ppy/Ontolog_VinayChaudhri_KB-Bio-101_chat-transcript_edited_20130627b.txt ------ Chat transcript from room: ontolog_20130627 2013-06-27 GMT-08:00 [PDT] ------ [9:09] PeterYim: Welcome to the = Ontolog Invited Speaker Presentation - Dr. Vinay Chaudhri - Thu 2013.06.27 = * Session Chair: Dr. LeoObrst (ONTOLOG; MITRE) * Invited Speaker: Dr. VinayChaudhri (SRI) * Title of Presentation: "KB_Bio_101: Conceptual Modeling Challenges in Creating a Biology Knowledge Base" Logistics: * 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) 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: AidaGandara, AlexShkotin, BobSmith, BobbinTeegarden, BrandonBennett, ChrisBaker, DougFoxvog, FranLightsom, FrankChum, GaryBergCross, GaryGannon, HansPolzer, HarolBoley, JackPark, JieZheng, KenBaclawski, KevinBurns, LamarHenderson, LeoObrst, NaicongLi, OliverKutz, PatrickMaroney, PeterYim, RamonWalls, RichKeller, RogerBurkhart, SiraraSarntivijai, TaraAthan, TonyWeida, VinayChaudhri == Proceedings: == [9:28] anonymous morphed into VinayChaudhri [9:30] anonymous morphed into NaicongLi [9:31] anonymous1 morphed into PatrickMaroney [9:31] anonymous morphed into RogerBurkhart [9:32] anonymous2 morphed into SiraratSarntivijai [9:32] anonymous morphed into KevinBurns [9:34] anonymous morphed into BrandonBennett [9:35] PeterYim: == LeoObrst starts the session and introduces the invited speaker, VinayChaudhri [9:39] PeterYim: == VinayChaudhri commences his talk ... see slides at: http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2013_06_27#nid3U3J [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 [9:41] anonymous2 morphed into DougFxovg [9:44] anonymous2 morphed into AidaGandara [9:46] FrankChum: Nice video! [9:46] GaryBergCross: Done [9:41] PeterYim: === VinayChaudhri's talk continues ... (back to the slides) [9:56] anonymous2 morphed into ChrisBaker [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 [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? [10:06] GaryBergCross: @Doug It would be good to know what the text says about red blood cells. [10:09] HaroldBoley: Because of the huge # Equality Assertions, a special treatment of (Ground) Equality would seem to make sense. [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 [10:28] LeoObrst: Is "Has Part" always transitive? (slide 28, e.g.) "Has Material": what is definition of "pervasive"? (slide 28) [10:31] JackPark: special event as final cause? [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. [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" ] [10:44] PatrickMaroney: What licensing models are available for non-commercial research applications in other domains? [10:51] LeoObrst: Path-based similarity: is it a strict path (class-relation-class... ) congruence, i.e., 1-1 similarity down the respective paths? [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] [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. [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] [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. [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 RichKeller [11:04] PeterYim: === going into the Q&A and discussion now ... [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 ] [11:13] PatrickMaroney: What AURA/Inquire licensing models are available for non-commercial research applications in other domains? ... [ VinayChaudhri: please contact me offline. ] [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"? [11:17] GaryBergCross: @Leo I was assuming that regulation referred to things like metabolic regulation, cell regulation etc. [11:18] LeoObrst: @Gary: ok, thanks, I wasn't sure. [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. ] [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? [11:36] PeterYim: great talk ... thank you, Vinay ... thanks everyone! [11:36] FrankChum: Interesting talk! Thanks [11:37] LeoObrst: Thanks, Vinay and all for participating! [11:36] PeterYim: -- session ended: 11:36 am PDT -- [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 ------