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Ontolog Forum

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 Mark Musen, MD Ph.D.

Panelists:

  • Dr. TaniaTudorache
  • Dr. TimRedmond
  • Dr. NatashaNoy

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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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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 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

  • Other registered participants who may have joined us after the roll call:
    • ... 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 <peter.yim@cim3.com> so that we can reserve enough resources to support everyone's participation. ...

Agenda & Proceedings

Agenda

1. Opening by session Chair (MarkMusen)

2. Briefings from Panelists -- Tania Tudorache, Tim Redmond, Natasha Noy

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

4. Summary and Next Steps (MarkMusen)

Proceedings

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)

Peter P. Yim: 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 Mark Musen, MD Ph.D.

Panelists:

  • Dr. Natasha Noy

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

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

Peter P. Yim: 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 Darren Ong

anonymous morphed into Kurt Conrad

anonymous morphed into Clarence Dillon

anonymous1 morphed into Timothy Redmond

anonymous1 morphed into Steve Ray

anonymous1 morphed into Bahareh Heravi

anonymous morphed into Cecil Lynch

VNC2: Natasha Noy 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...

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

Peter P. Yim: @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 Tania Tudorache

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

the extensions that folks have written to date?

Tania Tudorache: yes

Tania Tudorache: actually, partly

Tania Tudorache: only the UI part would change

Harold Solbrig: Should we wait then?

Tania Tudorache: depends

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

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

Harold Solbrig: Are you not satisfied with GWT? What are you considering?

Tania Tudorache: We like GWT

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

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

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

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

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

Harold Solbrig: So any GWT commitments will be durable.

Harold Solbrig: Perfect.

Tania Tudorache: yes

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

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

Tania Tudorache: Thanks for the suggestion!

Tania Tudorache: We'll look at uPortal

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

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

Harold Solbrig: SVN has pluggable diffs, however.

Harold Solbrig: Textual is just a default.

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

Tania Tudorache: @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

Arturo Sanchez: 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)

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

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

Mark Musen: 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.

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

Tania Tudorache: (at least for the OWL part)

Timothy Redmond: But using owl axioms as diffs is problematic

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

Timothy Redmond: prompt does a much more complicated algorithm

Tania Tudorache: sorry, i meant diffs at runtime

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

Tania Tudorache: not user-friendly diffs

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

Timothy Redmond: the server will use axiom diffs

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

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

that defines the concept of 'difference' between ontologies?

Tania Tudorache: we do for Protege 3

Tania Tudorache: not Protege 4 and OWL-API

Arturo Sanchez: So, naively speaking, can you implement this method as

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

Harold Solbrig: @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...

Timothy Redmond: a pluggable diff mechanism would be very helpful

Timothy Redmond: 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

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

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

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

Arturo Sanchez: 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?

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

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

Peter P. Yim: 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/

Arturo Sanchez: Thanks to all!

Harold Solbrig: Excellent presentations.

Mike Bennett: THanks all - most excellent

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

anonymous1: Thank you! Bye

Peter P. Yim: 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

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)
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