ppy/OntologySummit2013_s10_chat-transcript_unedited_20130321a.txt ------ Chat transcript from room: summit_20130321 2013-03-21 GMT-08:00 [PDT] ------ [9:16] PeterYim: Welcome to the = OntologySummit2013: Virtual Panel Session-10 - Thu 2013-03-21 = Summit Theme: Ontology Evaluation Across the Ontology Lifecycle * Summit Track Title: Track-D: Software Environments for Evaluating Ontologies Session Topic: Software Environments for Evaluating Ontologies - II * Session Co-chairs: Dr. MichaelDenny (MITRE) & Mr. PeterYim (Ontolog; CIM3) Panelists / Briefings: * Mr. AdamPease (Articulate Software) - "The Sigma Knowledge Engineering Environment" * Prof. Dr. TillMossakowski (University of Bremen) - "Ontohub.org - a web platform for distributed and heterogeneous ontologies" * Dr. TaniaTudorache (Stanford-BMIR) - "WebProtege and BioPortal as Infrastructures for Ontology Evaluation" * Professor MichelDumontier (Carleton University) - "Evaluation of ontology-powered scientific research as a means to assess and improve ontology quality" * Mr. KingsleyIdehen (OpenLink Software) - "Ontology life cycles and Linked Open Data (LOD)" Logistics: * Refer to details on session page at: http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2013_03_21 * (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: == . [9:17] PeterYim: Attn ALL: ... it has come to our attention that our conference bridge provider is running into some problems with the "joinconference" skype connections. In case anyone gets in trouble, please try to call the phone numbers instead (e.g. from your phone, skype-out, google-voice, etc.) . [7:42] anonymous morphed into K. Z. Watkins [9:22] anonymous morphed into MichaelDenny [9:26] anonymous morphed into Brian Haugh [9:27] anonymous morphed into anonymous2 [9:28] Michel Dumontier: howdy [9:28] anonymous1 morphed into TorstenHahmann [9:29] anonymous morphed into AdamPease [9:29] MichaelDenny: The survey of software capabilities for ontology quality & fitness across the ontology life cycle has launched at http://ontolog-02.cim3.net/wiki/OntologySummit2013_Survey. Spread the word! [9:29] MariaPoveda1 morphed into MariaPoveda [9:30] anonymous morphed into FranLightsom [9:30] MariaPoveda morphed into MariaPovedaVillalon [9:30] anonymous morphed into Rich Markeloff [9:30] anonymous1 morphed into Tania Tudorache [9:31] anonymous3 morphed into dougFoxvog [9:31] anonymous morphed into BriceSommacal [9:32] anonymous morphed into LamarHenderson [9:33] K. Z. Watkins: are slides only on skype? [9:36] Michel Dumontier: *7 [9:37] Michel Dumontier: skyping out [9:37] MeganKatsumi: @K.Z. You can download the slides here: http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2013_03_21#nid3NT2 [9:38] anonymous morphed into TomTinsley [9:39] PeterYim: == MikeDenny opens the session on behalf of the co-chairs ... see: the [0-Chair] slides [9:42] PeterYim: === slide#3 - MichaelDenny announcing the OntologySummit2013 Survey on software capabilities for quality and fitness of ontologies ... [9:44] PeterYim: see also: http://ontolog.cim3.net/forum/ontology-summit/2013-03/msg00197.html [9:45] PeterYim: the survey is at: http://ontolog-02.cim3.net/wiki/OntologySummit2013_Survey [9:47] Brian Haugh: Clap, Clap, Clap, Clap, ... [9:48] PeterYim: == AdamPease presenting ... see: the [1-Pease] slides [9:53] SimonSpero: What about horses that only have three legs [9:54] SimonSpero: "A horse like that, you don't eat all at once" [10:00] TillMossakowski: is the translation from SUO-KIF to OWL described somewhere? [10:00] AmandaVizedom: Question for @AdamPease: Any plans for support of Common Logic? [10:06] JoelBender: Isn't there a CL to KIF translator? [10:06] SimonSpero: Hets sort of does that [10:07] SimonSpero: for certain senses of KIF [10:07] MatthewWest: KIF is a dialect of CL [10:08] AmandaVizedom: Comment: I strongly agree with this point: having enough content to perform interesting inferences, and having ready/easy inference capability ready to hand, makes certain kinds of error detection and debugging much easier and more naturally integrated into development process. [10:08] SimonSpero: Hets module CommonLogic.Parse_KIF [10:09] anonymous1 morphed into PavithraKenjige [10:09] PeterYim: == TillMossakowski presenting ... see: the [2-Mossakowski] slides [10:09] anonymous1 morphed into SteveRay [10:10] anonymous1 morphed into RobertYao [10:11] anonymous2 morphed into Jcruanes [10:11] anonymous1 morphed into Daniel Couto Vale [10:11] MichaelGruninger: There is a long history behind the relationship of KIF and CL. KIF 3.0 (which is the last available document for KIF) evolved into Common Logic, but KIF also included a lot of other notions (such as set theory and metalanguage) that are not contained in Common Logic (which is the standard ISO 24707). Common Logic without sequence variables is first-order expressive. I'm not sure about the precise formal relationship of SUO-KIF and Common Logic -- this would require a closer look at the relationship of SUO-KIF and second-order logic. [10:11] anonymous1 morphed into LamarHenderson [10:12] Jcruanes morphed into Jorge Cruanes [10:13] TorstenHahmann: There is a CL to KIF, Prover9, and TPTP translator available from https://github.com/cmungall/cltools; it is in Prolog. It translates the first-order portion of CL. I have developed wrappers to translate (and evaluate) large sets of CL ontologies, I'm currently moving all the source to a Github project: https://github.com/thahmann/macleod [10:19] PeterYim: TillMossakowski - see: http://ontohub-new.informatik.uni-bremen.de/ [10:20] anonymous1 morphed into MarcelloBax [10:23] TorstenHahmann: @MichaelDenny: For the survey, I can't seem to login with my ontolog credentials - is there any extra signup required? [10:24] MichaelDenny: @Torsten If you are having problems, please use guest and ontolog-guest. [10:24] PeterYim: @TorstenHahmann & ALL: anyone having issues with the login (for the survey) can logiin with: username=guest ; password=ontolog-guest [10:25] PeterYim: == TaniaTudorache presenting ... see: the [3-Tudorache] slides [10:25] List of members: AdamPease, AmandaVizedom, AnatolyLevenchuk, anonymous, anonymous1, AstridDuqueRamos, Bob Smith, Brian Haugh, BruceBray, Daniel Couto Vale, dougFoxvog, FabianNeuhaus, FranLightsom, JoelBender, JohnBilmanis, Jorge Cruanes, K. Z. Watkins, KenBaclawski, Kingsley Idehen (kidehen)1, LamarHenderson, MarcelloBax, MariaPovedaVillalon, MatthewWest, MeganKatsumi, MichaelDenny, MichaelGruninger, Michel Dumontier, MikeDean, MikeRiben, OliverKutz, PavithraKenjige, PeterYim, Ram D. Sriram, Rich Markeloff, RobertYao1, SimonSpero, SteveRay, Tania Tudorache1, TerryLongstreth, TillMossakowski, ToddSchneider, TorstenHahmann, vnc2 [10:26] TorstenHahmann: @PeterYim & @MichaelDenny: thanks, that works. [10:30] dougFoxvog: Tania's Slide 4 mentions "Contextual notes and discussions attached to any entity in the ontology". Can such notes be attached to statements, or merely to the terms? [10:37] AmandaVizedom: Question for @TaniaTudorache: Is it correct to say that Web Protege supports collaborative manual evaluation, and potentially documentation of automated or semi-automated evaluation and/or metrics gathering that others may have done independently, but does not support such evaluation itself? [10:39] PeterYim: @TaniaTudorache: can one access the collected user review input, and slice-and-dice that data [10:41] PeterYim: ... I guess its the same question Amanda is asking [10:41] dougFoxvog: Ref Slide 12. What about an ontology for encoding the reviews using relations & terms defined in the ontology? [10:41] AdamPease: just reading the chat logs [10:41] PeterYim: == MichelDumontier presenting ... see: the [4-Dumontier] slides [10:42] AmandaVizedom: Comment: Tania's slide 12 regarding issues with review suggests, to me, that it would be helpful to have a common understanding of ontology characteristics and evaluation metrics/techniques, such that these could be explicitly addressed in reviews. One would like to see reviews evolve to focus on such shared questions. [10:42] AdamPease: KIF and SUO-KIF are quite different, so unless it's specifically a SUO-KIF translator, it won't work for SUMO [10:42] AdamPease: translating CL to the first-order subset of SUO-KIF should be easy [10:42] TillMossakowski: I think in Hets we have some translation of SUO-KIF into Common Logic [10:43] AdamPease: I included a presentation of that in Sigma at one point I think, mainly just renaming some of the logical symbols as I recall [10:44] AdamPease: that sounds great Til [10:45] PeterYim: @AdamPease: re your xx:43where can one find that presentation ... can you supply a link to it? [10:45] AdamPease: ? [10:45] AdamPease: oh, not a slide presentation [10:46] AdamPease: a presentation of logic [10:46] PeterYim: @Adam: this is in reference you your earlier statement "I included a presentation of that in Sigma at one point ..." ... can you supply a link to that presentation? [10:46] AdamPease: use the "traditionalLogic" menu option in the menu title "Formal Language" in the Sigma browser [10:47] PeterYim: Ah ... thanks, Adam [10:51] AmandaVizedom: Comment: Just noting, per @MichelDumontier's slide 3, that GO is a controlled vocabulary (common in domain, i think) -- i.e., the "nodes" are NL expressions. I wonder whether the significance of annotation change patterns, for example, would be different for a concept-centric ontology, with (potentially multiple) NL expressions associated, that for a controlled vocabulary like this. [10:53] AmandaVizedom: (I would think so; the concept-centric ontology with lexical mappings should be less brittle to language change than the controlled vocab. In any case, it's a good example of the importance of being clear what kind of KR artifact you are dealing with before you can understand what to evaluate and how to interpret it. [10:57] AmandaVizedom: @Michel - re slide 11: Great examples of how different kinds of evaluation can be more or less relevant depending on how the ontology is going to be used (or reused). [11:01] TorstenHahmann: @AdamPease: Adam, you mentioned that the KIF version of SUMO can be automatically translated to OWL. can you expand a little on how that works (or give me a pointer)? Which OWL variant (OWL-DL?) do you translate to? In particular, I would think you would need to consider all entailments of the first-order ontology to ensure that the translation is complete (with respect to the expressivity of OWL). How do get around this? [11:02] TillMossakowski: interesting question! [11:03] AdamPease: I make no claims that it's a complete translation [11:03] AdamPease: especially since OWL is so limited [11:03] AdamPease: but even within its limitations, we don't do anything extraordinary [11:03] AdamPease: all binary relations get translated [11:03] TerryLongstreth: @Michel - Slide 13 - did you subdivide the volunteer community by expertise? Did expertise/experience make any difference? [11:04] AdamPease: we translate all the builtin terms in OWL to their equivalents in SUMO [11:04] AdamPease: all rules get turned into comments [11:04] AdamPease: that's about it [11:06] TorstenHahmann: thanks, I was just wondering [11:10] Michel Dumontier: @Terry - the volunteers were experts at a conference on the topic [11:11] TerryLongstreth: Thanks, Michel. [11:11] PeterYim: == KingsleyIdehen presenting ... see: the [5-Idehen] slides [11:15] Michel Dumontier: @Amanda - The GO has made strides to be a more conformant "ontology", but I find it confusing/lacking in many respects, but doesn't diminish it's current utility in scientific research. Thanks for the positive comment on slide 11 :) [11:16] PeterYim: @ALL: note that Kingsley is working off a slightly updated deck of slides. If you downloaded the slide before he started talking, you might wanted to download the (the updated) slides again [11:23] Brian Haugh: slide number? [11:24] TillMossakowski: 12 [11:24] MatthewWest: Afraid I need to go now. [11:24] MatthewWest: 12 [11:25] Michel Dumontier: ugh oh [11:25] Brian Haugh: Yes [11:25] Michel Dumontier: kingsley we lost you! [11:25] MariaPovedaVillalon: yes [11:25] dougFoxvog: I hear Peter, but not Kingsley [11:26] SamirTartir: @Peter: SamirTartir I can hear you [11:26] PeterYim: Kingsley we lost you, on the voice line, can you dial in again, please [11:26] MichaelDenny: @Kingsley We've lost you! [11:28] PeterYim: === KingsleyIdehen's talk resumes ... (slide#13) [11:30] PeterYim: KingsleyIdehen request that AdamPease supply a URI for SUMO that he can link to [11:30] AdamPease: maybe I'm misunderstanding but we've had that for year [11:30] AdamPease: years [11:30] dougFoxvog: URI for terms that denote creators seems too much of a hack. Assertions about who is responsible for a terms set (which would have the same name space) seem to me to be more worthwhile. [11:30] AmandaVizedom: Must drop off. Thanks all! [11:31] AdamPease: http://sigma-01.cim3.net:8080/sigma/OWL.jsp?kb=SUMO&term=Object [11:31] AdamPease: for example [11:33] dougFoxvog: Individual assertion, e.g., (termCreatedBy ) can be used for attribution. [11:33] PeterYim: == Q&A and Open Discussion ... [11:33] PeterYim: Again, soliciting help from everyone here: -- for software environment stewards and tool developers, please make sure you participate in the upcoming survey ---and help us get these colleagues of yours to respond to the survey too: http://ontolog-02.cim3.net/wiki/OntologySummit2013_Survey -- ... or provide us with pointers to stewards of relevant software tools/systems/environments so we can reach out to them [11:37] PeterYim: join us again, same time next week, for OntologySummit2013 session-11: "Getting the "hackathon," "clinics" and related activities going" - Co-chairs: MikeDean, KenBaclawski & PeterYim - developing session details at: http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2013_03_28 [11:37] PeterYim: great session ... thanks everyone! [11:37] JoelBender: Thank you! [11:37] Michel Dumontier: Thanks! [11:37] Tania Tudorache1: Thank you! [11:38] PeterYim: -- session ended: 11:37 am PDT -- [11:38] MichaelDenny: Bye all! [11:39] List of attendees: AdamPease, AmandaVizedom, AnatolyLevenchuk, AstridDuqueRamos, Bob Smith, Brian Haugh, BriceSommacal, BruceBray, Daniel Couto Vale, FabianNeuhaus, FranLightsom, Jcruanes, JoelBender, JohnBilmanis, Jorge Cruanes, K. Z. Watkins, KenBaclawski, Kingsley Idehen (kidehen)1, LamarHenderson, MarcelloBax, MariaPoveda, MariaPoveda1, MariaPovedaVillalon, MatthewWest, MeganKatsumi, MichaelDenny, MichaelGruninger, Michel Dumontier, MikeDean, MikeRiben, MikeRiben1, OliverKutz, PavithraKenjige, PeterYim, Ram D. Sriram, Rich Markeloff, RobertYao, RobertYao1, SamirTartir, SimonSpero, SteveRay, Tania Tudorache, Tania Tudorache1, TerryLongstreth, TillMossakowski, ToddSchneider, TomTinsley, TorstenHahmann, anonymous, anonymous1, anonymous2, anonymous3, dougFoxvog, vnc2 ------