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Ontology Summit 2013: 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) and Mr. PeterYim (Ontolog; CIM3) - intro slides

Panelists / Briefings:

  • Mr. AdamPease (Articulate Software) - "The Sigma Knowledge Engineering Environment" slides
  • Prof. Dr. TillMossakowski (University of Bremen) - "Ontohub.org - a web platform for distributed and heterogeneous ontologies" slides
  • Dr. TaniaTudorache (Stanford-BMIR) - "WebProtege and BioPortal as Infrastructures for Ontology Evaluation" slides
  • Professor MichelDumontier (Carleton University) - "Evaluation of ontology-powered scientific research as a means to assess and improve ontology quality" slides
  • Mr. KingsleyIdehen (OpenLink Software) - "Ontology life cycles and Linked Open Data (LOD)" slides

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Abstract

OntologySummit2013 Session-10: "Software Environments for Evaluating Ontologies - II" - intro slides

This is our 8th Ontology Summit, a joint initiative by NIST, Ontolog, NCOR, NCBO, IAOA & NCO_NITRD with the support of our co-sponsors. The theme adopted for this Ontology Summit is: "Ontology Evaluation Across the Ontology Lifecycle."

Currently, there is no agreed methodology for development of ontologies, and there are no universally agreed metrics for ontology evaluation. At the same time, everybody agrees that there are a lot of badly engineered ontologies out there, thus people use -- at least implicitly -- some criteria for the evaluation of ontologies.

During this Ontology Summit, we seek to identify best practices for ontology development and evaluation. We will consider the entire lifecycle of an ontology -- from requirements gathering and analysis, through to design and implementation. In this endeavor, the Summit will seek collaboration with the software engineering and knowledge acquisition communities. Research in these fields has led to several mature models for the software lifecycle and the design of knowledge-based systems, and we expect that fruitful interaction among all participants will lead to a consensus for a methodology within ontological engineering. Following earlier Ontology Summit practice, the synthesized results of this season's discourse will be published as a Communique.

At the Launch Event on 17 Jan 2013, the organizing team provided an overview of the program, and how we will be framing the discourse around the theme of of this OntologySummit. Today's session is one of the events planned.

In this 10th virtual panel session of the Summit, we have invited the stewards of some exemplary ontology software tools and environments out there to join us on the panel. They will share with us their work, experience and insights - particularly on how the software environments/systems/tools they represent, support evaluating intrinsic aspects and extrinsic aspects of ontologies, and how they help assure quality across the lifecycle of the development (of the ontology or the ontology-driven application). We will also hear about what they think are the major obstacles now, toward quality excellence, relevant work they are embarking on, and wish lists of what have yet to be done in term of improving ontology quality.

We will also expecting to be "officially" launching the Ontology Summit 2013 Survey of Software Support for Ontology Quality and Fitness, which we alluded to earlier, at this session.

More details about this Ontology Summit is available at: OntologySummit2013 (homepage for this summit)

Briefings

  • Mr. AdamPease (Articulate Software) - "The Sigma Knowledge Engineering Environment" slides
    • Abstract: ... The Sigma system was created to support the development of the Suggested

Upper Merged Ontology (SUMO), starting over 12 years ago. It is an open source program, hosted on Source Forge (at http://sigmakee.sourceforge.net), and is coded in Java and JSP. Sigma includes interfaces to dozens of first-order and higher-order theorem provers, and optimization code to take best advantage of those provers when running over the SUMO theory. Sigma includes many static checks for testing the quality and correctness of expressive theories. It also has a growing body of textual analysis modules for information extraction and sentiment analysis. The system also supports browsing the WordNet lexico-semantic database, and its complete set of manually-coded links to SUMO. Sigma functions as a modern IDE for development of expressive theories, where actual coding is performed in a text editor and the IDE assists with debugging and visualization of the code. This talk will give a very brief introduction to these features.

  • Prof. Dr. TillMossakowski (University of Bremen) - "Ontohub.org - a web platform for distributed and heterogeneous ontologies" slides
    • Abstract: ... Ontohub.org is a web platform that goes beyond platforms like Bioportal in that it supports a multitude of ontology languagegs (OWL, RDF, Common Logic, first and higher-order logic, ...) as well as heterogeneous distributed ontologies. Ontohub also supports the structuring constructs of the distributed ontology language DOL, see http://www.ontoiop.org . Ontohub generally follows the architecture of the Open Ontology repository, see http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository_Architecture/Candidate03 , although currently it has not yet been fully split into a number of independent services. Ontohub is implemented in Ruby on Rails and is freely available at https://github.com/ontohub/ontohub . As analysis and reasoning backend, Ontohub uses the heterogeneous tool set (Hets), see http://hets.dfki.de , which is in turn connected to various theorem provers and model finders. In this talk, we will introduce Ontohub and discuss its use for ontology evaluation.
  • Dr. TaniaTudorache (Stanford-BMIR) - "WebProtege and BioPortal as Infrastructures for Ontology Evaluation" slides
    • Abstract: ... In the recent years, we have witnessed an increased adoption of ontologies in a wider range of domains, with biomedicine being the front runner. Users need now, more than ever, support for finding and assessing ontologies that are suitable for their particular task. Several approaches presented in this forum, are investigating the algorithmic side of evaluating ontologies. We will talk about the qualitative aspect of ontology evaluation, in which users act as reviewers of ontologies, similar to the process of scientific paper review. We will present Web Protege and BioPortal, two complementary Web-based systems that provide the essential infrastructure for documenting, reviewing, discussing and finding the "right" ontologies. Web Protege is a light weight ontology editor for the Web that provides extensive collaboration support. BioPortal is an open-source repository of over 300 biomedical ontologies with support for documentation, discussion and reviewing of ontologies. We will show how the seamless integration of Web Protege and BioPortal create a comprehensive infrastructure for ontology evaluation.
  • Professor MichelDumontier (Carleton University) - "Evaluation of ontology-powered scientific research as a means to assess and improve ontology quality" slides
    • Abstract: ... Ontologies are quickly becoming a core part of biomedical infrastructure, where they serve as a means to standardize terminology, to enable access to domain knowledge, to verify data consistency and to facilitate integrative analyses over heterogeneous biomedical data. Given the increased use of ontologies in scientific research, we must first consider the consistent evaluation of ontology-powered research so as to quantitatively evaluate the contribution of the ontology to the effort. Quantitative evaluation of research could then lead to systematic improvement of the application and performance of an ontology (as a key measures of quality) and enable the comparison of any ontology to the overall result. With the emergence of vast amounts of relatively schema-light biomedical Linked Open Data such as that provided by the open source Bio2RDF project, new opportunities arise for applying, evaluating and increasing the utility of ontologies in biomedical research.
  • Mr. KingsleyIdehen (OpenLink Software) - "Ontology life cycles and Linked Open Data (LOD)" slides

Agenda

OntologySummit2013 - Panel Session-10

  • Session Format: this is a virtual session conducted over an augmented conference call

Proceedings

Please refer to the above

IM Chat Transcript captured 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: summit_20130321

2013-03-21 GMT-08:00 [PDT]

[9:16] Peter P. Yim: Welcome to the

Ontology Summit 2013: 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

Panelists / Briefings:

- "The Sigma Knowledge Engineering Environment"

- "Ontohub.org - a web platform for distributed and heterogeneous ontologies"

- "WebProtege and BioPortal as Infrastructures for Ontology Evaluation"

- "Evaluation of ontology-powered scientific research as a means to assess and improve ontology quality"

- "Ontology life cycles and Linked Open Data (LOD)"

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: Adam Pease, Amanda Vizedom, Anatoly Levenchuk, AstridDuqueRamos, Bob Smith, Brian Haugh,

BriceSommacal, Bruce Bray, DanielCoutoVale, Doug Foxvog, Fabian Neuhaus, Fran Lightsom, JorgeCruanes,

Joel Bender, John Bilmanis, K. Z. Watkins, Ken Baclawski, Kingsley Idehen, Lamar Henderson, MarcelloBax,

MariaPovedaVillalon, Matthew West, Megan Katsumi, Michael Denny, Michael Grüninger, Michel Dumontier,

Mike Dean, Mike Riben, Oliver Kutz, Pavithra Kenjige, Peter P. Yim, Ram D. Sriram, Rich Markeloff, RobertYao,

Samir Tartir, Simon Spero, Steve Ray, Tania Tudorache, Terry Longstreth, Till Mossakowski, Todd Schneider,

Tom Tinsley, Torsten Hahmann, anonymous, ... vnc2

Proceedings:

[9:17] Peter P. Yim: 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 Michael Denny

[9:26] anonymous morphed into Brian Haugh

[9:27] anonymous morphed into anonymous2

[9:28] Michel Dumontier: howdy

[9:28] anonymous1 morphed into Torsten Hahmann

[9:29] anonymous morphed into Adam Pease

[9:29] Michael Denny: 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] MariaPovedaVillalon morphed into Maria Poveda

[9:30] anonymous morphed into Fran Lightsom

[9:30] Maria Poveda morphed into MariaPovedaVillalon

[9:30] anonymous morphed into Rich Markeloff

[9:30] anonymous1 morphed into Tania Tudorache

[9:31] anonymous3 morphed into Doug Foxvog

[9:31] anonymous morphed into BriceSommacal

[9:32] anonymous morphed into Lamar Henderson

[9:33] K. Z. Watkins: are slides only on skype?

[9:37] Megan Katsumi: @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 Tom Tinsley

[9:39] Peter P. Yim: == Mike Denny opens the session on behalf of the co-chairs ... see: the [0-Chair] slides

[9:42] Peter P. Yim: === slide#3 - Michael Denny announcing the Ontology Summit 2013 Survey on software

capabilities for quality and fitness of ontologies ...

[9:44] Peter P. Yim: see also: http://ontolog.cim3.net/forum/ontology-summit/2013-03/msg00197.html

[9:45] Peter P. Yim: the survey is at: http://ontolog-02.cim3.net/wiki/OntologySummit2013_Survey

[9:47] Brian Haugh: Clap, Clap, Clap, Clap, ...

[10:23] Torsten Hahmann: @MichaelDenny: For the survey, I can't seem to login with my ontolog

credentials - is there any extra signup required?

[10:24] Michael Denny: @Torsten If you are having problems, please use guest and ontolog-guest.

[10:24] Peter P. Yim: @TorstenHahmann & ALL: anyone having issues with the login (for the survey) can

login with: username=guest ; password=ontolog-guest

[10:26] Torsten Hahmann: @PeterYim & @MichaelDenny: thanks, that works.

[9:48] Peter P. Yim: == Adam Pease presenting ... see: the [1-Pease] slides

[9:53] Simon Spero: What about horses that only have three legs

[9:54] Simon Spero: "A horse like that, you don't eat all at once"

[10:00] Till Mossakowski: is the translation from SUO-KIF to OWL described somewhere?

[10:00] Amanda Vizedom: Question for @AdamPease: Any plans for support of Common Logic?

[10:11] Michael Grüninger: 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.

[10:13] Torsten Hahmann: 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

[10:08] Amanda Vizedom: 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.

[10:09] anonymous1 morphed into Pavithra Kenjige

[10:41] Adam Pease: just reading the chat logs

[10:42] Adam Pease: KIF and SUO-KIF are quite different, so unless it's specifically

a SUO-KIF translator, it won't work for SUMO

[10:42] Adam Pease: translating CL to the first-order subset of SUO-KIF should be easy

[10:42] Till Mossakowski: I think in Hets we have some translation of SUO-KIF into Common Logic

[10:43] Adam Pease: 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] Adam Pease: that sounds great Till

[10:45] Peter P. Yim: @AdamPease: re your xx:43where can one find that presentation ... can you supply a

link to it?

[10:45] Adam Pease: ?

[10:45] Adam Pease: oh, not a slide presentation

[10:46] Adam Pease: a presentation of logic

[10:46] Peter P. Yim: @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] Adam Pease: use the "traditionalLogic" menu option in the menu title "Formal Language" in the Sigma browser

[10:47] Peter P. Yim: Ah ... thanks, Adam

[11:01] Torsten Hahmann: @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] Till Mossakowski: interesting question!

[11:03] Adam Pease: I make no claims that it's a complete translation

[11:03] Adam Pease: especially since OWL is so limited

[11:03] Adam Pease: but even within its limitations, we don't do anything extraordinary

[11:03] Adam Pease: all binary relations get translated

[11:04] Adam Pease: we translate all the builtin terms in OWL to their equivalents in SUMO

[11:04] Adam Pease: all rules get turned into comments

[11:04] Adam Pease: that's about it

[11:06] Torsten Hahmann: thanks, I was just wondering

[10:09] Peter P. Yim: == Till Mossakowski presenting ... see: the [2-Mossakowski] slides

[10:09] anonymous1 morphed into Steve Ray

[10:10] anonymous1 morphed into RobertYao

[10:11] anonymous2 morphed into JorgeCruanes

[10:11] anonymous1 morphed into DanielCoutoVale

[10:11] anonymous1 morphed into Lamar Henderson

[10:20] anonymous1 morphed into MarcelloBax

[10:06] Joel Bender: Isn't there a CL to KIF translator?

[10:06] Simon Spero: Hets sort of does that

[10:07] Simon Spero: for certain senses of KIF

[10:08] Simon Spero: Hets module CommonLogic.Parse_KIF

[10:07] Matthew West: KIF is a dialect of CL

[10:19] Peter P. Yim: Till Mossakowski - see: http://ontohub-new.informatik.uni-bremen.de/

[10:25] Peter P. Yim: == Tania Tudorache presenting ... see: the [3-Tudorache] slides

[10:30] Doug Foxvog: 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] Amanda Vizedom: 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] Peter P. Yim: @TaniaTudorache: can one access the collected user review input, and

slice-and-dice that data ... I guess its, sort of, the same question Amanda is asking

[10:41] Doug Foxvog: Ref Slide 12. What about an ontology for encoding the reviews using relations &

terms defined in the ontology?

[10:42] Amanda Vizedom: 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.

[10:41] Peter P. Yim: == Michel Dumontier presenting ... see: the [4-Dumontier] slides

[10:51] Amanda Vizedom: 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] Amanda Vizedom: (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] Amanda Vizedom: @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).

[11:15] 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 :)

[11:03] Terry Longstreth: @Michel - Slide 13 - did you subdivide the volunteer community by

expertise? Did expertise/experience make any difference?

[11:10] Michel Dumontier: @Terry - the volunteers were experts at a conference on the topic

[11:11] Terry Longstreth: Thanks, Michel.

[11:11] Peter P. Yim: == Kingsley Idehen presenting ... see: the [5-Idehen] slides

[11:16] Peter P. Yim: @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

[11:24] Matthew West: Afraid I need to go now.

[11:25] Michel Dumontier: ugh oh ... Kingsley we lost you!

[11:25] MariaPovedaVillalon: yes

[11:25] Doug Foxvog: I hear Peter, but not Kingsley

[11:26] Samir Tartir: @Peter: I can hear you

[11:26] Peter P. Yim: Kingsley we lost you, on the voice line, can you dial in again, please

[11:26] Michael Denny: @Kingsley We've lost you!

[11:28] Peter P. Yim: === KingsleyIdehen's talk resumes ... (slide#13)

[11:30] Peter P. Yim: Kingsley Idehen request that Adam Pease supply a URI for SUMO that he can link to

[11:30] Adam Pease: maybe I'm misunderstanding but we've had that for years

[11:31] Adam Pease: http://sigma-01.cim3.net:8080/sigma/OWL.jsp?kb=SUMO&term=Object

[11:31] Adam Pease: for example

[11:30] Doug Foxvog: 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.

[11:33] Doug Foxvog: Individual assertion, e.g., (termCreatedBy <TERM> <AGENT>) can be used for

attribution.

[11:30] Amanda Vizedom: Must drop off. Thanks all!

[11:33] Peter P. Yim: == Q&A and Open Discussion ...

[11:33] Peter P. Yim: Again, soliciting help from everyone here:

-- for software environment stewards and tool developers, please make sure you participate in the Ontology Summit 2013 software 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] Peter P. Yim: join us again, same time next week, for Ontology Summit 2013 session-11: "Getting

the "hackathon," "clinics" and related activities going" - Co-chairs: Mike Dean, Ken Baclawski &

Peter P. Yim - developing session details at:

http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2013_03_28

[11:37] Peter P. Yim: great session ... thanks everyone!

[11:37] Joel Bender: Thank you!

[11:37] Michel Dumontier: Thanks!

[11:37] Tania Tudorache: Thank you!

[11:38] Peter P. Yim: -- session ended: 11:37 am PDT --

[11:38] Michael Denny: Bye all!

[11:51] 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_03_21#nid3NSZ

[11:52] Peter P. Yim: bye everyone!

-- end of in-session chat-transcript --

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Attendees

  • Expecting:
    • Ravi Sharma
    • ...
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