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Ontology Summit 2013: Panel Session-08 - Thu 2013-03-07

Summit Theme: "Ontology Evaluation Across the Ontology Lifecycle"

Summit Track Title: Track-A: Intrinsic Aspects of Ontology Evaluation

Session Topic: Intrinsic Aspects of Ontology Evaluation - II

Session Co-chairs: Dr. LeoObrst (Ontolog; MITRE) and Dr. StevenRay (CMU) - intro slides

Panelists / Briefings:

  • Professor PatrickLambrix (Linköping University, Sweden) - "Debugging is-a structure in ontologies" slides
  • Ms. MariaCopeland (University of Manchester) - "Ontology Evolution and Regression Testing" slides
  • Dr. MelissaHaendel (Oregon Health & Science University) - "A biologists' perspective on ontology utility" slides
  • Mr. EdBarkmeyer (NIST) - "Core components for an ontology: Modeling Codes and Code Lists" slides

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Abstract

OntologySummit2013 Session-08: "Intrinsic Aspects of Ontology Evaluation-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 8th virtual panel session of the Summit, we continue to explore intrinsic ontology evaluation, from basic structural evaluation through exploration of the "is-a" relation with Patrick Lambrix, software engineering concepts of regression testing with Maria Copeland, a biologist's perspective with Melissa Haendel, and finishing with some suggestions of the use of common elements with EdBarkmeyer. We hope that all of the participants in the open discussion and chat will join us in helping to flesh out the ingredients and methods for intrinsic evaluation.

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

Briefings

  • Professor PatrickLambrix (Linköping University, Sweden) - "Debugging is-a structure in ontologies" slides
    • Abstract: ... With the proliferation of ontologies and their use in semantically-enabled applications, detecting and repairing defects in ontologies has become increasingly important. In this talk we address the problem of defects in the is-a structure of ontologies. We briefly introduce the different kinds of defects and the problems of detection and repairing. Further, we introduce an approach for debugging that can deal with missing is-a relations as well as existing wrong is-a relations. We also show results of experiments on the ontologies of the Ontology Alignment Evaluation Initiative as well as results from work done on debugging ontologies for the Swedish National Food Administration.
  • Ms. MariaCopeland (University of Manchester) - "Ontology Evolution and Regression Testing" slides
    • Abstract: ... Understanding Ontology Evolution is becoming an active topic of interest

to ontology engineers. We have large collaborative developed ontologies but, unlike software engineering, comparatively little is understood about the dynamics of historical changes, especially when dealing with the re-introduction of unchanged content and information. We propose a method for analysing axiomatic change dynamics and identifying editing patterns that suggest regression errors. Understanding the frequency of these errors and the overall impact to the ontology is crucial when designing testing strategies in particular regression tests. This presentation is an introduction to ongoing research in this area and it provides an opportunity to discuss the impact of this work in the area of Ontology Evaluation and Evolution.

  • Dr. MelissaHaendel (Oregon Health & Science University) - "A biologists' perspective on ontology utility" slides
    • Abstract: ... Being both a developer of ontologies and a biologist lends an interesting perspective on ontology evaluation. Criteria such as as a complete subclass hierarchy, inclusion of both text definitions and class axioms, and examples of usage are all critical for the use of an ontology for annotation in biology. However, at the same time, when the ontology-related data is presented to an end-user, they better not be able to tell that there is an ontology "under the hood". Building in internal mechanisms that help make the ontology useful for ontology editors, annotators, and end-users of the annotated data is important. When gauging the potential reuse or integration of an existing ontology, it is important to take into account this plurality of diverse users.
    • You may also want to review a related presentation by Melissa Haendel delivered on March 6, 2013 here.
  • Mr. EdBarkmeyer (NIST) - "Core components for an ontology: Modeling Codes and Code Lists" slides
    • Abstract: ... One contribution to intrinsic quality of ontologies is recommended models of common information elements. (The effort to do this for business message elements in UN/CEFACT is called "core components".) This presentation introduces a general category of common elements -- code lists and code values -- and recommends an ontology modeling practice for them. There are international reference standards associated with these, and this presentation recommends simple ontology models that are consistent with those standards.

Agenda

OntologySummit2013 - Panel Session-08

  • 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_20130307

2013-03-07 GMT-08:00 [PST]

[09:26] Peter P. Yim: Welcome to the

Ontology Summit 2013: Virtual Panel Session-08 - Thu 2013-03-07

Summit Theme: Ontology Evaluation Across the Ontology Lifecycle

  • Summit Track Title: Track-A: Intrinsic Aspects of Ontology Evaluation

Session Topic: Intrinsic Aspects of Ontology Evaluation - II

Panelists / Briefings:

  • Professor Patrick Lambrix (Linkping University, Sweden) - "Debugging is-a structure in ontologies"
  • Ms. Maria Copeland (University of Manchester) - "Ontology Evolution and Regression Testing"
  • Dr. Melissa Haendel (Oregon Health & Science University) - "A biologists' perspective on ontology utility"
  • Mr. Ed Barkmeyer (NIST) - "Core components for an ontology: Modeling Codes and Code Lists"

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: Ali Hashemi, Amanda Vizedom, Anatoly Levenchuk, AstridDuqueRamos, Bijan Parsia, Bob Smith,

Bobbin Teegarden, David Whitten, Dennis Wisnosky, Dmitry Borisoglebsky, Doug Foxvog, Ed Barkmeyer,

Fabian Neuhaus, Fran Lightsom, Hans Polzer, Joanne Luciano, Joel Bender, John Bilmanis, Ken Baclawski,

Kevin Simkins, Leo Obrst, Ludger Jansen, Maria Copeland, Megan Katsumi, Melissa Haendel, Michael Grüninger,

Mike Dean, Patrick Lambrix, Pavithra Kenjige, Peter P. Yim, Ram D. Sriram, Steve Ray, Terry Longstreth,

Todd Schneider, Torsten Hahmann, ValentinaIvanova, Victor Agroskin, vnc2

proceedings:

[9:09] anonymous morphed into Patrick Lambrix

[9:23] anonymous morphed into Kevin Simkins

[9:29] 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.)

[9:30] anonymous morphed into Melissa Haendel

[9:30] Kevin Simkins: The IEEE Virtual World Standard Working Group (P1828) is focused on the

development of common standards for virtual environments. From assets to protocols and general

working models in order to facilitate the common interoperability scenario for all virtual

environments in the future. Our working group members are dedicated to multiple phases within this

process in order to accumulate further details and application methodologies over time. ... see:

http://www.metaversestandards.org/index.php?title=Main_Page

[9:32] Joel Bender: @Peter - attempting to enter the conference ID is failing, the bridge is missing

digits - I'm calling from a land line

[9:38] Anatoly Levenchuk: wrt skype: always mute microphone when you enter ID to skype (mic take

sound from your tone-digits and then can be "strange" processes of echo and digits suppressing or

doubling of click and "listened" digits).

[9:34] anonymous morphed into Bob Smith

[9:35] Melissa Haendel: yes, screen share doesn't work for me

[9:36] Fabian Neuhaus: Melissa, the screen share might not work if you are behind a firewall

[9:37] Fabian Neuhaus: just download the slides from the session page

http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2013_03_07

[9:39] Melissa Haendel: thanks Fabian, I have the slides

[9:35] anonymous morphed into Torsten Hahmann

[9:38] Peter P. Yim: == Steve Ray opening the session on behalf of the co-chairs ... ... see: the

[0-Chair] slides

[9:41] List of members: Amanda Vizedom, Anatoly Levenchuk, AstridDuqueRamos, Dennis Wisnosky,

Ed Barkmeyer, Fabian Neuhaus, Fran Lightsom, Hans Polzer, Joanne Luciano, Joel Bender, John Bilmanis,

Kevin Simkins, Leo Obrst, Maria Copeland, Melissa Haendel, Michael Grüninger, Mike Dean, Patrick Lambrix,

Peter P. Yim, Ram D. Sriram, Steve Ray, Terry Longstreth, Todd Schneider, Torsten Hahmann

[9:41] Peter P. Yim: == Patrick Lambrix presenting ... see: the [ 1-Lambrix ] slides

[9:44] anonymous morphed into Doug Foxvog

[9:51] Melissa Haendel: Question, so NCI is largely a human representation whilst MA is mouse. How do

you know there are not species-specific is_a absences or presence? Examples are correct, though :-).

[11:24] Patrick Lambrix: @Melissa [9:51]: For our experiments we had the help of a domain expert.

(This doesn't mean all the validations are correct. We have also noticed that a domain expert may

change his/her mind about the correctness of an is-a relation during the debugging session when more

is-a relations were debugged.)

[11:28] Melissa Haendel: @patrick. I understand biologists changing their mind! Also depends on the

way in which they are viewing the ontology and the debugging changes. Would be interested to view

this sometime, will look at your papers.

[9:54] Steve Ray: @Melissa: My understanding from his talk is that is why the repairs must be

validated by a domain expert.

[11:24] Patrick Lambrix: @Steve [9:54]: Yes, repairs need to be validated by a domain expert. For

missing is-a relations a system can compute repairs that guarantee that the missing is-a relations

will be logically derivable form the repaired ontology, but this does not necessarily mean that the

repair is correct according to the domain.

[9:54] Amanda Vizedom: @PatrickLambrix - I like your focus on a high-level division into syntactic,

semantic, defects; your calling out that detection and debugging of the modeling defects requires

domain knowledge, and your subsequent emphasis on very practical ways to detect and debug this third

category. In my experience, the syntactic and semantic evaluation and correction, while necessary,

are rarely sufficient. There seems, however, to be a widespread impression, or fear, that practical,

reliable evaluation of model accuracy is not possible. Thanks for showing this not to be true.

[11:24] Patrick Lambrix: @Amanda [9:54]: If I remember well, the different kinds of defects were

defined in Aditya Kalyanpur's PhD thesis. However, there is not so much work on systems for the

modeling defects yet.

[9:58] Doug Foxvog: For the example, concluding "limb_joint" is-a "joint" because all of its

subclasses are-a joint although it is not in any of the ontologies, the conclusion must be verified

by a human. It is quite possible that that common is-a is too general a term -- which may be the

reason the is-a was not asserted.

[9:58] Peter P. Yim: @PatrickLambrix - are there tools already implemented for the process outlined in

slide#26 ... if so, are they openly accessible (what is url?)

[9:58] Melissa Haendel: It would be great to have tools that present these things easily to the

domain expert. Actually, I would not classify a hip joint as a limb joint (sorry, I work on this

stuff ;-)).

[11:24] Patrick Lambrix: @Peter,@Melissa: [9:58]: We have systems and plan to make the first system

available soon. There are screenshots in the papers in the reference list of the talk.

[10:05] Doug Foxvog: @Melissa: That depends upon the ontology's definition of "limb joint". The term

could mean a joint within a limb or a joint which is to at least one bone in a limb. Bone joints vs.

body region joints are also a contrast; these two types are disjoint.

[10:01] Amanda Vizedom: @PatrickLambrix - I would note that "is-a" in your examples appears to be a

subClass or kind-of relationship (or, if also used for instances, it may be an under-specified

narrower concept used for both instancehood and subclass relationships, as found in some taxonomies,

less commonly ontologies, and other semantic models). I call attention to this simply because it can

be confusing to modelers who follow most contemporary ontology languages, in which "is-a" is used

only for the instancehood relationship, and a different relationship (subClassOf, kind-of, #$genls)

is used for the sub-class relationships in your examples.

[10:06] Melissa Haendel: well, many anatomists define limb as the free limb, as opposed to the limb

plus girdle. but that is perhaps neither here nor there.

[10:06] Melissa Haendel: @Patrick - I would love to have you experiment with our work on Uberon - see

http://uberon.org.

[11:25] Patrick Lambrix: @Melissa [10:06]: I would be interested at looking at Uberon.

[10:09] Doug Foxvog: @Amanda: many people use "is-a" to mean subclass of. Cyc uses #$isa to mean

instance of. I (growing up with Cyc) also find "is-a" used for subclass-of as grating.

Grammatically, it should be "a-is-a".

[11:24] Patrick Lambrix: @Amanda,@DougFoxvog [10:01]: Yes, is-a isSubClass or kind-of. Our system

works currently only on the concept level. For is-a we assume relexivity and transitivity.

[10:10] Amanda Vizedom: @doug, far fewer than used to. The two relationships are teased out, for

example, even in OWL.

[10:05] Joanne Luciano: is is-a a kind-of-kind-of is-a relationship? or is it a-kind-of-like

relation?

[11:24] Patrick Lambrix: @Joanne [10:05]: exactly :-)

[10:05] Joanne Luciano: :-) nice presentation!

[10:10] Leo Obrst: @Patrick: do repair actions ever cause additional problems for other parts of the

ontologies not yet analyzed?

[11:25] Patrick Lambrix: @Leo [10:10]: Repairing actions could cause additional problems. Therefore,

the system allows a user to switch between the different phases of detecting, validating and

repairing, as well as taxonomies and iteratively debug the whole network. The system also checks

whether a domain expert would want to remove a previously validated to be correct is-a relation. In

this case the user needs to retract the previous choice or the repair is not allowed. Similar when

the domain expert wants to add an is-a relation, that was previously validated as wrong.

[10:06] Peter P. Yim: == Maria Copeland presenting ... see: the [ 2-Copeland ] slides

[10:14] Ed Barkmeyer: @maria: Only some tested elements have meaning to the user. Many test elements

are intended to validate that the inferences work as expected for known cases. In many cases, the

user cannot recognize an erroneous inference, as Patrick mentioned.

[10:21] Ed Barkmeyer: @maria: Is it clear that these changes are "truth" and "bugs", or just

differences in educated opinion prevailing at different times in the maintenance cycle?

[10:21] Ali Hashemi: @Maria - are the graphs on slides 30 and 34(b) correct? It seems to me it should

be Effectually added (solid line) Ineffectually Removed (dotted line) Effectually Removed (no line)

Effectually Added ... otherwise, what do the lines represent?

[10:23] Doug Foxvog: @Maria: could these changes be a result of different users having different

ideas of what the terms (should) mean?

[10:23] Melissa Haendel: We (try to) keep track of such edits in the ontology metadata, it would be

fantastic to have a human readable version provided to the ontology editor/domain editor whilst they

are editing.

[10:23] anonymous morphed into David Whitten

[10:26] Amanda Vizedom: @MariaCopeland - could you explain your effectually / ineffectually

distinction a little more? I think I understood you to say that "effectual" presence means presence

as a directly asserted axiom, while "ineffectual" presence means absence from the directly asserted

axioms, but continued entailment by the ontology. Is that correct? If so, is this, as the label

ineffectual suggests, considered a fault? I ask because I imagine that presence as entailment only

would be desirable in some applications and undesirable in others. Specifically, if little to know

reasoning is done in an application and only directly asserted applications are usable, then

entailments are indeed "ineffectual". In other cases, where some degree of reasoning is used and is

efficient, assertions that are redundant with entailments may be removed for efficiency, if there is

not additional, provenance-related reason to make explicit assertions that rely on different

sources.

[11:24] Maria Copeland: @EdBarkmeyer, @AliHashemi, @DougFoxvog, @Melissa: Thanks for your questions

and comments. I will follow up offline.

[10:23] Peter P. Yim: == Melissa Haendel presenting ... see: the [ 3-Haendel ] slides

[10:30] Hans Polzer: (ref. slide#4) The example of fruit fly limbs vice human limbs underscores the

need for more explicit representation of context as it relates to ontologies

[10:32] Doug Foxvog: @Hans: the fruit fly vs. human Tibia presents an example of using NL words as

terms for concepts in an ontology. There should be mappings from the NL terms to (multiple)

concepts. But annotation of the concept should make its intended meaning crystal clear.

[10:34] Amanda Vizedom: @Hans - I don't disagree, exactly, but I'd add that it is also a good

illustration of why it is important not to confuse expressions and concepts. Arguably, the fruit fly

tibia is a subclass of some class of animal body parts that are not skelatal; the human tibia is a

subclass of some class of animal body parts that are skelatal. "limb" may be an expression used for

both of those classes, but the classes are different.

[10:35] Doug Foxvog: @Melissa : Having a key separation in an ontology whether something is

detectable seems to be setting oneself up to have the feature expire when new technology allows

something not previously detectable to become detectable.

[10:36] Doug Foxvog: I had trouble hearing for a while. But the sound has now come back

[10:36] Hans Polzer: But in some contexts the term "limb" represents the identical concept, for

example, when considering locomotion rather than anatomy (and not focusing on how exactly the

movement of the limb is activated/energized.)

[11:02] Melissa Haendel: @hans. we have disjoint axioms to prevent fruitfly tibia being equated with

human tibia. I wonder how much such disjoint axioms are leveraged in the ontology alignment

strategies? or if we can be providing them better for such purposes.

[11:04] Doug Foxvog: +1 Melissa. Disjointness axioms are crucial. Especially if they are enforced on

modification of an ontology to prevent the creation of classes that are disjoint with themselves.

[10:37] Amanda Vizedom: @Melissa -- Don't worry, it's not just biologists! I've lost track of the

number of domains I've worked in or with, and I don't think I've yet met a community of practice

that doesn't have these features (moving conceptual targets, reuse of labels, and expert

disagreements on definitions). I suspect there are fundamentals of human cognition, language, and

community knowledge development at work . :-)

[10:38] Doug Foxvog: One need to define multiple limbs: tree limb, animal limb, subclasses of animal

limb by exo/endo-skeleton, etc.

[10:38] Amanda Vizedom: @Hans - agreed. And that is, arguably a different concept, for which the same

expression is used.

[10:39] Doug Foxvog: @Amanda: Of course. Replace disagreement on definitions by modeling all

definitions with different (maybe overlapping) concepts.

[10:39] Steve Ray: This raises the point that different communities still want to use their own

terminologies, and they should, but we can separate those terminologies (expressions or labels) from

the concepts.

[10:41] Ed Barkmeyer: @melissa: As you say, people think ontology terms are words, and they think

definitions are circular when those words are reused, but the fact is that the definitions are in

natural language, the ontology symbols are "words" in a formal language. The issue is whether the

definitions themselves are circular.

[10:42] Doug Foxvog: OBO still has problems with different people having different ideas of what a

term is, even when the name is numeric. The NL description is not specific enough, so for example,

the plant people assume it means the plant definition of the term and the animal people assume it is

an animal definition. As a result, in the Cell (Line) Ontology, multiple cell types were subclasses

of both animal cell and plant cell.

[10:41] Terry Longstreth: @Melissa - Last bullet on slide 11 implies that speculative biology is not

in scope.

[11:04] Melissa Haendel: @terry I think what I was saying is that actually speculative biology is in

scope, but we just need to understand how to apply the ontology consistently when we are potentially

being speculative. (or maybe I misunderstand)

[10:41] Hans Polzer: We have an aversion to specifying context because it seems unnecessary in most

situations we find ourselves in - yet the internet and networked world exposes us to otherwise alien

contexts that are left implicit, thus leading to the arguments about definitions

[10:42] Hans Polzer: We want an absolute frame of reference, but usually assume our own frame of

reference is that absolute frame of reference.

[10:44] Hans Polzer: We need to learn to tolerate that there are multiple frames of reference and

multiple perspectives on those frames of reference and associated scope.

[10:44] Doug Foxvog: @Hans: You say "we" have an aversion to specifying context. *I* don't. 8)# I

find context crucial.

[10:45] Hans Polzer: It was the editorial "we" :-)

[10:45] Hans Polzer: Humans are very good at detecting context, except when it fails us - and thus

results in great literature

[10:46] Hans Polzer: and puns

[10:43] anonymous morphed into ValentinaIvanova

[10:44] Steve Ray: Gee, I'm thinking about a transiently transfected DNA expression construct and I'm

coming up blank :)

[10:45] Amanda Vizedom: @Melissa - slide 16: very nice illustration of refinement to include more

specific classes, corresponding with important functional distinctions.

[10:46] Ed Barkmeyer: @melissa: this is a great contribution! thanks.

[10:50] Peter P. Yim: @MelissaHaendel: do you have tools to augment the process(es) that you are

describing

[11:07] Melissa Haendel: @Peter - we have some scripts that help. We have been using Jenkins to help

too.

[11:12] Peter P. Yim: @MelissaHaendel - thank you, reason I am asking is because we are running

Ontology Clinic activities (as part of this Summit) by putting together ontology developers and

people with ontology evaluation methodologies and tool in the same (virtual) room to get some

interesting outcome, and we'll love to have you (and the other panelists today) to join us - see:

http://ontolog.cim3.net/cgi-bin/wiki.pl?OntologySummit2013_Hackathon_Clinics

[11:17] Melissa Haendel: @peter, it would be great to see if you could get Chris Mungall to

participate regarding his development of Jenkins. see http://wiki.geneontology.org/index.php/Jenkins

. Most of our work on the metadata is in the form of scripts and not integrated into tooling (though

we have some protege plugins).

[11:19] Peter P. Yim: @Melissa - thank you for the pointer ... this is helpful as we are doing a survey

on software and tools, as part of the Summit activities, too

[10:47] Doug Foxvog: Re slide 15. An ontology should not have synonyms. It should have mappings from

NL terms to the ontology terms. One NL term can map to multiple ontology terms and vice versa.

[10:47] Amanda Vizedom: @Melissa: slide 15: Do you mean that experts cannot articulate the

distinctions? Or that the modeling language is not expressive enough to capture it clearly?

[10:52] Steve Ray: @Amanda: How would you handle the example of the Senator who said "I can't define

it but I'll know it when I see it". ...in the context of porn. Quite seriously, it seems that

perhaps we sometimes operate with definitions only by example and are unable to define concepts.

[10:58] Amanda Vizedom: @Steve: I did mean to ask for clarification, not to imply that there are no

undefinable concepts. In fact, it is very common for us to use concepts operationally and regularly

without there being any set of necessary and sufficient conditions to accompany them. The less

technical the concept, I'd argue, the more this is likely to be true. IME, textual definitions that

mention and guide against potentially confused concepts can be very useful, though inherently

incomplete.

[11:00] Steve Ray: @Amanda: Agreed.

[10:54] Amanda Vizedom: @Melissa - slide 18, "true path" violations -- common problem indeed; human

brains are not good at keeping that kind of entailment trace. ;-) One technique that can help catch

these is the creation of tests that instantiate classes and draw the transitive inferences,

presenting the results to the experts, who are more likely to catch it at *that* point if they've

created either inconsistencies or undesired implications.

[11:10] Melissa Haendel: @amanda: I would love your idea "One technique that can help catch these is

the creation of tests that instantiate classes and draw the transitive inferences, presenting the

results to the experts, who are more likely to catch it at *that* point if they've created either

inconsistencies or undesired implications." This would help biologists enormously.

[10:49] Terry Longstreth: @Melissa Slide 17 - Curation status include provenance trace?

[10:47] Peter P. Yim: Ed & All: please provide some context wrt to your comment ... otherwise the

remarks won't mean much in the proceedings

[10:53] Hans Polzer: Peter, Melissa: my comments were aimed at the issue of ambiguity and controversy

in concept definitions. From a pragmatic/realism approach it may be worthwhile to make more of the

context assumptions specific to a given definition, allowing more flexibility in applying a specific

ontology or term in an ontology in a given situation/perspective/context.

[10:55] Peter P. Yim: @Hans - my comment is strictly aimed at messages people are typing into this

chat-room (like, "this is great!" would mean much less than "ref. your slide#12, this is great

insight!") since we captured the chat-transcript as part of the proceedings of the session.

[10:57] Melissa Haendel: (just lost of her voice connection as she got to the last slide) I'm all

done :-) ... Thank you.

[10:58] Fabian Neuhaus: @ Melisssa, the standards for documentation: is this an OBO Foundry effort?

[11:06] Melissa Haendel: @fabian this is a Melissa's team effort ;-). I would like it to be an OBO

effort, and I think we are getting traction.

[10:58] Peter P. Yim: == Ed Barkmeyer presenting ... see: the [ 4-Barkmeyer ] slides

[11:00] anonymous morphed into Ludger Jansen

[11:02] Joel Bender: Units! °F!

[11:04] Leo Obrst: @Ed: would you say that code-lists are controlled vocabularies, and that these map

to concepts/classes in a given ontology? Another example are digraphs and trigraphs for

countries/states.

[11:04] Steve Ray: @Ed: I'm interpreting your Code List to be what many call an Enumeration. Yes?

[11:05] Peter P. Yim: @EdBarkmeyer and All - some members of the Ontolog community had actually worked

on a project "CCT-Representation" back in 2004/2005 to map the ebXML Core Component Types ("CCT") to

a First Order Logic ontology (SUMO, MILO, QoS) - see: An Ontological Basis for ebXML Core Component

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

[11:06] Doug Foxvog: Code lists are controlled vocabularies. However, as Ed Barkmeyer is saying, the

meanings of the codes changes. So, dated uses of the codes is important.

[11:11] Leo Obrst: @Doug: yes, we see this all the time. There are extreme versioning issues involved

in maintaining the mappings from these controlled vocabularies to the ontology/ies.

[11:06] anonymous morphed into Pavithra Kenjige

[11:07] Doug Foxvog: I note that ISO country codes occasionally change.

[11:08] Hans Polzer: and countries change and come into being and go away

[11:11] Doug Foxvog: @Hans: I remember once finding an ISO code for an expired country being re-used

over a decade later for a new country. I forget what the example was.

[11:14] Amanda Vizedom: @EdBarkmeyer - Thanks for this presentation. I've seen this topic persist as

a point of conflict on ontology projects -- whether to go the string route or the

expression-for-thing route. Least-immediate-effort often pulls people toward the string route, but

if there is integration to be done, this is usually a mistake (or at best, pushes the effort down

the road, when it will have to be redone).

[11:14] Hans Polzer: Ref slide 6 in Ed's talk, it would seem to have some temporal context

specification - I suppose that's in the administrative records somewhere

[11:18] Hans Polzer: Looking up the code list is becoming more practical as things become more

connected over the internet. But there are also practical constraints on doing these lookups in real

time while processing transactions

[11:18] Doug Foxvog: @EdBarkmeyer: re slides 7 & 8. Having a term mapped to a code & code list is

intrinsically a ternary concept. An object that is an instance in a code list can have two mappings

from item, one to the code & the other to the code list. However, this only would work if the item

maps only to a single code & single code list.

[11:30] Victor Agroskin: To do such code models consistently is much easier if your ontology language

contains concept of class_of_class. Coding models of this type are very common for systems

implemented on ISO 15926. And ISO 15926-6 is partially a mapping of ISO 11179-3.

[11:18] == Q & A and Open Discussion ...

[11:18] Amanda Vizedom: I need to drop off -- thanks to all presenters! Good stuff.

[11:19] Doug Foxvog: Ciao, Amanda!

[11:24] Leo Obrst: Gramm Richardson et al gave a talk at STIDS 2012 on an 11179 registry addressing

these issues:

http://stids.c4i.gmu.edu/papers/STIDSPapers/STIDS2012_T04_RichardsonSchwarz_Constellation.pdf. STIDS

2012: http://stids.c4i.gmu.edu/agenda2012.php.

[11:25] Peter P. Yim: I am 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 (they'll be on a wiki, so everyone will know who

has or hasn't responded) ... or provide us with pointers so we can reach out to them -- we need

ontology evaluation experts and tool developers to participate in the "hackathon" and "clinics"

activities

[11:26] Peter P. Yim: also ... Join us at the "hackathon" and "clinics" activities -

http://ontolog.cim3.net/forum/ontology-summit/2013-02/msg00056.html &

http://ontolog.cim3.net/cgi-bin/wiki.pl?OntologySummit2013_Hackathon_Clinics

[11:35] Victor Agroskin: @Peter, @Patrick, @Valentina - we'll be really happy to see Patrick's team

to collaborate in our Clinics activity

http://ontolog.cim3.net/forum/ontology-summit/2013-03/msg00011.html ISO 15926 Reference Data Library

is a nice combination of taxonomies, quite suitable for exploration by methods described by Patrick.

[11:28] Pavithra Kenjige: About intrinsic and extrinsic evaluation .. those parts that are

manufactured by others .. is that considered extrinsic evaluation ??

[11:35] Leo Obrst: Thanks, all! Good session.

[11:35] Joanne Luciano: Would you repeat Peter's last point?

[11:35] Peter P. Yim: join us again, same time next week (Thu 2013.03.14), for Ontology Summit 2013

session-09: "Building Ontologies to Meet Evaluation Criteria - I" - Co-chairs: Mike Bennett &

Matthew West - see developing session page at

http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2013_03_14

[11:35] Joel Bender: Thank you!

[11:35] Melissa Haendel: Thanks everyone.

[11:36] Kevin Simkins: Thanks to all speakers and host.

[11:36] Peter P. Yim: great session ... thanks everyone!

[11:36] Joanne Luciano: Very interesting, thanks!

[11:36] anonymous morphed into Bijan Parsia

[11:36] Ali Hashemi: thank you all.

[11:36] David Whitten: Fascinating insights. Well Done all of you.

[11:36] Peter P. Yim: ... session ended ==

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

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