Ontolog Invited Speaker Presentation - Dr. Vinay Chaudhri - Thu 2013.06.27    (3TW5)

Session Chairs: Dr. LeoObrst (ONTOLOG; MITRE)    (3TXM)

Invited Speaker: Dr. VinayChaudhri (SRI)    (3TXN)

Title of Presentation: "KB_Bio_101: Conceptual Modeling Challenges in Creating a Biology Knowledge Base"    (3TXO)

Archive:    (3U3G)

Conference Call Details    (3TXP)

Attendees    (3TYM)

Agenda & Proceedings    (3U3N)

Abstract    (3U3V)

"KB_Bio_101: Conceptual Modeling Challenges in Creating a Biology Knowledge Base" ... [ slides ]    (3U3W)

http://ontolog.cim3.net/file/resource/presentation/VinayChaudhri_20130627/VinayChaudhri_20130627b.jpg [ Dr. Vinay Chaudhri ]    (3U3X)

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.    (3U3Y)

About the Speakers    (3U3Z)

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.    (3U40)

Transcript of the online chat during the session:    (3U41)

 see raw transcript here.    (3U42)
 (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.    (3U43)
    -- begin in-session chat-transcript --    (3U44)
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	Chat transcript from room: ontolog_20130627
	2013-06-27 GMT-08:00 [PDT]
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	[9:09] PeterYim: Welcome to the    (3UV5)
	 = Ontolog Invited Speaker Presentation - Dr. Vinay Chaudhri - Thu 2013.06.27 =    (3UV6)
	* Session Chair: Dr. LeoObrst (ONTOLOG; MITRE)    (3UV7)
	* Invited Speaker: Dr. VinayChaudhri (SRI)    (3UV8)
	* Title of Presentation: "KB_Bio_101: Conceptual Modeling Challenges in Creating a Biology Knowledge Base"    (3UV9)
	Logistics:    (3UVA)
	* Refer to details on session page at: http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2013_06_27    (3UVB)
	* (if you haven't already done so) please click on "settings" (top center) and morph from "anonymous" to your RealName (in WikiWord format)    (3UVC)
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	Attendees: AidaGandara, AlexShkotin, BobSmith, BobbinTeegarden, BrandonBennett, ChrisBaker, 
	DougFoxvog, FranLightsom, FrankChum, GaryBergCross, GaryGannon, HansPolzer, HaroldBoley, JackPark, 
	JieZheng, KenBaclawski, KevinBurns, LamarHenderson, LeoObrst, NaicongLi, OliverKutz, PatrickMaroney, 
	PeterYim, RamonaWalls, RichKeller, RogerBurkhart, SiraratSarntivijai, TaraAthan, TonyWeida, VinayChaudhri    (3UVF)
	 == Proceedings: ==    (3UVG)
	[9:28] anonymous morphed into VinayChaudhri    (3UVH)
	[9:30] anonymous morphed into NaicongLi    (3UVI)
	[9:31] anonymous1 morphed into PatrickMaroney    (3UVJ)
	[9:31] anonymous morphed into RogerBurkhart    (3UVK)
	[9:32] anonymous2 morphed into SiraratSarntivijai    (3UVL)
	[9:32] anonymous morphed into KevinBurns    (3UVM)
	[9:34] anonymous morphed into BrandonBennett    (3UVN)
	[9:35] PeterYim: == LeoObrst starts the session and introduces the invited speaker, VinayChaudhri    (3UVO)
	[9:39] PeterYim: == VinayChaudhri commences his talk ... see slides at: http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2013_06_27#nid3U3J    (3UVP)
	[9:41] PeterYim: === VinayChaudhri 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    (3UVQ)
	[9:41] anonymous2 morphed into DougFoxvog    (3UVR)
	[9:44] anonymous2 morphed into AidaGandara    (3UVS)
	[9:46] FrankChum: Nice video!    (3UVT)
	[9:46] GaryBergCross: Done    (3UVU)
	[9:41] PeterYim: === VinayChaudhri's talk continues ... (back to the slides)    (3UVV)
	[9:56] anonymous2 morphed into ChrisBaker    (3UVW)
	[9:57] LeoObrst: 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    (3UVX)
	[9:57] DougFoxvog: Aren't Red Blood Cells free of chromosomes? Slide 10 says all living cells have 
	chromosomes? Do you have an exception mechanism?    (3UVY)
	[10:06] GaryBergCross: @Doug It would be good to know what the text says about red blood cells.    (3UVZ)
	[10:09] HaroldBoley: Because of the huge # Equality Assertions, a special treatment of (Ground) 
	Equality would seem to make sense.    (3UW0)
	[10:27] TaraAthan: 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    (3UW1)
	[10:28] LeoObrst: Is "Has Part" always transitive? (slide 28, e.g.) "Has Material": what is 
	definition of "pervasive"? (slide 28)    (3UW2)
	[10:31] JackPark: special event as final cause?    (3UW3)
	[10:33] DougFoxvog: 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.    (3UW4)
	[10:40] PeterYim: #39 - triples? ... [ VinayChaudhri: yes ... all ABox knowledge are represented in 
	triples, which we store in our own knowledgebase, which we call KM "Knowledge Machine" ]    (3UW5)
	[10:44] PatrickMaroney: What licensing models are available for non-commercial research applications 
	in other domains?    (3UW6)
	[10:51] LeoObrst: Path-based similarity: is it a strict path (class-relation-class... ) congruence, 
	i.e., 1-1 similarity down the respective paths?    (3UW7)
	[10:53] PeterYim: 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]    (3UW8)
	[10:55] DougFoxvog: 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.    (3UW9)
	[10:56] PeterYim: @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]    (3UWA)
	[10:59] LeoObrst: 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.    (3UWB)
	[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?    (3UWC)
	[11:03] anonymous1 morphed into RichKeller    (3UWD)
	[11:04] PeterYim: === going into the Q&A and discussion now ...    (3UWE)
	[11:08] PeterYim: re. [10:53] PeterYim: 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 ]    (3UWF)
	[11:13] PatrickMaroney: What AURA/INQUIRE licensing models are available for non-commercial research 
	applications in other domains? ... [ VinayChaudhri: please contact me offline. ]    (3UWG)
	[11:16] LeoObrst: On slide 51, what do you mean by "regulation"? Is this "law-like"? Also, can you 
	talk about some of the issues with "causality"?    (3UWH)
	[11:17] GaryBergCross: @Leo I was assuming that regulation referred to things like metabolic 
	regulation, cell regulation etc.    (3UWI)
	[11:18] LeoObrst: @Gary: ok, thanks, I wasn't sure.    (3UWJ)
	[11:18] PeterYim: 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. ]    (3UWK)
	[11:19] LeoObrst: 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?    (3UWL)
	[11:36] PeterYim: great talk ... thank you, Vinay ... thanks everyone!    (3UWM)
	[11:36] FrankChum: Interesting talk! Thanks    (3UWN)
	[11:37] LeoObrst: Thanks, Vinay and all for participating!    (3UWO)
	[11:36] PeterYim: -- session ended: 11:36 am PDT --    (3UWP)
	[11:44] PeterYim: 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    (3UWQ)
    -- end of in-session chat-transcript --    (3U45)

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