ppy/Ontolog_VinayChaudhri_KB-Bio-101_chat-transcript_unedited_20130627a.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: DDr. 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. . == Proceedings: == . [9:28] anonymous morphed into vinay [9:28] vinay morphed into VinayChaudhri [9:30] anonymous morphed into NaicongLi [9:31] anonymous1 morphed into patrickmaroney [9:31] anonymous morphed into Roger Burkhart [9:32] anonymous2 morphed into Sirarat Sarntivijai [9:32] anonymous morphed into Kevin Burns [9:34] anonymous morphed into Brandon [9:41] anonymous2 morphed into dougFxovg [9:41] dougFxovg morphed into dougFoxvog [9:44] anonymous2 morphed into Aida Gandara [9:46] Frank Chum: Nice video! [9:46] Gary Berg-Cross: Done [9:56] anonymous2 morphed into ChrisB [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? [10:05] PeterYim: ERRATA (taking out the period at the end to make the link work properly) [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 [10:06] Gary Berg-Cross: @ Doug It would be good to know what the text says about red blood cells. [10:06] PeterYim: ... all: please do not append punctuation marks to url's [10:09] Harold Boley: 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. [10:28] LeoObrst: Is "Has Part" always transitive? (slide 28, e.g.) "Has Material": what is definition of "pervasive"? (slide 28) [10:30] TaraAthan: e.g. http://goldbook.iupac.org/S05708.html [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? [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? [10:55] dougFoxvog2: 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? [10:58] dougFoxvog2 morphed into dougFoxvog [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] Gary Berg-Cross: One of the listed challenges was "What are repeating patterns of axioms in KB_Bio_101?" Have any ODPs been abstracted to date? [11:00] List of members: Aida Gandara, AlexShkotin, anonymous, Bob Smith, BobbinTeegarden, Brandon, dougFoxvog, Frank Chum, FranLightsom, Gary Berg-Cross, Hans Polzer, Harold Boley, JackPark, JieZheng, KenBaclawski, LeoObrst, NaicongLi, OliverKutz, patrickmaroney, PeterYim, Roger Burkhart, TonyWeida1, VinayChaudhri, vnc2 [11:03] anonymous1 morphed into RichKeller [11:04] PeterYim: === going into the Q&A and discussion [11:08] PeterYim: re. [xx: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 [11:10] dougFoxvog2 morphed into dougFoxvog [11:13] patrickmaroney: What AURA/Inquire licensing models are available for non-commercial research applications in other domains? [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] Gary Berg-Cross: @Leo I was assuming that regulation referred to things like metabolic regulation, cell regulation etc. [11:18] PeterYim: re. [xx.56] 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. [11:18] LeoObrst: @Gary: ok, thanks, I wasn't sure. [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] Frank Chum: Interesting talk! Thanks [11:36] PeterYim: -- session ended: 11:36 am PDT -- [11:37] List of attendees: Aida Gandara, AlexShkotin, Bob Smith, BobbinTeegarden, Brandon, ChrisB, ChrisB1, FranLightsom, Frank Chum, Gary Berg-Cross, Gary Gannon, Hans Polzer, Harold Boley, JackPark, JieZheng, KenBaclawski, Kevin Burns, LeoObrst, NaicongLi, OliverKutz, PeterYim, Ramona Walls, RichKeller, Roger Burkhart, Sirarat Sarntivijai, TaraAthan, TonyWeida, TonyWeida1, VinayChaudhri, anonymous, anonymous1, anonymous2, dougFoxvog, dougFoxvog1, dougFoxvog2, dougFxovg, lamarhenderson, patrickmaroney, vinay, vnc2 [11:37] LeoObrst: Thanks, Vinay and all for participating! [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 ------