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Meeting minutes

From: Christophe Poulain <cpoulain@teranode.com>
Date: Thu, 18 May 2006 10:50:28 -0700
To: <public-semweb-lifesci@w3.org>
Message-ID: <000f01c67aa3$8caf1460$9c01a8c0@TERANET>
My notes from today's meeting are below. I tried to capture as much as I
could but I'm sure I missed a few things. Please feel free to point out
errors and omissions. 

 

Thanks,

 

Christophe Poulain, Ph.D.

Teranode Corporation

83 South King Street, Suite 800

Seattle, WA 98104

(206) 219-3023

www.teranode.com 

 

HCLSIG Teleconference

May 18, 2006

Time: 11:00 am EDT May 18, 2006 in America/New York

Phone: tel:+1-617-761-6200 

(Zakim) conference #4257 (HCLS) irc://irc.w3.org:6665/hcls

Attendees

Present 

tnbhat, Christophe_Poulain, Eric_Neumann, Alan_Ruttenberg, Emiller, olivier,
Davide, SeanM, Don_Doherty, Tanya_Hongsermeier, SusieS 

And TimC, JoanneL, LeeF

Regrets 

Chair 

EricN, TonyaH 

Scribe 

Christophe Poulain 

Contents

* Next HCLS call June 1, 2006

 

FYI, we didn't nominate a scribe, I'll volunteer to do it a second time.

 

* Introductions - No new participants since last call.

 

* Update of activities (BioRDF)

 

EN: Please read new-use case on) Chemical Taxonomies and Structures

(http://esw.w3.org/topic/HCLS/ChemicalTaxonomiesUseCase). Link added to SMID
use-case. Raise questions and suggestions.

 

EN: Discussions on mailing lists re: defining URI. No one from NCBI involved
in these discussion, yet effort has started within NCBI to define what URIs
should be like for NCBI DB entries. MattC and Kathy K? are persons involved.

 

  AlanR: Raises several issues:

 

*       Difference between URI used as identifier and de-referencing a URI.

*       What is the result of de-referencing a URI? What do you get?

*       What happens when multiple URIs are used for the same DB entry? How
are they made equivalent?

*       Support from data providers is needed. Otherwise, define our own
namespace/conventions.

 

  EM: Note that it is easy to confuse the issues. Helpful to break them
down. Suggests engaging NCBI folks in HCLS discussions. Also, supports use
of local conventions to get started. See link to Best practice for
publishing RDF vocabularies
(http://www.w3.org/TR/2006/WD-swbp-vocab-pub-20060314/).

 

  AlanR: Would like to see more transparency of NCBI process in defining
URIs.

 

  EM: Put a bridge in place by inviting the right NCBI persons to an HCLS
telecom. Helpful?

 

  Olivier: Can take advantage of physical proximity and offers to act as
liaison with people involved at NCBI.

 

  EN: Yes.

 

Susie gives other updates from BioRDF group. Two calls since last general
teleconference.

 

*       Outcome of call #1 is that it would be helpful to identify
vocabulary requirements so that a common vocabulary can be used by all
participants.

*       Oliver to give overview of UMLS

*       Call #2: Davide presented his work on NLP.

*       BioRDF group is on track with respect to where it wanted to be at
this point in time. Has deviated from initial objectives by using a wider
variety of data sources (instead of converting more NCBI data sources). Also
effort is currently more focused on bench-side.

 

    AlanR: Points that NLP work will be more clinical-side oriented.

 

    Joanne: Her work also more on clinical-side. Will have time after June
1st.

 

* Proposal to roll NLP task force into BioRDF task force.

 

  EN: No feedback received in past two weeks.

 

  TimC was offered to comment but he's not (back) on the phone.

 

  Davide: Wonders if not in BioRDF, then where? Open to other solutions.
Convenient to be in BioRDF because of close relationship to work already
going on. NLP produces structured data in XML formats that has to be
converted to RDF.

 

  EN: No need for NLP task force to re-create work already done in BioRDF.

 

  AlanR: Points to lack of critical mass to drive NLP projects. Makes sense
to merge in BioRDF now; can split again later. Also points that Davide has
delivered XML output file. Making them RDF would be first focus.

 

 

  AlanR: Objects to "best practices" as we are merely trying to figure out
"practices".

 

  EN: Goal is to establish "better practices".

 

  Davide: Has been in touch with NeuroCommons representatives. They don't
care much about location of NLP group. Most important is that all parties
are ready to work together.

 

  EM: Is work not getting done because of this situation?

 

  Susie: Seems to work.

 

  EN: One point is to show strong interactions between task forces by
merging them. Other point is to simplify; reduce # of task forces by
aggregating. Current objectives will not change.

 

  EN: Propose merging NLP task force to be part of BioRDF task force as a
sub-task and to continue with its current objectives. Vote proceeds:

 

  Yes: tnbhat, Christophe_Poulain, Eric_Neumann, Alan_Ruttenberg, Davide,
Don_Doherty, Tanya_Hongsermeier, SusieS

  Abstain: Emiller, Olivier, SeanM, JimM, Joanne

  Did not vote: LeeF, TimC (off-line)

 

  Resolution: NLP task force is merged into BioRDF sub-group.

 

  New Action: Front homepage needs to be updates (assigned to?)

 

  New Action: NLP group participants to update their site pages. BioRDF to
do same.

 

 

* Update of activities (BioOntology)

 

Vipul absent from this call. AlanR gave quick update (but the scribe missed
the gist of it... please fill in).

 

* Update of activities (Adaptive Clinical Protocol)

 

Davide: Wiki was updated. Charter was finalized. Started draft of ontology
and in-process of collecting comments. Today had call with Harvard professor
(name?); will follow-up and act on collaboration.

 

* Summary of Open Action Items:

 

[NEW] ACTION:  Tim Clarke to reach out to Matt Cockerill from Biomed 

Central to

collaborate on Scientific Publishing Lifecycle proposal

>> No update.

 

[NEW] ACTION: Eric Neumann, Tonya Hongsermeier, Susie Clark, and Joanne 

Luciano

to collaborate on agenda for Nov 6th Workshop in Athens, Georgia

>> Working on it.

 

[PENDING] ACTION: AlanR to review <http://esw.w3.org/topic/HCLS/>

ParkinsonUseCase and see if BioRDF task for translating data to RDF 

provide

answers to questions being asked [recorded in http://

www.w3.org/2006/04/20-hcls-minutes.html#action03]

>> See note on mailing list.

 

[PENDING] ACTION: SusieS to review <http://esw.w3.org/topic/HCLS/>

ParkinsonUseCase and see if BioRDF task for translating data to RDF 

provide

answers to questions being asked [recorded in http://

www.w3.org/2006/04/20-hcls-minutes.html#action04]

>> Seems good but unsure, at this time, how well it will link into BioRDF.

 

[PENDING] ACTION: Tonya will review BioRDF Task for intersection points 

with CDS

aspects of Ontology Use Cases, provide feedback [recorded in

http://www.w3.org/2006/04/20-hcls-minutes.html#action06

<http://www.w3.org/2006/04/20-hcls-minutes.html>]

>> No update.

 

[PENDING] ACTION: Vipul to follow up with Alan, Tonya and Susie on 

identifiying

intersection points between BioRDF and ONT use case task [recorded in

http://www.w3.org/2006/04/20-hcls-minutes.html#action05

<http://www.w3.org/2006/04/20-hcls-minutes.html>]

>> No update.

 

[PENDING] ACTION: Eric N, Vipul, Tonya talk about the Athens, GA 

conference and

possible organization of workshop. [recorded in http://

www.w3.org/2006/04/06-hcls-minutes.html#action05] Tonya to organize a 

telecon to take next step

>> No update.

 

* Several participants to attend next week

    @ www2006 -> EricN, Vipul, EricM, Susie, Joanne (possibly)  

 

 

IRC log is below:

 

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*** End of /MOTD command.

*** cpoulain [4051030a@128.30.52.23] has joined #hcls

*** cpoulain @em 

*** Channel created on Thu May 18 13:28:47 2006

*** Tonya [aadff63f@128.30.52.23] has joined #hcls

*** em changed the topic to: hcls May 18 telecon - @@ agenda @@

*** Zakim [rrs-bridgg@128.30.52.30] has joined #hcls

*** RRSAgent [rrs-loggee@128.30.52.30] has joined #hcls

<RRSAgent> logging to http://www.w3.org/2006/05/18-hcls-irc

<em> zakim, this will be HCLS

<Zakim> ok, em, I see SW_HCLS()11:00AM already started

<em> Meeting: HCLSIG 

<em> Agenda:
http://lists.w3.org/Archives/Public/public-semweb-lifesci/2006May/0114.html

*** alanr [alanr@206.123.75.20] has joined #hcls

*** em changed the topic to: HCLSIG May 18 telecon -
http://lists.w3.org/Archives/Public/public-semweb-lifesci/2006May/0114.html

<em> Chair: EricN, TonyaH

*** eneumann [eneumann@207.172.220.142] has joined #hcls

<em> Scribe: Christoph Poulain

<em> agenda+ Convene, take roll, review record

* Zakim notes agendum 1 added

*** Don [Don@71.253.9.92] has joined #hcls

<cpoulain> Scribe: Christophe Poulain

<em> agenda+ Propose next HCLS call June 1, 2006, nominate a scribe

* Zakim notes agendum 2 added

<em> agenda+ Introductions - New participants since last call.

* Zakim notes agendum 3 added

<Zakim> +Eric_Neumann

<em> agenda+ BIO RDF Update

* Zakim notes agendum 4 added

<em> agenda+ BioOntology Update

* Zakim notes agendum 5 added

<em> agenda+ Adaptive Clinical Protocol Update

* Zakim notes agendum 6 added

<em> agenda+ action item review

* Zakim notes agendum 7 added

<Zakim> +Alan_Ruttenberg

<em> zakim, dial emiller-bos

<Zakim> ok, em; the call is being made

<Zakim> +Emiller

<Zakim> +olivier

<em> zakim, who is here?

<Zakim> On the phone I see tnbhat, Christophe_Poulain, Eric_Neumann,
Alan_Ruttenberg, Emiller, olivier

<Zakim> On IRC I see Don, eneumann, alanr, RRSAgent, Zakim, Tonya, cpoulain,
em

<Zakim> + +1.617.864.aaaa

<em> zakim, +1.617.864.aaaa is Davide

<Zakim> +Davide; got it

*** Davide [davide@71.162.103.197] has joined #hcls

<em> zakim, who is here?

<Zakim> On the phone I see tnbhat, Christophe_Poulain, Eric_Neumann,
Alan_Ruttenberg, Emiller, olivier, Davide

<Zakim> + +1.617.794.aabb

<Zakim> On IRC I see Davide, Don, eneumann, alanr, RRSAgent, Zakim, Tonya,
cpoulain, em

<em> zakim, +1.617.794.aabb is SeanM

<Zakim> +Don_Doherty

<Zakim> +SeanM; got it

<Zakim> +Tanya_Hongsermeier

<Zakim> +??P7

<em> zakim, ??P7 is SusieS

*** Sean [sjmm@24.177.141.148] has joined #hcls

<Zakim> +SusieS; got it

* em thinks zakim is tired :(

*** Susie [945701aa@128.30.52.23] has joined #HCLS

<em> zakim, who is here?

* em pokes zakime

<Zakim> On the phone I see tnbhat, Christophe_Poulain, Eric_Neumann,
Alan_Ruttenberg, Emiller, olivier, Davide, SeanM, Don_Doherty,
Tanya_Hongsermeier, SusieS

<em> Present: tnbhat, Christophe_Poulain, Eric_Neumann, Alan_Ruttenberg,
Emiller, olivier, Davide, SeanM, Don_Doherty, Tanya_Hongsermeier, SusieS

<em> rrsagent, generate minutes

<RRSAgent> I have made the request to generate
http://www.w3.org/2006/05/18-hcls-minutes.html em

<em> rrsagent, make minutes world readable

<RRSAgent> I'm logging. I don't understand 'make minutes world readable',
em.  Try /msg RRSAgent help

<Zakim> On IRC I see Susie, Sean, Davide, Don, eneumann, alanr, RRSAgent,
Zakim, Tonya, cpoulain, em

<em> hmm

<Sean> Anyone know if there is there a way to mute my phone using Zakim? 

<em> agenda?

<Zakim> + +1.732.594.aacc

* Zakim sees 7 items remaining on the agenda:

* Zakim 1. Convene, take roll, review record [from em]

* Zakim 2. Propose next HCLS call June 1, 2006, nominate a scribe [from em]

* Zakim 3. Introductions - New participants since last call. [from em]

* Zakim 4. BIO RDF Update [from em]

* Zakim 5. BioOntology Update [from em]

* Zakim 6. Adaptive Clinical Protocol Update [from em]

* Zakim 7. action item review [from em]

<em> zakim, mute sean

<Zakim> +TimC

<Zakim> SeanM should now be muted

<Sean> Zakim mute me 

<em> zakim, unmute sean

<Zakim> SeanM should no longer be muted

<Sean> zakim, mute sean 

<Zakim> SeanM should now be muted

<em> zakim, who is here?

<Zakim> On the phone I see tnbhat, Christophe_Poulain, Eric_Neumann,
Alan_Ruttenberg, Emiller, olivier, Davide, SeanM (muted), Don_Doherty,
Tanya_Hongsermeier, SusieS, +1.732.594.aacc,

<Zakim> ... TimC

<Zakim> On IRC I see Susie, Sean, Davide, Don, eneumann, alanr, RRSAgent,
Zakim, Tonya, cpoulain, em

<em> zakim, +1.732.594.aacc is JimM

<Zakim> +JimM; got it

<em> zakim, who is here?

<Zakim> On the phone I see tnbhat, Christophe_Poulain, Eric_Neumann,
Alan_Ruttenberg, Emiller, olivier, Davide, SeanM (muted), Don_Doherty,
Tanya_Hongsermeier, SusieS, JimM, TimC

<Zakim> On IRC I see Susie, Sean, Davide, Don, eneumann, alanr, RRSAgent,
Zakim, Tonya, cpoulain, em

<em> Present: tnbhat, Christophe_Poulain, Eric_Neumann, Alan_Ruttenberg,
Emiller, olivier, Davide, SeanM (muted), Don_Doherty, Tanya_Hongsermeier,
SusieS, JimM, TimC

<em> agenda?

* Zakim sees 7 items remaining on the agenda:

<cpoulain> eneumann: next call June 1

* Zakim 1. Convene, take roll, review record [from em]

* Zakim 2. Propose next HCLS call June 1, 2006, nominate a scribe [from em]

* Zakim 3. Introductions - New participants since last call. [from em]

* Zakim 4. BIO RDF Update [from em]

* Zakim 5. BioOntology Update [from em]

* Zakim 6. Adaptive Clinical Protocol Update [from em]

* Zakim 7. action item review [from em]

<em> agenda+ NLP task force future

* Zakim notes agendum 8 added

<Zakim> +[IPcaller]

<em> zakim, +[IPcaller] is Joanne

<Zakim> sorry, em, I do not recognize a party named '+[IPcaller]'

<em> zakim, [IPcaller] is Joanne

<Zakim> +Joanne; got it

<em> .me please put new task force pointers in agenda (and now on IRC);
anyone have these handy?

<eneumann> q?

* Zakim sees no one on the speaker queue

<em> q+ 

* Zakim sees em on the speaker queue

<eneumann> ack em

* Zakim sees no one on the speaker queue

<em> Best Practice Recipes for Publishing RDF Vocabularies

<em> -> http://www.w3.org/TR/2006/WD-swbp-vocab-pub-20060314/

<alanr> btw, some people commented on the involvment of ncbi. I wanted to
say that one of the points of the note I sent out was that people from NCBI
are on our lists and hopefully would chime in.

<em> related to this...

<em> SKOS Core Vocabulary Specification

<em> -> http://www.w3.org/TR/swbp-skos-core-spec

<Sean> also related will be whatever caBIG decides their identifier standard
(hard to figure when this will be) 

*** Don [Don@71.253.9.92] has quit [Ping timeout]

<em> q+\

* Zakim sees \ on the speaker queue

<em> q+

* Zakim sees \, em on the speaker queue

<em> zakim, drop \

<Zakim> sorry, em, I do not see a party named '\'

<em> zakim, ack \

<Zakim> I see em on the speaker queue

<eneumann> ack em

* Zakim sees no one on the speaker queue

*** jluciano2 [52592586@128.30.52.23] has joined #hcls

<em> q+ 

* Zakim sees em on the speaker queue

<eneumann> ack em

* Zakim sees no one on the speaker queue

<Sean> I see Alan did provide a number to call 

<Sean> he is local it seems 

<em> q?

* Zakim sees no one on the speaker queue

<Tonya> Vipul is out of town, is he the only on in Bio-Ont?

<alanr> Discussion of identifiers in BioPAX:
http://cbio.mskcc.org/mailman/private/biopax-discuss/2006-April/001579.html

<em> zakim, unmite TimC

<Zakim> I don't understand 'unmite TimC', em

<em> zakim, unmute TimC

<Zakim> TimC was not muted, em

<em> hmm

<em> Tim?

<em> q+

* Zakim sees em on the speaker queue

*** LeeF [Lee@129.33.1.37] has joined #hcls

<alanr> q+

* Zakim sees em, alanr on the speaker queue

<eneumann> ack em

* Zakim sees alanr on the speaker queue

*** Don [Don@151.201.28.62] has joined #hcls

<Zakim> -TimC

<eneumann> ack alanr

* Zakim sees no one on the speaker queue

<jluciano2> I agree with Alan's comment about best practices - cant say best
yet

<em> zakim, who is here?

<Zakim> On the phone I see tnbhat, Christophe_Poulain, Eric_Neumann,
Alan_Ruttenberg, Emiller, olivier, Davide, SeanM (muted), Don_Doherty,
Tanya_Hongsermeier, SusieS, JimM, Joanne

<Zakim> On IRC I see Don, LeeF, jluciano2, Susie, Sean, Davide, eneumann,
alanr, RRSAgent, Zakim, Tonya, cpoulain, em

<alanr> BIORDF (Structured Data to RDF) -> BIORDF (Data to RDF)

<jluciano2> type question here:

<jluciano2> merge BioNLP taskforce ...

<jluciano2> into BioRDF 

<Sean> Abstain 

<Sean> Lee has note vote 

<Sean> no 

<Sean> no vote :-) 

<jluciano2> is that a vote of "NO" or not voting (abstain) :-)

<LeeF> i share sean's abstention

<LeeF> and maybe don't even get to do that =)

<em> q+

* Zakim sees em on the speaker queue

<eneumann> ack em

* Zakim sees no one on the speaker queue

<Sean> zakim, unmute sean 

<Zakim> SeanM should no longer be muted

<em> @ www2006 -> EricN, Vipul, EricM, Susie, Joanne (possibly)  

 

 
Received on Thursday, 18 May 2006 17:49:52 GMT

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