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ConferenceCall 2013 06 13 and ConferenceCall 2013 06 27: Difference between pages

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= [[ONTOLOG]] Community Event Planning Session - Thu 2013-06-13 =
= Ontolog Invited Speaker Presentation - Dr. Vinay Chaudhri - Thu 2013.06.27 =


Session Co-chairs: '''Dr. [[LeoObrst|Leo Obrst]] & Mr. PeterYim'''  
''Session Chairs:'' '''Dr. LeoObrst''' (ONTOLOG; MITRE)


To be Covered today:  
''Invited Speaker:'' '''Dr. VinayChaudhri''' (SRI)


* '''[[ONTOLOG]] Community Event Planning - Opening''' (co-chairs) ... [http://ontolog.cim3.net/file/work/Ontolog-planning/Event-Planning_2013/Ontolog-community-planning-intro--LeoObrst-PeterYim_20130613.pdf intro slides]
''Title of Presentation:'' "'''KB_Bio_101:  Conceptual Modeling Challenges in Creating a Biology Knowledge Base'''"
** What defines the [[Ontolog]] CoP?
** What do we want to achieve today?
* '''Open Discussion'''
** Outstanding follow-up activities
** Candidate Topics of interest to the community ...
** Coordinating current & new programs - annual events, mini-series, initiatives, ...
* '''Events & Action Plans'''  
** Candidate Speakers the community would want to invite ...
** Who will champion these activities ... ?
** Short / medium term event plans


==[http://ontolog.cim3.net/file/work/Ontolog-planning/Event-Planning_2013/ Archives]==
''[http://ontolog.cim3.net/file/resource/presentation/VinayChaudhri_20130627/ Archive]:''


* '''[[ConferenceCall_2013_06_13|Abstract]]'''  
* '''[ [[ConferenceCall_2013_06_27|Abstract]] ]'''  
* '''[[ConferenceCall_2013_06_13|Agenda]]'''  
* '''[ [[ConferenceCall_2013_06_27|Agenda & Proceedings]] ]'''  
* '''[[ConferenceCall_2013_06_13|Agenda Ideas]]'''
* '''[ [http://ontolog.cim3.net/file/resource/presentation/VinayChaudhri_20130627/KB-Bio-101--VinayChaudhri_20130627.pdf slides] ] . [ [http://www.aaaivideos.org/2012/inquire_intelligent_textbook/ video clip] ]''' (see: [[ConferenceCall_2013_06_27|applicable use license arrangements]])
* '''[http://ontolog.cim3.net/file/work/Ontolog-planning/Event-Planning_2013/Ontolog-community-planning-intro--LeoObrst-PeterYim_20130613.pdf Opening slides]'''  
* '''[[ConferenceCall_2013_06_27|transcript of the online chat]]''' during the session  
* '''[[ConferenceCall_2013_06_13|transcript of the online chat]]''' during the session  
* '''[http://ontolog.cim3.net/file/resource/presentation/VinayChaudhri_20130627/Ontolog_VinayChaudhri_KB-Bio-101_20130627b.mp3 Audio recording of the session]''' ... [ 1:53:13 ; mp3 ; 12.96 MB ]  
* '''[http://ontolog.cim3.net/file/work/Ontolog-planning/Event-Planning_2013/Ontolog-event-planning_20130613b.mp3 Audio recording of the session]''' ... [ 1:39:03 ; mp3 ; 11.34 MB ]  
** its best that you listen to the session while having the respective presentations (linked above) opened in front of you. You'll be prompted to advance slides by the speaker.  
** its best that you listen to the session while having the respective presentations (linked above) opened in front of you. You'll be prompted to advance slides by the speaker.  
* '''[[ConferenceCall_2013_06_13|Additional Resources]]'''


=== [[MeetingsCalls|Conference Call]] Details  ===
=== [[MeetingsCalls|Conference Call]] Details  ===


* Date: '''Thursday, 13-Jun-2013'''  
* Date: '''Thursday, 27-Jun-2013'''  
* Start Time: 8:30am PDT / 11:30am EDT / 12:30pm ART / 5:30pm CEST / 4:30pm BST / 15:30 UTC  
* Start Time: 9:30am PDT / 12:30pm EDT / 6:30pm CEST / 5:30pm BST / 16:30 UTC  
** ref: [http://www.timeanddate.com/worldclock/fixedtime.html?month=6&day=13&year=2013&hour=8&min=30&sec=0&p1=224 World Clock]  
** ref: [http://www.timeanddate.com/worldclock/fixedtime.html?month=6&day=27&year=2013&hour=9&min=30&sec=0&p1=224 World Clock]  
* Expected Call Duration: 1.5~2.0 hours  
* Expected Call Duration: ~1.5 hours  


* Dial-in:  
* Dial-in:  
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** view-only password: "ontolog"  
** 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.  
** 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 '''[[ConferenceCall_2013_06_13|slides above]]''' (where applicable) and running them locally. The speaker(s) will prompt you to advance the slides during the talk.  
** people behind corporate firewalls may have difficulty accessing this. If that is the case, please download the '''[[ConferenceCall_2013_06_27|slides above]]''' (where applicable) and running them locally. The speaker(s) will prompt you to advance the slides during the talk.  


* '''In-session chat'''-room url: http://webconf.soaphub.org/conf/room/ontolog_20130613
* '''In-session chat'''-room url: http://webconf.soaphub.org/conf/room/ontolog_20130627
** instructions: once you got access to the page, click on the "settings" button, and identify yourself (by modifying the Name field from "anonymous" to your real name, like "JaneDoe").  
** instructions: once you got access to the page, click on the "settings" button, and identify yourself (by modifying the Name field from "anonymous" to your real name, like "JaneDoe").  
** 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.  
** 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.  
** 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_20130613@soaphub.org ... Handy for mobile devices!  
** 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_20130627@soaphub.org ... Handy for mobile devices!  


* '''Discussions and Q & A:'''  
* '''Discussions and Q & A:'''  
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* '''RSVP''' '' to [mailto:peter.yim@cim3.com peter.yim@cim3.com] with your affiliation appreciated,'' ... or simply just by adding yourself to the "Expected Attendee" list below (if you are a member of the community already.)  
* '''RSVP''' '' to [mailto:peter.yim@cim3.com peter.yim@cim3.com] with your affiliation appreciated,'' ... or simply just by adding yourself to the "Expected Attendee" list below (if you are a member of the community already.)  


* 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?ConferenceCall_2013_06_13
* 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?ConferenceCall_2013_06_27


* 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 [[WikiHomePage#Intellectual_Property_Rights_.28IPR.29_Policy|our prevailing open IPR policy]].  
* 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 [[WikiHomePage#Intellectual_Property_Rights_.28IPR.29_Policy|our prevailing open IPR policy]].  
** Caveat: to allow us to share the latest in semantic technology, this session is being featured under a special waiver to our invited speaker on the prevailing Ontolog IPR Policy - the material for this talk is provided by the speaker under the CC-BY-NC-SA 3.0 license - http://creativecommons.org/licenses/by-nc-sa/3.0/ ... please pay special attention that the material is licensed for "non-commercial" use only.


== Attendees  ==
== Attendees  ==


* Attended:  
* Attended (including all registrants):  
** [[LeoObrst|Leo Obrst]] (co-chair)  
** [[VinayChaudhri|Vinay Chaudhri]] (invited speaker)
** [[PeterYim|Peter P. Yim]] (co-chair)
** [[LeoObrst|Leo Obrst]] (chair)  
** [[MichaelGruninger|Michael Grüninger]]  
** [[PeterYim|Peter P. Yim]]  
** [[ToddSchneider|Todd Schneider]]  
** [[CeciliaZanniMerk]]
** [[SteveRay|Steve Ray]]  
** [[PaulenaMeyer|Paulena Meyer]]
** [[MatthewWest|Matthew West]]  
** [[MatthewLange|Matthew Lange]]
** [[AmandaVizedom|Amanda Vizedom]]  
** [[BobSmith|Bob Smith]]
** [[RichKeller|Rich Keller]]
** [[FranLightsom|Fran Lightsom]]
** [[EnricoFranconi|Enrico Franconi]]
** [[BrianHaugh|Brian Haugh]]
** [[FrankChum|Frank Chum]]  
** [[TonyWeida|Tony Weida]]  
** [[BobbinTeegarden|Bobbin Teegarden]]  
** [[JieZheng|Jie Zheng]]  
** [[NaicongLi|Naicong Li]]  
** [[HaroldBoley|Harold Boley]]  
** [[HaroldBoley|Harold Boley]]  
** [[HensonGraves|Henson Graves]]  
** [[DavidNewman|David Newman]]  
** [[PavithraKenjige|Pavithra Kenjige]] (partially)  
** [[MarcoHernandez|Marco Hernandez]]  
** [[User:KennethBaclawski|Ken Baclawski]] (on chat, partially)
** [[RaviSharma|Ravi Sharma]]
** [[SimonSpero|Simon Spero]] (on chat, partially)
** [[BevCorwin|Bev Corwin]]
** [[FrancescaQuattri|Francesca Quattri]]
** [[JackPark|Jack Park]]
** [[ShariThurow|Shari Thurow]]
** [[AuronaGerber|Aurona Gerber]]
** [[GaryGannon|Gary Gannon]]
** [[AlexShkotin|Alex Shkotin]]
** [[RogerBurkhart|Roger Burkhart]]
** [[PatrickMaroney|Patrick Maroney]]
** [[MelissaHildebrand|Melissa Hildebrand]]
** [[MaraAbel|Mara Abel]] and students (from UFRGS, Brazil)  
** [[JoelCarbonera|Joel Carbonera]]
** [[ChrisBaker|Chris Baker]]
** [[HansPolzer|Hans Polzer]]
** [[MatthewMcKennirey]]
** [[DougFoxvog|Doug Foxvog]]
** [[AidaGandara|Aida Gandara]]
** [[BrandonBennett|Brandon Bennett]]
** [[GaryBergCross]]
** [[BobbinTeegarden|Bobbin Teegarden]]
** [[User:KennethBaclawski|Ken Baclawski]]  
** KevinBurns
** [[LamarHenderson|Lamar Henderson]]
** [[OliverKutz|Oliver Kutz]]
** [[RamonaWalls|Ramona Walls]]
** [[SiraratSarntivijai|Sirarat Sarntivijai]]
** [[TaraAthan|Tara Athan]]
** [[APatriceSeyed|A Patrice Seyed]]
** [[JackRing|Jack Ring]]
** [[PavelKocura|Pavel Kocura]]
** [[PeterMidford|Peter Midford]]  
** ...  
** ...  


* Expecting:  
* Expecting:  
** ''please add yourself to the list if you are a member of the [[WikiHomePage|Ontolog]] community, or, rsvp to <peter.yim@cim3.com> with your affiliation.''  
** ...
** ''please add yourself to the list if you are a member of the [[WikiHomePage|Ontolog]] or [[OntologySummit|Ontology Summit]] community, or, rsvp to <peter.yim@cim3.com> with your affiliation.''  


* Regrets:  
* Regrets:  
** [[MikeDean|Mike Dean]] (back in hospital)
** [[KiyongLee|Kiyong Lee]]  
** [[RexBrooks|Rex Brooks]] (may join for the last half-hour)
** [[AmandaVizedom|Amanda Vizedom]]  
** Nicola Guarino
** [[TerryLongstreth|Terry Longstreth]]
** [[TillMossakowski|Till Mossakowski]]
** [[ElisaKendall|Elisa Kendall]]
** [[BenjaminGrosof|Benjamin Grosof]]
** [[IgorIkonnikov|Igor Ikonnikov]]
** [[MikeBennett|Mike Bennett]]
** [[BobSmith|Bob Smith]]
** ...
 
== Abstract  ==
 
Now that the [[OntologySummit|Ontology Summit]] is over, we should start planning on how to best leverage the Ontolog Thursday event slots to do something that caters to the interests and desires of this community's membership. Our virtual sessions (and the knowledge we manage to capture out of those events) have always been a key asset/resource of our community.
 
There are ongoing initiatives, there are things we need to follow-up on, and there are things we've always wanted to do.
 
The plan is to lay out the options, and have members of the community chime in, and decide what events will be featured, and who will be championing those events. We hope we can have a good cross-section of the community participating at this session, so we can properly gauge the interest of the community members. If you want to influence what gets featured in the upcoming Thursday virtual session slots, please make sure you come join us at this session.
 
=== Agenda Ideas  ===
 
Some of the things that came to mind, include ...
 
* continuation of Ontology of Ontology Evaluation
* continuation of Ontolog content on PSMW, and [[OntologySummit|Ontology Summit]] website
* driving and coordination with Ontology-based Standards
** ICOM
** QUOMOS
** FIBO
** ...  
** ...  
* coordination with the OOR initiative
* coordination with PSMW-dev
* coordination with IAOA
* Reasoners (for those who were there, remember the FOIS 2008 conversation at Saarbrueken?)
* Logic Programming / Ontology-driven Applications (something like [[RuleLog]] sounds exciting)
* Integrated Ontology Visualization (e.g., visualizing both Description Logic and Horn Logic as in [[Grailog]])
* Smart Content - like, Ontolog BOK on [[OntologPSMW]]; AURA the "Smart Textbook" ([http://ontolog.cim3.net/forum/ontolog-forum/2012-07/msg00291.html ref.]); ...
* Reasoning over the LOD Cloud?
* Ontology for Big Data
* Ontology development methodologies
* Ontologies for Government and Citizens
* Ontologies and Healthcare
* Smart manufacturing and ontologies
* Computational science and ontologies
* Cyberspace and ontologies: cryptography, social networking, malware, access control, network incursion, identity theft
* Smart gadgets/devices - e.g. phones and ontologies
* Smart homes, vehicles, ...
* Smart Cities
* what other good initiatives to support?
* what other good topics to cover?
* what are good topics to get updates on?
** [[CLv2]]
** [[OntoIOp]]
** ...
* ... etc.
... ''send us your ideas too (post above, and identify yourself for follow-up purposes, or email that to the co-chairs so we can include them into the agenda!''
== Agenda  ==


'''[[ONTOLOG]] Community Event Planning'''
== Agenda & Proceedings  ==


* ''Session Format:'' this is a virtual session conducted over an augmented conference call
* '''Session Format and Agenda''':  
** ''this will be virtual session over a phone conference setting, augmented by in-session chat and shared computer screen support''
## The session will start with a brief self-introduction of the attendees (~10 min.) ... (We will be skipping this if there are more than 20 participants)
## Introduction of the invited speakers - session chair: [[LeoObrst|Leo Obrst]]
## Presentation by our invited speakers - [[VinayChaudhri|Vinay Chaudhri]] (~60 min.) ... ([[ConferenceCall_2013_06_27|slides]])
## Q&A and Open discussion (~20 min.)  ... (refer to [[ConferenceCall_2013_06_27|process above]])
## Closing (chair)


* 1. Session opening (co-chairs) - [[LeoObrst|Leo Obrst]] & [[PeterYim|Peter P. Yim]] (15 min.) ... [[ConferenceCall_2013_06_13|slides]]
=== Abstract ===


* 2. Open discussion-I: Brainstorm on what initiatives, activities, events we should be featuring - ALL (30 min.) ... (refer to [[ConferenceCall_2013_06_13|process above]])
:"'''KB_Bio_101:  Conceptual Modeling Challenges in Creating a Biology Knowledge Base'''" ... [ [http://ontolog.cim3.net/file/resource/presentation/VinayChaudhri_20130627/KB-Bio-101--VinayChaudhri_20130627.pdf slides] ]  


* 3. Open discussion-II: narrowing down on specific events plans - mini-series, topics, champions, speakers, dates - ALL (30 min.)
:http://ontolog.cim3.net/file/resource/presentation/VinayChaudhri_20130627/VinayChaudhri_20130627b.jpg [ Dr. Vinay Chaudhri ]


* 4. Recap Actions, Summary & Wrap-up - co-chairs: [[LeoObrst|Leo Obrst]] & [[PeterYim|Peter P. Yim]] (15 min.)
:KB_Bio_101 contains knowledge from an introductory college level biology textbook, has been developed as part of Project Halo, and is now freely available for research use. In this presentation, I will briefly introduce the knowledge representation used for creating the KB_Bio_101, and spend bulk of the time describing the design of an ontology for structure and function and the knowledge encoding process. KB_Bio_101 is a valuable resource for the ontology research community to study a variety of problems such as ontology quality, ontology design patterns, ontology modularization as well as for creating new ontologies for biological knowledge such as experiments, models, evolution, etc.  


== Proceedings ==
=== About the Speakers ===


Please refer to the [[ConferenceCall_2013_06_13|above]]  
:'''[[VinayChaudhri|Dr. Vinay K. Chaudhri]]''' is the Program Director at the Artificial Intelligence Center of SRI International (Menlo Park, California, USA.) His research focuses on the science and engineering of large knowledge base systems and spans knowledge representation and reasoning, deductive question answering, knowledge acquisition, and innovative applications. He is also interested in entrepreneurship, and transitioning research ideas into commercial products. He has worked with a wide range of knowledge representation and reasoning systems including LOOM, Ontolingua, Cyc, KM, and F-Logic. He was part of the team that developed the Open Knowledge Base Connectivity (OKBC) protocol for accessing knowledge bases. He contributed to storage, and multi-user software that underlies [http://www.sri.com/work/projects/ecocyc SRI's EcoCyc project]. Since 2000, he has been working on a system to capture knowledge from science textbooks, and to answer questions at the back of the book.


=== IM Chat Transcript captured during the session  ===
=== Transcript of the online chat during the session  ===


see raw transcript [http://ontolog.cim3.net/file/work/Ontolog-planning/Event-Planning_2013/Ontolog-planning_chat-transcript_unedited_20130613a.txt here].  
see raw transcript [http://ontolog.cim3.net/file/resource/presentation/VinayChaudhri_20130627/Ontolog_VinayChaudhri_KB-Bio-101_chat-transcript_unedited_20130627a.txt here].  


(for better clarity, the version below is a [http://ontolog.cim3.net/file/work/Ontolog-planning/Event-Planning_2013/Ontolog-planning_chat-transcript_edited_20130613b.txt re-organized and lightly edited chat-transcript].)
(for better clarity, the version below is a [http://ontolog.cim3.net/file/resource/presentation/VinayChaudhri_20130627/Ontolog_VinayChaudhri_KB-Bio-101_chat-transcript_edited_20130627b.txt re-organized and lightly edited chat-transcript].)


Participants are welcome to make light edits to their own contributions as they see fit.  
Participants are welcome to make light edits to their own contributions as they see fit.  
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-- begin in-session chat-transcript --  
-- begin in-session chat-transcript --  


[8:18] [[PeterYim|Peter P. Yim]]: Welcome to the
------
 
''' ONTOLOG Community Event Planning Session - Thu 2013-06-13 '''
 
Session Co-chairs: Dr. [[LeoObrst|Leo Obrst]] & Mr. [[PeterYim|Peter P. Yim]]
 
To be Covered today:    (3TR3)
 
* ONTOLOG Community Event Planning - Opening (co-chairs)  (3TR4)
 
** What defines the Ontolog CoP?    (3TR5)


** What do we want to achieve today?    (3TR6)
Chat transcript from room: ontolog_20130627


* Open Discussion    (3TR7)
2013-06-27 GMT-08:00 [PDT]


** Outstanding follow-up activities    (3TR8)
------


** Candidate Topics of interest to the community ...    (3TR9)
[9:09] [[PeterYim|Peter P. Yim]]: Welcome to the  


** Coordinating current & new programs - annual events, mini-series, initiatives, ...   (3TRB)
''' Ontolog Invited Speaker Presentation - Dr. Vinay Chaudhri - Thu 2013.06.27 '''


* Events & Action Plans    (3TRC)
* Session Chair: Dr. [[LeoObrst|Leo Obrst]] (ONTOLOG; MITRE)  


** Candidate Speakers the community would want to invite ...    (3TRA)
* Invited Speaker: Dr. [[VinayChaudhri|Vinay Chaudhri]] (SRI)  


** Who will champion these activities ... ?    (3TRD)
* Title of Presentation: "KB_Bio_101: Conceptual Modeling Challenges in Creating a Biology Knowledge Base"
 
** Short / medium term event plans    (3TRE)


Logistics:  
Logistics:  


* Refer to details on session page at: http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2013_06_13
* Refer to details on session page at: http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2013_06_27


* (if you haven't already done so) please click on "settings" (top center)  
* (if you haven't already done so) please click on "settings" (top center) and morph from "anonymous" to your RealName (in WikiWord format)  
 
and morph from "anonymous" to your <nowiki>RealName</nowiki> (in WikiWord format)  


* Mute control: *7 to un-mute ... *6 to mute  
* Mute control: *7 to un-mute ... *6 to mute  
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if the dialpad button is not shown in the call window you need to press the "d" hotkey to enable it.  
if the dialpad button is not shown in the call window you need to press the "d" hotkey to enable it.  


Attendees: [[LeoObrst|Leo Obrst]] (co-chair), [[PeterYim|Peter P. Yim]] (co-chair), [[AmandaVizedom|Amanda Vizedom]], [[HaroldBoley|Harold Boley]], [[HensonGraves|Henson Graves]],  
Attendees: [[AidaGandara|Aida Gandara]], [[AlexShkotin|Alex Shkotin]], [[BobSmith|Bob Smith]], [[BobbinTeegarden|Bobbin Teegarden]], [[BrandonBennett|Brandon Bennett]], [[ChrisBaker|Chris Baker]],  
 
[[User:KennethBaclawski|Ken Baclawski]], [[MatthewWest|Matthew West]], [[MichaelGruninger|Michael Gr&uuml;ninger]], [[PavithraKenjige|Pavithra Kenjige]], [[SimonSpero|Simon Spero]], [[SteveRay|Steve Ray]], [[ToddSchneider|Todd Schneider]]
 
''' Proceedings '''
 
[8:35] List of attendees: [[HaroldBoley|Harold Boley]], [[HensonGraves|Henson Graves]], [[User:KennethBaclawski|Ken Baclawski]], [[LeoObrst|Leo Obrst]],
 
[[MatthewWest|Matthew West]], [[MichaelGruninger|Michael Gr&uuml;ninger]], [[PeterYim|Peter P. Yim]], [[SteveRay|Steve Ray]], [[ToddSchneider|Todd Schneider]], vnc2
 
[8:36] [[PeterYim|Peter P. Yim]]: == session start ... Leo opens with the slides ...
 
[8:45] [[AmandaVizedom|Amanda Vizedom]]: No shortage of ideas!
 
[8:49] [[PeterYim|Peter P. Yim]]: == Discussion begins ... see some of the ideas already floated ... under:
 
http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2013_06_13#nid3TV0
 
[8:52] [[PeterYim|Peter P. Yim]]: === Brainstorming now ...
 
[8:49] [[SteveRay|Steve Ray]]: How about interleaving a good ol' seminar series, with highly selective criteria
 
for speakers? Some of the really interesting past seminars such as on Siri, or Watson, would be the
 
kind of thing I'm thinking.
 
[8:49] [[LeoObrst|Leo Obrst]]: I'd like to see a session or sessions on updates about some of the ongoing
 
initiatives like [[OntoIOp]] and [[CommonLogic_V2]], which the Ontolog community probably doesn't know much
 
about.
 
[8:53] [[ToddSchneider|Todd Schneider]]: Steve, Leo, Yes.
 
[8:57] [[PeterYim|Peter P. Yim]]: @SteveRay - indeed! ... that's something we would want to keep doing, specifically
 
under ever-running "Ontolog Invited Speakers" series
 
[8:58] [[LeoObrst|Leo Obrst]]: IAOA Education Committee has an ongoing ontology textbook/handbook effort, and
 
there may be potential collaboration with efforts like AURA.
 
[9:01] [[MichaelGruninger|Michael Gr&uuml;ninger]]: @Leo: we could start this with a special brainstorming session on the
 
coverage of topics that people would like to see in an ontology textbook
 
[8:59] [[ToddSchneider|Todd Schneider]]: What outcomes are expected for today's discussion? ... [ [[LeoObrst|Leo Obrst]] / [[PeterYim|Peter P. Yim]]:
 
hopefully event plans that covers the planning horizon for the rest of the year, say, until Nov or
 
Dec-2013 when activities of the next [[OntologySummit|Ontology Summit]] will start in earnest. ]
 
[9:01] [[HensonGraves|Henson Graves]]: I have to check out soon, but hope to be involved in activities
 
[9:04] [[MichaelGruninger|Michael Gr&uuml;ninger]]: what topics do people feel have been under-represented or overlooked by
 
past Ontolog sessions?
 
[9:04] [[ToddSchneider|Todd Schneider]]: Michael, reasoning.
 
[9:05] [[AmandaVizedom|Amanda Vizedom]]: I would love to do an "Ontology of ontology evaluation" series...
 
[9:28] [[MichaelGruninger|Michael Gr&uuml;ninger]]: With a big-picture view, we could be looking for opportunities for new
 
applications of ontologies, or new domains that are looking for ontologies
 
[9:18] [[PeterYim|Peter P. Yim]]: is there a lot of interest in Ontology Vizualization?
 
[9:20] [[AmandaVizedom|Amanda Vizedom]]: There is an *enormous* amount of interest in visualization and visual-based
 
creation and editing of ontologies... This was frequently talked about at
 
[http://semtechbizsf2013.semanticweb.com/agenda.cfm?confid=70&scheduleDay=PRINT [[SemTechBiz]]] last week.
 
[9:22] [[AmandaVizedom|Amanda Vizedom]]: E.g., it was one of 4 breakouts in FIBO because the frequent division between
 
imprecise visual techniques for conceptual/business model development, on the one hand, and
 
formalization of these models for operational purposes, on the other, is both a bottleneck and
 
lossy.
 
[9:20] [[LeoObrst|Leo Obrst]]: Harold: does GRAILOG also potentially address diagrammatic reasoning/proof
 
representations and visualizations?
 
[9:31] [[HaroldBoley|Harold Boley]]: Leo, Grailog includes Directed Labeled Graphs (DLGs) as a sublanguage, hence can
 
reuse DLG-based reasoning/proof representations. For n-ary relationships, Grailog's directed
 
hyperarcs can then be introduced. For subproofs, Grailog's recursive (complex) nodes. These options
 
are in support of readability.
 
[9:28] [[HensonGraves|Henson Graves]]: Given that Ontolog is interesting in achieving practical results that impact
 
communities such as the engineering and systems communities, there are a number of areas where this
 
might be possible. (1) collecting evidence where ontologies is being used in engineering, (2)
 
ontology standards, particular that can be used in engineering modeling languages, (3) identifying
 
relevant research on visualization with ontology, integration of reasoning with ontology use,
 
logic-based foundations for ontologies, ..
 
[9:31] [[HensonGraves|Henson Graves]]: I have used a product development ontology as the basis for developing a large


information management system. I can talk about the ideas used, but cannot talk about the specifics.
[[DougFoxvog|Doug Foxvog]], [[FranLightsom|Fran Lightsom]], [[FrankChum|Frank Chum]], [[GaryBergCross]], [[GaryGannon|Gary Gannon]], [[HansPolzer|Hans Polzer]], [[HaroldBoley|Harold Boley]], [[JackPark|Jack Park]],  


By the way the use of an ontology was a replacement for use of metadata to organize product
[[JieZheng|Jie Zheng]], [[User:KennethBaclawski|Ken Baclawski]], KevinBurns, [[LamarHenderson|Lamar Henderson]], [[LeoObrst|Leo Obrst]], [[NaicongLi|Naicong Li]], [[OliverKutz|Oliver Kutz]], [[PatrickMaroney|Patrick Maroney]],


information. Metadata was were we started, but while good, wasn't good enough
[[PeterYim|Peter P. Yim]], [[RamonaWalls|Ramona Walls]], [[RichKeller|Rich Keller]], [[RogerBurkhart|Roger Burkhart]], [[SiraratSarntivijai|Sirarat Sarntivijai]], [[TaraAthan|Tara Athan]], [[TonyWeida|Tony Weida]], [[VinayChaudhri|Vinay Chaudhri]]


[9:33] anonymous morphed into [[SimonSpero|Simon Spero]]
''' Proceedings: '''


[9:35] anonymous morphed into [[PavithraKenjige|Pavithra Kenjige]]  
[9:28] anonymous morphed into [[VinayChaudhri|Vinay Chaudhri]]  


[9:18] [[SteveRay|Steve Ray]]: How about we try to get Richard Cyganiak to revisit his Linked Open Data diagram
[9:30] anonymous morphed into [[NaicongLi|Naicong Li]]  


and explore if an ongoing map of SPARQL end-points and other LOD sources could be maintained? I have
[9:31] anonymous1 morphed into [[PatrickMaroney|Patrick Maroney]]


always been disappointed that the latest version froze at September 2011.
[9:31] anonymous morphed into [[RogerBurkhart|Roger Burkhart]]


[9:26] [[AmandaVizedom|Amanda Vizedom]]: I can speak to the LOC (Library of Congress) issue
[9:32] anonymous2 morphed into [[SiraratSarntivijai|Sirarat Sarntivijai]]  


[9:33] [[AmandaVizedom|Amanda Vizedom]]: Yes, [[LinkedOpenData]] (LOD), and LOD-* (e.g., LOD-LAM, where "LAM" = Libraries,
[9:32] anonymous morphed into KevinBurns


Archives, and Museums) specialized groups are abundant and very busy
[9:34] anonymous morphed into [[BrandonBennett|Brandon Bennett]]


[9:39] [[LeoObrst|Leo Obrst]]: At least some of the LD/LOD folks focus just on the graph structure, and so may be
[9:35] [[PeterYim|Peter P. Yim]]: == [[LeoObrst|Leo Obrst]] starts the session and introduces the invited speaker, [[VinayChaudhri|Vinay Chaudhri]]


re-inventing "semantic networks", i.e., an older style of knowledge representation, prior to the
[9:39] [[PeterYim|Peter P. Yim]]: == [[VinayChaudhri|Vinay Chaudhri]] commences his talk ... see slides at: http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2013_06_27#nid3U3J


rise of ontologies.  
[9:41] [[PeterYim|Peter P. Yim]]: === [[VinayChaudhri|Vinay Chaudhri]] asks participants to take the next 5 minutes to view the video


[9:41] [[HensonGraves|Henson Graves]]: using graphs, doesn't have to be reinvinting semantic networks
clip - link on slide or at: http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2013_06_27#nid3U3J


[9:42] [[HaroldBoley|Harold Boley]]: Graphs can be seen as a 2D *syntax* for logics, e.g. Description Logic and Horn
[9:41] anonymous2 morphed into [[DougFoxvog|Doug Foxvog]]  


Logic.
[9:44] anonymous2 morphed into [[AidaGandara|Aida Gandara]]


[9:45] [[LeoObrst|Leo Obrst]]: No, most complex representations (such as logics) have an underlying graph
[9:46] [[FrankChum|Frank Chum]]: Nice video!


structure. So OWL and CL, etc., have graph representations. However, the LOD folks and some of these
[9:46] [[GaryBergCross]]: Done


"knowledge graphs"" are just like semantic networks, i.e., named nodes and edges without a supporting
[9:41] [[PeterYim|Peter P. Yim]]: === VinayChaudhri's talk continues ... (back to the slides)


ontology defining them. So pre-logical.
[9:56] anonymous2 morphed into [[ChrisBaker|Chris Baker]]


[9:48] [[SimonSpero|Simon Spero]]: @Leo: things don't seem to be quite as bad as the pre-Woods forest
[9:57] [[LeoObrst|Leo Obrst]]: The link http://www.ai.sri.com/halo/public/exported-kb/owl/ is not accessible


... less everything is a isa
(among others): Forbidden Access! But the full archive is available: http://www.ai.sri.com/halo/public/exported-kb/exported-kb.zip


[9:47] [[AmandaVizedom|Amanda Vizedom]]: Indeed. What was striking about the [http://semtechbizsf2013.semanticweb.com/agenda.cfm?confid=70&scheduleDay=PRINT [[SemTechBiz]]] talks
[9:57] [[DougFoxvog|Doug Foxvog]]: Aren't Red Blood Cells free of chromosomes? Slide 10 says all living cells have


was that most of them weren't using ""knowledge graphs"" in that pre-semantic way. My feeling is that
chromosomes? Do you have an exception mechanism?


the acknowledged desires for some supporting ontology comes from the fact that they seem very
[10:06] [[GaryBergCross]]: @Doug It would be good to know what the text says about red blood cells.


focused on interoperability.
[10:09] [[HaroldBoley|Harold Boley]]: Because of the huge # Equality Assertions, a special treatment of (Ground)


[10:00] [[HaroldBoley|Harold Boley]]: Leo, yes, we have seen graphs used for logics on many levels: from the
Equality would seem to make sense.


domain-expert syntax level to the model-theoretic semantics level to the system-implementation
[10:27] [[TaraAthan|Tara Athan]]: A chemist would probably consider the skeleton as a part of an organic molecule.


pragmatics level. We could try to get LOD folks interested in logics by showing that all of these
There are standard definitions of such terminology. e.g. http://goldbook.iupac.org/S05708.html


levels are dealt with formally in logic.  
[10:28] [[LeoObrst|Leo Obrst]]: Is "Has Part" always transitive? (slide 28, e.g.) "Has Material": what is


[9:47] [[PeterYim|Peter P. Yim]]: == Let's doing the planning, assignment of champions & scheduling ...
definition of "pervasive"? (slide 28)


[9:47] [[PeterYim|Peter P. Yim]]: Harold: note possible conflicts with AAAI Seattle - Jul 14~18, 2013
[10:31] [[JackPark|Jack Park]]: special event as final cause?


[9:48] [[HaroldBoley|Harold Boley]]: http://www.aaai.org/Conferences/IAAI/iaai13.php
[10:33] [[DougFoxvog|Doug Foxvog]]: The discussion of "hasFunction" (slide 31) needs to be based on what meaning you


[9:49] (considering the possibility of taking a summer break and not staging any events in Aug-2013)
have for the relation. It should be clarified that meaning is a subrelation of hasCapability.


[[MichaelGruninger|Michael Gr&uuml;ninger]] initiated a vote - please click the Vote button to cast your ballot: Do we want to
[10:40] [[PeterYim|Peter P. Yim]]: #39 - triples? ... [ VinayChaudhri: yes ... all ABox knowledge are represented in


have any Ontolog sessions in August? (1) Yes (2) No This is a single choice vote.
triples, which we store in our own knowledgebase, which we call KM "Knowledge Machine" ]


[9:49] [[HaroldBoley|Harold Boley]] voted for: No
[10:44] [[PatrickMaroney|Patrick Maroney]]: What licensing models are available for non-commercial research applications


[9:49] [[ToddSchneider|Todd Schneider]] voted for: No
in other domains?


[9:49] [[SteveRay|Steve Ray]] voted for: No
[10:51] [[LeoObrst|Leo Obrst]]: Path-based similarity: is it a strict path (class-relation-class... ) congruence,


[9:50] [[AmandaVizedom|Amanda Vizedom]] abstains
i.e., 1-1 similarity down the respective paths?


[9:50] [[MichaelGruninger|Michael Gr&uuml;ninger]] voted for: No
[10:53] [[PeterYim|Peter P. Yim]]: is the INQUIRE system self contained, and all loaded into the tablet, or does it


[9:50] [[PeterYim|Peter P. Yim]] voted for: Yes
also depend on access to, say, other online resources? ... see VinayChaudhri's response below at [11:08]  


[9:50] [[LeoObrst|Leo Obrst]] voted for: No
[10:55] [[DougFoxvog|Doug Foxvog]]: Slide 48, "Prior Work", should recognize other work done for the HALO project


[9:51] [[MichaelGruninger|Michael Gr&uuml;ninger]] ended the vote - results: Do we want to have any Ontolog sessions in August?
(which this project derives from). Much of what is discussed was covered by Cycorp's work on HALO.


Tally Choice
This should be recognized as prior work, imho.


1 Yes
[10:56] [[PeterYim|Peter P. Yim]]: @Vinay - can you elaborate a bit more on how you arrived at the Component Library


5 No
(CLIB) as your Upper Ontology of choice; which other candidates were also evaluated? and what


1 Abstains
criteria did you use in your evaluation? ... see VinayChaudhri's response below at [11:08]


[9:52] [[PeterYim|Peter P. Yim]]: The consensus is: there will be no Ontolog Events in August-2013
[10:59] [[LeoObrst|Leo Obrst]]: Slide 48: Arp & Smith and others use "dispositions" that might correspond to some


[9:53] [[PeterYim|Peter P. Yim]]: I'm expecting two upcoming invited speaker sessions imminently - [[BenjaminGrosof|Benjamin Grosof]] on
of your "context-dependent" functions, i.e., these are almost always a (contrafactual) conditional,


"RULELOG" and [[VinayChaudhri|Vinay Chaudhri]] on "AURA" and - these two events are slated for the next two Thursdays
if there were some "stimulus", there could be some manifestation.


slots ... [confirmed subsequently: respectively, on Jun-20 (RuleLog) & Jun-27 (Aura)]  
[11:00] [[GaryBergCross]]: One of the listed challenges was "What are repeating patterns of axioms in


[9:55] [[MichaelGruninger|Michael Gr&uuml;ninger]]: [reserving] October 3: Brainstorming for an Ontology textbook (Ontolog-IAOA
KB_Bio_101?" Have any ODPs been abstracted to date?


collaboration)
[11:03] anonymous1 morphed into [[RichKeller|Rich Keller]]


[9:59] [[MichaelGruninger|Michael Gr&uuml;ninger]]: Sorry, but I need to leave now  
[11:04] [[PeterYim|Peter P. Yim]]: === going into the Q&A and discussion now ...


[10:03] [[LeoObrst|Leo Obrst]]: Reasoning on ontologies could cover: formalisms and foundational issues
[11:08] [[PeterYim|Peter P. Yim]]: re. [10:53] [[PeterYim|Peter P. Yim]]: is the INQUIRE system self contained, and all loaded into


(propositional, predicate, rule reasoning, SAT), and logic programming, rule-based systems,  
the tablet, or does it also depend on access to, say, other online resources?


DL-reasoners, first-order theorem provers, etc.,  
... [ VinayChaudhri: AURA/INQUIRE is a client-server system, AURA is the server and INQUIRE is


[10:04] [[LeoObrst|Leo Obrst]]: Folks, I must leave now, but am interested in helping to organize the "ontology reasoning" sessions.
the client, which will need AURA available online to function ]


[10:08] [[SteveRay|Steve Ray]]: I need to go also. Thanks.
[11:13] [[PatrickMaroney|Patrick Maroney]]: What AURA/INQUIRE licensing models are available for non-commercial research


[10:08] [[PavithraKenjige|Pavithra Kenjige]]: Peter, could you include Ontology for accessibility as a topic..
applications in other domains? ... [ VinayChaudhri: please contact me offline. ]  


( example accessibility to support disability like 508 compliance?)
[11:16] [[LeoObrst|Leo Obrst]]: On slide 51, what do you mean by "regulation"? Is this "law-like"? Also, can you


... [ [[PeterYim|Peter P. Yim]] responded: yes, if there are reasonable interest on this topic among
talk about some of the issues with "causality"?


Ontolog members, and members of the "accessibility" community. Could you find out
[11:17] [[GaryBergCross]]: @Leo I was assuming that regulation referred to things like metabolic


the level of interest please, Pavithra.]
regulation, cell regulation etc.  


[10:08] [[PeterYim|Peter P. Yim]]: I want a date in July for "[[OntologyBasedStandards]]" ... (possibly more focused on
[11:18] [[LeoObrst|Leo Obrst]]: @Gary: ok, thanks, I wasn't sure.  


restarting QUOMOS, etc.)
[11:18] [[PeterYim|Peter P. Yim]]: re. choice of Upper Ontology [10:56], were the more comprehensives ones (like Cyc


[10:08] [[PeterYim|Peter P. Yim]]: note to ALL: we generally black out Jul-4, Nov (Thanksgiving), and pretty much the
and SUMO) considered ... [VinayChaudhri: note that all knowledge capture work were done by


second half of December
biologists (in fact, biologists who are not even co-located; they were offshore) therefore a key


[10:07] [[AmandaVizedom|Amanda Vizedom]]: Issue: The Open Financial Data Group continues to have a weekly call at noon
criteria was ease of use. ]  


on Thursdays.
[11:19] [[LeoObrst|Leo Obrst]]: Vinay, do you have a notion of granularity of the answer (and so, granularity of


[10:13] [[AmandaVizedom|Amanda Vizedom]]: I can't find duration of the OFDG calls; will check with MikeBennett. I
the reasoning)? I.e., can you step down into more detail on prompting by the user?


believe that the group, and the FIBO leads, would also prefer not to have this conflict.  
[11:36] [[PeterYim|Peter P. Yim]]: great talk ... thank you, Vinay ... thanks everyone!


[10:16] [[PeterYim|Peter P. Yim]]: ^LeoObrst / [[HensonGraves|Henson Graves]] / [[HaroldBoley|Harold Boley]] ( [[BenjaminGrosof|Benjamin Grosof]] / MikeDean)- maybe we
[11:36] [[FrankChum|Frank Chum]]: Interesting talk! Thanks


should a planning session to plan out that rules / reasoning / ontology-driven applications series
[11:37] [[LeoObrst|Leo Obrst]]: Thanks, Vinay and all for participating!


... possibly Jul-25
[11:36] [[PeterYim|Peter P. Yim]]: -- session ended: 11:36 am PDT --  


[10:21] [[PeterYim|Peter P. Yim]]: that leave either Jul-11 or 18 for the "[[OntologyBasedStandards]]" session
[11:44] [[PeterYim|Peter P. Yim]]: the raw chat-transcript is online now; cleaned up version of the chat-transcript,


[10:22] [[PeterYim|Peter P. Yim]]: [[ToddSchneider|Todd Schneider]]: I will not be able to champion more things the rest of this year
the audio recording, attendee roster, etc. will be available in a day or two. Look under:


... will be in a better position to do that in 2014
http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2013_06_27#nid3U41
 
[10:22] [[PeterYim|Peter P. Yim]]: let's continue to work via the [ontolog-forum] mailing list
 
[10:22] [[PeterYim|Peter P. Yim]]: ... very productive session; thanks everyone!
 
[10:23] [[PeterYim|Peter P. Yim]]: -- session ended: 10:20 am PDT --


-- end of in-session chat-transcript --  
-- end of in-session chat-transcript --  


* '''Further Question & Remarks''' - please post them to the [ [http://ontolog.cim3.net/forum/ontolog-forum/ ontolog-forum] ] listserv
'''... More Questions?'''  
** if you are already subscribed, post to <ontolog-forum [at] ontolog.cim3.net>
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== Additional Resources  ==


* Homepage of '''OntologySummit''' - note that a brainstorm session for next year's [[OntologySummit|Ontology Summit]] topic has been scheduled for Thu 2013.09.19
* For those who have further questions or remarks on the topic, please [mailto:ontolog-forum@ontolog.cim3.net post them to the [ontolog-forum]] so that everyone in the community can benefit from the discourse.
* '''Ontology of Ontology Evaluation''' project - [[OntologySummit2013_Hackathon_Clinics_OntologyOfOntologyEvaluation]]
* if you are not a member of the Ontolog community (meaning to say you are not subscribed to the [ontolog-forum] list) yet, we cordially invite you to join us. See our "Membership" details at: http://ontolog.cim3.net/cgi-bin/wiki.pl?WikiHomePage#nid1J
* '''[[OntologPSMW]]''' - http://ontolog-02.cim3.net/wiki/OntologySummit2013 - [[OntologySummit2013_Hackathon_Clinics_SemanticContentHack]]  
* Homepage of the '''[[OntologyBasedStandards]]''' Initiative
* Homepage of the '''[[OpenOntologyRepository]] ([http://oor.net OOR])''' Initiative


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== How To Join (while the session is in progress)  ==
== How To Join (while the session is in progress)  ==


* '''1.''' Dial in with a phone or from skype: http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2013_06_13#nid3TRT
* '''1.''' Dial in with a phone or from skype: http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2013_06_27#nid3TXU
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* '''2.''' Open chat-workspace in a new browser window: http://webconf.soaphub.org/conf/room/ontolog_20130627
* '''3.''' Download the speakers' slides here: http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2013_06_13#nid3TRJ
* '''3.''' Download the speaker's slides here: http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2013_06_27#nid3U3J
** or, '''3.1''' optionally, [[ConferenceCall_2013_06_13|access our shared-screen vnc server]], if you are not behind a corporate firewall  
** or, '''3.1''' optionally, [[ConferenceCall_2013_06_27|access our shared-screen vnc server]], if you are not behind a corporate firewall  


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Latest revision as of 06:44, 9 January 2016

Ontolog Invited Speaker Presentation - Dr. Vinay Chaudhri - Thu 2013.06.27

Session Chairs: Dr. LeoObrst (ONTOLOG; MITRE)

Invited Speaker: Dr. VinayChaudhri (SRI)

Title of Presentation: "KB_Bio_101: Conceptual Modeling Challenges in Creating a Biology Knowledge Base"

Archive:

Conference Call Details

  • Date: Thursday, 27-Jun-2013
  • Start Time: 9:30am PDT / 12:30pm EDT / 6:30pm CEST / 5:30pm BST / 16:30 UTC
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Attendees

  • Expecting:
    • ...
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Agenda & Proceedings

  • Session Format and Agenda:
    • this will be virtual session over a phone conference setting, augmented by in-session chat and shared computer screen support
    1. The session will start with a brief self-introduction of the attendees (~10 min.) ... (We will be skipping this if there are more than 20 participants)
    2. Introduction of the invited speakers - session chair: Leo Obrst
    3. Presentation by our invited speakers - Vinay Chaudhri (~60 min.) ... (slides)
    4. Q&A and Open discussion (~20 min.) ... (refer to process above)
    5. Closing (chair)

Abstract

"KB_Bio_101: Conceptual Modeling Challenges in Creating a Biology Knowledge Base" ... [ slides ]
VinayChaudhri_20130627b.jpg [ Dr. Vinay Chaudhri ]
KB_Bio_101 contains knowledge from an introductory college level biology textbook, has been developed as part of Project Halo, and is now freely available for research use. In this presentation, I will briefly introduce the knowledge representation used for creating the KB_Bio_101, and spend bulk of the time describing the design of an ontology for structure and function and the knowledge encoding process. KB_Bio_101 is a valuable resource for the ontology research community to study a variety of problems such as ontology quality, ontology design patterns, ontology modularization as well as for creating new ontologies for biological knowledge such as experiments, models, evolution, etc.

About the Speakers

Dr. Vinay K. Chaudhri is the Program Director at the Artificial Intelligence Center of SRI International (Menlo Park, California, USA.) His research focuses on the science and engineering of large knowledge base systems and spans knowledge representation and reasoning, deductive question answering, knowledge acquisition, and innovative applications. He is also interested in entrepreneurship, and transitioning research ideas into commercial products. He has worked with a wide range of knowledge representation and reasoning systems including LOOM, Ontolingua, Cyc, KM, and F-Logic. He was part of the team that developed the Open Knowledge Base Connectivity (OKBC) protocol for accessing knowledge bases. He contributed to storage, and multi-user software that underlies SRI's EcoCyc project. Since 2000, he has been working on a system to capture knowledge from science textbooks, and to answer questions at the back of the book.

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 in-session chat-transcript --

Chat transcript from room: ontolog_20130627

2013-06-27 GMT-08:00 [PDT]

[9:09] Peter P. Yim: Welcome to the

Ontolog Invited Speaker Presentation - Dr. Vinay Chaudhri - Thu 2013.06.27

  • Session Chair: Dr. Leo Obrst (ONTOLOG; MITRE)
  • Title of Presentation: "KB_Bio_101: Conceptual Modeling Challenges in Creating a Biology Knowledge Base"

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Attendees: Aida Gandara, Alex Shkotin, Bob Smith, Bobbin Teegarden, Brandon Bennett, Chris Baker,

Doug Foxvog, Fran Lightsom, Frank Chum, GaryBergCross, Gary Gannon, Hans Polzer, Harold Boley, Jack Park,

Jie Zheng, Ken Baclawski, KevinBurns, Lamar Henderson, Leo Obrst, Naicong Li, Oliver Kutz, Patrick Maroney,

Peter P. Yim, Ramona Walls, Rich Keller, Roger Burkhart, Sirarat Sarntivijai, Tara Athan, Tony Weida, Vinay Chaudhri

Proceedings:

[9:28] anonymous morphed into Vinay Chaudhri

[9:30] anonymous morphed into Naicong Li

[9:31] anonymous1 morphed into Patrick Maroney

[9:31] anonymous morphed into Roger Burkhart

[9:32] anonymous2 morphed into Sirarat Sarntivijai

[9:32] anonymous morphed into KevinBurns

[9:34] anonymous morphed into Brandon Bennett

[9:35] Peter P. Yim: == Leo Obrst starts the session and introduces the invited speaker, Vinay Chaudhri

[9:39] Peter P. Yim: == Vinay Chaudhri commences his talk ... see slides at: http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2013_06_27#nid3U3J

[9:41] Peter P. Yim: === Vinay Chaudhri asks participants to take the next 5 minutes to view the video

clip - link on slide or at: http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2013_06_27#nid3U3J

[9:41] anonymous2 morphed into Doug Foxvog

[9:44] anonymous2 morphed into Aida Gandara

[9:46] Frank Chum: Nice video!

[9:46] GaryBergCross: Done

[9:41] Peter P. Yim: === VinayChaudhri's talk continues ... (back to the slides)

[9:56] anonymous2 morphed into Chris Baker

[9:57] Leo Obrst: The link http://www.ai.sri.com/halo/public/exported-kb/owl/ is not accessible

(among others): Forbidden Access! But the full archive is available: http://www.ai.sri.com/halo/public/exported-kb/exported-kb.zip

[9:57] Doug Foxvog: Aren't Red Blood Cells free of chromosomes? Slide 10 says all living cells have

chromosomes? Do you have an exception mechanism?

[10:06] GaryBergCross: @Doug It would be good to know what the text says about red blood cells.

[10:09] Harold Boley: Because of the huge # Equality Assertions, a special treatment of (Ground)

Equality would seem to make sense.

[10:27] Tara Athan: A chemist would probably consider the skeleton as a part of an organic molecule.

There are standard definitions of such terminology. e.g. http://goldbook.iupac.org/S05708.html

[10:28] Leo Obrst: Is "Has Part" always transitive? (slide 28, e.g.) "Has Material": what is

definition of "pervasive"? (slide 28)

[10:31] Jack Park: special event as final cause?

[10:33] Doug Foxvog: The discussion of "hasFunction" (slide 31) needs to be based on what meaning you

have for the relation. It should be clarified that meaning is a subrelation of hasCapability.

[10:40] Peter P. Yim: #39 - triples? ... [ VinayChaudhri: yes ... all ABox knowledge are represented in

triples, which we store in our own knowledgebase, which we call KM "Knowledge Machine" ]

[10:44] Patrick Maroney: What licensing models are available for non-commercial research applications

in other domains?

[10:51] Leo Obrst: Path-based similarity: is it a strict path (class-relation-class... ) congruence,

i.e., 1-1 similarity down the respective paths?

[10:53] Peter P. Yim: is the INQUIRE system self contained, and all loaded into the tablet, or does it

also depend on access to, say, other online resources? ... see VinayChaudhri's response below at [11:08]

[10:55] Doug Foxvog: Slide 48, "Prior Work", should recognize other work done for the HALO project

(which this project derives from). Much of what is discussed was covered by Cycorp's work on HALO.

This should be recognized as prior work, imho.

[10:56] Peter P. Yim: @Vinay - can you elaborate a bit more on how you arrived at the Component Library

(CLIB) as your Upper Ontology of choice; which other candidates were also evaluated? and what

criteria did you use in your evaluation? ... see VinayChaudhri's response below at [11:08]

[10:59] Leo Obrst: Slide 48: Arp & Smith and others use "dispositions" that might correspond to some

of your "context-dependent" functions, i.e., these are almost always a (contrafactual) conditional,

if there were some "stimulus", there could be some manifestation.

[11:00] GaryBergCross: One of the listed challenges was "What are repeating patterns of axioms in

KB_Bio_101?" Have any ODPs been abstracted to date?

[11:03] anonymous1 morphed into Rich Keller

[11:04] Peter P. Yim: === going into the Q&A and discussion now ...

[11:08] Peter P. Yim: re. [10:53] Peter P. Yim: is the INQUIRE system self contained, and all loaded into

the tablet, or does it also depend on access to, say, other online resources?

... [ VinayChaudhri: AURA/INQUIRE is a client-server system, AURA is the server and INQUIRE is

the client, which will need AURA available online to function ]

[11:13] Patrick Maroney: What AURA/INQUIRE licensing models are available for non-commercial research

applications in other domains? ... [ VinayChaudhri: please contact me offline. ]

[11:16] Leo Obrst: On slide 51, what do you mean by "regulation"? Is this "law-like"? Also, can you

talk about some of the issues with "causality"?

[11:17] GaryBergCross: @Leo I was assuming that regulation referred to things like metabolic

regulation, cell regulation etc.

[11:18] Leo Obrst: @Gary: ok, thanks, I wasn't sure.

[11:18] Peter P. Yim: re. choice of Upper Ontology [10:56], were the more comprehensives ones (like Cyc

and SUMO) considered ... [VinayChaudhri: note that all knowledge capture work were done by

biologists (in fact, biologists who are not even co-located; they were offshore) therefore a key

criteria was ease of use. ]

[11:19] Leo Obrst: Vinay, do you have a notion of granularity of the answer (and so, granularity of

the reasoning)? I.e., can you step down into more detail on prompting by the user?

[11:36] Peter P. Yim: great talk ... thank you, Vinay ... thanks everyone!

[11:36] Frank Chum: Interesting talk! Thanks

[11:37] Leo Obrst: Thanks, Vinay and all for participating!

[11:36] Peter P. Yim: -- session ended: 11:36 am PDT --

[11:44] Peter P. Yim: the raw chat-transcript is online now; cleaned up version of the chat-transcript,

the audio recording, attendee roster, etc. will be available in a day or two. Look under:

http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2013_06_27#nid3U41

-- end of in-session chat-transcript --

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