OOR/ConferenceCall 2011 09 13

= Joint NCBO-OOR Panel Discussion: "Kicking-off the Next Phase of Collaboration" - Tue 13-Sep-2011 =

'''This is an important milestone for the OpenOntologyRepository initiative, and will mark a new phase of collaboration between the NCBO-BioPortal team and the OOR team. Join us to find out more on where things stand, what changes are in store, some of the vision going forward, and provide us your input.'''

''Note that we have a hard stop at 10:00am PDT for this session. To make sure we can get the best out of the 90 minutes available for this session, we will start and end promptly on time. Please dial into the conference line a few minutes before the scheduled start time.''


 * Co-chairs: Dr. RayFergerson (NCBO; Stanford) and Mr. PeterYim (OOR; Ontolog; CIM3)


 * Panelists:
 * Professor MarkMusen (NCBO; Stanford)
 * Dr. NatashaNoy (NCBO; Stanford)
 * Dr. TrishWhetzel (NCBO; Stanford)
 * Dr. LeoObrst (OOR; MITRE)
 * Professor KenBaclawski (OOR; Northeastern U)
 * Dr. ToddSchneider (OOR; Raytheon)


 * Archive:
 * Agenda & Proceedings
 * Abstract
 * Prepared presentation material can be accessed by clicking on each of the title links below:
 * [ 0-Opening:Musen (no slides) ] . [ 1-[[BioPortal]:Fergerson] ] . [ 2-OOR:Yim-Obrst-Schneider-Baclawski) ]
 * audio recording of the session [ 1:23:44 ; mp3 ; 9.6MB ]
 * Transcript of the online chat session during the panel discussion
 * Other Resources

Agenda & Proceedings:
Session Topic: "Kicking-off the Next Phase of NCBO-OOR Collaboration"


 * Session Format & Agenda: this is a virtual session conducted over an augmented conference call:
 * 1. Opening Remarks - MarkMusen (5 min.)
 * 2. NCBO Briefing - RayFergerson (20 min.) ... [ slides ]
 * 3. OOR Briefings - LeoObrst-PeterYim, KenBaclawski-ToddSchneider (2 presentations, 10 min. each)
 * 3. Q & A and open discussion - All (30 min.) ... please refer to process above
 * 4. Conclusion / Follow-up - co-chairs

Abstracts:

 * Topic: "Kicking-off the Next Phase of NCBO-OOR Collaboration"
 * by PeterYim & RayFergerson


 * This is an important milestone for the OpenOntologyRepository initiative, and will mark a new phase of collaboration between the NCBO-BioPortal team and the OOR team.


 * Professor MarkMusen, Principal Investigator of NCBO, and a staunch supporter of the OOR initiative will kick-off this session for us. His opening will be followed by briefings from both the NCBO-BioPortal team and the OOR team. The briefings will include reports on the current status, important changes and plans that are underway, and how the teams see things both at a high-level (vision, strategy, ...) and low-level (tactics, implementations, coding, operations, ...) going forward.


 * The breifings will be followed by an extended discussion among the panelists and all participants at this session, where we hope to be able to collect input from the community on their expectations, as well as insights on how we can get the best synergy from this next phase of the NCBO-OOR collaboration.


 * Come join us at this session to find out more on where things stand, what changes are in store, some of the vision going forward, and provide us your input.

Transcript of the online chat during the session:
see raw transcript here.

(for better clarity, the version below is a re-organized and lightly edited chat-transcript.) Participants are welcome to make light edits to their own contributions as they see fit.

-- begin of chat session --

[08:19] PeterYim: Welcome to the

= Joint NCBO-OOR Panel Discussion - Tue 13-Sep-2011 =

Topic: : "Kicking-off the Next Phase of NCBO-OOR Collaboration"

Co-chairs: Dr. RayFergerson (NCBO; Stanford) and Mr. PeterYim (OOR; Ontolog; CIM3)

Panelists: Professor MarkMusen (NCBO; Stanford) Dr. NatashaNoy (NCBO; Stanford) Dr. TrishWhetzel (NCBO; Stanford) Dr. LeoObrst (OOR; MITRE) Professor KenBaclawski (OOR; Northeastern U) Dr. ToddSchneider (OOR; Raytheon)

Please refer to details on session page at: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_09_13

Participants will be muted before session starts To unmute phone: press *3 ... to put phone on mute again: *2

. = Proceedings: = .

[08:22] MikeDean: I'll need to drop off around 12:10, but will lurk until then

[08:24] PeterYim: Hi Mike ... thanks for being here

[08:26] ToddSchneider: Peter, I may need to leave after the first hour. I'll try and stay as long as possible.

[08:27] anonymous morphed into TimWilson

[08:28] TimWilson: Will there be sound on "hopper"? Does the VNC have sound?

[08:59] PeterYim: @Tim - the HOPPER server (i.e. vnc2) is only for screen sharing ... no voice support

[08:28] anonymous morphed into Niranjan Manjunath

[08:30] anonymous morphed into RayFergerson

[08:30] Kathy Ellis2 morphed into KathyEllis

[08:32] anonymous morphed into ElizabethFlorescu

[08:36] ToddSchneider: Peter, I'm having phone issues.

[08:37] KenBaclawski: Todd, let me know if you need me to take over for you in our talk.

[08:38] ToddSchneider: Ken, I now have a voice connection.

[08:36] anonymous morphed into ChuckRehberg

[08:38] anonymous morphed into Dave Hau (NCI) [DavidHau]

[08:40] ToddSchneider: Ray, can you speak louder?

[08:40] anonymous morphed into FrankOlken

[08:44] anonymous morphed into MyCoyne

[08:53] FrankOlken: I still did not catch which RDF triple store is being used.

[08:53] PeterYim: @Frank - let's ask Ray during the discussion later

[08:54] anonymous morphed into YefimZhuk

[08:40] pradeep: not able to dial from south korea

[08:40] pradeep: any help? sorry

[08:52] PeterYim: @pradeep - besides the US conference nbr, can you try some of the other (EU) phone numbers?

[09:04] pradeep: @PeterYim tried all the numbers not able to connect. Will wait for the audio files. Any possibility of using skype ? I am highly interested in the talk please help me.

[09:05] PeterYim: @pradeep - too bad ... the audio archive will be ready in a couple of days

[09:02] YefimZhuk: Ray, thanks for a very informative talk! which RDF Triplestore do you use in the BioPortal?

[09:06] ChuckRehberg: I need to leave - he can have my phone line

[09:06] PeterYim: @Chuck - thanks ... it's not the limitation of lines that is the problem, unfortunately

[09:10] pradeep: @PeterYim thank you.

[09:13] JohnBateman: @Todd: multiple representation languages: +10 :-)

[09:13] PeterYim: @JohnBateman - that's where you guys come in!

[09:14] ToddSchneider: John, support for multiple representation languages requires the independence of the functionality.

[09:21] LeoObrst: Ray, Mark, can you elaborate a bit on what you envision for licensing ontologies?

[09:40] FrankOlken: What backend are you planning to use? The audio is distorted? What triple store?

[09:42] FrankOlken: [RayFergerson mentioned 4store as a strong candidate] Looking at 4store triple store. Will it support SPQRQL 1.1?

[09:58] FrankOlken: http://4store.org/ is the web site for 4store triple store.

[09:44] ToddSchneider: Have to go. Cheers.

[09:59] LeoObrst: Thanks, all! Goodbye.

[09:59] PeterYim: great sessions ... thanks, everyone!

[09:59] PeterYim: -- session ended: 10:00 am PDT --

-- end of chat session --


 * Further Question & Remarks - please post them to the [ oor-forum ] listserv
 * if you are already subscribed, post to 
 * (if you are not yet subscribed) you may subscribe yourself to the [ oor-forum ] listserv listserv, by sending a blank email to  from your subscribing email address, and then follow the instructions you receive back from the mailing list system.

Resources

 * NCBO - National Center for Biomedical Ontology - http://www.bioontology.org/
 * The BioPortal - http://bioportal.bioontology.org/
 * OpenOntologyRepository - Homepage for the OOR initiative
 * A recent presentation on OOR - OOR Presentation at SemTech2010
 * The OOR_SandBox (powered by the NCBO BioPortal) instance, now online at: http://sandbox.oor.net
 * OOR Project site and code repository at SemWebCentral - http://oor.semwebcentral.org
 * OpenOntologyRepository_IPR Policy
 * 2010_09_17 - Friday: OOR Panel Discussion - "Getting OOR Development Going - Take-IV" Workshop - Co-chairs: Dr. ToddSchneider & Professor MichaelGruninger - Panelists: Dr. ToddSchneider (Raytheon), Mr. MikeDean (Raytheon-BBN), Dr. NatashaNoy (NCBO, Stanford University), Dr. ImmanuelNormann (Bremen University, BORG), Professor KenBaclawski (Northeastern University), Professor MichaelGruninger (University of Toronto) - OOR/ConferenceCall_2010_09_17
 * 2009_10_15 - Thursday: "OOR-BioPortal Comparative Analysis" panel discussion - Chair: ToddSchneider - Panelists: NatashaNoy, MichaelDorf, KenBaclawski, ElisaKendall & MikeDean - ConferenceCall_2009_10_15
 * 2009_07_30 - Thursday: Joint Ontolog-OOR Panel Discussion: "BioPortal and related Ontology Repository Implementations and Development" (Take-3) - Chair: NatashaNoy - Panelists: CarlosRueda, PaulAlexander, JohnGraybeal, MikeDean, StephenGranite, AlexGarcia, KenBaclawski - ConferenceCall_2009_07_30
 * 2009_02_19 - Thursday: Joint Ontolog-OOR Panel Discussion: "Getting OOR Development Off the Ground (Take-2): the work begins" - Chair: ToddSchneider; Panelists: MarkMusen, NatashaNoy, MikeDean, PaulBuitelaar / AndreasHarth, MathieuDaquin, KenBaclawski, MichaelGruninger - ConferenceCall_2009_02_19
 * 2008_08_22 - Friday: OOR Panel Discussion: "Getting OOR Development Off the Ground: Identifying Synergies & Gaps" (Take-1) - Chair: LeoObrst; Panelists: MikeDean, MarkMusen, LiDing, BruceBargmeyer & BillAndersen - ConferenceCall_2008_08_22
 * 2008_04_29 - Our team made a presentation with our history, status, OOR rationale and requirements, and a proposed roadmap at the OntologySummit2008 - see: http://ontolog.cim3.net/cgi-bin/wiki.pl?OntologySummit2008/FaceToFaceAgenda#nid1BLS
 * 2007_12_06 - Thursday: Invited Speaker - Professor MarkMusen: "If we build it, will they come? Social-engineering of new technology to disseminate biomedical ontologies" - ConferenceCall_2007_12_06
 * OntologySummit2008 - "Toward An Open Ontology Repository"
 * OntologySummit2008_Communique
 * our most recent regular OOR-team meeting - OOR/ConferenceCall_2011_09_06
 * [ oor-forum ] message archive - http://ontolog.cim3.net/forum/oor-forum/
 * (if you are not yet subscribed) you may subscribe yourself to the [ oor-forum ] listserv, by sending a blank email to  from your subscribing email address, and then follow the instructions you receive back from the mailing list system.
 * check out our other mailing lists and join us

Audio Recording of this Session

 * To download the audio recording of the session, click here
 * the playback of the audio files require the proper setup, and an MP3 compatible player on your computer.
 * Conference Date and Time:	13-Sep-2011 8:30am ~ 10:00pm Pacific Daylight Time
 * Duration of Recording:	1 Hour 24 Minutes
 * Recording File Size:	       9.6 MB (in mp3 format)


 * suggestion: its best that you listen to the session while having the presentation opened in front of you. You'll be prompted to advance slides by the speaker.
 * Take a look, also, at the rich body of knowledge that this community has built together, over the years, by going through the archives of noteworthy past Ontolog events. (References on how to subscribe to our podcast can also be found there.)

For the record ...

How To Join (while the session is in progress)

 * 1. Dial in with a phone: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_09_13#nid2WCB
 * 2. Open chat in a new browser window: http://webconf.soaphub.org/conf/room/ontolog_20110913
 * 3. Download presentations for each speaker here: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_09_13#nid2WWQ
 * or, 3.1 optionally, access our shared-screen vnc server, if you are not behind a corporate firewall

Conference Call Details:

 * Date: Tuesday, 13-Sep-2011
 * Start Time: 8:30am PDT / 11:30am EDT / 5:30pm CEST / 4:30pm BST / 15:30 UTC
 * ref: World Clock
 * Expected Call Duration: 1.5 hours
 * Dial-in Number:
 * from a US telephone (US): +1-218-844-8060 (domestic long distance cost will apply)
 * When calling in from a phone, use Conference ID: "4389979#"
 * from Europe, call:
 * Austria 0820-4000-1577
 * Belgium 070-35-9992
 * France 0826-100-280
 * Germany 01805-00-7642
 * Ireland 0818-270-037
 * Italy 848-390-179
 * Spain 0902-886-056
 * Switzerland 0848-560-327
 * UK 0844-581-9148
 * callers from other countries please dial into either one of the US or European numbers


 * Shared-screen support (VNC session) will be started 5 minutes before the call at: http://vnc2.cim3.net:5800/
 * view-only password: "ontolog"
 * if you plan to be logging into this shared-screen option (which the speaker may be navigating), and you are not familiar with the process, please try to call in 5 minutes before the start of the session so that we can work out the connection logistics. Help on this will generally not be available once the presentation starts.
 * people behind corporate firewalls may have difficulty accessing this. If that is the case, please download the slides above and running them locally. The speaker(s) will prompt you to advance the slides during the talk.


 * Discussions and Q & A:
 * (Unless the conference host has already muted everyone) Please mute your phone, by pressing "*2" on your phone keypad, when a presentation is in progress. To un-mute, press "*3"
 * You can type in your questions or comments through the browser based chat session by:
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 * or point your browser to: http://webconf.soaphub.org/conf/room/ontolog_20110913
 * instructions: once you got access to the page, click on the "settings" button, and identify yourself (by modifying the Name field). You can indicate that you want to ask a question verbally by clicking on the "hand" button, and wait for the moderator to call on you; or, type and send your question into the chat window at the bottom of the screen.
 * (when everyone is muted) If you want to speak or have questions or remarks to make, 'please "raise your hand (virtually)" by click on the "hand button" (lower right) on the chat session page. You may speak when acknowledged by the speaker or the session moderator (again, press "*3" on your phone to unmute). Test your voice and introduce yourself first before proceeding with your remarks, please.'' (Please remember to click on the "hand button" again (to lower your hand) and press "*2" on your phone to mute yourself after you are done speaking.)
 * thanks to the soaphub.org folks, one can now use a jabber/xmpp client (e.g. gtalk) to join this chatroom. Just add the room as a buddy - (in our case here) ontolog_20110913@soaphub.org ... Handy for mobile devices!


 * Please review our Virtual Session Tips and Ground Rules - see: VirtualSpeakerSessionTips


 * RSVP  to [mailto:peter.yim@cim3.com peter.yim@cim3.com] appreciated, ... or simply just by adding yourself to the "Expected Attendee" list below (if you are a member of the team.)


 * This session, like all other Ontolog events, is open to the public. Information relating to this session is shared on this wiki page: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_09_13


 * Please note that this session may be recorded, and if so, the audio archive is expected to be made available as open content, along with the proceedings of the call to our community membership and the public at-large under our prevailing open IPR policy.

Attendees

 * Attended (and a few registered participants who may have joined after the roll call):
 * RayFergerson (co-chair)
 * PeterYim (co-chair)
 * MarkMusen
 * NatashaNoy
 * TrishWhetzel
 * MikeDean
 * LeoObrst
 * KathleenEllis
 * KenBaclawski
 * ToddSchneider
 * YuriyMilov
 * TimWilson
 * Niranjan Manjunath (NEU)
 * TimDarr
 * YefimZhuk
 * Gilberto Fragoso (NIH/NCI)
 * ChuckRehberg
 * ElizabethFlorescu
 * JohnBateman
 * NancyWiegand
 * DavidHau
 * FrankOlken
 * MyCoyne
 * TerryLongstreth
 * DeborahMacPherson
 * PaulCourtney
 * ... if you are coming to the meeting, please add your name above (plus your affiliation, if you aren't already a member of the community) above, or e-mail  so that we can reserve enough resources to support everyone's participation.
 * ... if you are coming to the meeting, please add your name above (plus your affiliation, if you aren't already a member of the community) above, or e-mail  so that we can reserve enough resources to support everyone's participation.


 * Regrets:
 * MikeBennett
 * MichaelGruninger