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Ontology Summit 2013: Panel Session-08 - Thu 2013-03-07     (1)

Summit Theme: "Ontology Evaluation Across the Ontology Lifecycle"     (1A)

Summit Track Title: Track-A: Intrinsic Aspects of Ontology Evaluation     (1B)

Session Topic: Intrinsic Aspects of Ontology Evaluation - II     (1C)

Session Co-chairs: Dr. LeoObrst (Ontolog; MITRE) and Dr. StevenRay (CMU) - intro slides     (1D)

Panelists / Briefings:     (1E)

  • Professor PatrickLambrix (Link��ping University, Sweden) - "Debugging is-a structure in ontologies" slides     (1F)
  • Ms. MariaCopeland (University of Manchester) - "Ontology Evolution and Regression Testing" slides     (1G)
  • Dr. MelissaHaendel (Oregon Health & Science University) - "A biologists' perspective on ontology utility" slides     (1H)
  • Mr. EdBarkmeyer (NIST) - "Core components for an ontology: Modeling Codes and Code Lists" slides     (1I)

Abstract     (1K)

OntologySummit2013 Session-08: "Intrinsic Aspects of Ontology Evaluation-II" - intro slides     (1K1)

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."     (1K2)

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.     (1K3)

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.     (1K4)

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.     (1K5)

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.     (1K6)

More details about this Ontology Summit is available at: OntologySummit2013 (homepage for this summit)     (1K7)

Briefings     (1K8)

  • Professor PatrickLambrix (Link��ping University, Sweden) - "Debugging is-a structure in ontologies" slides     (1K8A)
    • 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.     (1K8A1)
  • Ms. MariaCopeland (University of Manchester) - "Ontology Evolution and Regression Testing" slides     (1K8B)
    • Abstract: ... Understanding Ontology Evolution is becoming an active topic of interest     (1K8B1)

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.     (1K8C)

  • Dr. MelissaHaendel (Oregon Health & Science University) - "A biologists' perspective on ontology utility" slides     (1K8D)
    • 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.     (1K8D1)
    • You may also want to review a related presentation by Melissa Haendel delivered on March 6, 2013 here.     (1K8D2)
  • Mr. EdBarkmeyer (NIST) - "Core components for an ontology: Modeling Codes and Code Lists" slides     (1K8E)
    • 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.     (1K8E1)

Agenda     (1L)

OntologySummit2013 - Panel Session-08     (1L1)

  • Session Format: this is a virtual session conducted over an augmented conference call     (1L2)

Proceedings     (1M)

Please refer to the above     (1M1)

IM Chat Transcript captured during the session    (1M2)

see raw transcript here.     (1M2A)

(for better clarity, the version below is a re-organized and lightly edited chat-transcript.)     (1M2B)

Participants are welcome to make light edits to their own contributions as they see fit.     (1M2C)

-- begin in-session chat-transcript --     (1M2D)


Chat transcript from room: summit_20130307     (1M2E)

2013-03-07 GMT-08:00 [PST]     (1M2F)


[09:26] Peter P. Yim: Welcome to the     (1M2G)

Ontology Summit 2013: Virtual Panel Session-08 - Thu 2013-03-07     (1M2H)

Summit Theme: Ontology Evaluation Across the Ontology Lifecycle     (1M2I)

  • Summit Track Title: Track-A: Intrinsic Aspects of Ontology Evaluation     (1M2J)

Session Topic: Intrinsic Aspects of Ontology Evaluation - II     (1M2K)

Panelists / Briefings:     (1M2M)

Logistics:     (1M2R)

  • (if you haven't already done so) please click on "settings" (top center) and morph from "anonymous" to your RealName (in WikiWord format)     (1M2T)

earlier Skype versions 2.x,) if the dialpad button is not shown in the call window you need to press     (1M2Y)

the "d" hotkey to enable it.     (1M2Z)

proceedings:     (1M2AG)

[9:09] anonymous morphed into Patrick Lambrix     (1M2AH)

[9:23] anonymous morphed into Kevin Simkins     (1M2AI)

[9:29] Peter P. Yim: Attn ALL: ... it has come to our attention that our conference bridge provider is     (1M2AJ)

running into some problems with the "joinconference" skype connections. In case anyone gets in     (1M2AK)

trouble, please try to call the phone numbers instead (e.g. from your phone, skype-out,     (1M2AL)

google-voice, etc.)     (1M2AM)

[9:30] anonymous morphed into Melissa Haendel     (1M2AN)

[9:30] Kevin Simkins: The IEEE Virtual World Standard Working Group (P1828) is focused on the     (1M2AO)

development of common standards for virtual environments. From assets to protocols and general     (1M2AP)

working models in order to facilitate the common interoperability scenario for all virtual     (1M2AQ)

environments in the future. Our working group members are dedicated to multiple phases within this     (1M2AR)

process in order to accumulate further details and application methodologies over time. ... see:     (1M2AS)

[9:32] Joel Bender: @Peter - attempting to enter the conference ID is failing, the bridge is missing     (1M2AU)

digits - I'm calling from a land line     (1M2AV)

[9:38] Anatoly Levenchuk: wrt skype: always mute microphone when you enter ID to skype (mic take     (1M2AW)

sound from your tone-digits and then can be "strange" processes of echo and digits suppressing or     (1M2AX)

doubling of click and "listened" digits).     (1M2AY)

[9:34] anonymous morphed into Bob Smith     (1M2AZ)

[9:35] Melissa Haendel: yes, screen share doesn't work for me     (1M2AAA)

[9:36] Fabian Neuhaus: Melissa, the screen share might not work if you are behind a firewall     (1M2AAB)

[9:37] Fabian Neuhaus: just download the slides from the session page     (1M2AAC)

[9:39] Melissa Haendel: thanks Fabian, I have the slides     (1M2AAE)

[9:35] anonymous morphed into Torsten Hahmann     (1M2AAF)

[9:38] Peter P. Yim: == Steve Ray opening the session on behalf of the co-chairs ... ... see: the     (1M2AAG)

[0-Chair] slides     (1M2AAH)

[9:41] Peter P. Yim: == Patrick Lambrix presenting ... see: the [ 1-Lambrix ] slides     (1M2AAM)

[9:44] anonymous morphed into Doug Foxvog     (1M2AAN)

[9:51] Melissa Haendel: Question, so NCI is largely a human representation whilst MA is mouse. How do     (1M2AAO)

you know there are not species-specific is_a absences or presence? Examples are correct, though :-).     (1M2AAP)

[11:24] Patrick Lambrix: @Melissa [9:51]: For our experiments we had the help of a domain expert.     (1M2AAQ)

(This doesn't mean all the validations are correct. We have also noticed that a domain expert may     (1M2AAR)

change his/her mind about the correctness of an is-a relation during the debugging session when more     (1M2AAS)

is-a relations were debugged.)     (1M2AAT)

[11:28] Melissa Haendel: @patrick. I understand biologists changing their mind! Also depends on the     (1M2AAU)

way in which they are viewing the ontology and the debugging changes. Would be interested to view     (1M2AAV)

this sometime, will look at your papers.     (1M2AAW)

[9:54] Steve Ray: @Melissa: My understanding from his talk is that is why the repairs must be     (1M2AAX)

validated by a domain expert.     (1M2AAY)

[11:24] Patrick Lambrix: @Steve [9:54]: Yes, repairs need to be validated by a domain expert. For     (1M2AAZ)

missing is-a relations a system can compute repairs that guarantee that the missing is-a relations     (1M2AAAA)

will be logically derivable form the repaired ontology, but this does not necessarily mean that the     (1M2AAAB)

repair is correct according to the domain.     (1M2AAAC)

[9:54] Amanda Vizedom: @PatrickLambrix - I like your focus on a high-level division into syntactic,     (1M2AAAD)

semantic, defects; your calling out that detection and debugging of the modeling defects requires     (1M2AAAE)

domain knowledge, and your subsequent emphasis on very practical ways to detect and debug this third     (1M2AAAF)

category. In my experience, the syntactic and semantic evaluation and correction, while necessary,     (1M2AAAG)

are rarely sufficient. There seems, however, to be a widespread impression, or fear, that practical,     (1M2AAAH)

reliable evaluation of model accuracy is not possible. Thanks for showing this not to be true.     (1M2AAAI)

[11:24] Patrick Lambrix: @Amanda [9:54]: If I remember well, the different kinds of defects were     (1M2AAAJ)

defined in Aditya Kalyanpur's PhD thesis. However, there is not so much work on systems for the     (1M2AAAK)

modeling defects yet.     (1M2AAAL)

[9:58] Doug Foxvog: For the example, concluding "limb_joint" is-a "joint" because all of its     (1M2AAAM)

subclasses are-a joint although it is not in any of the ontologies, the conclusion must be verified     (1M2AAAN)

by a human. It is quite possible that that common is-a is too general a term -- which may be the     (1M2AAAO)

reason the is-a was not asserted.     (1M2AAAP)

[9:58] Peter P. Yim: @PatrickLambrix - are there tools already implemented for the process outlined in     (1M2AAAQ)

slide#26 ... if so, are they openly accessible (what is url?)     (1M2AAAR)

[9:58] Melissa Haendel: It would be great to have tools that present these things easily to the     (1M2AAAS)

domain expert. Actually, I would not classify a hip joint as a limb joint (sorry, I work on this     (1M2AAAT)

stuff ;-)).     (1M2AAAU)

[11:24] Patrick Lambrix: @Peter,@Melissa: [9:58]: We have systems and plan to make the first system     (1M2AAAV)

available soon. There are screenshots in the papers in the reference list of the talk.     (1M2AAAW)

[10:05] Doug Foxvog: @Melissa: That depends upon the ontology's definition of "limb joint". The term     (1M2AAAX)

could mean a joint within a limb or a joint which is to at least one bone in a limb. Bone joints vs.     (1M2AAAY)

body region joints are also a contrast; these two types are disjoint.     (1M2AAAZ)

[10:01] Amanda Vizedom: @PatrickLambrix - I would note that "is-a" in your examples appears to be a     (1M2AAAAA)

subClass or kind-of relationship (or, if also used for instances, it may be an under-specified     (1M2AAAAB)

narrower concept used for both instancehood and subclass relationships, as found in some taxonomies,     (1M2AAAAC)

less commonly ontologies, and other semantic models). I call attention to this simply because it can     (1M2AAAAD)

be confusing to modelers who follow most contemporary ontology languages, in which "is-a" is used     (1M2AAAAE)

only for the instancehood relationship, and a different relationship (subClassOf, kind-of, #$genls)     (1M2AAAAF)

is used for the sub-class relationships in your examples.     (1M2AAAAG)

[10:06] Melissa Haendel: well, many anatomists define limb as the free limb, as opposed to the limb     (1M2AAAAH)

plus girdle. but that is perhaps neither here nor there.     (1M2AAAAI)

[10:06] Melissa Haendel: @Patrick - I would love to have you experiment with our work on Uberon - see     (1M2AAAAJ)

[11:25] Patrick Lambrix: @Melissa [10:06]: I would be interested at looking at Uberon.     (1M2AAAAL)

[10:09] Doug Foxvog: @Amanda: many people use "is-a" to mean subclass of. Cyc uses #$isa to mean     (1M2AAAAM)

instance of. I (growing up with Cyc) also find "is-a" used for subclass-of as grating.     (1M2AAAAN)

Grammatically, it should be "a-is-a".     (1M2AAAAO)

[11:24] Patrick Lambrix: @Amanda,@DougFoxvog [10:01]: Yes, is-a isSubClass or kind-of. Our system     (1M2AAAAP)

works currently only on the concept level. For is-a we assume relexivity and transitivity.     (1M2AAAAQ)

[10:10] Amanda Vizedom: @doug, far fewer than used to. The two relationships are teased out, for     (1M2AAAAR)

example, even in OWL.     (1M2AAAAS)

[10:05] Joanne Luciano: is is-a a kind-of-kind-of is-a relationship? or is it a-kind-of-like     (1M2AAAAT)

[11:24] Patrick Lambrix: @Joanne [10:05]: exactly :-)     (1M2AAAAV)

[10:05] Joanne Luciano: :-) nice presentation!     (1M2AAAAW)

[10:10] Leo Obrst: @Patrick: do repair actions ever cause additional problems for other parts of the     (1M2AAAAX)

ontologies not yet analyzed?     (1M2AAAAY)

[11:25] Patrick Lambrix: @Leo [10:10]: Repairing actions could cause additional problems. Therefore,     (1M2AAAAZ)

the system allows a user to switch between the different phases of detecting, validating and     (1M2AAAAAA)

repairing, as well as taxonomies and iteratively debug the whole network. The system also checks     (1M2AAAAAB)

whether a domain expert would want to remove a previously validated to be correct is-a relation. In     (1M2AAAAAC)

this case the user needs to retract the previous choice or the repair is not allowed. Similar when     (1M2AAAAAD)

the domain expert wants to add an is-a relation, that was previously validated as wrong.     (1M2AAAAAE)

[10:06] Peter P. Yim: == Maria Copeland presenting ... see: the [ 2-Copeland ] slides     (1M2AAAAAF)

[10:14] Ed Barkmeyer: @maria: Only some tested elements have meaning to the user. Many test elements     (1M2AAAAAG)

are intended to validate that the inferences work as expected for known cases. In many cases, the     (1M2AAAAAH)

user cannot recognize an erroneous inference, as Patrick mentioned.     (1M2AAAAAI)

[10:21] Ed Barkmeyer: @maria: Is it clear that these changes are "truth" and "bugs", or just     (1M2AAAAAJ)

differences in educated opinion prevailing at different times in the maintenance cycle?     (1M2AAAAAK)

[10:21] Ali Hashemi: @Maria - are the graphs on slides 30 and 34(b) correct? It seems to me it should     (1M2AAAAAL)

be Effectually added (solid line) Ineffectually Removed (dotted line) Effectually Removed (no line)     (1M2AAAAAM)

Effectually Added ... otherwise, what do the lines represent?     (1M2AAAAAN)

[10:23] Doug Foxvog: @Maria: could these changes be a result of different users having different     (1M2AAAAAO)

ideas of what the terms (should) mean?     (1M2AAAAAP)

[10:23] Melissa Haendel: We (try to) keep track of such edits in the ontology metadata, it would be     (1M2AAAAAQ)

fantastic to have a human readable version provided to the ontology editor/domain editor whilst they     (1M2AAAAAR)

are editing.     (1M2AAAAAS)

[10:23] anonymous morphed into David Whitten     (1M2AAAAAT)

[10:26] Amanda Vizedom: @MariaCopeland - could you explain your effectually / ineffectually     (1M2AAAAAU)

distinction a little more? I think I understood you to say that "effectual" presence means presence     (1M2AAAAAV)

as a directly asserted axiom, while "ineffectual" presence means absence from the directly asserted     (1M2AAAAAW)

axioms, but continued entailment by the ontology. Is that correct? If so, is this, as the label     (1M2AAAAAX)

ineffectual suggests, considered a fault? I ask because I imagine that presence as entailment only     (1M2AAAAAY)

would be desirable in some applications and undesirable in others. Specifically, if little to know     (1M2AAAAAZ)

reasoning is done in an application and only directly asserted applications are usable, then     (1M2AAAAAAA)

entailments are indeed "ineffectual". In other cases, where some degree of reasoning is used and is     (1M2AAAAAAB)

efficient, assertions that are redundant with entailments may be removed for efficiency, if there is     (1M2AAAAAAC)

not additional, provenance-related reason to make explicit assertions that rely on different     (1M2AAAAAAD)

[11:24] Maria Copeland: @EdBarkmeyer, @AliHashemi, @DougFoxvog, @Melissa: Thanks for your questions     (1M2AAAAAAF)

and comments. I will follow up offline.     (1M2AAAAAAG)

[10:23] Peter P. Yim: == Melissa Haendel presenting ... see: the [ 3-Haendel ] slides     (1M2AAAAAAH)

[10:30] Hans Polzer: (ref. slide#4) The example of fruit fly limbs vice human limbs underscores the     (1M2AAAAAAI)

need for more explicit representation of context as it relates to ontologies     (1M2AAAAAAJ)

[10:32] Doug Foxvog: @Hans: the fruit fly vs. human Tibia presents an example of using NL words as     (1M2AAAAAAK)

terms for concepts in an ontology. There should be mappings from the NL terms to (multiple)     (1M2AAAAAAL)

concepts. But annotation of the concept should make its intended meaning crystal clear.     (1M2AAAAAAM)

[10:34] Amanda Vizedom: @Hans - I don't disagree, exactly, but I'd add that it is also a good     (1M2AAAAAAN)

illustration of why it is important not to confuse expressions and concepts. Arguably, the fruit fly     (1M2AAAAAAO)

tibia is a subclass of some class of animal body parts that are not skelatal; the human tibia is a     (1M2AAAAAAP)

subclass of some class of animal body parts that are skelatal. "limb" may be an expression used for     (1M2AAAAAAQ)

both of those classes, but the classes are different.     (1M2AAAAAAR)

[10:35] Doug Foxvog: @Melissa : Having a key separation in an ontology whether something is     (1M2AAAAAAS)

detectable seems to be setting oneself up to have the feature expire when new technology allows     (1M2AAAAAAT)

something not previously detectable to become detectable.     (1M2AAAAAAU)

[10:36] Doug Foxvog: I had trouble hearing for a while. But the sound has now come back     (1M2AAAAAAV)

[10:36] Hans Polzer: But in some contexts the term "limb" represents the identical concept, for     (1M2AAAAAAW)

example, when considering locomotion rather than anatomy (and not focusing on how exactly the     (1M2AAAAAAX)

movement of the limb is activated/energized.)     (1M2AAAAAAY)

[11:02] Melissa Haendel: @hans. we have disjoint axioms to prevent fruitfly tibia being equated with     (1M2AAAAAAZ)

human tibia. I wonder how much such disjoint axioms are leveraged in the ontology alignment     (1M2AAAAAAAA)

strategies? or if we can be providing them better for such purposes.     (1M2AAAAAAAB)

[11:04] Doug Foxvog: +1 Melissa. Disjointness axioms are crucial. Especially if they are enforced on     (1M2AAAAAAAC)

modification of an ontology to prevent the creation of classes that are disjoint with themselves.     (1M2AAAAAAAD)

[10:37] Amanda Vizedom: @Melissa -- Don't worry, it's not just biologists! I've lost track of the     (1M2AAAAAAAE)

number of domains I've worked in or with, and I don't think I've yet met a community of practice     (1M2AAAAAAAF)

that doesn't have these features (moving conceptual targets, reuse of labels, and expert     (1M2AAAAAAAG)

disagreements on definitions). I suspect there are fundamentals of human cognition, language, and     (1M2AAAAAAAH)

community knowledge development at work . :-)     (1M2AAAAAAAI)

[10:38] Doug Foxvog: One need to define multiple limbs: tree limb, animal limb, subclasses of animal     (1M2AAAAAAAJ)

limb by exo/endo-skeleton, etc.     (1M2AAAAAAAK)

[10:38] Amanda Vizedom: @Hans - agreed. And that is, arguably a different concept, for which the same     (1M2AAAAAAAL)

expression is used.     (1M2AAAAAAAM)

[10:39] Doug Foxvog: @Amanda: Of course. Replace disagreement on definitions by modeling all     (1M2AAAAAAAN)

definitions with different (maybe overlapping) concepts.     (1M2AAAAAAAO)

[10:39] Steve Ray: This raises the point that different communities still want to use their own     (1M2AAAAAAAP)

terminologies, and they should, but we can separate those terminologies (expressions or labels) from     (1M2AAAAAAAQ)

the concepts.     (1M2AAAAAAAR)

[10:41] Ed Barkmeyer: @melissa: As you say, people think ontology terms are words, and they think     (1M2AAAAAAAS)

definitions are circular when those words are reused, but the fact is that the definitions are in     (1M2AAAAAAAT)

natural language, the ontology symbols are "words" in a formal language. The issue is whether the     (1M2AAAAAAAU)

definitions themselves are circular.     (1M2AAAAAAAV)

[10:42] Doug Foxvog: OBO still has problems with different people having different ideas of what a     (1M2AAAAAAAW)

term is, even when the name is numeric. The NL description is not specific enough, so for example,     (1M2AAAAAAAX)

the plant people assume it means the plant definition of the term and the animal people assume it is     (1M2AAAAAAAY)

an animal definition. As a result, in the Cell (Line) Ontology, multiple cell types were subclasses     (1M2AAAAAAAZ)

of both animal cell and plant cell.     (1M2AAAAAAAAA)

[10:41] Terry Longstreth: @Melissa - Last bullet on slide 11 implies that speculative biology is not     (1M2AAAAAAAAB)

[11:04] Melissa Haendel: @terry I think what I was saying is that actually speculative biology is in     (1M2AAAAAAAAD)

scope, but we just need to understand how to apply the ontology consistently when we are potentially     (1M2AAAAAAAAE)

being speculative. (or maybe I misunderstand)     (1M2AAAAAAAAF)

[10:41] Hans Polzer: We have an aversion to specifying context because it seems unnecessary in most     (1M2AAAAAAAAG)

situations we find ourselves in - yet the internet and networked world exposes us to otherwise alien     (1M2AAAAAAAAH)

contexts that are left implicit, thus leading to the arguments about definitions     (1M2AAAAAAAAI)

[10:42] Hans Polzer: We want an absolute frame of reference, but usually assume our own frame of     (1M2AAAAAAAAJ)

reference is that absolute frame of reference.     (1M2AAAAAAAAK)

[10:44] Hans Polzer: We need to learn to tolerate that there are multiple frames of reference and     (1M2AAAAAAAAL)

multiple perspectives on those frames of reference and associated scope.     (1M2AAAAAAAAM)

[10:44] Doug Foxvog: @Hans: You say "we" have an aversion to specifying context. *I* don't. 8)# I     (1M2AAAAAAAAN)

find context crucial.     (1M2AAAAAAAAO)

[10:45] Hans Polzer: It was the editorial "we" :-)     (1M2AAAAAAAAP)

[10:45] Hans Polzer: Humans are very good at detecting context, except when it fails us - and thus     (1M2AAAAAAAAQ)

results in great literature     (1M2AAAAAAAAR)

[10:43] anonymous morphed into ValentinaIvanova     (1M2AAAAAAAAT)

[10:44] Steve Ray: Gee, I'm thinking about a transiently transfected DNA expression construct and I'm     (1M2AAAAAAAAU)

coming up blank :)     (1M2AAAAAAAAV)

[10:45] Amanda Vizedom: @Melissa - slide 16: very nice illustration of refinement to include more     (1M2AAAAAAAAW)

specific classes, corresponding with important functional distinctions.     (1M2AAAAAAAAX)

[10:46] Ed Barkmeyer: @melissa: this is a great contribution! thanks.     (1M2AAAAAAAAY)

[10:50] Peter P. Yim: @MelissaHaendel: do you have tools to augment the process(es) that you are     (1M2AAAAAAAAZ)

[11:07] Melissa Haendel: @Peter - we have some scripts that help. We have been using Jenkins to help     (1M2AAAAAAAAAB)

[11:12] Peter P. Yim: @MelissaHaendel - thank you, reason I am asking is because we are running     (1M2AAAAAAAAAD)

Ontology Clinic activities (as part of this Summit) by putting together ontology developers and     (1M2AAAAAAAAAE)

people with ontology evaluation methodologies and tool in the same (virtual) room to get some     (1M2AAAAAAAAAF)

interesting outcome, and we'll love to have you (and the other panelists today) to join us - see:     (1M2AAAAAAAAAG)

[11:17] Melissa Haendel: @peter, it would be great to see if you could get Chris Mungall to     (1M2AAAAAAAAAI)

participate regarding his development of Jenkins. see http://wiki.geneontology.org/index.php/Jenkins     (1M2AAAAAAAAAJ)

. Most of our work on the metadata is in the form of scripts and not integrated into tooling (though     (1M2AAAAAAAAAK)

we have some protege plugins).     (1M2AAAAAAAAAL)

[11:19] Peter P. Yim: @Melissa - thank you for the pointer ... this is helpful as we are doing a survey     (1M2AAAAAAAAAM)

on software and tools, as part of the Summit activities, too     (1M2AAAAAAAAAN)

[10:47] Doug Foxvog: Re slide 15. An ontology should not have synonyms. It should have mappings from     (1M2AAAAAAAAAO)

NL terms to the ontology terms. One NL term can map to multiple ontology terms and vice versa.     (1M2AAAAAAAAAP)

[10:47] Amanda Vizedom: @Melissa: slide 15: Do you mean that experts cannot articulate the     (1M2AAAAAAAAAQ)

distinctions? Or that the modeling language is not expressive enough to capture it clearly?     (1M2AAAAAAAAAR)

[10:52] Steve Ray: @Amanda: How would you handle the example of the Senator who said "I can't define     (1M2AAAAAAAAAS)

it but I'll know it when I see it". ...in the context of porn. Quite seriously, it seems that     (1M2AAAAAAAAAT)

perhaps we sometimes operate with definitions only by example and are unable to define concepts.     (1M2AAAAAAAAAU)

[10:58] Amanda Vizedom: @Steve: I did mean to ask for clarification, not to imply that there are no     (1M2AAAAAAAAAV)

undefinable concepts. In fact, it is very common for us to use concepts operationally and regularly     (1M2AAAAAAAAAW)

without there being any set of necessary and sufficient conditions to accompany them. The less     (1M2AAAAAAAAAX)

technical the concept, I'd argue, the more this is likely to be true. IME, textual definitions that     (1M2AAAAAAAAAY)

mention and guide against potentially confused concepts can be very useful, though inherently     (1M2AAAAAAAAAZ)

[11:00] Steve Ray: @Amanda: Agreed.     (1M2AAAAAAAAAAB)

[10:54] Amanda Vizedom: @Melissa - slide 18, "true path" violations -- common problem indeed; human     (1M2AAAAAAAAAAC)

brains are not good at keeping that kind of entailment trace. ;-) One technique that can help catch     (1M2AAAAAAAAAAD)

these is the creation of tests that instantiate classes and draw the transitive inferences,     (1M2AAAAAAAAAAE)

presenting the results to the experts, who are more likely to catch it at *that* point if they've     (1M2AAAAAAAAAAF)

created either inconsistencies or undesired implications.     (1M2AAAAAAAAAAG)

[11:10] Melissa Haendel: @amanda: I would love your idea "One technique that can help catch these is     (1M2AAAAAAAAAAH)

the creation of tests that instantiate classes and draw the transitive inferences, presenting the     (1M2AAAAAAAAAAI)

results to the experts, who are more likely to catch it at *that* point if they've created either     (1M2AAAAAAAAAAJ)

inconsistencies or undesired implications." This would help biologists enormously.     (1M2AAAAAAAAAAK)

[10:49] Terry Longstreth: @Melissa Slide 17 - Curation status include provenance trace?     (1M2AAAAAAAAAAL)

[10:47] Peter P. Yim: Ed & All: please provide some context wrt to your comment ... otherwise the     (1M2AAAAAAAAAAM)

remarks won't mean much in the proceedings     (1M2AAAAAAAAAAN)

[10:53] Hans Polzer: Peter, Melissa: my comments were aimed at the issue of ambiguity and controversy     (1M2AAAAAAAAAAO)

in concept definitions. From a pragmatic/realism approach it may be worthwhile to make more of the     (1M2AAAAAAAAAAP)

context assumptions specific to a given definition, allowing more flexibility in applying a specific     (1M2AAAAAAAAAAQ)

ontology or term in an ontology in a given situation/perspective/context.     (1M2AAAAAAAAAAR)

[10:55] Peter P. Yim: @Hans - my comment is strictly aimed at messages people are typing into this     (1M2AAAAAAAAAAS)

chat-room (like, "this is great!" would mean much less than "ref. your slide#12, this is great     (1M2AAAAAAAAAAT)

insight!") since we captured the chat-transcript as part of the proceedings of the session.     (1M2AAAAAAAAAAU)

[10:57] Melissa Haendel: (just lost of her voice connection as she got to the last slide) I'm all     (1M2AAAAAAAAAAV)

done :-) ... Thank you.     (1M2AAAAAAAAAAW)

[10:58] Fabian Neuhaus: @ Melisssa, the standards for documentation: is this an OBO Foundry effort?     (1M2AAAAAAAAAAX)

[11:06] Melissa Haendel: @fabian this is a Melissa's team effort ;-). I would like it to be an OBO     (1M2AAAAAAAAAAY)

effort, and I think we are getting traction.     (1M2AAAAAAAAAAZ)

[10:58] Peter P. Yim: == Ed Barkmeyer presenting ... see: the [ 4-Barkmeyer ] slides     (1M2AAAAAAAAAAAA)

[11:00] anonymous morphed into Ludger Jansen     (1M2AAAAAAAAAAAB)

[11:02] Joel Bender: Units! ��F!     (1M2AAAAAAAAAAAC)

[11:04] Leo Obrst: @Ed: would you say that code-lists are controlled vocabularies, and that these map     (1M2AAAAAAAAAAAD)

to concepts/classes in a given ontology? Another example are digraphs and trigraphs for     (1M2AAAAAAAAAAAE)

countries/states.     (1M2AAAAAAAAAAAF)

[11:04] Steve Ray: @Ed: I'm interpreting your Code List to be what many call an Enumeration. Yes?     (1M2AAAAAAAAAAAG)

[11:05] Peter P. Yim: @EdBarkmeyer and All - some members of the Ontolog community had actually worked     (1M2AAAAAAAAAAAH)

on a project "CCT-Representation" back in 2004/2005 to map the ebXML Core Component Types ("CCT") to     (1M2AAAAAAAAAAAI)

a First Order Logic ontology (SUMO, MILO, QoS) - see: An Ontological Basis for ebXML Core Component     (1M2AAAAAAAAAAAJ)

[11:06] Doug Foxvog: Code lists are controlled vocabularies. However, as Ed Barkmeyer is saying, the     (1M2AAAAAAAAAAAL)

meanings of the codes changes. So, dated uses of the codes is important.     (1M2AAAAAAAAAAAM)

[11:11] Leo Obrst: @Doug: yes, we see this all the time. There are extreme versioning issues involved     (1M2AAAAAAAAAAAN)

in maintaining the mappings from these controlled vocabularies to the ontology/ies.     (1M2AAAAAAAAAAAO)

[11:06] anonymous morphed into Pavithra Kenjige     (1M2AAAAAAAAAAAP)

[11:07] Doug Foxvog: I note that ISO country codes occasionally change.     (1M2AAAAAAAAAAAQ)

[11:08] Hans Polzer: and countries change and come into being and go away     (1M2AAAAAAAAAAAR)

[11:11] Doug Foxvog: @Hans: I remember once finding an ISO code for an expired country being re-used     (1M2AAAAAAAAAAAS)

over a decade later for a new country. I forget what the example was.     (1M2AAAAAAAAAAAT)

[11:14] Amanda Vizedom: @EdBarkmeyer - Thanks for this presentation. I've seen this topic persist as     (1M2AAAAAAAAAAAU)

a point of conflict on ontology projects -- whether to go the string route or the     (1M2AAAAAAAAAAAV)

expression-for-thing route. Least-immediate-effort often pulls people toward the string route, but     (1M2AAAAAAAAAAAW)

if there is integration to be done, this is usually a mistake (or at best, pushes the effort down     (1M2AAAAAAAAAAAX)

the road, when it will have to be redone).     (1M2AAAAAAAAAAAY)

[11:14] Hans Polzer: Ref slide 6 in Ed's talk, it would seem to have some temporal context     (1M2AAAAAAAAAAAZ)

specification - I suppose that's in the administrative records somewhere     (1M2AAAAAAAAAAAAA)

[11:18] Hans Polzer: Looking up the code list is becoming more practical as things become more     (1M2AAAAAAAAAAAAB)

connected over the internet. But there are also practical constraints on doing these lookups in real     (1M2AAAAAAAAAAAAC)

time while processing transactions     (1M2AAAAAAAAAAAAD)

[11:18] Doug Foxvog: @EdBarkmeyer: re slides 7 & 8. Having a term mapped to a code & code list is     (1M2AAAAAAAAAAAAE)

intrinsically a ternary concept. An object that is an instance in a code list can have two mappings     (1M2AAAAAAAAAAAAF)

from item, one to the code & the other to the code list. However, this only would work if the item     (1M2AAAAAAAAAAAAG)

maps only to a single code & single code list.     (1M2AAAAAAAAAAAAH)

[11:30] Victor Agroskin: To do such code models consistently is much easier if your ontology language     (1M2AAAAAAAAAAAAI)

contains concept of class_of_class. Coding models of this type are very common for systems     (1M2AAAAAAAAAAAAJ)

implemented on ISO 15926. And ISO 15926-6 is partially a mapping of ISO 11179-3.     (1M2AAAAAAAAAAAAK)

[11:18] == Q & A and Open Discussion ...     (1M2AAAAAAAAAAAAL)

[11:18] Amanda Vizedom: I need to drop off -- thanks to all presenters! Good stuff.     (1M2AAAAAAAAAAAAM)

[11:24] Leo Obrst: Gramm Richardson et al gave a talk at STIDS 2012 on an 11179 registry addressing     (1M2AAAAAAAAAAAAO)

[11:25] Peter P. Yim: I am soliciting help from everyone here: -- for software environment stewards and     (1M2AAAAAAAAAAAAS)

tool developers, please make sure you participate in the upcoming survey ---and help us get these     (1M2AAAAAAAAAAAAT)

colleagues of yours to respond to the survey too (they'll be on a wiki, so everyone will know who     (1M2AAAAAAAAAAAAU)

has or hasn't responded) ... or provide us with pointers so we can reach out to them -- we need     (1M2AAAAAAAAAAAAV)

ontology evaluation experts and tool developers to participate in the "hackathon" and "clinics"     (1M2AAAAAAAAAAAAW)

[11:26] Peter P. Yim: also ... Join us at the "hackathon" and "clinics" activities -     (1M2AAAAAAAAAAAAY)

[11:35] Victor Agroskin: @Peter, @Patrick, @Valentina - we'll be really happy to see Patrick's team     (1M2AAAAAAAAAAAAAB)

to collaborate in our Clinics activity     (1M2AAAAAAAAAAAAAC)

is a nice combination of taxonomies, quite suitable for exploration by methods described by Patrick.     (1M2AAAAAAAAAAAAAE)

[11:28] Pavithra Kenjige: About intrinsic and extrinsic evaluation .. those parts that are     (1M2AAAAAAAAAAAAAF)

manufactured by others .. is that considered extrinsic evaluation ??     (1M2AAAAAAAAAAAAAG)

[11:35] Leo Obrst: Thanks, all! Good session.     (1M2AAAAAAAAAAAAAH)

[11:35] Joanne Luciano: Would you repeat Peter's last point?     (1M2AAAAAAAAAAAAAI)

[11:35] Peter P. Yim: join us again, same time next week (Thu 2013.03.14), for Ontology Summit 2013     (1M2AAAAAAAAAAAAAJ)

session-09: "Building Ontologies to Meet Evaluation Criteria - I" - Co-chairs: Mike Bennett &     (1M2AAAAAAAAAAAAAK)

Matthew West - see developing session page at     (1M2AAAAAAAAAAAAAL)

[11:36] Kevin Simkins: Thanks to all speakers and host.     (1M2AAAAAAAAAAAAAP)

[11:36] Peter P. Yim: great session ... thanks everyone!     (1M2AAAAAAAAAAAAAQ)

[11:36] Joanne Luciano: Very interesting, thanks!     (1M2AAAAAAAAAAAAAR)

[11:36] anonymous morphed into Bijan Parsia     (1M2AAAAAAAAAAAAAS)

[11:36] David Whitten: Fascinating insights. Well Done all of you.     (1M2AAAAAAAAAAAAAU)

[11:36] Peter P. Yim: ... session ended ==     (1M2AAAAAAAAAAAAAV)

-- end of in-session chat-transcript --     (1M2AAAAAAAAAAAAAW)

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