http://www.gnu.org/licenses/lgpl.html
  [6] https://more-reasoner.googlecode.com/svn/trunk/resources/readme.txt
  [7] https://groups.google.com/forum/#!forum/more-reasoner-users


  -- 
  Ernesto Jiménez-Ruiz
  Research Assistant
  Department of Computer Science
  University of Oxford
  Wolfson Building, Parks Road, Oxford OX1 3QD, UK

  http://krono.act.uji.es/people/Ernesto
  http://www.cs.ox.ac.uk/people/ernesto.jimenez-ruiz/








-- 

Michel Dumontier
Associate Professor of Bioinformatics, Carleton University
Chair, W3C Semantic Web for Health Care and the Life Sciences Interest Group
http://dumontierlab.com

Clinical Pharmacogenomics teleconference SUMMER BREAK

[Matthias Samwald]

Dear all,

Because the past has shown that too many participants are unavailable 
throughout the summer months, there will be no Clinical Pharmacogenomics 
teleconferences until September. Please use the mailing list or private e-mails 
for ad-hoc discussions during this time. 

Have a nice summer!
 - Matthias 

International partners describe global alliance to enable secure sharing of genomic and clinical data (with several references to W3C)

[Matthias Samwald]

"Over 70 leading health care, research, and disease advocacy organizations that 
together involve colleagues in over 40 countries have taken the first steps to 
form an international alliance dedicated to enabling secure sharing of genomic 
and clinical data. "

News item: https://www.broadinstitute.org/news/5046-0
White paper: 
https://www.broadinstitute.org/files/news/pdfs/GAWhitePaperJune3.pdf

What is remarkable is that the white paper makes several references to the W3C 
as a model that inspires how they want to build this alliance. I wonder if they 
also considered doing this AS PART of the W3C? Or if someone at W3C gave that 
consideration? 

Cheers,
Matthias

Minutes: Clinical Pharmacogenomics Teleconference

[Matthias Samwald]

The minutes of the teleconference are available at
http://www.w3.org/2013/06/05-hcls-minutes.html

Cheers,
Matthias

Reminder: Clinical Pharmacogenomics Teleconference

[Matthias Samwald]

This is a reminder of the Clinical Pharmacogenomics Teleconference on Wednesday 
at 10:15 Eastern Time (16:15 Central European Time). Here is the suggested 
agendaa.. Simon Lin (Marshfield Clinic) to present/discuss "Big Data Needs in 
Clinical Genomics". Simon aims to work with the group to collaboratively edit a 
use case document. 
a.. Google-Doc: 
docs.google.com/document/d/12leHdI-GT2dzRgvVIx13wsXAaCLj6eNGvQ-L2B749f4/edit 
  b.. Discussion of schedule - 
http://www.w3.org/wiki/HCLSIG/Pharmacogenomics#Schedule - Are you making 
progress as planned? Are you blocked somewhere and need help? Do you have new 
suggestions? 
Meeting:  Clinical Pharmacogenomics
Date: June 05, 2013
Time: 10:15 Eastern Time (16:15 Central European Time)
Frequency:1st and 3rd Wednesday of the month
Conveners:Michel Dumontier, Matthias Samwald
Dial-In #:+1.617.761.6200 (Cambridge, MA)
VoIP address: sip:za...@voip.w3.org
Participant   Access Code: 4257 ("HCLS")
IRC Channel:  irc.w3.org port 6665 channel #HCLSURL: 
http://www.w3.org/wiki/HCLSIG/Pharmacogenomics/Meetings/2013-06-05_Conference_Call
Cheers,Matthias

Minutes: Clinical Pharmacogenomics Teleconference

[Matthias Samwald]

The meeting minutes can be found on the wiki at
http://www.w3.org/wiki/HCLSIG/Pharmacogenomics/Meetings/2013-05-15_Conference_Call

The discussion on "Big Data Needs in Clinical Genomics" was postponed to the 
next call.

Cheers,
Matthias




From: Matthias Samwald 
Sent: Wednesday, May 15, 2013 12:08 PM
To: public-semweb-lifesci@w3.org 
Cc: Simon Lin MD 
Subject: Reminder: Clinical Pharmacogenomics Teleconference


This is a reminder of the Clinical Pharmacogenomics Teleconference today at 
10:15 Eastern Time (16:15 Central European Time). Here is the suggested agenda:
  a.. Simon Lin (Marshfield Clinic) to present/discuss the topic "Big Data 
Needs in Clinical Genomics". Simon aims to work with the group to 
collaboratively edit a use case document. 
  b.. Continuation of planning and priorities meeting from last teleconference. 
Prepare for this meeting by jotting down specific outcomes you want to see in 
the next 3, 6, 12 months (if you have not reported on this already). The 
minutes of the last teleconference are available at 
http://www.w3.org/wiki/HCLSIG/Pharmacogenomics/Meetings/2013-05-01_Conference_Call

 Meeting:  Clinical Pharmacogenomics
 Date: May 15, 2013
 Time: 10:15 Eastern Time (16:15 Central European Time)
 Frequency:1st and 3rd Wednesday of the month
 Conveners:    Michel Dumontier, Matthias Samwald
 Dial-In #:+1.617.761.6200 (Cambridge, MA)
 VoIP address: sip:za...@voip.w3.org
 Participant   Access Code: 4257 ("HCLS")
 IRC Channel:  irc.w3.org port 6665 channel #HCLS
 URL: 
http://www.w3.org/wiki/HCLSIG/Pharmacogenomics/Meetings/2013-05-15_Conference_Call


Cheers,
Matthias

Reminder: Clinical Pharmacogenomics Teleconference

[Matthias Samwald]

This is a reminder of the Clinical Pharmacogenomics Teleconference today at 
10:15 Eastern Time (16:15 Central European Time). Here is the suggested agenda:
  a.. Simon Lin (Marshfield Clinic) to present/discuss the topic "Big Data 
Needs in Clinical Genomics". Simon aims to work with the group to 
collaboratively edit a use case document. 
  b.. Continuation of planning and priorities meeting from last teleconference. 
Prepare for this meeting by jotting down specific outcomes you want to see in 
the next 3, 6, 12 months (if you have not reported on this already). The 
minutes of the last teleconference are available at 
http://www.w3.org/wiki/HCLSIG/Pharmacogenomics/Meetings/2013-05-01_Conference_Call

 Meeting:  Clinical Pharmacogenomics
 Date: May 15, 2013
 Time: 10:15 Eastern Time (16:15 Central European Time)
 Frequency:1st and 3rd Wednesday of the month
 Conveners:Michel Dumontier, Matthias Samwald
 Dial-In #:+1.617.761.6200 (Cambridge, MA)
 VoIP address: sip:za...@voip.w3.org
 Participant   Access Code: 4257 ("HCLS")
 IRC Channel:  irc.w3.org port 6665 channel #HCLS
 URL: 
http://www.w3.org/wiki/HCLSIG/Pharmacogenomics/Meetings/2013-05-15_Conference_Call


Cheers,
Matthias

Minutes: Clinical Pharmacogenomics Teleconference

[Matthias Samwald]

The meeting minutes and some notes about plans for the next months are now 
available on the meeting wiki page:
http://www.w3.org/wiki/HCLSIG/Pharmacogenomics/Meetings/2013-05-01_Conference_Call

The discussion was very productive and there was not enough time to discuss 
everything. We will continue the discussion in the next meeting.

- Matthias

Reminder: Clinical Pharmacogenomics Teleconference

[Matthias Samwald]

This is a reminder of the Clinical Pharmacogenomics Teleconference today at 
10:15 Eastern Time (16:15 Central European Time). Here is the suggested agenda:

* Planning and priorities meeting. Prepare for this meeting by jotting down 
specific outcomes you want to see in the next 3, 6, 12 months. We will discuss 
these and determine what specifically needs to be done to achieve them. Then we 
will prioritize tasks and identify who wants to work on what.

* Submission about Genomic CDS (and other ontologies you have in the field of 
pharmacogenomics?) to the OWL Reaser Evaluation Workshop 2013 
http://ore2013.cs.manchester.ac.uk/ (Deadline 3rd of May!!)


Meeting:  Clinical Pharmacogenomics
 Date: May 01, 2013
 Time: 10:15 Eastern Time (16:15 Central European Time)
 Frequency:1st and 3rd Wednesday of the month
 Conveners:Michel Dumontier, Matthias Samwald
 Dial-In #:+1.617.761.6200 (Cambridge, MA)
 VoIP address: sip:za...@voip.w3.org
 Participant   Access Code: 4257 ("HCLS")
 IRC Channel:  irc.w3.org port 6665 channel #HCLS


Cheers,
Matthias

Meeting minutes: Clinical Pharmacogenomics Teleconference

[Matthias Samwald]

The meeting minutes are available at
http://www.w3.org/2013/04/03-HCLS-minutes.html

Cheers,
Matthias



From: Matthias Samwald 
Sent: Wednesday, April 03, 2013 2:56 PM
To: public-semweb-lifesci@w3.org 
Subject: Reminder: Clinical Pharmacogenomics Teleconference


This is a reminder of the Clinical Pharmacogenomics Teleconference today at 
10:15 Eastern Time (16:15 Central European Time). Here is the suggested agenda:
  a.. Jeremy Carroll will present his work on VCF and RDF. 
a.. Presentation slides: 
http://lists.w3.org/Archives/Public/www-archive/2013Apr/att-0002/W3C-JJC-LifeSci.pdf
 
b.. Topics: business background, Syapse Discovery; some background on VCF 
as a knowledge representation format; some initial results on mapping 1000 
genomes into RDF 
  a.. Optional: Pharmacogenomics of depression as a potential driving use-case? 
(Input from Joanne Luciano, Richard Boyce, others) 
Meeting:  Clinical Pharmacogenomics
Date: April 03, 2013
Time: 10:15 Eastern Time (16:15 Central European Time)
Frequency:1st and 3rd Wednesday of the month
Conveners:Michel Dumontier, Matthias Samwald
Dial-In #:+1.617.761.6200 (Cambridge, MA)
VoIP address: sip:za...@voip.w3.org
Participant   Access Code: 4257 ("HCLS")
IRC Channel:  irc.w3.org port 6665 channel #HCLS
URL: 
http://www.w3.org/wiki/HCLSIG/Pharmacogenomics/Meetings/2013-04-03_Conference_Call

Cheers,
Matthias

Reminder: Clinical Pharmacogenomics Teleconference

[Matthias Samwald]

This is a reminder of the Clinical Pharmacogenomics Teleconference today at 
10:15 Eastern Time (16:15 Central European Time). Here is the suggested agenda:
  a.. Jeremy Carroll will present his work on VCF and RDF. 
a.. Presentation slides: 
http://lists.w3.org/Archives/Public/www-archive/2013Apr/att-0002/W3C-JJC-LifeSci.pdf
 
b.. Topics: business background, Syapse Discovery; some background on VCF 
as a knowledge representation format; some initial results on mapping 1000 
genomes into RDF 
  a.. Optional: Pharmacogenomics of depression as a potential driving use-case? 
(Input from Joanne Luciano, Richard Boyce, others) 
Meeting:  Clinical Pharmacogenomics
Date: April 03, 2013
Time: 10:15 Eastern Time (16:15 Central European Time)
Frequency:1st and 3rd Wednesday of the month
Conveners:Michel Dumontier, Matthias Samwald
Dial-In #:+1.617.761.6200 (Cambridge, MA)
VoIP address: sip:za...@voip.w3.org
Participant   Access Code: 4257 ("HCLS")
IRC Channel:  irc.w3.org port 6665 channel #HCLS
URL: 
http://www.w3.org/wiki/HCLSIG/Pharmacogenomics/Meetings/2013-04-03_Conference_Call

Cheers,
Matthias

Canceled: Clinical Pharmacogenomics Telecon

[Matthias Samwald]

Dear all,

Since some of the usual participants are visting (and presenting at) the AMIA 
Joint Summit this week, the clinical pharmacogenomics teleconference today is 
canceled.

Best,
Matthias

Re: HCLSIG F2F @ CSHALS

[Matthias Samwald]

Dear all,

It turns out that the meeting place near CSHALS we originally had in mind is 
not really fit for accommodating a F2F meeting. Instead, we are having the 
meeting in the CSHALS lunch area during lunch time. Unfortunately, this means 
that only participants registered for CSHALS can participate. If you have any 
input (discussions points, suggestions for future directions) but cannot come, 
please post it to the wiki page or this mailing list. 

http://www.w3.org/wiki/HCLSIG/Cambridge_F2F_2013

Cheers,
Matthias




From: Michel Dumontier 
Sent: Wednesday, January 16, 2013 11:14 AM
To: HCLS 
Subject: HCLSIG F2F @ CSHALS


Hi everybody, 
  on the current clinical pharmacogenomics call we raised the possibility of 
have an impromptu face to face meeting at CSHALS in boston at the end of 
february


http://www.iscb.org/cshals2013-program/cshals2013-agenda


who would be interested in meeting up during CSHALS?  


m.


-- 

Michel Dumontier
Associate Professor of Bioinformatics, Carleton University
Chair, W3C Semantic Web for Health Care and the Life Sciences Interest Group
http://dumontierlab.com

Canceled: Clinical Pharmacogenomics Telecon

[Matthias Samwald]

Michel and I decided to cancel the teleconference today -- sorry for the short 
notice. 

The next teleconference will be held in two weeks, on March 06. Feel free to 
add suggested agenda items to 
http://www.w3.org/wiki/HCLSIG/Pharmacogenomics/Meetings/2013-03-06_Conference_Call

Cheers,
Matthias

Re: Local HCLS meeting during CSHALS on Friday March 1, 2013

[Matthias Samwald]

Dear Steven,

Thanks for the hint, this sounds like a very good idea.

Best,
Matthias


From: Steven Leard 
Sent: Thursday, February 07, 2013 3:57 PM
To: Matthias Samwald 
Cc: Steven Leard ; Luciano, Joanne S. ; Ted Slater ; Michel Dumontier ; 
public-semweb-lifesci hcls ; Charlie Mead ; Eric Prud'hommeaux 
Subject: Re: Local HCLS meeting during CSHALS on Friday March 1, 2013


Matthias, will your group then meet somewhere else in the hotel?   There is a 
restaurant on the main level that could work --- delegates could bring their 
plate down and non-delegates could buy a lunch? 


Thanks,

Steven


Steven Leard
ste...@marketwhys.ca
Phone: 780•414•1663


On 2013-02-07, at 3:01 AM, Matthias Samwald wrote:


  Dear Steven,

  Sorry for the confusion, I could not access my e-mail after we had the W3C 
teleconference yesterday.
  In that teleconference we found that Wednesday late evening (after the poster 
session) did not work out for some potential participants. We then decided to 
have the meeting on Friday, during the lunch break.

  Thanks a lot for your effort, and again, sorry for the confusion!

  With kind regards,
  Matthias


  From: Steven Leard 
  Sent: Wednesday, February 06, 2013 11:07 PM
  To: Luciano, Joanne S. 
  Cc: Steven Leard ; Ted Slater ; Michel Dumontier ; public-semweb-lifesci hcls 
; Charlie Mead ; Eric Prud'hommeaux ; Matthias Samwald 
  Subject: Re: Local HCLS meeting during CSHALS on Friday March 1, 2013


  hi Joanne, Matthias Samwald has already been in touch with me regarding 
holding a meeting on Wednesday evening on W3C Health Care and Life Science F2F 
meeting. I believe you are referring to the same meeting. 


  Please let me know so we can coordinate.




  Thank you,


  Steven


  Steven Leard
  ISCB Conferences Director
  ste...@iscb.org
  1+780-414-1663


  On 2013-02-06, at 3:00 PM, Luciano, Joanne S. wrote:


Michel, Ted, Steven, Charlie, Eric,


Re: http://www.w3.org/wiki/HCLSIG/Cambridge_F2F_2013 


Let's be sure we arrange ahead of time that those interested in attending 
the HCLSIG meeting during CSHALS on Friday March 1, 2013 can attend.  


Perhaps the CSHALS participants get box lunch? or there's some space we can 
meet that's not behind CSHALS doors? Or we get special permission for them to 
buy lunch or bring their lunch. Whatever works, but let's get this worked out 
ahead of time.


I'm sure a count and names of those planning to attend the HCSLIG meeting 
will be helpful to make this happen.


Thanks,


Joanne



~~

Joanne S. Luciano, PhD Tetherless World 
Constellation 
Research Associate Professor Rensselaer Polytechnic Institute
Deputy Director, Web Science Research Center 110 8th Street, Winslow 2143   
  
Email: jluci...@rpi.edu Troy, NY 12180, USA 
Office Tel. +1.518.276.4939   Global Tel. 
+1.617.440.4364 (skypeIn)
~~

Re: Local HCLS meeting during CSHALS on Friday March 1, 2013

[Matthias Samwald]

Dear Steven,

Sorry for the confusion, I could not access my e-mail after we had the W3C 
teleconference yesterday.
In that teleconference we found that Wednesday late evening (after the poster 
session) did not work out for some potential participants. We then decided to 
have the meeting on Friday, during the lunch break.

Thanks a lot for your effort, and again, sorry for the confusion!

With kind regards,
Matthias


From: Steven Leard 
Sent: Wednesday, February 06, 2013 11:07 PM
To: Luciano, Joanne S. 
Cc: Steven Leard ; Ted Slater ; Michel Dumontier ; public-semweb-lifesci hcls ; 
Charlie Mead ; Eric Prud'hommeaux ; Matthias Samwald 
Subject: Re: Local HCLS meeting during CSHALS on Friday March 1, 2013


hi Joanne, Matthias Samwald has already been in touch with me regarding holding 
a meeting on Wednesday evening on W3C Health Care and Life Science F2F meeting. 
I believe you are referring to the same meeting. 


Please let me know so we can coordinate.




Thank you,


Steven


Steven Leard
ISCB Conferences Director
ste...@iscb.org
1+780-414-1663


On 2013-02-06, at 3:00 PM, Luciano, Joanne S. wrote:


  Michel, Ted, Steven, Charlie, Eric,


  Re: http://www.w3.org/wiki/HCLSIG/Cambridge_F2F_2013 


  Let's be sure we arrange ahead of time that those interested in attending the 
HCLSIG meeting during CSHALS on Friday March 1, 2013 can attend.  


  Perhaps the CSHALS participants get box lunch? or there's some space we can 
meet that's not behind CSHALS doors? Or we get special permission for them to 
buy lunch or bring their lunch. Whatever works, but let's get this worked out 
ahead of time.


  I'm sure a count and names of those planning to attend the HCSLIG meeting 
will be helpful to make this happen.


  Thanks,


  Joanne



  ~~

  Joanne S. Luciano, PhD Tetherless World 
Constellation 
  Research Associate Professor Rensselaer Polytechnic Institute
  Deputy Director, Web Science Research Center 110 8th Street, Winslow 2143 

  Email: jluci...@rpi.edu Troy, NY 12180, USA 
  Office Tel. +1.518.276.4939   Global Tel. 
+1.617.440.4364 (skypeIn)
  ~~

Reminder: Clinical Pharmacogenomics Telecon (was Re: PK Ontology)

[Matthias Samwald]

There is a Clinical Pharmacogenomics telecon scheduled for tomorrow, Wednesday, 
10:15 Eastern Time (remember that we decided to have the telecon a bit 
earlier). I suggest that we use the teleconference to discuss this!
If you have other agenda items to suggest, please add them to the wiki page.

http://www.w3.org/wiki/HCLSIG/Pharmacogenomics/Meetings/2013-02-06_Conference_Call
Meeting:  HCLS Pharmacogenomics
Date: February 06, 2013
Time: 10:15 Eastern Time (16:15 Middle European Time)
Frequency:1st and 3rd Wednesday of the month
Convener: Michel Dumontier, Matthias Samwald
Dial-In #:+1.617.761.6200 (Cambridge, MA)
VoIP address: sip:za...@voip.w3.org
Participant   Access Code: 4257 ("HCLS")
IRC Channel:  irc.w3.org port 6665 channel #HCLS
Suggested Agenda

  a.. PK Ontology 
  b.. Discussing a potential HCLS IG / task force meetup around CSHALS 2013 in 
Boston this year 
  c.. (add other agenda items to the wiki page) 
Cheers,
Matthias



From: Richard Boyce 
Sent: Tuesday, February 05, 2013 8:34 PM
To: public-semweb-lifesci@w3.org 
Subject: Re: PK Ontology


This is relevant, thanks for finding Bob. Lang Li's group has been doing some 
interesting work. This ontology is a start in the right direction but has some 
issues (see below). I  would certainly be interested in discussing this and 
related work on a call. As you know, I would like to lead an effort to build a 
DDI ontology for the semantic web that meets pharmacist use cases. 

Comments:
- The ontology uses almost no formal definitions except for those imported. 

- It is inconsistent according to Hermit 1.3.6 and Fact++ (Protege 4.2)

- a quick inspection finds evidence that formal relationships are not being 
used e.g., why are CYP probe inhibitors and inducers sub-classes of specific 
CYP families? As it is, Omeprazole is_a CYP1A2-inducer-probe is_a CYP1A2 is_a 
Metabolism-enzyme!? Seems this should be a relationship between a set of a 
drug/chemicals as the domain and a CYP family as the range.

- The enzymes themselves are not mapped to anything!

- Its good to see muon's and positrons in there just in case... ;)

- variants come from the Sequence ontology

- the paper refers to a 2006 guidance to industry on drug-drug interaction 
studies for probe inhibitors, inducers, and substrates (see page 7 URL). This 
was updated in 2012 
(http://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Guidances/ucm292362.pdf)
 and its not clear if the ontology has been updated with it (I know that I need 
to update the Drug Interaction Knowledge Base).

- There are at least two other DDI corpuses out there besides Li's and the 
SemEval 2011. SemEval 2013 has a new corpus with MedLine and DrugBank 
annotations that will be publicly released in a couple of months when this 
years' the SemEval DDI challenge is completed 
(http://www.cs.york.ac.uk/semeval-2013/task9/). Also, we have made public a 
corpus of pharmacokinetic PDDIs manually annotated from drug product labeling: 
<http://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/package-insert-DDI-NLP-corpus.html>.
 

-Rich

On 02/05/2013 12:04 PM, Freimuth, Robert, Ph.D. wrote:

  URLs to save you time...

  The article abstract and provisional pdf are available at:
  http://www.biomedcentral.com/1471-2105/14/35/abstract

  The ontology is at:
  http://rweb.compbio.iupui.edu/corpus/ontology/

  The PK corpuses that were used are at:
  http://rweb.compbio.iupui.edu/corpus/

  Thanks, 
  Bob 






From: public-semweb-lifesci-requ...@listhub.w3.org 
[mailto:public-semweb-lifesci-requ...@listhub.w3.org] On Behalf Of Freimuth, 
Robert, Ph.D.
Sent: Tuesday, February 05, 2013 10:20 AM
To: public-semweb-lifesci@w3.org
Subject: PK Ontology




Hi All,

I haven't read this yet, but thought the abstract sounded interesting.  
Perhaps it is a topic for a future meeting?

Thanks,
Bob


BMC Bioinformatics. 2013 Feb 1;14(1):35. [Epub ahead of print]

An integrated pharmacokinetics ontology and corpus for text mining.

Wu HY, Karnik S, Subhadarshini A, Wang Z, Philips S, Han X, Chiang C, Liu 
L, Boustani M, Rocha LM, Quinney SK, Flockhart D, Li L.

Abstract


ABSTRACT: BACKGROUND: Drug pharmacokinetics parameters, drug interaction 
parameters, and pharmacogenetics data have been unevenly collected in different 
databases and published extensively in the literature. Without appropriate 
pharmacokinetics ontology and a well annotated pharmacokinetics corpus, it will 
be difficult to develop text mining tools for pharmacokinetics data collection 
from the literature and pharmacokinetics data integration from multiple 
databases.Description: A comprehensive pharmacokinetics ontology was 
constructed. It can annotate all aspects of in vitro pharmacokinetics 
experiments and in vivo pharmacokinetics studies. It cover

Re: HCLSIG F2F @ CSHALS

[Matthias Samwald]

I created a wiki page for planning the face-to-face meeting:
http://www.w3.org/wiki/HCLSIG/Cambridge_F2F_2013

Please add your name if you are interested in attending (I already added the 
names of those who replied via e-mail).
I guess we don't know yet know how many interested participants we will have 
(and hence, whether we might want to have a dedicated, quiet space for the 
meeting, or are fine with meeting at a dinner table). Just in case: Does 
anybody know of opportunities for securing a small conference room? Would it be 
feasible to reserve a room at the W3C offices? 

 - Matthias




From: Michel Dumontier 
Sent: Wednesday, January 16, 2013 5:14 PM
To: HCLS 
Subject: HCLSIG F2F @ CSHALS


Hi everybody, 
  on the current clinical pharmacogenomics call we raised the possibility of 
have an impromptu face to face meeting at CSHALS in boston at the end of 
february


http://www.iscb.org/cshals2013-program/cshals2013-agenda


who would be interested in meeting up during CSHALS?  


m.


-- 

Michel Dumontier
Associate Professor of Bioinformatics, Carleton University
Chair, W3C Semantic Web for Health Care and the Life Sciences Interest Group
http://dumontierlab.com

Re: Reminder: Clinical Pharmacogenomics teleconference

[Matthias Samwald]

Atif wrote:
> Also in the meeting invite the 'Frequency' description mentions "1st and 3rd 
> Thursday of the month".  Should this not be "Wednesday" instead.

Thanks for pointing that out. Of course, this should have been "Wednesday".

- Matthias



From: Atif Khan 
Sent: Wednesday, January 16, 2013 2:13 PM
To: Matthias Samwald 
Cc: HCLS 
Subject: Re: Reminder: Clinical Pharmacogenomics teleconference


I second the motion to change the meeting time  to 10:00 AM.

Also in the meeting invite the 'Frequency' description mentions "1st and 3rd 
Thursday of the month".  Should this not be "Wednesday" instead.


Cheers,

-Atif




On Wed, Jan 16, 2013 at 8:01 AM, Matthias Samwald 
 wrote:

Dear all,This is a reminder of the teleconference on Clinical Pharmacogenomics, 
starting today at 11:00 Eastern Time.Meeting:  HCLS Pharmacogenomics
Date: January 16, 2013
Frequency:    1st and 3rd Thursday of the month
Convener: Michel Dumontier, Matthias Samwald
Dial-In #:+1.617.761.6200 (Cambridge, MA)
VoIP address: sip:za...@voip.w3.org
Participant   Access Code: 4257 ("HCLS")
IRC Channel:  irc.w3.org port 6665 channel #HCLS
Suggested Agenda 

a.. Possibility of moving the timeslot of this call from 11:00 to 10:00 or 
10:30? (request by Michel) 
b.. New developments regarding annotation of pharmacogenomic statements in 
FDA abstracts with the Annotation Ontology (Richard) 
c.. Quick update on experiences with working with TrOWL for reasoning with 
pharmacogenetic ontologies for decision support. Should we seek cooperation 
with OWL reasoner developers on this demanding use-case? (Matthias) 
d.. Discussing a potential HCLS IG / task force meetup around CSHALS 2013 
in Boston this year (Matthias) 
e.. Other new developments 
  Cheers,
  Matthias



-- 
Atif Khan
PhD Candidate
David R. Cheriton School of Computer Science
University of Waterloo
http://www.cs.uwaterloo.ca/~a78khan/

Reminder: Clinical Pharmacogenomics teleconference

[Matthias Samwald]

Dear all,This is a reminder of the teleconference on Clinical Pharmacogenomics, 
starting today at 11:00 Eastern Time.Meeting:  HCLS Pharmacogenomics
Date: January 16, 2013
Frequency:1st and 3rd Thursday of the month
Convener: Michel Dumontier, Matthias Samwald
Dial-In #:+1.617.761.6200 (Cambridge, MA)
VoIP address: sip:za...@voip.w3.org
Participant   Access Code: 4257 ("HCLS")
IRC Channel:  irc.w3.org port 6665 channel #HCLS
Suggested Agenda 

  a.. Possibility of moving the timeslot of this call from 11:00 to 10:00 or 
10:30? (request by Michel) 
  b.. New developments regarding annotation of pharmacogenomic statements in 
FDA abstracts with the Annotation Ontology (Richard) 
  c.. Quick update on experiences with working with TrOWL for reasoning with 
pharmacogenetic ontologies for decision support. Should we seek cooperation 
with OWL reasoner developers on this demanding use-case? (Matthias) 
  d.. Discussing a potential HCLS IG / task force meetup around CSHALS 2013 in 
Boston this year (Matthias) 
  e.. Other new developments 
Cheers,
Matthias

Clinical Pharmacogenomics telecon canceled, a look back, and a look forward

[Matthias Samwald]

Dear all,

The Clinical Pharmacogenomics Telecon today is canceled, since some key persons 
are not able to attend. The next call is scheduled for January 16, next year.

Best,
Matthias

Re: Preview of OWL 2 ontology for clinical pharmacogenomics and decision support (now called 'Genomic CDS')

[Matthias Samwald]

Quick reply: SNPs and drugs are already linked to the Bio2RDF versions of dbSNP 
and DrugBank, i.e., the ontology is already part of the linked data cloud! The 
entities are linked via rdfs:seeAlso.

Cheers,
Matthias

From: Michel Dumontier 
Sent: Wednesday, November 21, 2012 6:40 PM
To: Matthias Samwald 
Cc: public-semweb-lifesci@w3.org ; Simon Lin MD 
Subject: Re: Preview of OWL 2 ontology for clinical pharmacogenomics and 
decision support (now called 'Genomic CDS')


Matthias, 
 First, great work. I think this embodies an initial approach we've envisioned 
for using OWL ontologies for clinical pharmacogenomics.  It's able to 
i) define complex genotypes (as a union/conjunction of alleles)
ii) it can define copy number variation (zero, one or more copies of a 
gene/gene variant), or capture uncertainty in the copy number (e.g. at least 
one). 
iii) it points to specific snps variants for a given variant


so, here are some comments:
1. can you provide a description of the specific snp-containing entry e.g. 
rs9332239_C - i'll generate the appropriate descriptions for Bio2RDF version 
dbsnp that i'm working on.


2. The class 'Human' specifies 2 of all the genes, so this restricts our cases 
where CNV plays an important role (from 0 copies to dozens). To what extent is 
the use of the cardinality restriction on this parent class *essential* for 
generating the inferred classification?   Should this instead be done at the 
patient level?


3. We should be generating linked data -> Warfarin can point to any of : 
drugbank or SPL (since PharmGKB and PubChem gets their drug information from 
DrugBank). Since Bio2RDF hosts Drugbank, we could use those URIs.


m.


On Wed, Nov 21, 2012 at 10:19 AM, Matthias Samwald 
 wrote:

  Dear all,

  A preview release (version 0.8) of the Genomic CDS ontology is now available 
at 
  http://www.genomic-cds.org/ont/genomic-cds.owl

  There is also a demo version that contains some example patient data:
  http://www.genomic-cds.org/ont/genomic-cds-demo.owl

  Among other things, it contains logical representations of pharmacogenetic 
alleles and their defining SNPs, as well as logical representations of selected 
pharmacogenetic guidelines from the Clinical Pharmacogenetics Implementation 
Consortium and the Dutch Pharmacogenetics Working Group. The Genomic CDS 
ontology aims to unify several functionalities in a single resource, being:
  * A knowledge base for clinical pharmacogenomics/pharmacogenetics that can be 
used for question-answering (e.g., which SNPs are associated with this drug?)
  * A rule base for clinical decision support (e.g., inferring that a patient 
with a specific set of SNPs requires a lowered dose of warfarin and generating 
a CDS message that can be viewed by clinicians)
  * A tool for checking data consistency (e.g., highlighting which allele 
definitions in PharmGKB are overlapping, or which clinical decision support 
rules are matching the same group of patients)

  The ontology is OWL 2 DL serialized in Manchester Syntax. Protege 4 with the 
TrOWL reasoner plugin is recommended for working with the ontology. Please note 
that it the ontology is quite complex, so reasoning only works on decent 
hardware.

  The use of OWL 2 (and Manchester Syntax) makes it possible to capture complex 
pharmacogenetic definitions and data in a relatively intuitive, yet 
ontology-based and machine-readable format. For example, the OWL description of 
a few SNPs of a patient looks like this:
---Individual: example_patient
Types:
human,
(has some rs10929302_A)  and (has some rs10929302_G),
(has some rs1208_A)  and (has some rs1208_G),
(has some rs12571421_A)  and (has some rs12571421_G),
(has some rs12769205_A)  and (has some rs12769205_G),
has exactly 2 rs10264272_C,
has exactly 2 rs10276036_T,
has exactly 2 rs1041983_C,
has exactly 2 rs1042713_G,
---Equally, a logical description of SNPs associated with the CYP2C9*3 
allele look like this...---Class: 'human with CYP2C9 *3'
EquivalentTo: has some rs1057910_C

SubClassOf: has some 'CYP2C9 *3',(has some rs1057910_C) 
and (has some rs1057911_A) and (has some rs1799853_C) 
and (has some rs2256871_A)
 and (has some rs28371685_C)
 and (has some rs28371686_C) and (has some rs56165452_T)
 and (has some rs57505750_C) and (has some rs67807361_C) and 
(has some rs72558184_G) and (has some rs72558187_T)

 and (has some rs72558188_AGAAATGGAA) and (has some 
rs72558189_G) and (has some rs72558190_C) and (has some 
rs72558192_A) and (has some rs72558193_A) and (has some 
rs7900194_G)

 and (has some rs9332130_A) and (has some rs9332131_A) 
and (has some rs9332239_C),---.

Reminder: Clinical Genomics telecon (new!)

[Matthias Samwald]

Dear all,

This is a reminder that the teleconference of the Clinical Genomics task force 
will start soon. This task force was created by merging the Clinical 
Pharmacogenomics and the Clinical Decision Support task forces (which turned 
out to be tightly integrated anyways). The teleconferences will now be held on 
the 2nd and 4th Wednesday of the month, replacing the Thursday teleconferences

== Conference Details ==
 Clinical Genomics
 
 Date of Call: Wednesday November 21 2012
 Time of Call: 11:00am - 12:00pm ET 
 Dial-In #: +1.617.761.6200 (Cambridge, MA) 
 Dial-In #: +33.4.26.46.79.03 (Paris, France) 
 Dial-In #: +44.203.318.0479 (London, UK) 
 Participant Access Code: 4257 ("HCLS")
 IRC Channel: irc.w3.org port 6665 channel #HCLS
 Duration: 1h 
 Conveners: Michel Dumontier & Matthias Samwald

== Agenda ==
* News about the Genomic CDS ontology (http://www.genomic-cds.org/)
* Building an extended clinical pharmacogenomics knowledge base

http://www.w3.org/wiki/HCLSIG/Pharmacogenomics/Meetings/2012-11-21_Conference_Call

Cheers,
Matthias Samwald

Preview of OWL 2 ontology for clinical pharmacogenomics and decision support (now called 'Genomic CDS')

[Matthias Samwald]

Dear all,

A preview release (version 0.8) of the Genomic CDS ontology is now available at 
http://www.genomic-cds.org/ont/genomic-cds.owl

There is also a demo version that contains some example patient data:
http://www.genomic-cds.org/ont/genomic-cds-demo.owl

Among other things, it contains logical representations of pharmacogenetic 
alleles and their defining SNPs, as well as logical representations of selected 
pharmacogenetic guidelines from the Clinical Pharmacogenetics Implementation 
Consortium and the Dutch Pharmacogenetics Working Group. The Genomic CDS 
ontology aims to unify several functionalities in a single resource, being:
* A knowledge base for clinical pharmacogenomics/pharmacogenetics that can be 
used for question-answering (e.g., which SNPs are associated with this drug?)
* A rule base for clinical decision support (e.g., inferring that a patient 
with a specific set of SNPs requires a lowered dose of warfarin and generating 
a CDS message that can be viewed by clinicians)
* A tool for checking data consistency (e.g., highlighting which allele 
definitions in PharmGKB are overlapping, or which clinical decision support 
rules are matching the same group of patients)

The ontology is OWL 2 DL serialized in Manchester Syntax. Protege 4 with the 
TrOWL reasoner plugin is recommended for working with the ontology. Please note 
that it the ontology is quite complex, so reasoning only works on decent 
hardware.

The use of OWL 2 (and Manchester Syntax) makes it possible to capture complex 
pharmacogenetic definitions and data in a relatively intuitive, yet 
ontology-based and machine-readable format. For example, the OWL description of 
a few SNPs of a patient looks like this:
---Individual: example_patient
Types:
human,
(has some rs10929302_A)  and (has some rs10929302_G),
(has some rs1208_A)  and (has some rs1208_G),
(has some rs12571421_A)  and (has some rs12571421_G),
(has some rs12769205_A)  and (has some rs12769205_G),
has exactly 2 rs10264272_C,
has exactly 2 rs10276036_T,
has exactly 2 rs1041983_C,
has exactly 2 rs1042713_G,
---Equally, a logical description of SNPs associated with the CYP2C9*3 
allele look like this...---Class: 'human with CYP2C9 *3'
EquivalentTo: has some rs1057910_CSubClassOf: has some 
'CYP2C9 *3',(has some rs1057910_C) and (has some rs1057911_A)   
  and (has some rs1799853_C) and (has some rs2256871_A) and 
(has some rs28371685_C) and (has some rs28371686_C) and (has 
some rs56165452_T) and (has some rs57505750_C) and (has some 
rs67807361_C) and (has some rs72558184_G) and (has some 
rs72558187_T) and (has some rs72558188_AGAAATGGAA) and (has 
some rs72558189_G) and (has some rs72558190_C) and (has some 
rs72558192_A) and (has some rs72558193_A) and (has some 
rs7900194_G) and (has some rs9332130_A) and (has some 
rs9332131_A) and (has some rs9332239_C),---... and a logical 
description of the group of humans that might require a specific initial 
warfarin dose based on their genetic traits looks like this:---Class: 
'human triggering CDS rule 7'Annotations: label "human triggering 
CDS rule 7",'CDS message' "3-4 mg warfarin per day should be considered 
as a starting dose range for a patient with this genotype according to the 
Warfarin drug label (Bristol-Myers Squibb).",'relevant for' 
<http://www.genomic-cds.org/ont/genomic-cds.owl#Warfarin>EquivalentTo:  
   (has some 'CYP2C9 *1') and (has some 'CYP2C9 *3') and 
(has exactly 2 rs9923231_C)SubClassOf: 'Human triggering CDS 
rule'---To make long-term development and maintenance easier, the 
ontology is generated from intuitive spreadsheets (so that independent domain 
experts can easily edit and validate the knowledge) and automated imports from 
primary datasets such as dbSNP.An issue tracker for ontology development is 
available athttp://code.google.com/p/genomic-cds/issues/listAlso, a website for 
the project is under construction at
http://www.genomic-cds.org/

The ontology also has a home on BioPortal at
http://bioportal.bioontology.org/ontologies/3179

Needless to say, all of this is just a partial research prototype. Not all 
required information is in the ontology, some information might be several 
months out of date, and accuracy and quality have not been validated. 
We can discuss the ontology in today's teleconference call (the first in the 
new Wednesday timeslot, an announcement will be sent out soon).

Cheers,
Matthias Samwald
http://samwald.info/

CDS Telecon today cancelled; updated ontology available soon

[Matthias Samwald]

Dear all,

Please note that the Clinical Decision Support teleconference today is 
cancelled.

I can report that I am close to finalizing the first release of the ontology 
for pharmacogenomics-based clinical decision support, including an OWL 2-based 
representation of clinical guidelines of the CPIC and the Royal Dutch 
Pharmacogenetics Working Group, as well as OWL 2 based definitions of 
clinically relevant alleles and phenotypes. I will keep you updated via e-mail.

Cheers,
Matthias

Re: Reminder: CDS Telecon about to start

[Matthias Samwald]

The minutes of the CDS call are available at
http://www.w3.org/2012/10/11-hcls-minutes.html

Thanks to Bob Powers for scribing.

 - Matthias



From: Matthias Samwald 
Sent: Thursday, October 11, 2012 5:00 PM
To: public-semweb-lifesci@w3.org 
Subject: Reminder: CDS Telecon about to start


Dear all,

This is a reminder that the CDS teleconference is about to start right now.

- Matthias

Reminder: CDS Telecon about to start

[Matthias Samwald]

Dear all,

This is a reminder that the CDS teleconference is about to start right now.

- Matthias

Cancelled: Clinical Decision Support telecon on Thursday

[Matthias Samwald]

Dear all,

The Clinical Decision Support teleconference today is cancelled (conflicting 
schedules).

Best,
Matthias

Reminder of CDS telecon / Re: OpenDDx project

[Matthias Samwald]

Hello Alejandro et al.,

We have a teleconference of the Clinical Decision Support task force this 
Thursday. Maybe you can join and present / discuss  your project there? Here 
are the dial-in details:

Clinical Decision Support for Personalized Medicine
http://www.w3.org/wiki/HCLSIG/CDS

Date of Call: Thursday September 13 2012
Time of Call: 11:00am - 12:00pm ET 
Dial-In #: +1.617.761.6200 (Cambridge, MA) 
Dial-In #: +33.4.26.46.79.03 (Paris, France) 
Dial-In #: +44.203.318.0479 (London, UK) 
Participant Access Code: 4257 ("HCLS")
IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, 
or see Web IRC) 
Mibbit quick start: Click on mibbit for instant IRC access
Duration: 1h 
Convener: Matthias SamwaldCheers,Matthias Samwald 



From: Alejandro Rodríguez González 
Sent: Wednesday, September 12, 2012 12:19 PM
To: public-semweb-lifesci@w3.org ; semantic-...@w3.org ; public-...@w3.org 
Cc: Cam Webb 
Subject: OpenDDx project


Dear colleagues,


I want to introduce you the OpenDDx project.


OpenDDx is a project which aims to create an open, reliable and global database 
that associates clinical findings with diseases, something that we consider 
that will be very useful for medical researchers and practitioners. The main 
technological cornerstone in which will be based this project are the semantic 
technologies. I attach in this email the main url of the project [1] where you 
can find more information such as concept document [2], initial blog post [3] 
done by Dr. Campbell O. Webb, the precursor of this project, or the mailing 
list [4] where we are discussing about the project.


We are seeking for people interested in the development of this project that 
can provide new ideas to the current model that Dr. Webb already have developed 
or interact in the mailing list providing new points of view, ideas, or 
opinions.


Warm regards,


Alejandro Rodríguez


[1] http://openddx.net/
[2] 
https://docs.google.com/document/d/1T05Ao-7uVtOW0rjn_qZray9DK5VtJiIoZ7aU7Q6tA8k/edit
[3] http://camwebb.info/blog/2012-03-14/
[4] http://lists.openddx.net/listinfo.cgi/oddx-design-openddx.net


-- 

Dr. Alejandro Rodríguez González - PhD


Bioinformatics at Centre for Plant Biotechnology and Genomics UPM-INIA
Polytechnic University of Madrid
http://www.alejandrorg.com
Phone: +34 914524900 . Ext: 25550 





Once the game is over, the king and the pawn go back in the same box. - Italian 
proverb

Re: Teleconference Reminder: Clinical Decision Support for Personalized Medicine

[Matthias Samwald]

The meeting minutes are available at 
http://www.w3.org/2012/08/23-hcls-minutes.html
Thanks to Eric and Scott for scribing.

Cheers,
Matthias


From: Matthias Samwald 
Sent: Thursday, August 23, 2012 1:01 PM
To: public-semweb-lifesci@w3.org 
Subject: Teleconference Reminder: Clinical Decision Support for Personalized 
Medicine


This is a reminder of the teleconference today. Agenda:
  a.. Continue discussion about standardized, OWL-based representation of core 
pharmacogenomic markers and clinical decision support rules 
  b.. Other topics suggested by participants
Cheers,
Matthias
Clinical Decision Support for Personalized Medicine
http://www.w3.org/wiki/HCLSIG/CDS

Date of Call: Thursday August 23 2012
Time of Call: 11:00am - 12:00pm ET 
Dial-In #: +1.617.761.6200 (Cambridge, MA) 
Dial-In #: +33.4.26.46.79.03 (Paris, France) 
Dial-In #: +44.203.318.0479 (London, UK) 
Participant Access Code: 4257 ("HCLS")
IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, 
or see Web IRC) 
Mibbit quick start: Click on mibbit for instant IRC access
Duration: 1h 
Convener: Matthias Samwald

Teleconference Reminder: Clinical Decision Support for Personalized Medicine

[Matthias Samwald]

This is a reminder of the teleconference today. Agenda:
  a.. Continue discussion about standardized, OWL-based representation of core 
pharmacogenomic markers and clinical decision support rules 
  b.. Other topics suggested by participants
Cheers,
Matthias
Clinical Decision Support for Personalized Medicine
http://www.w3.org/wiki/HCLSIG/CDS

Date of Call: Thursday August 23 2012
Time of Call: 11:00am - 12:00pm ET 
Dial-In #: +1.617.761.6200 (Cambridge, MA) 
Dial-In #: +33.4.26.46.79.03 (Paris, France) 
Dial-In #: +44.203.318.0479 (London, UK) 
Participant Access Code: 4257 ("HCLS")
IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, 
or see Web IRC) 
Mibbit quick start: Click on mibbit for instant IRC access
Duration: 1h 
Convener: Matthias Samwald

Re: seeks input on Study Data Exchange Standards

[Matthias Samwald]

Peter wrote:
> Using both SQL and subsumption you can automatically find things like this: 
> "find all disorders that are a kind of adverse drug reaction where drug is a 
> subtype of antibiotic and was given for a kind of gram negative bacterial 
> infection of the digestive system". 

Simple subsumption such as that can be inferred by basic, RDFS-type reasoning. 
I don't see any potential problems caused by OWL's open world assumption here 
(please point them out if there are any).
Indeed, the open-world assumption of OWL can make creating expressive 
ontologies and using reasoners tricky. However, I do not see why the same 
should be true for using RDF, basic RDFS subsumptions and SPARQL. Could you 
provide some examples?

If we wanted to use more expressive ontologies with "intensional" entities 
(i.e., defined classes) in the overall system, we could simply run a reasoner 
and materialize the inferred statements for each ontology before it is 
'shipped' for use by other systems. These other systems could then use simple 
RDF(S) and SPARQL (and maybe SPARQL rules), without the performance issues and 
potential unexpected consequences of open-world reasoning with expressive OWL 
ontologies. Specifying if and how exactly each specific node should be reasoned 
upon sounds so complex that I cannot imagine it working in any practical 
setting.

Best,
Matthias

Telecon CANCELED: Clinical Decision Support for Personalized Medicine

[Matthias Samwald]

The CDS teleconference tomorrow is cancelled.

(once again, let's reduce the number of teleconferences while several people 
are on vacation over the summer months, and use e-mail instead)

Cheers,
Matthias

Teleconference Reminder: Clinical Decision Support for Personalized Medicine

[Matthias Samwald]

This is a reminder of the teleconference that will start in less than an hour. 
Agenda:
  a.. Quick update and discussion on recent developments and ideas, open to all 
topics
Cheers,MatthiasClinical Decision Support for Personalized Medicine
http://www.w3.org/wiki/HCLSIG/CDS

Date of Call: Thursday July 26 2012
Time of Call: 11:00am - 12:00pm ET 
Dial-In #: +1.617.761.6200 (Cambridge, MA) 
Dial-In #: +33.4.26.46.79.03 (Paris, France) 
Dial-In #: +44.203.318.0479 (London, UK) 
Participant Access Code: 4257 ("HCLS")
IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, 
or see Web IRC) 
Mibbit quick start: Click on mibbit for instant IRC access
Duration: 1h 
Convener: Matthias Samwald

Telecon CANCELED: Clinical Decision Support for Personalized Medicine

[Matthias Samwald]

The CDS teleconference today is cancelled.
(let's reduce the number of teleconferences now that several people are on 
vacation over the summer months, and use e-mail instead)

Cheers,
Matthias

Medical Microdata Compendium (Open Biomedical Datasets with schema.org annotation) -- was: Re: New proposal: health & medical extensions to schema.org

[Matthias Samwald]

Dear all,

I published a first prototype of the "Medical Microdata Compendium", a 
collection of open medical and pharmacological datasets with markup conforming 
to the recently updated schema.org and the microdata format. The long-term goal 
of this project is to provide structured medical and pharmacological 
information to search engines to enable better decision making by doctors and 
patients. The far more humble short-term goal is to research how microdata can 
be used for retrieving and querying biomedical information, and to come up with 
interesting demonstrations and use-cases.

The data can be viewed here:

http://samwald.info/medical_microdata/

At the moment this is a flat list of web pages, with each page describing a 
formulated pharmaceutical or a substance. The data were derived from the 
DailyMed and DrugBank datasets from the LODD collection. 

Example of a DrugBank resource:
http://samwald.info/medical_microdata/drugbank_resource_drugs_DB00175.html

Example of a DailyMed resource:
http://samwald.info/medical_microdata/dailymed_resource_drugs_3580.html

You can extract the structured data from these pages with a variety of tools. 
For example, You can use the Sindice inspector:
http://inspector.sindice.com/inspect?url=http%3A%2F%2Fsamwald.info%2Fmedical_microdata%2Fdrugbank_resource_drugs_DB00175.html

At the moment I am evaluating how different search engines can cope with the 
data. For example, the microdata can already be used by Google Custom Search 
Engines. Other 'semantic' search engines such as http://sindice.com/ or the 
medical search engine developed by the http://khresmoi.eu/ project should also 
be evaluated. 

If you are interested in joining the effort to evaluate how semantic markup can 
be used to improve medical information search and decision making, please send 
me an e-mail! I would like to see this work published as a journal paper, and 
could use some co-authors. I appreciate every feedback or idea!

Regarding the Medical Microdata Compendium, there are several issues that still 
need to be taken care of:

1) The DailyMed resources are still riddled with character encoding issues -- 
this is a problem of the LODD data source and will be remedied by switching to 
a newer version of this dataset, Richard's 'Linked Structured Product Labels'.
2) Only a fraction of the properties of the source datasets have been mapped, 
namely those where a close fit between a property in the source dataset and 
schema.org could be found. This means that a lot of useful data is not 
captured. I will look into using the proposed schema.org extension mechanism to 
see if it could help to capture these additional properties and types.
3) More datasets need to be converted, such as ClinicalTrials.gov (and its 
linked data mirror http://linkedct.org/). This will also help to better 
demonstrate interlinking of different datasets (e.g., from disease to drug to 
ongoing clinical trials in the area).
4) The generation of http://schema.org/MedicalCode entities needs to be fixed. 
Also, we need to check how we can align with controlled vocabularies that 
already have URIs (e.g. to BioPortal taxonomies)
5) General clean-up, code formatting and improvement of web design

Cheers,
Matthias Samwald

Meeting Minutes: Clinical Decision Support for Personalized Medicine

[Matthias Samwald]

The meeting minutes are available at:
http://www.w3.org/2012/06/28-hcls-minutes.html

Cheers,
Matthias





From: Matthias Samwald 
Sent: Wednesday, June 27, 2012 11:58 PM
To: public-semweb-lifesci@w3.org 
Subject: Teleconference Reminder: Clinical Decision Support for Personalized 
Medicine



Agenda 
  a.. Continue discussions from last Thursday (dbSNP etc.) 
  b.. Deciding on extensions of the Translational Medicine Ontology (TMO) - 
what should be covered in the TMO and what should be left to ad-hoc schemas 
based on source data? 
  c.. Revisiting the plans for a journal submission 
Conference Details 
Clinical Decision Support for Personalized Medicine
http://www.w3.org/wiki/HCLSIG/CDS

Date of Call: Thursday June 28 2012
Time of Call: 11:00am - 12:00pm ET 
Dial-In #: +1.617.761.6200 (Cambridge, MA) 
Dial-In #: +33.4.26.46.79.03 (Paris, France) 
Dial-In #: +44.203.318.0479 (London, UK) 
Participant Access Code: 4257 ("HCLS")
IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, 
or see Web IRC) 
Mibbit quick start: Click on mibbit for instant IRC access
Duration: 1h 
Convener: Matthias Samwald

Teleconference Reminder: Clinical Decision Support for Personalized Medicine

[Matthias Samwald]

Agenda 
  a.. Continue discussions from last Thursday (dbSNP etc.) 
  b.. Deciding on extensions of the Translational Medicine Ontology (TMO) - 
what should be covered in the TMO and what should be left to ad-hoc schemas 
based on source data? 
  c.. Revisiting the plans for a journal submission 
Conference Details 
Clinical Decision Support for Personalized Medicine
http://www.w3.org/wiki/HCLSIG/CDS

Date of Call: Thursday June 28 2012
Time of Call: 11:00am - 12:00pm ET 
Dial-In #: +1.617.761.6200 (Cambridge, MA) 
Dial-In #: +33.4.26.46.79.03 (Paris, France) 
Dial-In #: +44.203.318.0479 (London, UK) 
Participant Access Code: 4257 ("HCLS")
IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, 
or see Web IRC) 
Mibbit quick start: Click on mibbit for instant IRC access
Duration: 1h 
Convener: Matthias Samwald

Re: Schema.org Discussion

[Matthias Samwald]

A quick update: The medical schema.org extension was published:
http://blog.schema.org/2012/06/health-and-medical-vocabulary-for.html

I'm almost done exposing some core Linked Open Drug Data (LODD) based on the 
extended schema.org vocabulary in RDFa 1.1 format (microdata will follow as 
well). While the mapping is already finished, I am still working on the code to 
to convert the resulting RDF into HTML+RDFa or HTML+Microdata. I wasted an 
awful amount of time with trying to use XSLT for that purpose (e.g., as used by 
[1]), but the results were not good enough. Now I am writing the transformation 
as simple Java code...

Cheers,
Matthias

[1] http://rhizomik.net/html/redefer/



From: Matthias Samwald 
Sent: Friday, June 01, 2012 6:05 PM
To: public-semweb-lifesci@w3.org 
Subject: Meeting minutes: Schema.org Discussion 


The minutes of the call are available at
http://www.w3.org/2012/06/01-HCLS-minutes.html

Unfortunately, only the second half of the call (after Aaron joined) is 
captured in the minutes.

Cheers,
Matthias

Re: aTag and conclusion sections from PubMed

[Matthias Samwald]

Hi Richard,

Thanks for digging this up. As a reminder:  aTags = a convention for using 
the SIOC vocabulary for the simple representation of scientific assertions 
annotated with terms from controlled vocabularies.


The aTag website fell in disrepair when I left DERI (a fate of so many 
research-driven projects...), but I will now work with Lena to bring at 
least parts of it back online. So far, aTags were adopted in the context of 
some research projects, but not on any broader scale or independent from 
this group (at least I am not aware of it).


However, I will revisit aTags in the context of ongoing work (e.g., 
summarizing biomedical articles quickly to make research findings easier to 
consume in time-constrained clinical settings). It might be interesting to 
switch from the SIOC vocabulary to a very simple extension of Schema.org... 
so far, Schema.org does not really cover this, but extending it would be 
very simple.


aTags should be very simple to create, integrate and consume (you don't have 
the problem of different ontology design patterns), so I can encourage you 
to expose some of the data you are working on in this format!


Cheers,
Matthias



--
From: "Richard Boyce" 
Sent: Friday, June 22, 2012 9:05 PM
To: 
Subject: aTag and conclusion sections from PubMed

A few years ago Matthias and others did some interesting work on aTags 
 and an initial extraction 
of conclusions from PubMed abstracts still queryable in the HCLS knowledge 
base. Does anyone know what the status of the atag approach is? Did it 
gain traction in the SW community or is has work progressed in some way?


Also, I would be interested to expand the conclusions section demo, any 
way that could be accomplished?


I see that most of the related links seem to be dead on the HCLS site: 
. The 
science commons still provides a text annotation service that embeds atags 
.


Since I didn't start working with this group until 2010 I am still 
discovering work done by members of the group several years ago!


-Rich

--
Richard Boyce, PhD
Assistant Professor of Biomedical Informatics
Faculty, Geriatric Pharmaceutical Outcomes and Gero-Informatics Research 
and Training Program

Scholar, Comparative Effectiveness Research Program
University of Pittsburgh
rd...@pitt.edu
412-648-9219 (W), 206-371-6186 (C)
Twitter: @bhaapgh

Meeting minutes: Clinical Decision Support for Personalized Medicine

[Matthias Samwald]

The meeting minutes are available at 
http://www.w3.org/2012/06/14-hcls-minutes.html

Thanks to Eric for scribing.

 - Matthias




From: Matthias Samwald 
Sent: Wednesday, June 13, 2012 6:23 PM
To: public-semweb-lifesci@w3.org 
Cc: Gökhan Karakülah 
Subject: Teleconference Reminder: Clinical Decision Support for Personalized 
Medicine


Agenda 

  a.. The Medicine Safety Code project -- A 2D barcode that helps predict a 
patient's personal response to medical therapy (based on pharmacogenomic rules 
and RDF/SPARQL). See http://safety-code.org/ 

  b.. Extending the pharmacogenomic CDS decision support table, see 
https://docs.google.com/spreadsheet/pub?hl=en_US&hl=en_US&key=0AiGT-vnkGcoLdFFVMEdqcFdYaDFqS0xHTnlUT0N3cEE&output=html
 

  c.. Structured Product Label data for European countries -- discussion on how 
to make them available and what that could enable. For example, Diagnosia 
(http://www.diagnosia.com) made drug package inserts from 12 European countries 
available on the web. 

  d.. Other topics suggested by participants 
Conference Details 

Clinical Decision Support for Personalized Medicine
http://www.w3.org/wiki/HCLSIG/CDS

Date of Call: Thursday June 14 2012
Time of Call: 11:00am - 12:00pm ET 
Dial-In #: +1.617.761.6200 (Cambridge, MA) 
Dial-In #: +33.4.26.46.79.03 (Paris, France) 
Dial-In #: +44.203.318.0479 (London, UK) 
Participant Access Code: 4257 ("HCLS")
IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, 
or see Web IRC) 
Mibbit quick start: Click on mibbit for instant IRC access
Duration: 1h 
Convener: Matthias Samwald

Re: Minutes from BioRDF/LODD telcon Monday 06/12/2012

[Matthias Samwald]

I would also be interested in extending this with data extracted from 
European product labels. Compared to the US and Dailymed, this is far 
trickier. The data is not openly available for many countries, content has 
different languages, and structured product labels are even harder to come 
by.


A Viennese startup called http://www.diagnosia.com/de/ recently made package 
insert texts from 12 European countries openly available. I plan to contact 
them and see if they would also be interested in cooperating with research 
projects. We might not end up with a resource that can be shared without 
restrictions, but at least we could end up with something that allows us to 
run SPARQL queries for analysis and research.


Other ideas for how such a multilingual, pan-European ressource are welcome!

Cheers,
Matthias



Hi, Richard,

Very nice work. Building the linked data source for SPLs is very important
for facilitating its wide use. It is impressive that you keep the source
updated once per week.

As you have pointed out that the SPLs are semi-structured, the combination
of NLP and standard terminologies will be crucial for producing structured
data out of the SPLs. As you know, our team at Mayo Clinic is 
investigating

the SPLs from the perspective of Adverse Drug Events. We would like to
collaborate to see whether we could link our ADEpedia data
(http://adepedia.org) with your LinkedSPLs.

The following are our preliminary works,

1)  Jiang G, Solbrig H, Chute CG. ADEpedia: a scalable and standardized
knowledge base of Adverse Drug Events using semantic web technology. AMIA
Annu Symp Proc. 2011;2011:607-16. Epub  2011 Oct 22.
http://www.ncbi.nlm.nih.gov/pubmed?term=adepedia

2) Zhu Q, Jiang G, Chute CG. Profiling Structured Product Labeling using
RxNorm and NDF-RT. ICBO 2012 Workshop (to be held in July 21-25, 2012).

Best regards,

Guoqian


Guoqian Jiang, M.D., Ph.D.
===
Assistant Professor of Medical Informatics
Division of Biomedical Statistics & Informatics,
Mayo Clinic College of Medicine
200 First Street, SW,
Rochester, MN, 55905
Tel: 1-507-266-1327
Fax: 1-507-284-0360
Email: jiang.guoq...@mayo.edu
===




On 6/14/12 12:47 PM, "Richard Boyce"  wrote:


Minutes from BioRDF/LODD telcon Monday 06/12/2012

Rich Boyce (University of Pittsburgh) presented "LinkedSPLs - a
dynamically updated and comprehensive linked data node for US drug
package inserts"

Link to his slides:


Summary of discussion:

Richard: Purpose of presenting is to attract collaborators...consider
Linked Structured Product Labels an important data resource to keep up
to date and improved, hopefully with partners.

Richard: Structured Product Labels are the standard in the U.S.
Medscape, Micromedex echo product labels and add information that is
missing. If a recent IOM report (http://tinyurl.com/cxovshm) is acted
on, we should see some progress in how the product labels are formed in
the next few years

ericP: q+ to ask if the SPLs reflect the areas of concensus and that
affects the degree to which not being on the SPL indicates variation of
information from the various resources

Richard: (answering EricP): Interesting question. Warfarin is an example
of how consensus from the community ended up in the product label. Often
the information is not complete and it is left up to third parties to
complete - dynamic process.

Richard: FDA wrote laws the dictate the types of claims that should be
present in each section. This gives us an opportunity to link to related
resources such as for evidence.

Richard: FDA wrote laws the dictate the types of claims that should be
present in each section.
..This gives us an opportunity to link to related resources such as for
evidence.
..[slide8]DailyMed is the public source of SPLs
..[slide9] "SPL IDs are not static, so a label's URL may change if
..the label is updated. However, DailyMed provides permanent
..URLs to view or download the latest version of an SPL²

Richard: LinkedSPLs started with Anja's PHP for DailyMed and ported to
python

EricP: correcting for multiple active ingredients require modeling 
changes?

Richard: Modeling changes
UNII -
Unique Ingredient Identifier
sounds like Unicode when spoken!
CODE: http://swat-4-med-safety.googlecode.com/svn/trunk/linkedSPLs/

JoanneLuciano Health Care Delivery Grants from ???

Simon Lee: Maybe use for AHRQ grants

JoanneLuciano NIN NLM grants
JoanneLuciano I'm thinking this can be linked with Safety-Code.org

Richard: Think it's a little early for AHRQ grants, more research 
necessary


Simon: agree.
Simon: need working prototype.
Simon Lin - Marshfield Clinic

michel DrugBank is the best to link to, i think
michel they then link out to many other sources

JoanneLuciano safety-code.org

michel BTW - I've built a new parser for drugbank
michel
http://bio2rdf.semanticscience.org:8022/descri

Teleconference Reminder: Clinical Decision Support for Personalized Medicine

[Matthias Samwald]

Agenda 

  a.. The Medicine Safety Code project -- A 2D barcode that helps predict a 
patient's personal response to medical therapy (based on pharmacogenomic rules 
and RDF/SPARQL). See http://safety-code.org/ 

  b.. Extending the pharmacogenomic CDS decision support table, see 
https://docs.google.com/spreadsheet/pub?hl=en_US&hl=en_US&key=0AiGT-vnkGcoLdFFVMEdqcFdYaDFqS0xHTnlUT0N3cEE&output=html
 

  c.. Structured Product Label data for European countries -- discussion on how 
to make them available and what that could enable. For example, Diagnosia 
(http://www.diagnosia.com) made drug package inserts from 12 European countries 
available on the web. 

  d.. Other topics suggested by participants 
Conference Details 

Clinical Decision Support for Personalized Medicine
http://www.w3.org/wiki/HCLSIG/CDS

Date of Call: Thursday June 14 2012
Time of Call: 11:00am - 12:00pm ET 
Dial-In #: +1.617.761.6200 (Cambridge, MA) 
Dial-In #: +33.4.26.46.79.03 (Paris, France) 
Dial-In #: +44.203.318.0479 (London, UK) 
Participant Access Code: 4257 ("HCLS")
IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, 
or see Web IRC) 
Mibbit quick start: Click on mibbit for instant IRC access
Duration: 1h 
Convener: Matthias Samwald

Meeting minutes: Schema.org Discussion

[Matthias Samwald]

The minutes of the call are available at
http://www.w3.org/2012/06/01-HCLS-minutes.html

Unfortunately, only the second half of the call (after Aaron joined) is 
captured in the minutes.

Cheers,
Matthias

Re: RDF Schema / LODD mapping -- Re: New proposal: health & medical extensions to schema.org

[Matthias Samwald]

Dear all,

I have finished a first conversion of some key datasets from the "Linked Open 
Drug Data" collection to schema.org with medical extensions. At the moment, I 
converted the datasets from Drugbank [1] and Dailymed [2]. I can work on 
mapping other datasets such as RxNorm, DBpedia and ClinicalTrials.gov as well, 
if this pilot leads to promising results.

The RDF of the conversion is available at
http://samwald.info/res/medical-schema-org/pharmaceutical-information-according-to-schema-org.ttl

Beware that this file is quite large (33 MB). I have published it uncompressed 
so that it is more transparent to web crawlers.

How this was done
To create this file, I extracted the RDF triples from the RDFa file provided by 
Aaron (outcome available at [3]). I had to fix a minor bug to make that happen 
correctly (there was whitespace in some of the labels and URIs). Then I 
manually created a mapping file between the schema.org extensions and the 
entities and properties used in the Drugbank and Dailymed datasets. This 
mapping is based on RDF Schema and Simple SPARQL Rules, and is available at [4] 
-- please have a look. I loaded all these files together with the LODD datasets 
into a triplestore with RDFS reasoning and executed the SPARQL Rules, yielding 
the final pharmaceutical-information-according-to-schema-org.ttl file.

Where to go from here
It would be great to evaluate how Google and other search engines (such as 
Khresmoi [5]) can use structured information based on schema.org to improve 
access to medical / pharmaceutical information. To do this, we could set up web 
sites based on these datasets with embedded Microdata (or RDFa lite?) 
statements. Then we could compare the usability of schema.org-aware search 
engines with standard search engines (e.g., a normal Google Custom Search 
Engine). I think this could provide a very impressive example of what 
schema.org markup enables (and probably a nice scientific article).

@ Aaron: What do you suggest as the next steps for setting up such a test 
scenario? Are there any prototypical search tools from Google on the horizon 
that we could use?
@ Aaron: If you want to get some more detailed feedback from me about the 
schema.org extensions and some modelling choices, we should probably get in 
contact via Skype.
@ All: Do you have any suggestions for automatically publishing RDF datasets as 
HTML-with-Microdata or HTML-with-RDFa? Or do we need to write a script from 
scratch?

[1] http://drugbank.ca/ 
[2] http://dailymed.nlm.nih.gov/dailymed/
[3] http://samwald.info/res/medical-schema-org/schema_org_rdfa.ttl
[4] http://samwald.info/res/medical-schema-org/schema_org_2_LODD_mapping.ttl
[5] http://khresmoi.eu/

Best,
Matthias




From: Matthias Samwald 
Sent: Monday, May 21, 2012 1:35 PM
To: Aaron Brown 
Cc: Dan Brickley ; public-semweb-lifesci@w3.org 
Subject: RDF Schema / LODD mapping -- Re: New proposal: health & medical 
extensions to schema.org


Dear Aaron,

I think it might be an interesting exercise to publish some of the "Linked Open 
Drug Data" [1] datasets as microdata that adheres to the proposed extensions. 
These datasets were published in RDF format by members of the W3C Health Care 
and Life Science Interest Group. Mapping these datasets to your proposed 
schema.org extensions would be much easier if we had an RDF Schema of those 
extensions (which is available for the official schema.org via [2] and [3]). 
Could you make an RDF schema of your extensions available?

[1] http://www.w3.org/wiki/HCLSIG/LODD/Data
[2] http://schema.org/docs/schemaorg.owl
[3] http://schema.rdfs.org/all.ttl

Cheers,
Matthias Samwald



From: Michel Dumontier 
Sent: Wednesday, May 16, 2012 4:05 PM
To: w3c semweb hcls 
Cc: Aaron Brown ; Dan Brickley 
Subject: New proposal: health & medical extensions to schema.org


Hi all, 


 Aaron Brown (@google) and others have been working on a health/medical 
extension to schema.org ->  http://schemaorg-medicalext.appspot.com/. It's also 
linked on the W3 wiki at
http://www.w3.org/wiki/WebSchemas/MedicalHealthProposal, along with other 
proposals - http://www.w3.org/wiki/WebSchemas. Have a look at the 
medical/health proposal and tell us what you think - I'd love to hear from 
those that are active in creating or consuming web page content (SciDisc, 
atags, Mark Wilkinson's Personal Health Lens, etc).


 Reserve Friday June 1 @ 11am (Terminology task force slot) for a special 
meeting discuss the proposal and we'll craft some feedback for the public 
mailing list at public-voc...@w3.org. 


Cheers!


m.


-- Forwarded message --
From: Dan Brickley 
Date: Tue, May 15, 2012 at 10:49 AM
Subject: Fwd: New proposal: health & medical extensions to schema.org
To: e...@w3.org, team-hcls-cha...@w3.org, Aaron Brown 
Cc: i...@w3.org


Eric, HCLS folk, Ivan,

I want to introduce you to Aaron Brown, and pass along his msg below
introducing some work on healt

Clinical Decision Support Telecon cancelled

[Matthias Samwald]

Dear all,

I have to cancel the Clinical Decision Support Teleconference this Thursday 
(because of conflicting schedules). I will follow up with an e-mail on recent 
progress.

Best,
Matthias

Re: RDF Schema / LODD mapping -- Re: New proposal: health & medical extensions to schema.org

[Matthias Samwald]

Dear all,

I think these details are relevant for reasoning about patient data et 
cetera., but the documentation of schema.org and the proposed medical 
extensions make it very clear that they are not intended for such tasks. I 
think that the issues highlighted here are not highly relevant for basic 
entity annotation and capturing basic statements used for improved retrieval 
of information on the web -- as intended by the people driving these 
projects. Let's try not to scare them away! :-)


I made some progress with mapping the schema.org extensions to some Linked 
Open Drug Data classes and properties, but have to pause this work for the 
rest of the week because of teaching duties. I will try to publish a first 
draft next week.


- Matthias



--
From: "Stuart Turner" 
Sent: Wednesday, May 23, 2012 10:55 PM
To: "Luciano, Joanne S." 
Cc: "Solbrig, Harold R." ; "R. Cornet" 
; "Michel Dumontier" ; 
"Freimuth, Robert, Ph.D." ; "Jim McCusker" 
; "Aaron Brown" ; "Dan 
Brickley" ; "Renato Iannella" ; 
"Lin MD, Simon" ; "Matthias Samwald" 
; 
Subject: Re: RDF Schema / LODD mapping -- Re: New proposal: health & medical 
extensions to schema.org


A patient (human or non-human) continues to be a patient after their 
death. Medical procedures continue (e.g. autopsy/necropsy). Medical 
records are revised and persisted naturally, and by law. A death 
certificate is issued. And so on. HL7 modeling isn't ideal for guidance 
here, especially when referring to patients of the non-human variety :)


~ Stuart
-
Stuart Turner, DVM, MS
Biomedical Informaticist | Principal, Leafpath Informatics, LLC
stu...@leafpath.org | +1.916.596.0255 | @ Skype 
http://leafpath.org | FOAF: http://stuartturner.org/foaf.rdf


On May 23, 2012, at 1:45 PM, Luciano, Joanne S. wrote:


Do they? The body does. The memory doesn't, in digital space:

What happens to their data?
Does their data disappear? Their medical record?
They "were" a patient.  Not sure what that means - maybe we need, in 
addition to is_a   a new class was_a   (for the has beens).


some things to muse about.

joanne

~
Joanne S. Luciano, PhD Rensselaer 
Polytechnic Institute
Research Associate Professor  110 8th Street, Winslow 
2143

Tetherless World Constellation Troy, NY 12180, USA
Department of Computer Science Email: jluci...@rpi.edu
Office Tel. +1.518.276.4939  Global Tel. 
+1.617.440.4364 (skypeIn)

~~

On May 23, 2012, at 3:37 PM, Solbrig, Harold R. wrote:


Although, if the patient dies, the person goes away as well, no?  ;-)

From: public-semweb-lifesci-requ...@listhub.w3.org 
[mailto:public-semweb-lifesci-requ...@listhub.w3.org] On Behalf Of R. 
Cornet

Sent: Wednesday, May 23, 2012 2:26 PM
To: Michel Dumontier; Freimuth, Robert, Ph.D.
Cc: Jim McCusker; Aaron Brown; Dan Brickley; Renato Iannella; Lin MD, 
Simon; Matthias Samwald; public-semweb-lifesci@w3.org
Subject: RE: RDF Schema / LODD mapping -- Re: New proposal: health & 
medical extensions to schema.org


I would say that if you follow ontoclean, being a patient is a non-rigid 
property of a person.


Ronald


Ronald Cornet, PhDemail: r.cor...@amc.uva.nl
dept. of Medical Informatics   phone: +31 (0)20 566 5188
Academic Medical Center, Room J1B-115  fax:   +31 (0)20 691 9840
P.O.Box 22700  www: kik.amc.uva.nl/home/rcornet/
1100 DE  Amsterdam
The Netherlands

From: Michel Dumontier [mailto:michel.dumont...@gmail.com] 

RDF Schema / LODD mapping -- Re: New proposal: health & medical extensions to schema.org

[Matthias Samwald]

Dear Aaron,

I think it might be an interesting exercise to publish some of the "Linked Open 
Drug Data" [1] datasets as microdata that adheres to the proposed extensions. 
These datasets were published in RDF format by members of the W3C Health Care 
and Life Science Interest Group. Mapping these datasets to your proposed 
schema.org extensions would be much easier if we had an RDF Schema of those 
extensions (which is available for the official schema.org via [2] and [3]). 
Could you make an RDF schema of your extensions available?

[1] http://www.w3.org/wiki/HCLSIG/LODD/Data
[2] http://schema.org/docs/schemaorg.owl
[3] http://schema.rdfs.org/all.ttl

Cheers,
Matthias Samwald



From: Michel Dumontier 
Sent: Wednesday, May 16, 2012 4:05 PM
To: w3c semweb hcls 
Cc: Aaron Brown ; Dan Brickley 
Subject: New proposal: health & medical extensions to schema.org


Hi all, 


 Aaron Brown (@google) and others have been working on a health/medical 
extension to schema.org ->  http://schemaorg-medicalext.appspot.com/. It's also 
linked on the W3 wiki at
http://www.w3.org/wiki/WebSchemas/MedicalHealthProposal, along with other 
proposals - http://www.w3.org/wiki/WebSchemas. Have a look at the 
medical/health proposal and tell us what you think - I'd love to hear from 
those that are active in creating or consuming web page content (SciDisc, 
atags, Mark Wilkinson's Personal Health Lens, etc).


 Reserve Friday June 1 @ 11am (Terminology task force slot) for a special 
meeting discuss the proposal and we'll craft some feedback for the public 
mailing list at public-voc...@w3.org. 


Cheers!


m.


-- Forwarded message --
From: Dan Brickley 
Date: Tue, May 15, 2012 at 10:49 AM
Subject: Fwd: New proposal: health & medical extensions to schema.org
To: e...@w3.org, team-hcls-cha...@w3.org, Aaron Brown 
Cc: i...@w3.org


Eric, HCLS folk, Ivan,

I want to introduce you to Aaron Brown, and pass along his msg below
introducing some work on health/medical markup for use in the public
Web, part of the schema.org project which is a collaboration amongst
several search engines to improve structured data usage within HTML.

Aaron has been busy with a pretty substantial medical/health
vocabulary, and yesterday circulated a first public version for
feedback/comments. I wanted to ask your advice on how best we might
connect this with the various activities of the HCLS W3C group. The
message below is public (see
http://lists.w3.org/Archives/Public/public-vocabs/2012May/0057.html
), so we could just pass it along to the public HCLS list
http://lists.w3.org/Archives/Public/public-semweb-lifesci/ but if
you've any thoughts on how best to interact with HCLS that would be
really useful. The emphasis with the vocabulary Aaron's working on is
on in-page HTML markup rather than full/deep ontology engineering,
though there are obviously points of connection to such activities.
I'll leave Aaron to discuss the details (see his note below or ask in
this thread).

Thanks for any advice,

cheers,

Dan


ps. for a bit more background -
The public-voc...@w3.org list is the main feedback/discussion forum
for the schema.org initiative. Within W3C it is the 'Web Schemas'
taskforce of the Semantic Web group, which I  chair. I also btw have
an @google affiliation for my schema.org work, though I don't formally
represent Google at W3C. Basically the Web Schemas group serves as a
liaison point between schema.org as an external entity, the W3C
community, and other groups producing metadata vocabularies. More
details c/o http://www.w3.org/wiki/WebSchemas ...


-- Forwarded message --
From: Aaron Brown 
Date: 14 May 2012 22:56
Subject: New proposal: health & medical extensions to schema.org
To: public-voc...@w3.org


Hi all,

As I’ve alluded to before on this list
(http://lists.w3.org/Archives/Public/public-vocabs/2012Feb/0053.html),
over the past 6 months, a few of us at Google and other institutions
have been working on a set of schema.org extensions to cover the
health and medical domain. After several internal iterations and a lot
of feedback from initial reviewers (including the US NCBI; physicians
at Harvard, Stanford, and Duke; the major search engines; and a few
health web sites), we think we have a solid draft and would like to
open it for public feedback as a step toward incorporating it into
schema.org.

The proposed health/medical schema can be found at
http://schemaorg-medicalext.appspot.com/ which includes an
introduction as well as a snapshot of the type hierarchy and several
markup examples. It's also linked on the w3 wiki at
http://www.w3.org/wiki/WebSchemas/MedicalHealthProposal. As you'll see
this is a substantial piece of work, so we’d welcome feedback and
detailed review comments on the specifics (please follow up to this
email).

For those interested in more background on the approach: our goal is
to create schema that w

RDF Schema / LODD mapping -- Re: New proposal: health & medical extensions to schema.org

[Matthias Samwald]

Dear Aaron,

I think it might be an interesting exercise to publish some of the "Linked Open 
Drug Data" [1] datasets as microdata that adheres to the proposed extensions. 
These datasets were published in RDF format by members of the W3C Health Care 
and Life Science Interest Group. Mapping these datasets to your proposed 
schema.org extensions would be much easier if we had an RDF Schema of those 
extensions (which is available for the official schema.org via [2] and [3]). 
Could you make an RDF schema of your extensions available?

[1] http://www.w3.org/wiki/HCLSIG/LODD/Data
[2] http://schema.org/docs/schemaorg.owl
[3] http://schema.rdfs.org/all.ttl

Cheers,
Matthias Samwald



From: Michel Dumontier 
Sent: Wednesday, May 16, 2012 4:05 PM
To: w3c semweb hcls 
Cc: Aaron Brown ; Dan Brickley 
Subject: New proposal: health & medical extensions to schema.org


Hi all, 


 Aaron Brown (@google) and others have been working on a health/medical 
extension to schema.org ->  http://schemaorg-medicalext.appspot.com/. It's also 
linked on the W3 wiki at
http://www.w3.org/wiki/WebSchemas/MedicalHealthProposal, along with other 
proposals - http://www.w3.org/wiki/WebSchemas. Have a look at the 
medical/health proposal and tell us what you think - I'd love to hear from 
those that are active in creating or consuming web page content (SciDisc, 
atags, Mark Wilkinson's Personal Health Lens, etc).


 Reserve Friday June 1 @ 11am (Terminology task force slot) for a special 
meeting discuss the proposal and we'll craft some feedback for the public 
mailing list at public-voc...@w3.org. 


Cheers!


m.


-- Forwarded message --
From: Dan Brickley 
Date: Tue, May 15, 2012 at 10:49 AM
Subject: Fwd: New proposal: health & medical extensions to schema.org
To: e...@w3.org, team-hcls-cha...@w3.org, Aaron Brown 
Cc: i...@w3.org


Eric, HCLS folk, Ivan,

I want to introduce you to Aaron Brown, and pass along his msg below
introducing some work on health/medical markup for use in the public
Web, part of the schema.org project which is a collaboration amongst
several search engines to improve structured data usage within HTML.

Aaron has been busy with a pretty substantial medical/health
vocabulary, and yesterday circulated a first public version for
feedback/comments. I wanted to ask your advice on how best we might
connect this with the various activities of the HCLS W3C group. The
message below is public (see
http://lists.w3.org/Archives/Public/public-vocabs/2012May/0057.html
), so we could just pass it along to the public HCLS list
http://lists.w3.org/Archives/Public/public-semweb-lifesci/ but if
you've any thoughts on how best to interact with HCLS that would be
really useful. The emphasis with the vocabulary Aaron's working on is
on in-page HTML markup rather than full/deep ontology engineering,
though there are obviously points of connection to such activities.
I'll leave Aaron to discuss the details (see his note below or ask in
this thread).

Thanks for any advice,

cheers,

Dan


ps. for a bit more background -
The public-voc...@w3.org list is the main feedback/discussion forum
for the schema.org initiative. Within W3C it is the 'Web Schemas'
taskforce of the Semantic Web group, which I  chair. I also btw have
an @google affiliation for my schema.org work, though I don't formally
represent Google at W3C. Basically the Web Schemas group serves as a
liaison point between schema.org as an external entity, the W3C
community, and other groups producing metadata vocabularies. More
details c/o http://www.w3.org/wiki/WebSchemas ...


-- Forwarded message --
From: Aaron Brown 
Date: 14 May 2012 22:56
Subject: New proposal: health & medical extensions to schema.org
To: public-voc...@w3.org


Hi all,

As I’ve alluded to before on this list
(http://lists.w3.org/Archives/Public/public-vocabs/2012Feb/0053.html),
over the past 6 months, a few of us at Google and other institutions
have been working on a set of schema.org extensions to cover the
health and medical domain. After several internal iterations and a lot
of feedback from initial reviewers (including the US NCBI; physicians
at Harvard, Stanford, and Duke; the major search engines; and a few
health web sites), we think we have a solid draft and would like to
open it for public feedback as a step toward incorporating it into
schema.org.

The proposed health/medical schema can be found at
http://schemaorg-medicalext.appspot.com/ which includes an
introduction as well as a snapshot of the type hierarchy and several
markup examples. It's also linked on the w3 wiki at
http://www.w3.org/wiki/WebSchemas/MedicalHealthProposal. As you'll see
this is a substantial piece of work, so we’d welcome feedback and
detailed review comments on the specifics (please follow up to this
email).

For those interested in more background on the approach: our goal is
to create schema that w

Re: New proposal: health & medical extensions to schema.org

[Matthias Samwald]

Hi Michel, 

Last time I checked schema.org I researched whether it contained any vocabulary 
for capturing basic scientific statements/assertions/hypotheses, similar to 
aTags and the various formats created by participants of the SciDisc task force 
and the Nanopublications project. I found that schema.org did not really 
contain anything like that -- except maybe http://schema.org/ScholarlyArticle, 
which is too coarse grained for capturing single scientific assertions. Adding 
something like this to schema.org should be fairly simple!

Cheers,
Matthias



From: Michel Dumontier 
Sent: Wednesday, May 16, 2012 4:05 PM
To: w3c semweb hcls 
Cc: Aaron Brown ; Dan Brickley 
Subject: New proposal: health & medical extensions to schema.org


Hi all, 


 Aaron Brown (@google) and others have been working on a health/medical 
extension to schema.org ->  http://schemaorg-medicalext.appspot.com/. It's also 
linked on the W3 wiki at
http://www.w3.org/wiki/WebSchemas/MedicalHealthProposal, along with other 
proposals - http://www.w3.org/wiki/WebSchemas. Have a look at the 
medical/health proposal and tell us what you think - I'd love to hear from 
those that are active in creating or consuming web page content (SciDisc, 
atags, Mark Wilkinson's Personal Health Lens, etc).


 Reserve Friday June 1 @ 11am (Terminology task force slot) for a special 
meeting discuss the proposal and we'll craft some feedback for the public 
mailing list at public-voc...@w3.org. 


Cheers!


m.


-- Forwarded message --
From: Dan Brickley 
Date: Tue, May 15, 2012 at 10:49 AM
Subject: Fwd: New proposal: health & medical extensions to schema.org
To: e...@w3.org, team-hcls-cha...@w3.org, Aaron Brown 
Cc: i...@w3.org


Eric, HCLS folk, Ivan,

I want to introduce you to Aaron Brown, and pass along his msg below
introducing some work on health/medical markup for use in the public
Web, part of the schema.org project which is a collaboration amongst
several search engines to improve structured data usage within HTML.

Aaron has been busy with a pretty substantial medical/health
vocabulary, and yesterday circulated a first public version for
feedback/comments. I wanted to ask your advice on how best we might
connect this with the various activities of the HCLS W3C group. The
message below is public (see
http://lists.w3.org/Archives/Public/public-vocabs/2012May/0057.html
), so we could just pass it along to the public HCLS list
http://lists.w3.org/Archives/Public/public-semweb-lifesci/ but if
you've any thoughts on how best to interact with HCLS that would be
really useful. The emphasis with the vocabulary Aaron's working on is
on in-page HTML markup rather than full/deep ontology engineering,
though there are obviously points of connection to such activities.
I'll leave Aaron to discuss the details (see his note below or ask in
this thread).

Thanks for any advice,

cheers,

Dan


ps. for a bit more background -
The public-voc...@w3.org list is the main feedback/discussion forum
for the schema.org initiative. Within W3C it is the 'Web Schemas'
taskforce of the Semantic Web group, which I  chair. I also btw have
an @google affiliation for my schema.org work, though I don't formally
represent Google at W3C. Basically the Web Schemas group serves as a
liaison point between schema.org as an external entity, the W3C
community, and other groups producing metadata vocabularies. More
details c/o http://www.w3.org/wiki/WebSchemas ...


-- Forwarded message --
From: Aaron Brown 
Date: 14 May 2012 22:56
Subject: New proposal: health & medical extensions to schema.org
To: public-voc...@w3.org


Hi all,

As I’ve alluded to before on this list
(http://lists.w3.org/Archives/Public/public-vocabs/2012Feb/0053.html),
over the past 6 months, a few of us at Google and other institutions
have been working on a set of schema.org extensions to cover the
health and medical domain. After several internal iterations and a lot
of feedback from initial reviewers (including the US NCBI; physicians
at Harvard, Stanford, and Duke; the major search engines; and a few
health web sites), we think we have a solid draft and would like to
open it for public feedback as a step toward incorporating it into
schema.org.

The proposed health/medical schema can be found at
http://schemaorg-medicalext.appspot.com/ which includes an
introduction as well as a snapshot of the type hierarchy and several
markup examples. It's also linked on the w3 wiki at
http://www.w3.org/wiki/WebSchemas/MedicalHealthProposal. As you'll see
this is a substantial piece of work, so we’d welcome feedback and
detailed review comments on the specifics (please follow up to this
email).

For those interested in more background on the approach: our goal is
to create schema that webmasters and content publishers can use to
mark up health and medical content on the web, with a particular focus
on markup that will help patients, physicians, and generally
health-interested consumers find r

Reminder: Telconference on Clinical Decision Support for Personalized Medicine

[Matthias Samwald]

Conference Details 

Clinical Decision Support for Personalized Medicine
http://www.w3.org/wiki/HCLSIG/CDS

Date of Call: Thursday May 10 2012
Time of Call: 11:00am - 12:00pm Eastern Time (17:00 - 18:00 Central European 
Time) 
Dial-In #: +1.617.761.6200 (Cambridge, MA) 
Dial-In #: +33.4.26.46.79.03 (Paris, France) 
Dial-In #: +44.203.318.0479 (London, UK) 
Participant Access Code: 4257 ("HCLS")
IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, 
or see Web IRC) 
Mibbit quick start: Click on mibbit for instant IRC access
Duration: 1h 
Convener: Matthias Samwald
Agenda 

  a.. Bob Freimuth will talk to us about CPIC, the clinical pharmacogenomics 
implementation consortium, which is crafting clinically actionable notes for 
pharmacogenomic-labeled drugs. 

Re: Minutes from Clinical Decision Support teleconference

[Matthias Samwald]

Hi Richard,

>Were the entries blank in "Germ-line genetic marker (curated SNPs)" because 
>the 2C9 variants were not present in a curated resource?

We discussed this a bit after you had left. Some entries for curated SNPs in 
[1] are blank because the warfarin drug label there refers to CPY2C9*1 alleles, 
i.e., the wild-type alleles. These are a bit tricky, because these wild-type 
alleles can be defined by not having any SNP that would turn it into a 
non-wildtype allele (i.e., you would need to know the status of a great number 
of SNPs to make a wild-type call, while you only need to know one or two SNPs 
to make a non-wildtype call). 

Generally, it seems a bit problematic to use alleles denoted with the * 
notation in drug labels without referring to the concrete SNPs or genetic 
sequences, because the definition of alleles can change when new variants are 
discovered.

> What is the meaning of the evidence column? 

I think for the time being it is sufficient to capture from which source the 
rule was derived in a short text and a URL that points to that resource, if 
available online. I added such a text to the table now. In general, I think we 
won't derive these rules from primary datasets, but mostly from already curated 
(albeit unstructured) and authoritative sources.

> It might also be interesting to link to the evidence that motivated that 
> decision for which one would have to go to a different source e.g., 
>  or 
> 

I don't understand -- could you elaborate?

> It might help communicate the rules more clearly if you provide a label for 
> VKORC1 variants in the column "Germ-line genetic marker (as appearing in 
> source)" 

Done.

> The "level of evidence" and "clinical significance" columns are very 
> challenging things to assign. The level of evidence could be some 
> evidence-based ranking 
> (e.g.,
>  ) or a consensus-based scale (e.g., SORT, 
> ). I think that there is no 
> standard rating scale but that most will agree some kind of rating is 
> important. So, it might make sense to include a triple that has the rating 
> and metadata describing the scale used and who did the rating. 

There exist some evidence classification schemes in the pharmacogenomics domain 
(e.g. from PharmGKB, of course). I documented the PharmGKB schemes at 
https://docs.google.com/spreadsheet/pub?hl=en_US&key=0AiGT-vnkGcoLdFFVMEdqcFdYaDFqS0xHTnlUT0N3cEE&hl=en_US&gid=1
 (values in the decision table are auto-completed based on the entities there). 
I guess for this project we should standardize to using a single scale, rather 
than mixing different scales. 

TODO: Would you (or someone else) be interested in looking into these 
classification schemes to see what would fit best? Are some of these schemes 
available as ontologies, e.g. via BioPortal? However, I guess we should at 
least retain some compatibility with PharmGKB, CPIC and other such initiatives!


Cheers,
Matthias

[1] 
https://docs.google.com/spreadsheet/pub?hl=en_US&hl=en_US&key=0AiGT-vnkGcoLdFFVMEdqcFdYaDFqS0xHTnlUT0N3cEE&single=true&gid=3&output=html







From: Richard Boyce 
Sent: Thursday, April 26, 2012 8:26 PM
To: public-semweb-lifesci@w3.org 
Subject: Re: Minutes from Clinical Decision Support teleconference


I wanted to first thank Matthias and the CDS group for doing a very nice job on 
some initial OWL and SPARQL rules for pharmacogenomic clinical decision support 
[1]. I had a few comments and questions regarding the rules...

Questions:

- Were the entries blank in "Germ-line genetic marker (curated SNPs)" because 
the 2C9 variants were not present in a curated resource?

- What is the meaning of the evidence column? I could imagine assigning and 
evidence type, an OBI description of the study from which the evidence was 
derived, or a citation. Thinking about the big picture, it would be neat if the 
evidence was a URI or SPARQL query to an annotation of the text (human or 
computer) complete with metadata on when the annotation was created and the 
expertise of the group providing the annotation. Perhaps there should be both 
an entry for the annotation and metadata about the scientific provenance of the 
data from which the rule was derived. In this case, the scientific provenance 
would be that the statement came from a decision made by an authoritative 
source (the FDA). It might also be interesting to link to the evidence that 
motivated that decision for which one would have to go to a different source 
e.g.,  or 


Comments:

- It might help communicate the rules more clearly if you provide a label for 
VKORC1 variants in the column "Germ-line genetic marker (as appearing in 
source)" 

- I think 

Re: Teleconference Reminder: Clinical Decision Support for Personalized Medicine

[Matthias Samwald]

Hi Jerven,
(CCing the mailing list)

Yes, I experimented with SPIN a lot.
The idea of simple SPARQL rules is to be a *simple* alternative to SPIN that 
is very easy to understand and to implement. SPIN is powerful, but also very 
complex, and the RDF serialization of SPARQL queries and templates can 
easily make generating SPIN rules quite awkward. Simple SPARQL Rules can be 
implemented with any triplestore or RDF application within minutes, while 
implementations of SPIN are still rather sparse (as far as I know there is 
only the Jena-based reference implementation by TopQuadrant, and a partial 
implemntation in recent versions of AllegroGraph).


Cheers,
Matthias

--
From: "Jerven Bolleman" 
Sent: Thursday, April 26, 2012 4:44 PM
To: "Matthias Samwald" 
Subject: Re: Teleconference Reminder: Clinical Decision Support for 
Personalized Medicine



Hi Matthias,

Have you  had a look at SPIN inferencing? Quite similar to your Simple
SPARQL rules. Except seems to be much more complete.
www.spinrdf.org

Regards,
Jerven

On Thu, Apr 26, 2012 at 12:16 PM, Matthias Samwald
 wrote:

Dear all,

This is a reminder of the CDS telecon today at 11am EST (17:00 Central
European Time). Agenda:

Discussing Matthias' "Simple SPARQL Rules" (A very light-weight approach 
to

formulating rules for decision support and other purposes with SPARQL
queries). First version of the ontology: http://purl.org/zen/ssr.ttl
Pharmacogenomics Decision Support Table in Google Docs that automatically
generates Simple SPARQL Rules for decision support based on the
Translational Medicine Ontology(and its pharmacogenomics extensions) -
https://docs.google.com/spreadsheet/pub?hl=en_US&hl=en_US&key=0AiGT-vnkGcoLdFFVMEdqcFdYaDFqS0xHTnlUT0N3cEE&single=true&gid=3&output=html
Feedback and discussion
Other topics suggested by participants

Cheers,
Matthias




''' Conference Details'''
 Clinical Decision Support for Personalized Medicine
 http://www.w3.org/wiki/HCLSIG/CDS

 Date of Call: Thursday April 26 2012

 Time of Call: 11:00am - 12:00pm ET
 Dial-In #: +1.617.761.6200 (Cambridge, MA)
 Dial-In #: +33.4.26.46.79.03 (Paris, France)
 Dial-In #: +44.203.318.0479 (London, UK)
 Participant Access Code: 4257 ("HCLS")
 IRC Channel: irc.w3.org port 6665 channel #HCLS (see
[http://www.w3.org/Project/IRC/ W3C IRC page] for details, or see
[http://cgi.w3.org/member-bin/irc/irc.cgi Web IRC])
 Mibbit quick start: Click on
[http://www.mibbit.com/chat/?server=irc.w3.org:6665&channel=%23hcls 
mibbit]

for instant IRC access
 Duration: 1h
 Convener: Matthias Samwald

''' Agenda'''
* "Simple SPARQL Rules" - First version of the ontology:
http://purl.org/zen/ssr.ttl
* Pharmacogenomics Decision Support Table in Google Docs that 
automatically

generates Simple SPARQL Rules for decision support based on the
Translational Medicine Ontology(and its pharmacogenomics extensions)
* Feedback and discussion

* Other topics suggested by participants




--
Jerven Bolleman
m...@jerven.eu

Teleconference Reminder: Clinical Decision Support for Personalized Medicine

[Matthias Samwald]

Dear all,

This is a reminder of the CDS telecon today at 11am EST (17:00 Central European 
Time). Agenda:
  a.. Discussing Matthias' "Simple SPARQL Rules" (A very light-weight approach 
to formulating rules for decision support and other purposes with SPARQL 
queries). First version of the ontology: http://purl.org/zen/ssr.ttl 
  b.. Pharmacogenomics Decision Support Table in Google Docs that automatically 
generates Simple SPARQL Rules for decision support based on the Translational 
Medicine Ontology(and its pharmacogenomics extensions) - 
https://docs.google.com/spreadsheet/pub?hl=en_US&hl=en_US&key=0AiGT-vnkGcoLdFFVMEdqcFdYaDFqS0xHTnlUT0N3cEE&single=true&gid=3&output=html
 
  c.. Feedback and discussion 
  d.. Other topics suggested by participants
Cheers,
Matthias


 

''' Conference Details''' 
 Clinical Decision Support for Personalized Medicine
 http://www.w3.org/wiki/HCLSIG/CDS
 
 Date of Call: Thursday April 26 2012
 Time of Call: 11:00am - 12:00pm ET 
 Dial-In #: +1.617.761.6200 (Cambridge, MA) 
 Dial-In #: +33.4.26.46.79.03 (Paris, France) 
 Dial-In #: +44.203.318.0479 (London, UK) 
 Participant Access Code: 4257 ("HCLS")
 IRC Channel: irc.w3.org port 6665 channel #HCLS (see 
[http://www.w3.org/Project/IRC/ W3C IRC page] for details, or see 
[http://cgi.w3.org/member-bin/irc/irc.cgi Web IRC]) 
 Mibbit quick start: Click on 
[http://www.mibbit.com/chat/?server=irc.w3.org:6665&channel=%23hcls mibbit] for 
instant IRC access
 Duration: 1h 
 Convener: Matthias Samwald

''' Agenda'''
* "Simple SPARQL Rules" - First version of the ontology: 
http://purl.org/zen/ssr.ttl
* Pharmacogenomics Decision Support Table in Google Docs that automatically 
generates Simple SPARQL Rules for decision support based on the Translational 
Medicine Ontology(and its pharmacogenomics extensions)
* Feedback and discussion
* Other topics suggested by participants

Re: Telcon Schedule.... logistics

[Matthias Samwald]

This sounds like a good idea, Elgar (especially since we already have a Google 
Calendar that is poorly advertised and not updated when meetings are 
cancelled). It also seems like you can change the description of each event 
separately (even though they are recurring), so the agenda could probably also 
be kept in these event descriptions.

I think an automated reminder 1 day prior  the event could be sufficient (and 
would keep the number of reminders per week at a bearable level). Looking at 
the Google calendar, on average there seem to be one teleconference per working 
day at the moment! 

 - Matthias


From: Elgar Pichler 
Sent: Thursday, April 19, 2012 8:51 PM
To: Michel Dumontier 
Cc: Joanne Luciano ; Helena Deus ; public-semweb-lifesci hcls ; M. Scott 
Marshall 
Subject: Re: Telcon Schedule logistics


I personally am a fan of Google Calendar, and all the problems described in 
this thread could be solved with it. Why not 
  a.. Task and HCLS chairs should set up the proper recurring events on Google 
Calendar. 
  b.. Explicitly set the time zone for those events. 
  c.. Then explicitly invite "public-semweb-lifesci hcls" 
 to each recurring event. 
  d.. Add reminders for 1d and 1h prior to event (or set those 2 reminders as 
default for the HCLS calendar overall). 
  e.. Change the agenda for the single events as needed, or cancel a single 
event if the meeting is off. 
Doing that will insure that
  a.. the event/agenda is up to date 
  b.. time zone differences will be handled automatically 
  c.. event updates and cancellations will be sent to the 
 list 
  d.. reminders will be sent automatically to the 
 list 
  e.. (Google) users who poll the HCLS calendar will always get the correct and 
most up to date events on their calendar, at the correct time slot.
That doesn't take care of the wiki yet, but maybe we could do a Google Calendar 
display or list of events feed on our wiki pages. 
(http://support.google.com/calendar/bin/answer.py?hl=en&answer=1186917#site)


Cheers,
Elgar




On Thu, Apr 19, 2012 at 13:24, Michel Dumontier  
wrote:

  Hi!
Each call has a reserved time slot, but the reminders are the official 
declaration that a meeting will happen. Task and HCLS chairs should prepare and 
send out the agenda no later than the day prior (and preferably a week before). 
I have to apologize, as I have been traveling extensively in April to far 
flung places in Canada with poor Internet.  I'll be resuming my regular calls 
as of May 1.
 Cheers,
  m.


  On 2012-04-19, at 12:05 PM, Joanne Luciano  wrote:


Hi Helena, 


I'm very appreciative of the reminders +1


I'd like the wiki to be reliable too. (I think may have I've 
over-compensated and missed too many meetings in the past - now I'm showing up 
when it scheduled and there's no call (although Matthias also dialed in.)


Joanne




On Apr 19, 2012, at 11:59 AM, Helena Deus wrote:


  I agree with Joanne, the calendar can't entirely be trusted so the most 
distracted among us will need a reminder from the chairs as to when these hcls 
telcos happen :)


  On Thu, Apr 19, 2012 at 4:53 PM, Joanne Luciano  
wrote:

Hi Michele, Scott,


I dialed into the the telcon today, 2nd time this happened recently and 
it was only Matthias and me that were there. No reminder was sent, but we do 
have a regularly scheduled telcon, so I made sure to catch an early train so I 
could be back at my desk in time.   So, are we having regularly scheduled 
telcons or are we having telcons only when reminders are sent?  (Just so I can 
plan accordingly)


I'm needing to schedule a meeting and need to know if there's going to 
be a call this coming Tuesday (April 24th).  The Wiki isn't clear re: Linked 
Life Data -- Is "Tuesday at 12pm EST"  every Tuesday (in which it would be goo 
to have the plural (or to be explicit) or is it once a month?
Is Maximizing the utility -- the un-indentation and bullets are 
confusing -- I'd fix, but I don't know what's correct.


Thanks!!!


Joanne


I'm also confused as to whether there is a meeting this coming tuesday. 
 I can't tell from the Wiki -- 
Life Sciences 
Maximizing the utility of linked life science data, ontologies and 
services. 
2nd Tuesday at 11am EST. Next call May 8, 2012.
  a.. Linked Life Data: Best practices in creating, publishing, 
linking, querying and visualizing linked life data. Tuesday at 12pm EST. 








  -- 
  Helena F. Deus 
  Post-Doctoral Researcher at DERI/NUIG
  http://lenadeus.info/

Re: Teleconference Reminder: Clinical Decision Support for Personalized Medicine

[Matthias Samwald]

A a point of discussion for today's meeting, here is the source of an extension 
to TMO that describes the variants of the approx. 380 core pharmacogenomics 
biomarkers in dbSNP:
http://code.google.com/p/translationalmedicineontology/source/browse/trunk/ontology/extensions/dbsnp_pharmacogenomics_core.ttl

I created that file with a script that parses the output produced by the dbSNP 
batch query service at http://www.ncbi.nlm.nih.gov/projects/SNP/batchquery.html

@EricP: The namespace for this extension is still not settled -- maybe we could 
use a W3C namespace as we did for the TMO ontology itself?
@Michel: I tried to link to your Bio2RDF version of dbSNP, currently only via 
rdfs:seeAlso links to your dev server (the data still does not seem to be 
available on the public Bio2RDF server. We should try to do this properly as 
soon as possible.

 - Matthias



From: Matthias Samwald 
Sent: Thursday, April 12, 2012 10:55 AM
To: public-semweb-lifesci@w3.org 
Cc: Gökhan Karakülah 
Subject: Teleconference Reminder: Clinical Decision Support for Personalized 
Medicine


Dear all,

The CDS telecon today at 11am EST (17:00 Central European Time) will focus on 
advancing the "big pharmacogenomics paper" that some of us have been working on 
(trying to demonstrate RDF-based pharmacogenomics data integration and decision 
support). If you have pharmacogenomic data in RDF / Linked Data format, it 
would be great if you could join -- maybe we could integrate your data into our 
demo.

Cheers,
Matthias


''' Conference Details''' 
 Clinical Decision Support for Personalized Medicine
 http://www.w3.org/wiki/HCLSIG/CDS
 
 Date of Call: Thursday April 12 2012
 Time of Call: 11:00am - 12:00pm ET 
 Dial-In #: +1.617.761.6200 (Cambridge, MA) 
 Dial-In #: +33.4.26.46.79.03 (Paris, France) 
 Dial-In #: +44.203.318.0479 (London, UK) 
 Participant Access Code: 4257 ("HCLS")
 IRC Channel: irc.w3.org port 6665 channel #HCLS (see 
[http://www.w3.org/Project/IRC/ W3C IRC page] for details, or see 
[http://cgi.w3.org/member-bin/irc/irc.cgi Web IRC]) 
 Mibbit quick start: Click on 
[http://www.mibbit.com/chat/?server=irc.w3.org:6665&channel=%23hcls mibbit] for 
instant IRC access
 Duration: 1h 
 Convener: Matthias Samwald

''' Agenda'''
* Advancing the "big pharmacogenomics paper" that some of us have been working 
on (for pharmacogenomics data integration and RDF-based decision support).
* Other topics suggested by participants.

Teleconference Reminder: Clinical Decision Support for Personalized Medicine

[Matthias Samwald]

Dear all,

The CDS telecon today at 11am EST (17:00 Central European Time) will focus on 
advancing the "big pharmacogenomics paper" that some of us have been working on 
(trying to demonstrate RDF-based pharmacogenomics data integration and decision 
support). If you have pharmacogenomic data in RDF / Linked Data format, it 
would be great if you could join -- maybe we could integrate your data into our 
demo.

Cheers,
Matthias


''' Conference Details''' 
 Clinical Decision Support for Personalized Medicine
 http://www.w3.org/wiki/HCLSIG/CDS
 
 Date of Call: Thursday April 12 2012
 Time of Call: 11:00am - 12:00pm ET 
 Dial-In #: +1.617.761.6200 (Cambridge, MA) 
 Dial-In #: +33.4.26.46.79.03 (Paris, France) 
 Dial-In #: +44.203.318.0479 (London, UK) 
 Participant Access Code: 4257 ("HCLS")
 IRC Channel: irc.w3.org port 6665 channel #HCLS (see 
[http://www.w3.org/Project/IRC/ W3C IRC page] for details, or see 
[http://cgi.w3.org/member-bin/irc/irc.cgi Web IRC]) 
 Mibbit quick start: Click on 
[http://www.mibbit.com/chat/?server=irc.w3.org:6665&channel=%23hcls mibbit] for 
instant IRC access
 Duration: 1h 
 Convener: Matthias Samwald

''' Agenda'''
* Advancing the "big pharmacogenomics paper" that some of us have been working 
on (for pharmacogenomics data integration and RDF-based decision support).
* Other topics suggested by participants.

Teleconfereced today cancelled -- W3C HCLS Task Force: Clinical Decision Support for Personalized Medicine

[Matthias Samwald]

Dear all,

The CDS call today is cancelled -- several people (including myself) are still 
at the AMIA Summit and can't make it.

Cheers,
Matthias

Re: HCLS - visualization task force?

[Matthias Samwald]

Regarding visualisation of Linked Data, it should be avoided to fall victim to 
what was called "the pathetic fallacy of RDF" in one publication [1], i.e., 
visualising RDF data as graphs because the underlying datamodel is a graph, not 
because the use-case at hand requires this kind of visualisation (many do not).

[1] http://eprints.ecs.soton.ac.uk/12911/1/the_pathetic_fallacy_of_rdf-33.html

I have not found many _generic_ RDF visualisations that would even be remotely 
useful to end-users. However, if tailored/specialised SPARQL queries are needed 
to distil the data for visualisation, I wonder if visualisation of data from 
Linked Data sources is so much different from visualizing other kinds of 
complex data (?)

Cheers,
Mattias Samwald




From: Helena Deus 
Sent: Tuesday, March 13, 2012 7:37 PM
To: Luciano, Joanne Sylvia ; Eric Pru'dhommeaux 
Cc: Chris Baker ; Michel Dumontier ; w3c semweb hcls 
Subject: Re: HCLS - visualization task force?


Hi all,  


During the telco today Eric mentioned  http://www.distilbio.com/ , which was 
apparently built on top of exhibit3, seems like a great way to start.


I would propose not to limit ourselves to "ways to visualize RDF graphs", but 
to actually try to plug linked data into data visualization paradigms already 
widely adopted, like dendrograms, heatmaps, sunburst plots, etc


Example of a heatmap built from a SPARQL query (medicines VS their classes):

http://mathbiol-lena.googlecode.com/hg/dendroheat/dendroheat_cma.html 



Finally, in the same lime of thinking,  a TED talk by Jer Thorp (NYT) about 
visualization 
-http://www.youtube.com/watch?feature=player_embedded&v=Q9wcvFkWpsM



There's lots of really REALLY cool js libraries that we could use for very 
quickly prototyping!
Best, 
Lena



On Tue, Mar 13, 2012 at 5:12 PM, Luciano, Joanne Sylvia  wrote:

  Michel,

  A task force on visualization is a great idea.  And it would make sense to 
have it aimed at and work with helping each of the other task forces utilize 
visualization capabilities.  It's something I've been thinking about with 
respect to the work we did on the TMO/TMKB. How do we demonstrate beyond sparql 
queries?

  cheers,
  joanne


  On Mar 13, 2012, at 12:58 PM, Chris Baker wrote:

  > Related to this topic .
  >
  > Changing the Equation on Scientific Data Visualization
  > by: Peter Fox, James Hendler
  > http://www.sciencemag.org/content/331/6018/705
  >
  > The changing face of visualisation in a world of data intensive science.
  > http://eresearchau.files.wordpress.com/2011/11/peter-fox.pdf
  >
  > On Tue, Mar 13, 2012 at 1:15 PM, Michel Dumontier
  >  wrote:
  >>
  >> Hi all,
  >>   At today's HCLS Life Sciences Forum (see minutes [1]) we had Alex Garcia 
present on the topic of RDF visualization, indeed important for the whole of 
the HCLS community. In addition to a Semantic Web Journal review article [2], 
is anybody aware of comprehensive lists of use-cases for human computer 
interaction with semantic web data (e.g. browse, search, query, discovery)?
  >>
  >>   Second, I would like to gauge the interest of our community in 
visualization, and whether it would be worthwhile to set up a task force around 
HCLS visualization (use cases, requirements, tools and technologies, 
collaborative development, deployment, evaluation). Please reply indicating 
your interest.
  >>
  >> Cheers!
  >>
  >> m.
  >>
  >> [1] http://www.w3.org/2012/03/13-HCLS-minutes.html
  >> [2] http://iospress.metapress.com/content/2822p340453463g1
  >>
  >>
  >> --
  >> Michel Dumontier
  >> Associate Professor of Bioinformatics, Carleton University
  >> Visiting Associate Professor, Stanford University
  >> Chair, W3C Semantic Web for Health Care and the Life Sciences Interest 
Group
  >> http://dumontierlab.com
  >>
  >
  >
  >
  > --
  > Christopher J. O. Baker Ph. D.
  > Associate Professor
  > Dept. Computer Science and Applied Statistics
  > University of New Brunswick, Canada
  > http://ca.linkedin.com/in/christopherjobaker
  >









-- 
Helena F. Deus 
Post-Doctoral Researcher at DERI/NUIG
http://lenadeus.info/

W3C HCLS Task Force: Clinical Decision Support for Personalized Medicine

[Matthias Samwald]

Dear all,

Please join us this Thursday at 11am EST (17:00 Central European Time) to 
discuss how we can use semantic technologies for realizing personalized, 
molecular medicine through computational decision support. This is the first 
teleconference of this new task force, so feel free to contribute your ideas 
and help to shape the work that will be done over the next year!

http://www.w3.org/wiki/HCLSIG/CDS

Cheers,
Matthias Samwald



Conference Details
 Clinical Decision Support for Personalized Medicine
 http://www.w3.org/wiki/HCLSIG/CDS
 
 Date of Call: Thursday March 8 2012
 Time of Call: 11:00am - 12:00pm ET 
 Dial-In #: +1.617.761.6200 (Cambridge, MA) 
 Dial-In #: +33.4.26.46.79.03 (Paris, France) 
 Dial-In #: +44.203.318.0479 (London, UK) 
 Participant Access Code: 4257 ("HCLS")
 IRC Channel: irc.w3.org port 6665 channel #HCLS (see 
[http://www.w3.org/Project/IRC/ W3C IRC page] for details, or see 
[http://cgi.w3.org/member-bin/irc/irc.cgi Web IRC]) 
 Mibbit quick start: Click on 
[http://www.mibbit.com/chat/?server=irc.w3.org:6665&channel=%23hcls mibbit] for 
instant IRC access
 Duration: 1h 
 Convener: Matthias Samwald

Agenda
* Overview
* Three major proposed use-cases:
** OWL and SPARQL Rules for Pharmacogenomic Clinical Decision Support 
** Embedding semantic technologies in clinical environments (alignment with HL7 
and OpenCDS)
** Biomedical Linked Data for targeted cancer therapy
* Ideas and suggestions from participants

Re: TM conference call -- cancelled

[Matthias Samwald]

Several people sent their regrets, so we will cancel the teleconference today. 
I suggest we coordinate further action via the mailing list or Google Group.

The next teleconference will be on January 5 next year.

Cheers,
Matthias


From: Matthias Samwald 
Sent: Wednesday, December 21, 2011 3:04 PM
To: public-semweb-lifesci@w3.org 
Subject: TM conference call this Thursday, minutes from last week


Here is a reminder for the TM conference call this Thursday -- the last one of 
this year!

''' Conference Details''' 
 * Date of Call: Thursday December 21 2011 
 * Time of Call: 12:00pm - 1:00pm ET 
 * Dial-In #: +1.617.761.6200 (Cambridge, MA) 
 * Dial-In #: +33.4.26.46.79.03 (Paris, France) 
 * Dial-In #: +44.203.318.0479 (London, UK) 
 * Participant Access Code: 42572 ("HCLS2") 
 * IRC Channel: irc.w3.org port 6665 channel #HCLS2 (see 
[http://www.w3.org/Project/IRC/ W3C IRC page] for details, or see 
[http://cgi.w3.org/member-bin/irc/irc.cgi Web IRC]) 
 * Mibbit quick start: Click on 
[http://www.mibbit.com/chat/?server=irc.w3.org:6665&channel=%23hcls2 mibbit] 
for instant IRC access
 * Duration: 1h 
 * Convener: Matthias

''' Agenda'''
Work on a submission to the ICBO2012 conference on extending the Translational 
Medicine Ontology for pharmacogenomics and personalized medicine and applying 
OWL reasoning for clinical decision support.

''' Minutes '''
Thanks to Bob Powers for scribing the minutes for last week: 
http://www.w3.org/2011/12/15-hcls2-minutes.html


Cheers,
Matthias Samwald

Re: Evidence of Significance of Semantic Web for Life Sciences

[Matthias Samwald]

Hi Lena,

"Although this was not achieved using the LODD cloud or semantic web 
technologies, it illustrates the same type of network analysis that we are 
trying to enable for linked life sciences and health care data. "

Then it is a problematic example -- after all this could also be interpreted as 
an illustration of how such things can be achieved without SW technologies!

 - Matthias


From: Helena Deus 
Sent: Thursday, December 22, 2011 1:16 PM
To: Oliver Ruebenacker 
Cc: public-semweb-lifesci 
Subject: Re: Evidence of Significance of Semantic Web for Life Sciences


Hi Oliver, 


Related example:
http://www.sciencenews.org/view/generic/id/337088/title/Network_analysis_predicts_drug_side_effects?utm_medium=referral&utm_source=pulsenews
 


“To clear some of the haze surrounding side effects, scientists from Harvard 
Medical School and Children’s Hospital Boston created a network linking 809 
medications to 852 side effects that were known as of 2005. The team also added 
information to their network on chemical properties, such as the drug’s melting 
point and molecular weight, and where the drug does its stuff in the body. 
Using these data and relationships alone, the computer predicted side effects 
that were reported in later years, such as the seizure drug zonisamide causing 
suicidal thoughts in some people and the antibiotic norfloxacin’s link to 
ruptured tendons. It also linked the controversial diabetes drug Avandia 
(rosiglitazone) to heart attacks, a connection that is supported by some 
research.”




Although this was not achieved using the LODD cloud or semantic web 
technologies, it illustrates the same type of network analysis that we are 
trying to enable for linked life sciences and health care data. 


Best,
Lena


On Wed, Dec 21, 2011 at 4:39 PM, Oliver Ruebenacker  wrote:

  Hello,

   I am looking for evidence I can quote to convince non-experts of the
  significance of applying Semantic Web to biomedical research,
  especially computational cell biology.

   I need a recorded public statement from a source recognizable as
  authoritative to a non-expert: e.g. could be from a relevant
  government agency, a well-known research institution (including major
  grad schools and companies), a well-known (i.e. well-known outside the
  field) expert, some one where a brief look at the biography
  immediately suggests he or she is an authority, some one quoted in
  major media, etc.

   Significance could mean abstract things like advancing science and
  health care, but even better would be tangible things like: saves
  lives, saves money, cures cancer/malaria/AIDS, creates jobs, etc.

   Thanks a lot!

  Take care
  Oliver

  --
  Oliver Ruebenacker, Computational Cell Biologist
  Virtual Cell (http://vcell.org)
  SBPAX: Turning Bio Knowledge into Math Models (http://www.sbpax.org)
  http://www.oliver.curiousworld.org







-- 
Helena F. Deus 
Post-Doctoral Researcher at DERI/NUIG
http://lenadeus.info/

TM conference call this Thursday, minutes from last week

[Matthias Samwald]

Here is a reminder for the TM conference call this Thursday -- the last one of 
this year!

''' Conference Details''' 
 * Date of Call: Thursday December 21 2011 
 * Time of Call: 12:00pm - 1:00pm ET 
 * Dial-In #: +1.617.761.6200 (Cambridge, MA) 
 * Dial-In #: +33.4.26.46.79.03 (Paris, France) 
 * Dial-In #: +44.203.318.0479 (London, UK) 
 * Participant Access Code: 42572 ("HCLS2") 
 * IRC Channel: irc.w3.org port 6665 channel #HCLS2 (see 
[http://www.w3.org/Project/IRC/ W3C IRC page] for details, or see 
[http://cgi.w3.org/member-bin/irc/irc.cgi Web IRC]) 
 * Mibbit quick start: Click on 
[http://www.mibbit.com/chat/?server=irc.w3.org:6665&channel=%23hcls2 mibbit] 
for instant IRC access
 * Duration: 1h 
 * Convener: Matthias

''' Agenda'''
Work on a submission to the ICBO2012 conference on extending the Translational 
Medicine Ontology for pharmacogenomics and personalized medicine and applying 
OWL reasoning for clinical decision support.

''' Minutes '''
Thanks to Bob Powers for scribing the minutes for last week: 
http://www.w3.org/2011/12/15-hcls2-minutes.html


Cheers,
Matthias Samwald

Reminder: TM teleconference call on Thursday

[Matthias Samwald]

Dear colleagues, 

Please join us tomorrow for a TM call focused on extending the translational 
medicine ontology with pharmacogenomics terms. Please review current terms in 
TMO and try to add required new terms to the Google-Docs spreadsheet [1] 
(notify me if you don't have access but feel like you can contribute). 

The current terms in TMO are listed in the second and third sheet of that 
document. The goal is to finalize the extension of the TMO and to demonstrate 
querying and reasoning functionality based on TMO for clinical decision support 
in the context of personalized medicine. Our achievements should be documented 
in a submission to International Conference on Biomedical Ontology (ICBO) -- 
the submission deadline is January 31.

[1] 
https://docs.google.com/spreadsheet/ccc?key=0AiGT-vnkGcoLdEJrOTU4blAtME04S3plUW5XQ1FwcHc&hl=en_US#gid=0

Cheers,
Matthias


''' Conference Details''' 
 * Date of Call: Thursday December 14 2011 
 * Time of Call: 12:00pm - 1:00pm ET 
 * Dial-In #: +1.617.761.6200 (Cambridge, MA) 
 * Dial-In #: +33.4.26.46.79.03 (Paris, France) 
 * Dial-In #: +44.203.318.0479 (London, UK) 
 * Participant Access Code: 42572 ("HCLS2") 
 * IRC Channel: irc.w3.org port 6665 channel #HCLS2 (see 
[http://www.w3.org/Project/IRC/ W3C IRC page] for details, or see 
[http://cgi.w3.org/member-bin/irc/irc.cgi Web IRC]) 
 * Mibbit quick start: Click on 
[http://www.mibbit.com/chat/?server=irc.w3.org:6665&channel=%23hcls2 mibbit] 
for instant IRC access
 * Duration: 1h 
 * Convener: Matthias Samwald

No TM teleconference call this week

[Matthias Samwald]

Dear all,

I will will in for Michel in chairing the remaining the remaining TM 
teleconferences this month (he is travelling).
There will be no TM teleconference this week because of SWAT4LS and the fact 
that Thursday is a Holiday in some European countries.

The next TM teleconference will be next week on December 15.

With kind regards,
Matthias Samwald

Re: A new potential HCLS use case (scientific discourse)

[Matthias Samwald]

I think we should find some mode of operation where all the documents are in 
the wiki. The split between wiki and Google-Docs seems problematic (especially 
when each use-case doc is shared differently).

 - Matthias



From: Michel Dumontier 
Sent: Sunday, October 09, 2011 10:18 PM
To: boy...@u.washington.edu 
Cc: public-semweb-lifesci@w3.org 
Subject: Re: A new potential HCLS use case (scientific discourse)


Super! I put the use case in a google document for any to comment: 


https://docs.google.com/document/d/1QpW-axtGL7Tuhd_Zcaf30a4-s4S_lveIJtpKL5QBLfQ/edit?hl=en_US


m.


On Thu, Oct 6, 2011 at 7:30 AM, Richard Boyce  wrote:

  In response to the recent request, I have attached a draft of a new potential 
HCLS  use case focused especially on scientific discourse.

  Any comments, critiques, or suggestions would be welcome.

  kind regards,

  Richard Boyce, PhD
  Assistant Professor of Biomedical Informatics
  Scholar, Comparative Effectiveness Research Program
  University of Pittsburgh
  rd...@pitt.edu
  412-648-6768



  On 09/26/2011 09:15 AM, Waard, Anita de A (ELS-AMS) wrote:

Dear all,

Further to the first agenda point, use cases, for our call in 42 minutes, 
I'd like to review:

a) The new HCLS Use Case template which can be found here: 
https://docs.google.com/document/d/1DRnwXw7xIOLTjZ4TUiDtT80ouSQYfUqM9KWKXVgr60s/edit?hl=en_US

b) Our current three use cases: 
http://www.w3.org/wiki/HCLSIG/SWANSIOC/Actions/RhetoricalStructure#Use_Cases

and ask ourselves and each other:

1) Are these use cases still valid, or have they been addressed by our work 
so far?
2) If they are valid, how can we get them to be compliant with the new 
format: can someone take on each use cases?
3) If there's time: brainstorm about other use cases, or otherwise make a 
plan to gather more use cases before the next meeting.

Talk in a bit! Best,

- Anita.

Anita de Waard
Disruptive Technologies Director, Elsevier Labs
http://elsatglabs.com/labs/anita/
a.dewa...@elsevier.com



-Original Message-
From: Tim Clark [mailto:tim.cl...@rcn.com]
Sent: Fri 9/23/2011 11:04
To: HCLS IG; scidiscou...@googlegroups.com
Cc: Alberto Accomazzi; Allen, Bradley P (ELS-SDG); Sophia Ananiadou; Philip 
Bourne; Gully Burns; Daniel, Ronald (ELS-SDG); Rahul Dave; Waard, Anita de A 
(ELS-AMS); Alf Eaton; Alexander Garcia Castro; Matthew Gamble; Yolanda Gil; 
Alyssa Goodman; Paul Groth; Tudor Groza; Hays, Ellen (ELS-BUR); Maryann 
Martone; David R Newman; Scerri, Antony (ELS-CAM); Jack Park; Silvio Peroni; 
Steve Pettifer; Philippe Rocca-Serra; Cartic Ramakrishnan; Jodi Schneider; 
David Shotton; Kaitlin Thaney; Karin Verspoor; Lynette Hirschman; 
Susanna-Assunta Sansone; Kees van Bochove; Katy Wolstencroft; Jun Zhao
Subject: Reminder: HCLS Sci Disc call - ISA-RDF&  Use Case Review- Mon 26 
Sept 10am-11am EDT / 14:00-15:00 UTC

Colleagues:

This is a reminder for the biweekly HCLS Scientific Discourse concall 
scheduled for Monday, 26 Sept 10am-11am EDT / 14:00-15:00 UTC.

As discussed in the previous call, we'll be focusing on defined tasks and 
use cases for the coming year.

- we will begin a review and update of our use cases

- ISA-RDF will be discussed as a potential shared task for 2011-12 (see 
underlying ISA-TAB project here:  http://isa-tools.org/  for some background)
 Dial-in&  IRC Information

Dial-In #: +1.617.761.6200 (Cambridge, MA)
Dial-In #: +33.4.26.46.79.03 (Paris, France)
Dial-In #: +44.203.318.0479 (London, UK)
Participant Access Code: 42572 ("HCLS2")
IRC Channel: irc.w3.org port 6665 channel #HCLS2 use IRC direct link or 
(see W3C IRC page for details, or see Web IRC)
Mibbit quick start: Click on mibbit for instant IRC access
Duration: 1hr
Best

Tim



Elsevier B.V. Registered Office: Radarweg 29, 1043 NX Amsterdam, The 
Netherlands, Registration No. 33156677 (The Netherlands)











-- 
Michel Dumontier
Associate Professor of Bioinformatics
Carleton University
http://dumontierlab.com

regrets -- Re: TM call

[Matthias Samwald]

Dear Michel, all,

I will not be available on Thursday during the entire day. Please go ahead and 
edit the manuscript where you see fit. Currently I am still pondering on the 
best visual metaphor for explaining how OWL reasoning can help with classifying 
individual patients into classes based on genetic and other clinical markers 
(preferably incorporating warfarin as an example). 
I can work on formatting and submitting the manuscript on Friday.

 - Matthias



From: Michel Dumontier 
Sent: Wednesday, September 28, 2011 7:19 PM
To: w3c semweb hcls 
Subject: TM call


Hi all,
  Just a friendly reminder for tomorrow's conference call. Please take a moment 
to read and review the short report and provide extensive comments to identify 
gaps and to contribute to the writing of the article.


Cheers!


m.


''' Conference Details''' 
 * Date of Call: Thursday September 29 2011 
 * Time of Call: 12:00pm - 1:00pm ET 
 * Dial-In #: +1.617.761.6200 (Cambridge, MA) 
 * Dial-In #: +33.4.26.46.79.03 (Paris, France) 
 * Dial-In #: +44.203.318.0479 (London, UK) 
 * Participant Access Code: 42572 ("HCLS2") 
 * IRC Channel: irc.w3.org port 6665 channel #HCLS2 (see 
[http://www.w3.org/Project/IRC/ W3C IRC page] for details, or see 
[http://cgi.w3.org/member-bin/irc/irc.cgi Web IRC]) 
 * Mibbit quick start: Click on 
[http://www.mibbit.com/chat/?server=irc.w3.org:6665&channel=%23hcls2 mibbit] 
for instant IRC access
 * Duration: 1h 
 * Convener: Michel



''' Agenda'''
* Short Report [matthias, michel]
* use cases and kb (snp) development [all]
* AOB


Minutes for last week's minutes are [http://www.w3.org/2011/09/22-hcls2-irc 
here]




-- 
Michel Dumontier
Associate Professor of Bioinformatics
Carleton University
http://dumontierlab.com

Re: "molar" for concentration

[Matthias Samwald]

Besides the ontologies already mentioned, the unit ontology / UO 
(http://obofoundry.org/cgi-bin/detail.cgi?id=unit) also has a class for "mole" 
and one for "molar mass unit". But you actually wanted a URI for a datatype so 
this (as well as the other ontologies mentioned before) is probably not what 
you wanted.

Does anybody know of an ontology that defines scientific datatypes in OWL 2?

 - Matthias



From: Helena Deus 
Sent: Tuesday, August 16, 2011 5:23 PM
To: W3C HCLSIG hcls 
Subject: "molar" for concentration


Hi all, 


Wondering if anyone ever needed/came across a URI for datatype "M" (molar, as 
in 10 M -> 10 Molar). 
http://en.wikipedia.org/wiki/Molar_concentration



Cheers,
-- 
Helena F. Deus 
Post-Doctoral Researcher at DERI/NUIG
http://lenadeus.info/

Re: Version 1.0 of Bio2RDF and Chembl webapps released

[Matthias Samwald]

I will look at it again. Is there an open source implementation by the
way? I have been using SPARQL CONSTRUCT queries to do virtually
everything that I thought SPIN could do, with a more familiar
notation. I didn't find the SPIN notation easy to understand.


Yes, the way SPARQL is formulated with RDF might be turn out to be a bit too 
complex.

They have an open source reference implementation built on the Jena API:
http://topbraid.org/spin/api/1.2.0/index.html

Never tried using so far, though.

Cheers,
Matthias 

Re: Version 1.0 of Bio2RDF and Chembl webapps released

[Matthias Samwald]

Hi Peter,

Great work! On the example page you provided 
(http://bio2rdf.org/page/geneid:12334) I also see properties such as 
http://purl.org/science/owl/sciencecommons/describes_gene_or_gene_product_mentioned_by 
which come from the Science Commons KB (and the HCLS Knowledge Base 
developed in the first charter of the HCLS interest group). Did those 
properties go into Bio2RDF because you imported some data from the Science 
Commons KB, or did you deliberately choose to re-use those properties 
because you considered them useful?



If you want to make changes to any of the datasources, you can
normalise results (and denormalise queries) using rules. This version
allows you to use XSLT and SPARQL in addition to Regular Expressions
that were already supported. For example this now means that if there
are XML datasources, you can convert them to RDF using the
normalisation rules in the server. The software now uses Sesame 2.4.0
which contains support for SPARQL Query 1.1 so any SPARQL rules that
are applied to intermediate results can be transformed using the new
functions and language features. In particular, SPARQL 1.1 allows you
to create new URIs inside queries, so if you know that there are
literals in an rdf document that you could create a URI out of, you
can do it using a SPARQL normalisation rule for that datasource.


Do you have an example of how this could be done with SPARQL 1.1?


In addition, if anyone wants to suggest a way to do any other rule
based normalisation I would be happy to extend the software to support
it. I have always had RIF rules in the back of my head, but have not
experimented with them yet. If anyone uses RIF rules in their work, it
would be great to get some example code to guide a future extension to
this software.


Did you consider using SPARQL Inference Notation (SPIN, 
http://spinrdf.org/)? I don't think there is an implementation for Sesame 
out there yet, though.


Cheers,
Matthias


--
From: "Peter Ansell" 
Sent: Thursday, June 30, 2011 8:58 AM
To: "Bio2Rdf Mailing List" ; "w3c semweb hcls" 


Subject: Version 1.0 of Bio2RDF and Chembl webapps released


Hi all,

The 1.0.1 version of the Bio2RDF server software has been released on
Sourceforge. The software is designed to be a Linked Data interface to
a range of RDF datasources, with the current examples being Bio2RDF
and Chembl. (There was a small bug fix needed to enable endpoint
round-robin between 1.0.0 and 1.0.1.)

The Bio2RDF version now contains 1655 namespaces, 111 query types, 455
data providers and 197 normalisation rules. In addition to the Bio2RDF
server interface [1], I made up a version suitable for browsing
through resources located in Egon Willighagen's Chembl RDF dataset [2]
from http://rdf.farmbio.uu.se/chembl/sparql . I picked this dataset as
it did not seem to have a linked data interface to go with its URIs.

If anyone has any other RDF or SPARQL datasets that they want to have
a linked data interface then feel free to either mention them and/or
experiment with the software yourself based on the Chembl sources (all
of the Bio2RDF and Chembl configuration files can be found in the
sourceforge Git repository at [3]). The Bio2RDF configuration files
may be easier to find examples in, but they are quite large, so you
may want to start by looking at how Chembl was implemented using the
software. The software is designed to merge data from different
locations, so if you want to do a mashup with the data you can make up
queries/providers/normalisation rules to do it and publish them as a
server configuration using the configuration interface in the server
(/admin/configuration/n3 , For example:
http://config.bio2rdf.org/admin/configuration/n3 ) so that others can
extend/integrate/re-use them easily in their own instances of the
software.

The HTML interface for the software is configurable using Apache
Velocity templates, so don't feel that you have to stick to the
current design if you want to reuse the software.

This version allows you to optionally perform 303 redirections along
with the in-built HTTP content negotiation using the Accept header.
This allows access to the results of queries in the following RDF
formats:

* RDF/XML - using /rdfxml/ or Accept:application/rdf+xml
** For example: http://bio2rdf.org/rdfxml/geneid:12334
* N3 - using /n3/ or Accept:text/rdf+n3
** For example: http://bio2rdf.org/n3/geneid:12334
* HTML and RDFa - using /page/ or Accept:text/html
** For example: http://bio2rdf.org/page/geneid:12334 (RDFa embedded in
the HTML representation)
* NTriples - /ntriples/ or Accept:text/plain
** For example: E.g. http://bio2rdf.org/ntriples/geneid:12334 (this
and the following two formats will not work until we actually do the
upgrade on bio2rdf.org in the next few days.)
* NQuads  - /nquads/ or Accept:text/x-nquads
** E.g. http://bio2rdf.org/nquads/geneid:12334 (The graph names match
the provider URI that the data came from. I.e., 

Re: HCLS chartering/next steps Thur 16 June

[Matthias Samwald]

Eric wrote:

Join me tomorrow at the usual time (11.00 EDT, 15.00Z)?


I somehow missed that sentence and was not aware of the HCLS telecon 
today -- sorry I didn't attend!


- Matthias 

Re: TM conference call

[Matthias Samwald]

The minutes of the teleconference can be viewed at 
http://www.w3.org/2011/06/09-hcls2-minutes.html

Thanks to Bob for scribing (once again!)

Cheers,
Matthias


From: Matthias Samwald 
Sent: Thursday, June 09, 2011 2:25 PM
To: public-semweb-lifesci@w3.org 
Subject: Re: TM conference call


Dear all,

This is a reminder for the TM conference call today. We will discuss and 
coordinate ongoing work around the pharmacogenomics paper, and check the 
progress we made with the various TODO items on our list.
 

Conference Details'
 * Date of Call: Thursday June 9 2011 
 * Time of Call: 12:00pm - 1:00pm ET (18:00 - 19:00 Central European Time)
 * Dial-In #: +1.617.761.6200 (Cambridge, MA) 
 * Dial-In #: +33.4.26.46.79.03 (Paris, France) 
 * Dial-In #: +44.203.318.0479 (London, UK) 
 * Participant Access Code: 42572 ("HCLS2") 
 * IRC Channel: irc.w3.org port 6665 channel #HCLS2 (see 
[http://www.w3.org/Project/IRC/ W3C IRC page] for details, or see 
[http://cgi.w3.org/member-bin/irc/irc.cgi Web IRC]) 
 * Mibbit quick start: Click on 
[http://www.mibbit.com/chat/?server=irc.w3.org:6665&channel=%23hcls2 mibbit] 
for instant IRC access
 * Duration: 1h 
 * Convener: Matthias 



''' Agenda'''
* Paper: warfarin predictive pharmacogenomics: overview of methods (Elgar)
* Paper: warfarin relevant text-mined relations: triples (Adrien, Iker)
* Paper: ontology: diagram + nomenclature (see 
http://85.48.202.13:8080/webprotege/ (requires login), 
https://docs.google.com/document/d/1BeaU3VJW1S_R3eB5ncrcW9wJ-lMU4xdmxCdjH8E0i5s/edit?hl=en_US
 and http://www.hgvs.org/mutnomen/recs.html) (Matthias, Adrien, Michel, Scott, 
BobF)
* Paper: conversion of warfarin pharmacogenomic data - http://bit.ly/k7Exjc 
(Joanne, etc)
* Paper: crawling RDF from SNPedia with a linked data crawler (Matthias)
* Paper: priority conversion of other data (discuss)
* Paper: kb development (Iker, EricP)

* Paper: opinions on renaming "Translational Medicine Ontology" to 
"Translational and Personalized Medicine Ontology"
* AOB



Unfortunately, Michel and Scott cannot join the meeting today.



Thanks to Bob Powers for scribing last week's 
[http://www.w3.org/2011/06/02-hcls2-minutes.html minutes]

 

 

Cheers,
Matthias Samwald

// http://samwald.info 

Re: TM conference call

[Matthias Samwald]

Dear all,

This is a reminder for the TM conference call today. We will discuss and 
coordinate ongoing work around the pharmacogenomics paper, and check the 
progress we made with the various TODO items on our list.
 

Conference Details'
 * Date of Call: Thursday June 9 2011 
 * Time of Call: 12:00pm - 1:00pm ET (18:00 - 19:00 Central European Time)
 * Dial-In #: +1.617.761.6200 (Cambridge, MA) 
 * Dial-In #: +33.4.26.46.79.03 (Paris, France) 
 * Dial-In #: +44.203.318.0479 (London, UK) 
 * Participant Access Code: 42572 ("HCLS2") 
 * IRC Channel: irc.w3.org port 6665 channel #HCLS2 (see 
[http://www.w3.org/Project/IRC/ W3C IRC page] for details, or see 
[http://cgi.w3.org/member-bin/irc/irc.cgi Web IRC]) 
 * Mibbit quick start: Click on 
[http://www.mibbit.com/chat/?server=irc.w3.org:6665&channel=%23hcls2 mibbit] 
for instant IRC access
 * Duration: 1h 
 * Convener: Matthias 



''' Agenda'''
* Paper: warfarin predictive pharmacogenomics: overview of methods (Elgar)
* Paper: warfarin relevant text-mined relations: triples (Adrien, Iker)
* Paper: ontology: diagram + nomenclature (see 
http://85.48.202.13:8080/webprotege/ (requires login), 
https://docs.google.com/document/d/1BeaU3VJW1S_R3eB5ncrcW9wJ-lMU4xdmxCdjH8E0i5s/edit?hl=en_US
 and http://www.hgvs.org/mutnomen/recs.html) (Matthias, Adrien, Michel, Scott, 
BobF)
* Paper: conversion of warfarin pharmacogenomic data - http://bit.ly/k7Exjc 
(Joanne, etc)
* Paper: crawling RDF from SNPedia with a linked data crawler (Matthias)
* Paper: priority conversion of other data (discuss)
* Paper: kb development (Iker, EricP)

* Paper: opinions on renaming "Translational Medicine Ontology" to 
"Translational and Personalized Medicine Ontology"
* AOB



Unfortunately, Michel and Scott cannot join the meeting today.



Thanks to Bob Powers for scribing last week's 
[http://www.w3.org/2011/06/02-hcls2-minutes.html minutes]

 

 

Cheers,
Matthias Samwald

// http://samwald.info 

Re: HCLS chartering/next steps Thur 26 May

[Matthias Samwald]

I agree with Tim's ideas. The different task forces should be problem-focused. 
This would also help to reduce the redundancy between task forces (for example, 
the original idea of BioRDF was mainly to convert biomedical data to RDF, but 
over the years this also became a major focus of other task forces such as 
LODD).

 - Matthias


From: Tim Clark 
Sent: Thursday, May 26, 2011 3:55 PM
To: HCLS IG 
Cc: Mikel Egaña Aranguren ; Helena Deus 
Subject: Re: HCLS chartering/next steps Thur 26 May


Dear HCLS colleagues 


I guess my comment would be, setting Translational Medicine as a major priority 
= ok, making it the only priority = not ok.   


TM applications are important, and do potentially integrate many of the things 
we have all been working on. But they are far from covering all the bases, and 
far from covering all the use cases of critical concern to people in my Task 
Group, Scientific Discourse. 


I'll just observe that since we launched the multiple task groups we have ended 
up with two kinds of groups:  


(1) Problem Centric, e.g. TM and Scientific Discourse 
(2) Solution Centric, e.g. LODD, BioRDF, Terminology


My personal recommendation would be to formulate the charter around 
accelerating biomedical research and promoting cross-discipline sharing, across 
the full scientific and clinical life cycle.  I would begin by dividing into 
several distinct problem focused areas. I would lose the solution-based Task 
Groups and reformulate them as problem-based.


for example, BioRDF has been working on gene lists for transcriptomic 
experiments, we might recharter that Task Group to work on Genomic Experiments, 
for example, or whatever concept area the Task members like and is a logical 
step from what they are doing now, but with a PROBLEM FOCUS ... you see the 
point. 


I think each of the solution centric groups has a potential problem centric 
group hiding inside it, waiting to come out.


Best


Tim


On May 26, 2011, at 9:31 AM, Helena Deus wrote:


  Hi, 

  That is a very good point, thanks Mikel and Andrea!
  Do you have pointers to such type of data? Shall we consider an IG for 
"basic" life sciences?


  The LS part of HCLS has indeed been gaining adepts rapidly and it may make 
sense to reflect that in the charter. 


  Cheers,
  Lena


  2011/5/26 Mikel Egaña Aranguren 

Hi;

I should attend the conference call but I just want to add that I concur 
with Andrea in that the HCLS IG should consider the environmental realm, since 
loads of new ecological/environment data, with new challenges to be addressed, 
are waiting to be represented semantically. That's precisely one of the lines 
we are trying to open here at OEG-UPM.

Cheers 


On og., 2011.eko mairen 26a 15:08, Andrea Splendiani wrote:

  Hi,

  I see myself as more involved in the next incarnation of the charter ;)
  Unfortunately, today is a travel day and I cannot attend the conference
  call.

  I have two questions/ideas, which don't really map to the current
  sub-groups, but just in case they ring some bell:

  -) Is the HCLS exclusively oriented on HeathCare ? (that is, is the "and" 
in
  Heath Care and Life Sciences IG and AND or an OR ?). Here in Rothamsted, 
we
  are just starting to evaluate the Ecological/Agricultural/Environmental
  connections to Life Sciences. Does this fall into the remit of the IG 
group
  ?

  -) Does the evaluation/ coordination of development of systems which link
  information representation and analysis side fall within the remit of the 
IG
  ? I think interfaces to linked data, as well as tools which can analyze
  linked data are important to improve the acceptance of Semantic Web
  technologies in the Life Sciences.

  ciao,
  Andrea




  Il giorno 24/mag/2011, alle ore 04.04, Eric Prud'hommeaux ha scritto:


Hi all, as some of you reallize, the charter ends at the end of this
month. I've been polling around to see what alternative formulations
would give us the most resources and impact. In the process, I wrote
up some of our high-level use cases (elevator speeches) to help us
approach the relevant parties in pharmas, health services and
research:.

I'd like to discuss the landscape and potential strategies with the
community. I'd particularly like to invite those who have been active
or see themselves as being active in the next incarnation of the group.
We'll discuss the current, fairly conservative draft charter
, as well as ways to
optimize both its message and the paths for dissemination. An example
of a messaging alternative would be to characterize the HCLS IG work
in terms of e.g. overarching translational medicine use cases:
"
 The W3C Semantic Web in Health Care a

Re: Fwd: [open-science] LODD Hack Session Notes - Is It Open request signatories needed

[Matthias Samwald]

Five databases have a non-commercial clause involved, making it Open
according to the LODD definitions (correct?), but not Open following
the OFKN's standards. The original plan was to set up an informative
package of information explaining why the NC clause causes problems,
but we did not get around to this. From a LODD perspective, this is a
non-issue, as I understood (I have not been around when "LODD" was
defined).


I'm not sure if clear-cut rules for LODD have been defined. However, many 
people interested/involved in LODD come from commercially oriented companies 
(mostly pharmaceutical companies). Therefore it certainly IS a reason for 
concern if 5 out of 12 datasets disallow commercial use without permission. 
It would certainly be helpful to convince these data providers of removing 
the NC clause, but it seems unlikely. Looking at the list of datasets with 
NC clauses (including Drugbank, LinkedCT, major parts of SIDER, STITCH), I 
get the feeling that the providers did not choose to include NC clauses on a 
whim. I guess the best we can realistically do for these datasets is to 
improve the visibility of these licensing restrictions for people that want 
to use them.


- Matthias 

Re: Fwd: Linked Data Book: HTML Version Live at linkeddatabook.com (was: Re: ANN: New book about Linked Data published)

[Matthias Samwald]

The references to Linked Data applications in the life sciences could be 
improved in the next revision of the (otherwise great) book.


Quote:
"A Life Science application that relies on knowledge from more than 200 
publicly available ontologies in order to support its users in exploring 
biomedical resources is the NCBO Resource Index. A second example of a 
Linked Data application from this domain is Diseasome Map. The application 
combines data from various Life Science data sources in order to generate a 
'network of disorders and disease genes linked by known disorder-gene 
associations, indicating the common genetic origin of many diseases.'"


To my knowledge the NCBO Resource Index does not access linked data 
(although BioPortal is exposing lots of data in RDF, of course). Diseasome 
data was converted to Linked Data as part of the LODD effort, but the actual 
diseasome project and the map are completely independent of these efforts, 
and do not use RDF or Linked Data.


- Matthias

--
From: "M. Scott Marshall" 
Sent: Wednesday, March 02, 2011 4:07 PM
To: "HCLS" 
Subject: Fwd: Linked Data Book: HTML Version Live at linkeddatabook.com 
(was:  Re: ANN: New book about Linked Data published)



FYI
-- Forwarded message --
From: Kingsley Idehen 
Date: Wed, Mar 2, 2011 at 3:23 PM
Subject: Re: Linked Data Book: HTML Version Live at linkeddatabook.com
(was:  Re:  ANN: New book about Linked Data published)
To: Tom Heath 
Cc: public-lod , Semantic Web 


On 3/2/11 8:32 AM, Tom Heath wrote:

Hi all,

As promised in Chris's original mail, the freely accessible HTML
version of the Linked Data book went online yesterday at:

http://linkeddatabook.com/

Today the text has been enhanced with some basic RDFa markup using
BIBO, FOAF and DC terms vocabularies:


Links to access/order electronic and hard copies of the book are also
listed on the http://linkeddatabook.com/ site.

We'd like to thank the publisher Morgan & Claypool for agreeing to
this version of the book being made freely accessible.

Hope you enjoy the book :)

Cheers,

Tom Heath and Christian Bizer.


Tom,

Here's what I see so far re. Linked Data dog-fooding:

1. 
http://linkeddata.uriburner.com/describe/?url=http%3A%2F%2Flinkeddatabook.com%2Feditions%2F1.0%2F%23book

--  resource description (note navigation control at the bottom re.
paging)

2. 
http://linkeddata.uriburner.com/describe/?url=http%3A%2F%2Flinkeddata.uriburner.com%2Fabout%2Fid%2Fentity%2Fhttp%2Flinkeddatabook.com%2Feditions%2F1.0%2F

-- a different view showing some of the effects of dropping this
resource into URIBurner's data space

3. http://linkeddata.uriburner.com/fct/facet.vsp?cmd=load&fsq_id=76 --
current URIBurner Zeitgeist

4. http://linkeddata.uriburner.com/c/DTIRYD -- random PivotViewer page
generated from text pattern search

5. http://linkeddata.uriburner.com/c/DTHBZO -- variant of above based
on SPARQL query

6. http://linkeddata.uriburner.com/c/DTDV4L -- edit link should you
want to tweak the SPARQL that serves the PivotViewer control.


BTW - Adding "linkeddata" to you list of
 property values will increase SDQ
(serendipitous discovery quotient) etc.. For instance, I could then
make a query based on things associated with a Tag where the Tag label
contains "linkeddata" which will result in a much richer Linked Data
graph than what I've used in the examples above :-)



--

Regards,

Kingsley Idehen
President & CEO
OpenLink Software
Web: http://www.openlinksw.com
Weblog: http://www.openlinksw.com/blog/~kidehen
Twitter/Identi.ca: kidehen



--
M. Scott Marshall, W3C HCLS IG co-chair, http://www.w3.org/blog/hcls
http://staff.science.uva.nl/~marshall

Re: call for paper in pharmacogenomics - Journal of Biomedical Informatics

[Matthias Samwald]

Very interesting indeed. It is unfortunate that the deadline is so close!

 - Matthias





From: Helena Deus 
Sent: Sunday, February 27, 2011 2:13 PM
To: public-semweb-lifesci@w3.org 
Subject: call for paper in pharmacogenomics - Journal of Biomedical Informatics




This call for papers may be interesting to some people in this list [1]. 
Submission deadline is 15 March 2011




[1]
http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WHD-52899SC-2&_user=103680&_coverDate=02/28/2011&_rdoc=1&_fmt=high&_orig=gateway&_origin=gateway&_sort=d&_docanchor=&view=c&_acct=C07922&_version=1&_urlVersion=0&_userid=103680&md5=ab744a2ede2cf2d33d4b7ae2f6479170&searchtype=a




-- 
Helena F. Deus 
Post-Doctoral Researcher at DERI/NUIG
http://lenadeus.info/

Re: beefing up PharmaOntology Queries #Q6

[Matthias Samwald]

Hi Eric,

I'm not an expert, but this seems a bit hard to answer. Bapineuzumb does not 
seem to bind or directly regulate Apolipoprotein and its variants. The APOE4 
allele is merely a biomarker which can be used to stratify the patient 
population into likely responders and non-responders. Looking at the HCLS 
KB, TMKB and http://lod.openlinksw.com, the (almost) only information that 
can be found about Bapineuzumab are clinical trials from LinkedCT. 
hypothesis.alzforum.org does not have much either, unfortunately.


- Matthias

--
From: "Eric Prud'hommeaux" 
Sent: Monday, February 14, 2011 10:37 PM
To: 
Cc: "Helena Deus" 
Subject: beefing up PharmaOntology Queries #Q6


Query six¹ matches patients without the APOE4 allel, putatively to
match the inclusion criterial for a clinical trial involving
Bapineuzumab. Do we have any drug data which links Bapineuzumab to
APOE4, so that we query for *any* protein regulated by Beelzebub,
rather than specifically APOE4?


¹ 
http://www.w3.org/wiki/HCLSIG/PharmaOntology/Queries#Q6._Are_there_any_AD_patients_without_the_APOE4_allele_as_these_would_be_good_candidates_for_the_clinical_trial_involving_Bapineuzumab.3F


--
-ericP

Re: An Universal Exchange Language

[Matthias Samwald]

Jim wrote:
"Like it or not, they were probably thinking of HL7 and ISO 21090. We would 
need to show how semweb solutions are a better solution, or how it is tied too 
much to healthcare, leaving out life sciences, population science, chemistry, 
etc. We don't yet have *a* solution for this, we have several. :-) "

Besides the fact that HL7 et al. are already better established in the current 
healthcare IT infrastructure than RDF/OWL, it does not seem too hard to come up 
with reasonable arguments in favour of RDF/OWL. I also read other seemingly 
RDF-friendly pieces of text in that document:

"As mentioned, ONC's CDA is a foundational step in the right direction. 
However, the thrust of CDA seems 
largely that it be an extensible wrapper that can hold a variety of structured 
reports or documents, each 
with vocabulary ­controlled metadata. While this shares many features with the 
universal exchange 
language that we envisage, it lacks many others. In particular, it perpetuates 
the record­ centric notion 
that data elements should "live" inside documents (albeit metadata tagged). We 
think that a universal 
exchange language must facilitate the exchange of metadata tagged elements at a 
more atomic and 
disaggregated level, so that their varied assembly into documents or reports 
can itself be a robust, 
entrepreneurial marketplace of applications. In a similar vein, we view the 
semantics of metadata tags 
as an arena in which new players can participate (by "publishing"), not as one 
limited to a vocabulary 
controlled by the government"

Cheers,
Matthias Samwald

// DERI Galway, Ireland
// Information Retrieval Facility, Austria
// http://samwald.info

Google Refine

[Matthias Samwald]

I guess almost everyone on this list will find this highly interesting...
http://code.google.com/p/google-refine/

"Google Refine is a power tool for working with messy data, cleaning it up, 
transforming it from one format into another, extending it with web services, 
and linking it to databases like Freebase."


Cheers,
Matthias Samwald

// DERI Galway, Ireland
// Information Retrieval Facility, Austria
// http://samwald.info

Re: LODD Telcon

[Matthias Samwald]

Dear all,

I have compiled some agenda items and points of discussion for today's telecon 
about the LODD paper:

 * Finding consensus on style of the paper and target audience. I suggest that 
we focus on a high-level, not-too-technical view of the problem and our 
solution. Should appeal to all stakeholders.
 * Agreeing on overall paper structure (keeping in mind that we have a limit of 
only 1500 words for the main section).
 * Ask @Claus and @Susie if they could provide a paragraph about requirements 
from pharma perspective. 
 * What is _part_ of LODD and what is only _related_ and connected to LODD? 
Where do we draw the line? A bit difficult to decide for some data sets.
 * We should decide on a demo scenario. Neuropharmacology (including novel 
datasets, possibly ABA) would be a good candidate. Should we also use some of 
the queries presented by @Eric in his presentation?
 * Problems with integrating the Allen Brain Atlas (ABA) in its current version 
(the result of the GRDDL transform of ABA XML is only mildly useful for our 
purposes, since many key entities are not identified with URIs)
 * Interfaces we use for the demo: TripleMap, Sig.ma, maybe Exhibit (based on a 
simple script that digests SPARQL results). Any others?
 * @Chris, can you provide a short paragraph about TripleMap? Also, we might 
need your help formulating queries in TripleMap and providing screenshots once 
we have decided on a demo scenario.
 * How to deal with SPARQL queries and code -- I suggest placing most queries 
and code on a wiki page and reference it from the paper, instead of integrating 
them into the paper.
 * The paper should end with with a paragraph describing the next steps we plan 
with LODD. What are they? Could @Susie formulate this paragraph?
 * Discussion of other ideas by LODD participants.

The deadline for submission is November 29. Given that this should be a rather 
condensed paper, it currently seems achievable to finish the paper in time. 
Please use the Google-Doc to collect ideas and text snippets.

Cheers,
Matthias Samwald

// DERI Galway, Ireland
// Information Retrieval Facility, Austria
// http://samwald.info




From: Susie Stephens 
Sent: Tuesday, November 09, 2010 1:56 PM
To: public-semweb-lifesci hcls 
Subject: LODD Telcon


Here's the reminder for Wednesday's LODD telcon. The main focus of the call 
will be making progress on the paper.

Cheers,

Susie

== Conference Details ==
* Date of Call: Wednesday November 10, 2010
* Time of Call: 11:00am Eastern Time (ET)
* Dial-In #: +1.617.761.6200 (Cambridge, MA)
* Dial-In #: +33.4.26.46.79.03 (Paris, France) 
* Dial-In #: +44.203.318.0479 (London, UK) 
* Participant Access Code: 4257 ("HCLS"). 
* IRC Channel: irc.w3.org port 6665 channel #HCLS
* Duration: ~1h
* Convener: Susie 

== Agenda ==
* J Cheminformatics paper
* Mapping experimental data
* Data updates
* AOB

Re: Representing conflicting evidence and refutation

[Matthias Samwald]

Dear all,

Interesting connections -- one of the main developers of the CADIAG-2 system 
(Prof. Klaus-Peter Adlassnig) was my PhD supervisor. While I was mainly 
interested in crisp reasoning back then, I also played around with 
fuzzy/probabilistic OWL reasoning. However, the scalability of these 
reasoners (such as Pronto) seemed to be very limited back then (two years 
ago). It is exciting to hear that this situation has seemingly improved in 
the meantime.


The trend towards personalized medicine could generate some very interesting 
use-cases, since the information about effects of certain SNPs, molecular 
pathway alterations, lifestyle and demographic factors are still quite 
incomplete and sometimes contradictory. One could extract the relevant data 
for each disease/drug and each patient to yield a knowledge base fragment of 
a manageable size, and then try to judge disease risk, drug efficacy or risk 
of adverse events based on imprecise reasoning.


Cheers,
Matthias Samwald

// DERI Galway, Ireland
// Konrad Lorenz Institute for Evolution and Cognition Research, Austria
// http://samwald.info



--
From: "Joanne Luciano" 
Sent: Wednesday, October 13, 2010 4:28 PM
To: "M. Scott Marshall" 
Cc: "HCLS" ; "Andrey Rzhetsky" 
; ; "Deborah 
McGuinness" ; "Jim McCusker" ; 
"Dominic DiFranzo" ; 

Subject: Re: Representing conflicting evidence and refutation


Hi Scott,

Interesting you should being this up.  Last week when I was at  Manchester 
I attended the DL (Description Logics) lunch talk by PhD  Student Pavel 
Klinov, The talk was on an analysis of CADIAG-2 KB. The  aim of the 
project is to analyze (in)consistency of CADIAG-2 -- the  large medical 
diagnosing system developed in Vienna in the 80s. The  approach is to 
translate CADIAG-2 into a P-SH KB and compute all (or  most of) minimal 
sets of conflicting rules. This is a joint work with  David Picado from 
the Technical University of Vienna, who provided the  system and developed 
its translation into P-SH.


Conflicting information in text is exactly what Andrey was working  with. 
His focus was in biological pathways.


After the talk I had a chat with Pavel and thought that there we other 
applications of his work, but we'd need to identify some data sets.  I 
immediately thought of Andrey Rzhetsky's work on Geneways where he 
addressed representing complementary data. I wrote to Andrey in hopes  of 
getting some data with inconsistencies to see what Pavel's methods  would 
uncover.


I've copied both Andrey and Pavel on this email as well as a few form  the 
TWC.


Cheers,
Joanne



On Oct 13, 2010, at 9:43 AM, M. Scott Marshall wrote:


Lilly recently halted development of of the Alzheimer's drug
"semagacestat" because it was making patients worse in two late stage
clinical trials. This type of knowledge seems like very valuable
information to researchers in Alzheimer's. However, in recent searches
of http://clinicaltrials.gov such as
http://clinicaltrials.gov/ct2/results?term=semagacestat, it seems that
the news hasn't been incorporated into the data on the website.
However, assuming that it had been added, I am curious how 'cancelled
clinical trials' can be found in the linked data. Has anyone looked at
this?

http://prescriptions.blogs.nytimes.com/2010/08/17/lilly-halts-alzheimers-drug-trial/?scp=2&sq=alzheimer's%20disease&st=cse

Another example of contradiction/refutation, this time found in
PubMed, is that Metformin apparently doesn't work (only) along the
pathways that previous research indicated:

"Metformin inhibits hepatic gluconeogenesis in mice independently of
the LKB1/AMPK pathway via a decrease in hepatic energy state"
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2898585/

Has anyone seen a way to deal with conflicting information like this
in text mining? If we were to represent this information in RDF, could
we do it in such a way that we could observe the change of the
Metformin association with LKB1/AMPK pathways over time in the
literature?

Cheers,
Scott

P.S. Oktie - It is pure coincidence that the first example is from
clinical trials. :)

--
M. Scott Marshall, W3C HCLS IG co-chair
Leiden University Medical Center / University of Amsterdam
http://staff.science.uva.nl/~marshall






~
Joanne S. Luciano, PhD   Email:   jluci...@cs.rpi.edu
Research Associate Professor 110 8th Street, Winslow 2143
Tetherless World Constellation   Troy, NY 12180, USA
Rensselaer Polytechnic Institute Office Tel.  +1.518.276.4939
Global Tel. +1.617.440.4364 (skypeIn)Office Fax   +1.518.276.4464
~