ConferenceCall 2009 07 16

= Joint Ontolog-OOR Panel Discussion Session - Thu 16-July-2009 =

Topic: Integrated tools for ontology development and management: A field guide to the Stanford technology
Session Chair: Professor MarkMusen, MD Ph.D.

Panelists:


 * Dr. TaniaTudorache
 * Dr. TimRedmond
 * Dr. NatashaNoy

Archives

 * Our panel's prepared slides can be accessed by clicking on each of the title links below:
 * Slides: . [ 1-Tudorache ] . [ 2-Redmond ] . [ 3-Noy ] 
 * [ Audio Recording of the session ] (mp3)
 * [ Transcript of the online chat session ] during the panel discussion

Conference Call Details

 * Date: Thursday, July 16, 2009 
 * Start Time: 10:30am PDT / 1:30pm EDT / 7:30pm CEST / 6:30pm BST / 17:30 UTC
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 * Expected Call Duration: 1.5~2.0 hours
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Abstract:. . . by MarkMusen

'''For the past 20 years, workers at Stanford University have been developing tools to assist with different aspects of the ontology life cycle. This panel will present several inter-related tools that assist with ontology editing, management, and peer review that are available to the entire Ontolog community. These tools include:'''


 * The Protégé ontology editor, which now supports both distributed, collaborative ontology development and a Web-based client


 * The Ontolog Collaborative Ontology Development Service (CODS), which allows users to edit and access ontologies from a shared server


 * BioPortal, the open ontology repository of the National Center for Biomedical Ontology (NCBO), developed by groups at Stanford, Mayo, and Victoria for ontology browsing, visualization, mapping, search, and annotation. Through an interactive "notes" features, users can enter threaded discussion about ontologies in BioPortal and engage in community-based peer review


 * Ontology-oriented Web services, which allow programmatic ontology access to BioPortal ontologies and use of those ontologies for a number of useful tasks

In this session, the panelists will describe the functionality of these different tools, and discuss how they can be used in concert to develop and manage significant ontology-related projects.

Attendees

 * Attended:
 * MarkMusen
 * TaniaTudorache
 * NatashaNoy
 * TimRedmond
 * PeterYim
 * JenniferVendetti
 * MikeDean
 * KeithDeWeese
 * KurtConrad
 * PatCassidy
 * CecilLynch
 * Blake Shepard (Cycorp)
 * GailHodge
 * DougHolmes
 * HaroldSolbrig
 * MichaelGruninger
 * DarrenOng
 * Randy Kerber (Sandpiper Software)
 * BaharehHeravi
 * MikeBennett
 * ArturoSanchez
 * Clarence Dillon
 * BartGajderowicz
 * SteveRay


 * Other registered participants who may have joined us after the roll call:
 * NigamShah
 * BrandNiemann
 * Sylvere Krima (NIST)
 * RoyRoebuck
 * MichaelDorf
 * GaryBergCross
 * Xenia Fiorentini (NIST)
 * ... if you are coming to the session, please add your name above (please include your affiliation, if you aren't already a member of the community); or e-mail  so that we can reserve enough resources to support everyone's participation. ...
 * ... if you are coming to the session, please add your name above (please include your affiliation, if you aren't already a member of the community); or e-mail  so that we can reserve enough resources to support everyone's participation. ...


 * Regrets:
 * ToddSchneider

Agenda
1. Opening by session Chair (MarkMusen)

2. Briefings from Panelists -- TaniaTudorache, TimRedmond, NatashaNoy

3. Q & A and Open Discussion (All) -- please refer to process above

4. Summary and Next Steps (MarkMusen)

Discussion:

 * Please refer to the process above


 * See related material under the archives section above

IM Chat Transcript captured during the session: ... (Chat Transcript has been lightly edited for clarity)

PeterYim: Welcome to the Joint Ontolog-OOR Panel Discussion Session - Thu 16-July-2009

Topic: Integrated tools for ontology development and management: A field guide to the Stanford technology

Session Chair: Professor MarkMusen, MD Ph.D.

Panelists:


 * Dr. TaniaTudorache
 * Dr. TimRedmond
 * Dr. NatashaNoy

PeterYim: See details on the session page at: http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2009_07_16

PeterYim: To mute your phone line, press " *2 " ... and un-mute press " *3 "

PeterYim: anonymous users please change your names to a WikiWord format name (with the "Settings" button at top center of window)

anonymous morphed into meena

anonymous morphed into Rafat

anonymous morphed into DarrenOng

anonymous morphed into KurtConrad

anonymous morphed into Clarence Dillon

anonymous1 morphed into TimothyRedmond

anonymous1 morphed into SteveRay

anonymous1 morphed into BaharehHeravi

anonymous morphed into CecilLynch

VNC2: NatashaNoy is presenting ...

anonymous: @Peter: Where are the slides? Shes on slide 3 and Im not seeing anything but a room full of people. Please advise...

PeterYim: slides are under: http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2009_07_16#nid1ZM5

PeterYim: @person with your hand up ... are you able to get to the slides yet? (...you can lower you hand by clicking on the "hand button" again, it toggles)

anonymous morphed into TaniaTudorache

HaroldSolbrig: A question about the new widget library... If you migrate, does it invalidate the extensions that folks have written to date?

TaniaTudorache: yes

TaniaTudorache: actually, partly

TaniaTudorache: only the UI part would change

HaroldSolbrig: Should we wait then?

TaniaTudorache: depends

HaroldSolbrig: I'd like not to - this looks really great and I'd like to get started sooner rather than later

TaniaTudorache: we expect that the migration to the new UI library for the extensions will not be difficult

HaroldSolbrig: Are you not satisfied with GWT? What are you considering?

TaniaTudorache: We like GWT

TaniaTudorache: but,the GWT-ext lib is not so good

TaniaTudorache: @Harold: Sorry, I had to drop the conversation before

TaniaTudorache: We're going to use GWT, but we may replace the GWT-ext UI library that we are using

HaroldSolbrig: Oh - that isn't so bad, then.

TaniaTudorache: if someone would develop a portlet using GWT, then there would be no problem, no migration needed

HaroldSolbrig: So any GWT commitments will be durable.

HaroldSolbrig: Perfect.

TaniaTudorache: yes

ArturoSanchez: @TaniaTudorache - Did you consider using open source portal development platforms?

ArturoSanchez: About open source portal development platforms, one that comes to mind is uPortal

TaniaTudorache: Thanks for the suggestion!

TaniaTudorache: We'll look at uPortal

ArturoSanchez: Another suggestion for Ms. Tudorache: Use "Elluminate" as the collaboration platform ...

VNC: TimRedmond is presenting ... (on slide#5 now)

HaroldSolbrig: SVN has pluggable diffs, however.

HaroldSolbrig: Textual is just a default.

ArturoSanchez: @TaniaTudorache - How ontology-driven is the portal tool itself?

TaniaTudorache: @Arturao: Thank you for the suggestion. Our collaboration framework is very much "ontology-oriented". We'll have to see if Elluminate can be easily integrated

ArturoSanchez: Comment for Mr. Redmond Re: Version Control platforms, you might want to consider 'Git' ... I do not know if it supports pluggable diffs (which is a good point in connection to SVN)

HaroldSolbrig: It seems like the change management requires a standardized diff format?

HaroldSolbrig: The ability to exchange ontology deltas, with sufficient information to detect collisions.

MarkMusen: The problem is that an OWL ontology is a collection of unordered axioms. There is no canonical serialization for such ontologies. This is why standard diffs fail.

TaniaTudorache: The plan is to use the OWL-API Axioms as diffs

TaniaTudorache: (at least for the OWL part)

TimothyRedmond: But using owl axioms as diffs is problematic

TaniaTudorache: all operations in the OWL-API are addition and deletion of axioms

TimothyRedmond: prompt does a much more complicated algorithm

TaniaTudorache: sorry, i meant diffs at runtime

TimothyRedmond: so a refactor will show a very complex set of addition and deletions

TaniaTudorache: not user-friendly diffs

TimothyRedmond: oh yes - this depends on whether we are talking about version control or a server

TimothyRedmond: the server will use axiom diffs

TimothyRedmond: version control needs a better method because it will need to be user  friendly.

ArturoSanchez: Question for Mr. Redmond and Ms. Tudorache: do you have a model that defines the concept of 'difference' between ontologies?

TaniaTudorache: we do for Protege 3

TaniaTudorache: not Protege 4 and OWL-API

ArturoSanchez: So, naively speaking, can you implement this method as a pluggable diff for SVN? (or Git, if it supports it)

HaroldSolbrig: @Mark: perhaps you need axiom identities and/or state (I changed axiom #1111732 edition 17 from A to B) or, if it is is simply editions and deletions (troubling - I'd like to correct the spelling of an xml:literal without being totally destructive...), then the identifiers allow the discovery of overlapping changes. The other issue, however, is that changes aren't always atomic...

TimothyRedmond: a pluggable diff mechanism would be very helpful

TimothyRedmond: prompt gives a very useful definition of a diff but I think that it would need some work to be sufficient for a version control mechanism

HaroldSolbrig: What I like about the SVN approach is that "what" is also the "how".

TimothyRedmond: There are other diff mechanisms running about that I haven't fully tested (e.g. owldiff). I had trouble with that one and the nci thesaurus

ArturoSanchez: NatashaNoy is presenting ... (on slide#41 now)

ArturoSanchez: Question for Ms. Noy: what is the 'meta-model' that defines the concept of 'mapping'? In other words, what is the 'formal' definition of a mapping?

BartGajderowicz: @NatashaNoy - What format are the mappings in, for download?

BartGajderowicz: Peter, the [3-Noy] presentation is a *.pdf, but wiki link is pointing to *.ppt

PeterYim: Natasha wanted to present from the powperpoint deck (where some slides were hidden), the pdf is full length ... both versions are avilable at: http://ontolog.cim3.net/file/work/OOR-Ontolog-Panel/2009-07-16_Stanford-NCBO-Ontology-Tools/

ArturoSanchez: Thanks to all!

HaroldSolbrig: Excellent presentations.

MikeBennett: THanks all - most excellent

BartGajderowicz: Thank you. It was a great set of presentations. Looking forward to the next OOR session

anonymous1: Thank you! Bye

PeterYim: Huge thank you to Mark, Tania, Tim & Natasha ... thanks everyone for your participation ... bye!


 * Further Question & Remarks - please post them to the [ontolog-forum] listserv
 * see Ontolog membership details. We welcome your participation if you are not already a member of the community
 * for those who would like to participate in the OOR initiative, see: OpenOntologyRepository

Audio Recording of this Session

 * To download the recording of the session, click here
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 * Conference Date and Time:	16-Jul-2009 10:38am~12:12 pm PDT
 * Duration of Recording:	1 Hour 29 Minutes
 * Recording File Size:	       10.2 MB (in mp3 format)
 * suggestions:
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 * Take a look, also, at the rich body of knowledge that this community has built together, over the years, by going through the archives of noteworthy past Ontolog events. (References on how to subscribe to our podcast can also be found there.)

For the record ...

How To Join (while the session is in progress)

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