ppy/chat-transcript_20090716d.txt // 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: . 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 "Settings" button at top center of window) PeterYim: . anonymous morphed into meena anonymous morphed into Rafat anonymous morphed into DarrenOng anonymous morphed into KurtConrad anonymous morphed into ClarenceDillon 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) HaroldSolbrig: We are on slide 9 PeterYim: slide 10 now PeterYim: on slide 17 now HaroldSolbrig: We are on 19 now, not 18 PeterYim: correct 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 cna 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-Portfolio/ 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!