Joint Ontolog-OOR Panel Discussion Session - Thu 16-July-2009    (1Z52)

Topic: Integrated tools for ontology development and management: A field guide to the Stanford technology    (1Y4S)

Session Chair: Professor MarkMusen, MD Ph.D.    (1Z4P)

Panelists:    (1Z4Q)

Archives    (1ZM4)

Conference Call Details    (1ZIR)

Abstract: . . . by MarkMusen    (1Z4V)

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:    (1Z4W)

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.    (1Z51)

Attendees    (1Z53)

Agenda & Proceedings    (1ZMA)

Agenda    (1ZMB)

1. Opening by session Chair (MarkMusen)    (1ZMC)

2. Briefings from Panelists -- TaniaTudorache, TimRedmond, NatashaNoy    (1ZMD)

3. Q & A and Open Discussion (All) -- please refer to process above    (1ZME)

4. Summary and Next Steps (MarkMusen)    (1ZMF)

Proceedings    (1ZMG)

Discussion:    (1ZMH)

Please refer to the process above    (1ZMI)

See related material under the archives section above    (1ZMJ)

IM Chat Transcript captured during the session: ... (Chat Transcript has been lightly edited for clarity)    (1ZMK)

 PeterYim: Welcome to the Joint Ontolog-OOR Panel Discussion Session - Thu 16-July-2009    (1ZML)
 Topic: Integrated tools for ontology development and management: A field guide to the Stanford technology    (1ZPD)
 Session Chair: Professor MarkMusen, MD Ph.D.    (1ZPE)
 Panelists:    (1ZPF)
    * Dr. TaniaTudorache   
    * Dr. TimRedmond    
    * Dr. NatashaNoy    (1ZPG)
 PeterYim: See details on the session page at: http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2009_07_16    (1ZPH)
 PeterYim: To mute your phone line, press " *2 " ... and un-mute press " *3 "    (1ZPJ)
 PeterYim:  anonymous users please change your names to a WikiWord format name 
            (with the "Settings" button at top center of window)    (1ZPK)
 anonymous morphed into meena    (1ZPM)
 anonymous morphed into Rafat    (1ZPN)
 anonymous morphed into DarrenOng    (1ZPO)
 anonymous morphed into KurtConrad    (1ZPP)
 anonymous morphed into Clarence Dillon    (1ZPQ)
 anonymous1 morphed into TimothyRedmond    (1ZPR)
 anonymous1 morphed into SteveRay    (1ZPS)
 anonymous1 morphed into BaharehHeravi    (1ZPT)
 anonymous morphed into CecilLynch    (1ZPU)
 VNC2: NatashaNoy is presenting ...    (1ZPV)
 anonymous: @Peter: Where are the slides? Shes on slide 3 and Im not seeing anything 
            but a room full of people. Please advise...    (1ZPW)
 PeterYim: slides are under: http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2009_07_16#nid1ZM5    (1ZPX)
 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)    (1ZPY)
 anonymous morphed into TaniaTudorache    (1ZQ4)
 HaroldSolbrig: A question about the new widget library... If you migrate, does it invalidate 
                the extensions that folks have written to date?    (1ZQ5)
 TaniaTudorache: yes    (1ZQ6)
 TaniaTudorache: actually, partly    (1ZQ7)
 TaniaTudorache: only the UI part would change    (1ZQ8)
 HaroldSolbrig: Should we wait then?    (1ZQ9)
 TaniaTudorache: depends    (1ZQA)
 HaroldSolbrig: I'd like not to - this looks really great and I'd like to get started sooner rather than later    (1ZQB)
 TaniaTudorache: we expect that the migration to the new UI library for the extensions will not be difficult    (1ZQC)
 HaroldSolbrig: Are you not satisfied with GWT?  What are you considering?    (1ZQD)
 TaniaTudorache: We like GWT    (1ZQE)
 TaniaTudorache: but,the GWT-ext lib is not so good    (1ZQF)
 TaniaTudorache: @Harold: Sorry, I had to drop the conversation before    (1ZQG)
 TaniaTudorache: We're going to use GWT, but we may replace the GWT-ext UI library that we are using    (1ZQH)
 HaroldSolbrig: Oh - that isn't so bad, then.    (1ZQI)
 TaniaTudorache: if someone would develop a portlet using GWT, then there would be no problem, no migration needed    (1ZQJ)
 HaroldSolbrig: So any GWT commitments will be durable.    (1ZQK)
 HaroldSolbrig: Perfect.    (1ZQL)
 TaniaTudorache: yes    (1ZQM)
 ArturoSanchez: @TaniaTudorache - Did you consider using open source portal development platforms?    (1ZQN)
 ArturoSanchez: About open source portal development platforms, one that comes to mind is uPortal    (1ZQO)
 TaniaTudorache: Thanks for the suggestion!    (1ZQP)
 TaniaTudorache: We'll look at uPortal    (1ZQQ)
 ArturoSanchez: Another suggestion for Ms. Tudorache: Use "Elluminate" as the collaboration platform ...    (1ZQR)
 VNC: TimRedmond is presenting ... (on slide#5 now)    (1ZQS)
 HaroldSolbrig: SVN has pluggable diffs, however.    (1ZQT)
 HaroldSolbrig: Textual is just a default.    (1ZQU)
 ArturoSanchez: @TaniaTudorache - How ontology-driven is the portal tool itself?    (1ZQV)
 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    (1ZQW)
 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)    (1ZQX)
 HaroldSolbrig: It seems like the change management requires a standardized diff format?    (1ZQY)
 HaroldSolbrig: The ability to exchange ontology deltas, with sufficient information to detect collisions.    (1ZQZ)
 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.    (1ZR0)
 TaniaTudorache: The plan is to use the OWL-API Axioms as diffs    (1ZR1)
 TaniaTudorache: (at least for the OWL part)    (1ZR2)
 TimothyRedmond: But using owl axioms as diffs is problematic    (1ZR3)
 TaniaTudorache: all operations in the OWL-API are addition and deletion of axioms    (1ZR4)
 TimothyRedmond: prompt does a  much more complicated algorithm    (1ZR5)
 TaniaTudorache: sorry, i meant diffs at runtime    (1ZR6)
 TimothyRedmond: so a refactor will show a very complex set of addition and deletions    (1ZR7)
 TaniaTudorache: not user-friendly diffs    (1ZR8)
 TimothyRedmond: oh yes  - this depends on whether we are talking about version control or a server    (1ZR9)
 TimothyRedmond: the server will use axiom diffs    (1ZRA)
 TimothyRedmond: version control  needs a better method because it will need to be user  friendly.    (1ZRB)
 ArturoSanchez: Question for Mr. Redmond and Ms. Tudorache: do you have a model 
                that defines the concept of 'difference' between ontologies?    (1ZRC)
 TaniaTudorache: we do for Protege 3    (1ZRD)
 TaniaTudorache: not Protege 4 and OWL-API    (1ZRE)
 ArturoSanchez: So, naively speaking, can you implement this method as 
                a pluggable diff for SVN? (or Git, if it supports it)    (1ZRF)
 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...    (1ZRG)
 TimothyRedmond: a pluggable diff  mechanism would be very helpful    (1ZRH)
 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    (1ZRI)
 HaroldSolbrig: What I like about the SVN approach is that "what" is also the "how".    (1ZRJ)
 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    (1ZRK)
 ArturoSanchez: NatashaNoy is presenting ... (on slide#41 now)    (1ZRL)
 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?    (1ZRM)
 BartGajderowicz: @NatashaNoy - What format are the mappings in, for download?    (1ZRN)
 BartGajderowicz: Peter, the [3-Noy] presentation is a *.pdf, but wiki link is pointing to *.ppt    (1ZRO)
 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/    (1ZRP)
 ArturoSanchez: Thanks to all!    (1ZRQ)
 HaroldSolbrig: Excellent presentations.    (1ZRR)
 MikeBennett: THanks all - most excellent    (1ZRS)
 BartGajderowicz: Thank you. It was a great set of presentations. Looking forward to the next OOR session    (1ZRT)
 anonymous1: Thank you! Bye    (1ZRU)
 PeterYim: Huge thank you to Mark, Tania, Tim & Natasha ... thanks everyone for your participation ... bye!    (1ZRV)

Audio Recording of this Session    (1ZMO)

For the record ...    (1ZRX)

How To Join (while the session is in progress)    (1ZLY)