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

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

Session Chair: Professor Mark Musen, MD Ph.D.     (1A1)

Panelists:     (1A2)

Archives     (1A6)

  • Shared-screen support (VNC session), if applicable, will be started 5 minutes before the call at:     (1A7E)
    • view-only password: "ontolog"     (1A7E1)
    • if you plan to be logging into this shared-screen option (which the speaker may be navigating), and you are not familiar with the process, please try to call in 5 minutes before the start of the session so that we can work out the connection logistics. Help on this will generally not be available once the presentation starts.     (1A7E2)
    • people behind corporate firewalls may have difficulty accessing this. If that is the case, please download the slides above and running them locally. The speaker(s) will prompt you to advance the slides during the talk.     (1A7E3)
  • Discussions and Q & A:     (1A7F)
    • (Unless the conference host has already muted everyone) Please mute your phone, by pressing "*2" on your phone keypad, when a presentation is in progress. To un-mute, press "*3"     (1A7F1)
    • You can type in your questions or comments through the browser based chat session by:     (1A7F2)
      • instructions: once you got access to the page, click on the "settings" button, and identify yourself (by modifying the Name field). You can indicate that you want to ask a question verbally by clicking on the "hand" button, and wait for the moderator to call on you; or, type and send your question into the chat window at the bottom of the screen.     (1A7F3A)
    • (when everyone is muted) If you want to speak or have questions or remarks to make, please "raise your hand (virtually)" by click on the "hand button" (lower right) on the chat session page. You may speak when acknowledged by the speaker or the session moderator (again, press "*3" on your phone to unmute). Test your voice and introduce yourself first before proceeding with your remarks, please. (Please remember to click on the "hand button" again (to lower your hand) and press "*2" on your phone to mute yourself after you are done speaking.)     (1A7F4)
    • thanks to the folks, one can now use a jabber/xmpp client (e.g. gtalk) to join this chatroom. Just add the room as a buddy - (in our case here) ... Handy for mobile devices!     (1A7F5)
  • Please note that this session will be recorded, and the entire proceedings including the audio archives are expected to be made available as open content to our community membership and the public at-large under our prevailing open IPR policy.     (1A7J)

Abstract: . . . by MarkMusen     (1A7K)

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:     (1A7L)

  • The Ontolog Collaborative Ontology Development Service (CODS), which allows users to edit and access ontologies from a shared server     (1A7N)
  • 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     (1A7O)
  • Ontology-oriented Web services, which allow programmatic ontology access to BioPortal ontologies and use of those ontologies for a number of useful tasks     (1A7P)

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.     (1A7Q)

Attendees     (1A8)

Agenda & Proceedings     (1B)

1. Opening by session Chair (MarkMusen)     (1B1A)

2. Briefings from Panelists -- Tania Tudorache, Tim Redmond, Natasha Noy     (1B1B)

3. Q & A and Open Discussion (All) -- please refer to process above     (1B1C)

4. Summary and Next Steps (MarkMusen)     (1B1D)

Proceedings     (1C)

Discussion     (1C1)

Please refer to the process above     (1C1A)
See related material under the archives section above     (1C1B)

===IM Chat Transcript captured during the session=== ... (Chat Transcript has been lightly edited for clarity)     (1C1C)

Peter P. Yim: Welcome to the Joint Ontolog-OOR Panel Discussion Session - Thu 16-July-2009     (1C1D)

Topic: Integrated tools for ontology development and management: A field guide to the Stanford technology     (1C1E)

Session Chair: Professor Mark Musen, MD Ph.D.     (1C1F)

Panelists:     (1C1G)

Peter P. Yim: To mute your phone line, press " *2 " ... and un-mute press " *3 "     (1C1L)

Peter P. Yim: anonymous users please change your names to a WikiWord format name     (1C1M)

(with the "Settings" button at top center of window)     (1C1N)

anonymous morphed into meena     (1C1O)

anonymous morphed into Rafat     (1C1P)

anonymous morphed into Darren Ong     (1C1Q)

anonymous morphed into Kurt Conrad     (1C1R)

anonymous morphed into Clarence Dillon     (1C1S)

anonymous1 morphed into Timothy Redmond     (1C1T)

anonymous1 morphed into Steve Ray     (1C1U)

anonymous1 morphed into Bahareh Heravi     (1C1V)

anonymous morphed into Cecil Lynch     (1C1W)

VNC2: Natasha Noy is presenting ...     (1C1X)

anonymous: @Peter: Where are the slides? Shes on slide 3 and Im not seeing anything     (1C1Y)

but a room full of people. Please advise...     (1C1Z)

Peter P. Yim: @person with your hand up ... are you able to get to the slides yet?     (1C1AB)

( can lower you hand by clicking on the "hand button" again, it toggles)     (1C1AC)

anonymous morphed into Tania Tudorache     (1C1AD)

Harold Solbrig: A question about the new widget library... If you migrate, does it invalidate     (1C1AE)

the extensions that folks have written to date?     (1C1AF)

Tania Tudorache: only the UI part would change     (1C1AI)

Harold Solbrig: Should we wait then?     (1C1AJ)

Harold Solbrig: I'd like not to - this looks really great and I'd like to get started sooner rather than later     (1C1AL)

Tania Tudorache: we expect that the migration to the new UI library for the extensions will not be difficult     (1C1AM)

Harold Solbrig: Are you not satisfied with GWT? What are you considering?     (1C1AN)

Tania Tudorache: but,the GWT-ext lib is not so good     (1C1AP)

Tania Tudorache: @Harold: Sorry, I had to drop the conversation before     (1C1AQ)

Tania Tudorache: We're going to use GWT, but we may replace the GWT-ext UI library that we are using     (1C1AR)

Harold Solbrig: Oh - that isn't so bad, then.     (1C1AS)

Tania Tudorache: if someone would develop a portlet using GWT, then there would be no problem, no migration needed     (1C1AT)

Harold Solbrig: So any GWT commitments will be durable.     (1C1AU)

Arturo Sanchez: @TaniaTudorache - Did you consider using open source portal development platforms?     (1C1AX)

Arturo Sanchez: About open source portal development platforms, one that comes to mind is uPortal     (1C1AY)

Tania Tudorache: Thanks for the suggestion!     (1C1AZ)

Tania Tudorache: We'll look at uPortal     (1C1AAA)

Arturo Sanchez: Another suggestion for Ms. Tudorache: Use "Elluminate" as the collaboration platform ...     (1C1AAB)

VNC: Tim Redmond is presenting ... (on slide#5 now)     (1C1AAC)

Harold Solbrig: SVN has pluggable diffs, however.     (1C1AAD)

Harold Solbrig: Textual is just a default.     (1C1AAE)

Arturo Sanchez: @TaniaTudorache - How ontology-driven is the portal tool itself?     (1C1AAF)

Tania Tudorache: @Arturao: Thank you for the suggestion. Our collaboration framework     (1C1AAG)

is very much "ontology-oriented". We'll have to see if Elluminate can be easily integrated     (1C1AAH)

Arturo Sanchez: Comment for Mr. Redmond Re: Version Control platforms, you might want     (1C1AAI)

to consider 'Git' ... I do not know if it supports pluggable diffs     (1C1AAJ)

(which is a good point in connection to SVN)     (1C1AAK)

Harold Solbrig: It seems like the change management requires a standardized diff format?     (1C1AAL)

Harold Solbrig: The ability to exchange ontology deltas, with sufficient information to detect collisions.     (1C1AAM)

Mark Musen: The problem is that an OWL ontology is a collection of unordered axioms.     (1C1AAN)

There is no canonical serialization for such ontologies. This is why standard diffs fail.     (1C1AAO)

Tania Tudorache: The plan is to use the OWL-API Axioms as diffs     (1C1AAP)

Tania Tudorache: (at least for the OWL part)     (1C1AAQ)

Timothy Redmond: But using owl axioms as diffs is problematic     (1C1AAR)

Tania Tudorache: all operations in the OWL-API are addition and deletion of axioms     (1C1AAS)

Timothy Redmond: prompt does a much more complicated algorithm     (1C1AAT)

Tania Tudorache: sorry, i meant diffs at runtime     (1C1AAU)

Timothy Redmond: so a refactor will show a very complex set of addition and deletions     (1C1AAV)

Tania Tudorache: not user-friendly diffs     (1C1AAW)

Timothy Redmond: oh yes - this depends on whether we are talking about version control or a server     (1C1AAX)

Timothy Redmond: the server will use axiom diffs     (1C1AAY)

Timothy Redmond: version control needs a better method because it will need to be user friendly.     (1C1AAZ)

Arturo Sanchez: Question for Mr. Redmond and Ms. Tudorache: do you have a model     (1C1AAAA)

that defines the concept of 'difference' between ontologies?     (1C1AAAB)

Tania Tudorache: we do for Protege 3     (1C1AAAC)

Tania Tudorache: not Protege 4 and OWL-API     (1C1AAAD)

Arturo Sanchez: So, naively speaking, can you implement this method as     (1C1AAAE)

a pluggable diff for SVN? (or Git, if it supports it)     (1C1AAAF)

Harold Solbrig: @Mark: perhaps you need axiom identities and/or state (I changed     (1C1AAAG)

axiom #1111732 edition 17 from A to B) or, if it is is simply editions     (1C1AAAH)

and deletions (troubling - I'd like to correct the spelling of an xml:literal     (1C1AAAI)

without being totally destructive...), then the identifiers allow the discovery     (1C1AAAJ)

of overlapping changes. The other issue, however, is that changes aren't always atomic...     (1C1AAAK)

Timothy Redmond: a pluggable diff mechanism would be very helpful     (1C1AAAL)

Timothy Redmond: prompt gives a very useful definition of a diff but I think that     (1C1AAAM)

it would need some work to be sufficient for a version control mechanism     (1C1AAAN)

Harold Solbrig: What I like about the SVN approach is that "what" is also the "how".     (1C1AAAO)

Timothy Redmond: 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     (1C1AAAP)

Arturo Sanchez: Natasha Noy is presenting ... (on slide#41 now)     (1C1AAAQ)

Arturo Sanchez: Question for Ms. Noy: what is the 'meta-model' that defines the concept     (1C1AAAR)

of 'mapping'? In other words, what is the 'formal' definition of a mapping?     (1C1AAAS)

Bart Gajderowicz: @NatashaNoy - What format are the mappings in, for download?     (1C1AAAT)

Bart Gajderowicz: Peter, the [3-Noy] presentation is a *.pdf, but wiki link is pointing to *.ppt     (1C1AAAU)

Peter P. Yim: Natasha wanted to present from the powperpoint deck (where some slides were hidden),     (1C1AAAV)

the pdf is full length ... both versions are avilable     (1C1AAAW)

Harold Solbrig: Excellent presentations.     (1C1AAAZ)

Mike Bennett: THanks all - most excellent     (1C1AAAAA)

Bart Gajderowicz: Thank you. It was a great set of presentations. Looking forward to the next OOR session     (1C1AAAAB)

anonymous1: Thank you! Bye     (1C1AAAAC)

Peter P. Yim: Huge thank you to Mark, Tania, Tim & Natasha ... thanks everyone for your participation ... bye!     (1C1AAAAD)

Audio Recording of this Session     (1D)

For the record ...     (1D6)

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

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