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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
  • Expected Call Duration: ~1.5 hours
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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"

Logistics:

  • (if you haven't already done so) please click on "settings" (top center) and morph from "anonymous" to your RealName (in WikiWord format)
  • Mute control: *7 to un-mute ... *6 to mute
  • Can't find Skype Dial pad?
    • for Windows Skype users: it's under the "Call" dropdown menu as "Show Dial pad"
    • for Linux Skype users: please note that the dial-pad is only available on v4.1 (or later or the earlier Skype versions 2.x,)

if the dialpad button is not shown in the call window you need to press the "d" hotkey to enable it.

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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