Ontolog Forum
OOR Panel Discussion: "Getting OOR Development Going - Take-IV" - Fri 17-Sep-2010
This session is sometimes referred to as the "fork" session. The key issue being addressed at this virtual workshop session is on how we should manage to incorporate various ongoing OOR-related software development efforts, and how best to "fork" from the BioPortal codebase while staying synergistic.
- Co-chairs: Dr. ToddSchneider (Raytheon) and Professor MichaelGruninger (U of Toronto)
- Panelists:
- Dr. ToddSchneider (OOR; Raytheon) - "Getting OOR Development Going - a proposal" - [ slides ]
- Mr. MikeDean (OOR; Raytheon-BBN) - "The OOR Code Repository" - [ slides ] - presented by Peter P. Yim on MikeDean's behalf
- Dr. NatashaNoy (NCBO; Stanford-BMIR) - "Forking OOR Development: Thoughts from NCBO" - [ slides ]
- Dr. ImmanuelNormann (Bremen U; BORG) - "More Service Orientation to open Ontology Repositories - HeTS, TNTBase, and OOR" - [ slides ]
- Professor KenBaclawski (Northeastern U) - "OOR: Architecture and Interfaces" - [ slides ]
- Professor MichaelGruninger (U of Toronto; IAOA) - "Concerns from the vantage point of COLORE"
- Archive:
- Agenda & Proceedings
- Abstracts
- Prepared presentation material can be accessed by clicking on each of the title links below:
- [ 1-Schneider ] . [ 2-Dean(Yim) ] . [ 3-Noy ] . [ 4-Normann ] . [ 5-Baclawski ] . [ 6-Gruninger (no slides) ]
- [ audio recording of the session ] ( 1:51:56 ; mp3 ; 12.8 MB )
- Transcript of the online chat session during the panel discussion
- Other Resources
Conference Call Details
- Date: Friday, 17-September-2010
- Start Time: 12:00pm EDT / 9:00am PDT / 6:00pm CEST / 5:00pm BST / 16:00 UTC
- ref: World Clock
- Expected Call Duration: ~2.0 hours
- Dial-in Number:
- from a US telephone (US): +1-218-844-8060 (domestic long distance cost will apply)
- When calling in from a phone, use Conference ID: "4389979#"
- from Europe, call:
- Austria 0820-4000-1577
- Belgium 070-35-9992
- France 0826-100-280
- Germany 01805-00-7642
- Ireland 0818-270-037
- Italy 848-390-179
- Spain 0902-886-056
- Switzerland 0848-560-327
- UK 0844-581-9148
- callers from other countries please dial into either one of the US or European numbers
- Shared-screen support (VNC session) will be started 5 minutes before the call at: http://vnc2.cim3.net:5800/
- view-only password: "ontolog"
- 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.
- 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.
- Discussions and Q & A:
- (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"
- You can type in your questions or comments through the browser based chat session by:
- pointing a separate browser tab (or window) to http://webconf.soaphub.org/conf/room and enter: Room="ontolog_20100917" and My Name="Your Own Name" (e.g. "JaneDoe")
- or point your browser to: http://webconf.soaphub.org/conf/room/ontolog_20100917
- 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.
- (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.)
- thanks to the soaphub.org 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) ontolog_20100917@soaphub.org ... Handy for mobile devices!
- Please review our Virtual Session Tips and Ground Rules - see: VirtualSpeakerSessionTips
- RSVP to peter.yim@cim3.com appreciated.
- This session, like all other Ontolog events, is open to the public. Information relating to this session is shared on this wiki page: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2010_09_17
- Please note that this session will be recorded, and the audio archive is expected to be made available as open content to our community membership and the public at-large under our prevailing open IPR policy.
Attendees
- Attended:
- Todd Schneider (co-chair)
- Michael Grüninger (co-chair)
- Immanuel Normann
- Peter P. Yim
- Cameron Ross
- Ken Baclawski
- Roger Burkhart
- Alan Rector
- Paul Alexander
- Nikkia Anderson (Information International Associates)
- Natasha Noy
- Simon Spero
- Terry Longstreth
- Misha Dorf
- Elizabeth Florescu
- Frank Olken
- Yuriy Milov
- Expecting:
-
- ... if you are coming to the session, please add your name above (plus your affiliation, if you aren't already a member of the community) above; or e-mail <peter.yim@cim3.com> so that we can reserve enough resources to support everyone's participation. ...
- Regrets:
- Mike Dean
- Amanda Vizedom (will view/listen asynchronously)
- Bart Gajderowicz
- AlexGarcia
Resources
- OpenOntologyRepository - Homepage for the OOR initiative
- A recent presentation on OOR - OOR Presentation at SemTech2010
- The OOR-sandbox v2.5 (powered by the NCBO BioPortal Core v2.5) instance, now online at: http://oor-01.cim3.net ref.
- OOR Project site and code repository at SemWebCentral - http://oor.semwebcentral.org
- 2009_07_30 - Thursday: Joint Ontolog-OOR Panel Discussion: "BioPortal and related Ontology Repository Implementations and Development" (Take-3) - Chair: Natasha Noy - Panelists: Carlos Rueda, Paul Alexander, John Graybeal, Mike Dean, StephenGranite, AlexGarcia, Ken Baclawski - ConferenceCall_2009_07_30
- 2009_02_19 - Thursday: Joint Ontolog-OOR Panel Discussion: "Getting OOR Development Off the Ground (Take-2): the work begins" - Chair: Todd Schneider; Panelists: Mark Musen, Natasha Noy, Mike Dean, Paul Buitelaar / Andreas Harth, Mathieu Daquin, Ken Baclawski, Michael Grüninger - ConferenceCall_2009_02_19
- 2008_08_22 - Friday: OOR Panel Discussion: "Getting OOR Development Off the Ground: Identifying Synergies & Gaps" (Take-1) - Chair: Leo Obrst; Panelists: Mike Dean, Mark Musen, Li Ding, Bruce Bargmeyer & Bill Andersen - ConferenceCall_2008_08_22
- 2008_04_29 - Our team made a presentation with our history, status, OOR rationale and requirements, and a proposed roadmap at the Ontology Summit 2008 - see: http://ontolog.cim3.net/cgi-bin/wiki.pl?OntologySummit2008/FaceToFaceAgenda#nid1BLS
- OntologySummit2008_Communique
- our last regular OOR-team meeting - OOR/ConferenceCall_2010_08_20
- [ oor-forum ] message archive - http://ontolog.cim3.net/forum/oor-forum/
- (if you are not yet subscribed) you may subscribe yourself to the [ oor-forum ] listserv, by sending a blank email to <oor-forum-join [at] ontolog.cim3.net> from your subscribing email address, and then follow the instructions you receive back from the mailing list system.
- check out our other mailing lists and join us
Agenda & Proceedings
Session Topic: "Getting OOR Development Going - Take-IV"
- Session Format & Agenda: this is a virtual session conducted over an augmented conference call:
- 1. Opening - co-chairs ... [ slides ]
- 2. Panelists presentations - Todd Schneider, Peter P. Yim (for MikeDean), Natasha Noy, Immanuel Normann, Ken Baclawski, Michael Grüninger (10~15 min. each)
- 3. Q & A and open discussion - All (30 min.) ... please refer to process above
- 4. Conclusion / Follow-up - co-chairs
Abstracts
- Workshop Topic: "Getting OOR Development Going - Take-IV"
- This session is sometimes referred to as the "fork" session. The key issue being addressed at this virtual workshop session (as the new OOR code repository at http://oor.semwebcentral.org emerges) is on how we should manage to incorporate various ongoing OOR-related software development efforts, and how best to "fork" from the BioPortal codebase while staying synergistic.
- Figure 1: A Concept Map on OOR Development
Transcript of the online chat during the session
see raw transcript here.
(for better clarity, the version below is a re-organized and lightly edited chat-transcript.)
Participants are welcome to make light edits to their own contributions as they see fit.
-- begin of chat session --
Peter P. Yim: .
Welcome to the OOR Panel Discussion: "Getting OOR Development Going - Take-IV" - Fri 17-Sep-2010
This session is sometimes referred to as the "fork" session. The key issue being addressed
at this virtual workshop session is on how we should manage to incorporate various ongoing
OOR-related software development efforts, and how best to "fork" from
the BioPortal codebase while staying synergistic.
- Co-chairs: Professor Michael Grüninger (U of Toronto) and Dr. Todd Schneider (Raytheon)
- Panelists: (2H0V)
o Dr. Todd Schneider (OOR; Raytheon) - "Getting OOR Development Going - a proposal"
o Mr. Mike Dean (OOR; Raytheon-BBN) - "The OOR Code Repository"
- to be presented by Peter P. Yim on MikeDean's behalf
o Dr. Natasha Noy (NCBO; Stanford-BMIR) - "Forking OOR Development: Thoughts from NCBO"
o Dr. Immanuel Normann (Bremen U; BORG) - "More Service Orientation to open Ontology Repositories - HeTS, TNTBase, and OOR"
o Professor Ken Baclawski (Northeastern U) - "OOR: Architecture and Interfaces"
o Dr. Alexander Garcia (Bremen U BORG) - "The ORATE Contribution"
o Professor Michael Grüninger (U of Toronto; IAOA) - "Concerns from the vantage point of COLORE"
Please refer to details on the session page
at: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2010_09_17
anonymous morphed into Paul Alexander
anonymous1 morphed into Todd Schneider
anonymous morphed into Nikkia Anderson
Alan Rector: Todd - could you speak louder? thanks
anonymous morphed into Elizabeth Florescu
Cameron Ross: +1 OMV
Cameron Ross: @All - The BioPortal resource model seems oriented around OWL-based(?) terms like
concepts, instances and properties etc. This doesn't seem to align well with general CL theories.
Does anyone have ideas on how to rationalize this?
Simon Spero: Github (and git in general)++
Simon Spero: But can track svn repository
Cameron Ross: @NatashaNoy - Is all BioPortal data stored as triples within MySQL?
Paul Alexander: @Cameron: BioPortal data is not currently stored as triples, but that's where we'll
be moving in the future. Currently OWL/Protege ontologies are stored in a Protege back-end. OBO,
RRF, etc are stored using LexEVS. Metadata is stored in a Protege back-end as well.
Cameron Ross: @PaulAlexander - Is the Protege back-end just and XML file, or is it some kind of
database?
Paul Alexander: It's a database
Paul Alexander: MySQL with one table per ontology and another table for the metadata
Cameron Ross: Thanks
Cameron Ross: @All - I think storing general CL in a triple store will be a challenge.
Paul Alexander: RE: Common Logic fitting the OWL model. It wouldn't be difficult to have a separate
set of REST services to handle common logic. Of course this would make it so there is no common
method for accessing all of the resources in the repository.
Cameron Ross: @PaulAlexander - I wonder if the resource interface could be generalized... if not then
supporting unique resource interfaces would be useful.
Natasha Noy: RE: Common logic: it is true though that our user interface is very much class-centric,
and so are our REST services. That's what *our* users needed. Adapting it to CL is definitely a
challenge as it is a very different view of ontologies.
Cameron Ross: @NatashaNoy - Thanks... I tend to agree.
Simon Spero: Q: What do you mean by "SKOS-based"?
Natasha Noy: @Simon SKOS-based: when we move to a triple store, we want to have a simple model for
representing ontologies and terminologies, including things like preferred names, synonyms,
definitions, etc. This will be a unifying layer among the different formats that we have. SKOS
provides this layer, and we may need to extend it with a few additional properties
Simon Spero: @NatashaNoy: So you just want to use it for labeling of ontologies, right?
Natasha Noy: for labeling of ontology concepts, not ontologies themselves
Simon Spero: @NatashaNoy: good - have had a lot of problems with people confusing the word
butterfly with butterflies.
Natasha Noy: @Simon: yes we have that model now as well. But it is a bit idiosyncratic. So, we want
something more thought-out and standards based for the next major version. SKOS is a perfect
standard for that
Paul Alexander: @Cameron: I'm not very familiar with common logic. If there are enough commonalities
between CL and OWL/OBO/RRF it should be do-able. However, it would be a major change and require a
significant amount of work to restructure all of the service signatures and XML responses (assuming
you can't shoe-horn CL into the existing resource model).
Cameron Ross: @PaulAlexander - The resource difference on the interface tier might be manageable, but
representing CL in a triple store would probably be futile.
Natasha Noy: @Paul: Michael Grüninger looked at trying to shoe-horn CL into the class-centric model of
BioPortal, and I think the conclusion was that it pretty much didn't work. CL is axiom-based and so
it is a very different focus
Paul Alexander: @Cameron: Sure, but there's nothing stopping running a different store alongside the
triplestore. We very much respect OOP and already have our code handling different formats/stores.
Very soon we'll have MySQL, LexEVS, Protege Server, and a triple store all running different parts
of BioPortal.
Natasha Noy: On CL: I think it is the UI that is more of a problem. Our UI is coompletely focused on
browsing classes and class hierarchies. My understanding is that it's pretty useless for CL
(Cameron, am I right?)
Cameron Ross: @NatashaNoy - I guess it depends on the CL theories you're considering, but in general,
I believe so.
Simon Spero: @ImmanuelNormann: Does using a version control repository that deals in files make
properly tracking provenance of assertions harder?
Simon Spero: @NastashaNoy: As long as you ignore the SKOS support for of Non-Transitive hierarchical
relations which was forced in due to butterfly/"butterfly" confusions
Natasha Noy: @Simon: not sure i understand
Simon Spero: @Natasha: SKOS was changed so that everything about Concept A is always also about
Concept B, everything about Concept B is always also about Concept C. but it is possible for
something to be about Concept A but not about Concept C
Natasha Noy: Simon: Sorry, still confused. What is the relationship between concepts A, B, and C in
your example
Simon Spero: A broader B , B broader C
Natasha Noy: There are two "broader" properties in SKOS: one is transitive, one is not
Cameron Ross: @Immanuel - The general architecture I think you're proposing sounds very familiar to
JohnSowa's Flexible Modular Framework for Intelligent Systems.
Simon Spero: @Natasha: yes - that was a bug introduced after the SMEs left
Natasha Noy: @Simon: Still don't see why this is a bug. As long as you choose the appropriate
broader property, you are ok, aren't you? There are cases for both of them, aren't there?
Simon Spero: @NatashaNoy: when you add the note that you're not supposed to assert the (traditional
KOS) BT relationship, which was called broader until 2004, but then renamed to broaderTransitive.
Simon Spero: @Natasha: can take off line
Simon Spero: To take this point further: a lot of the functionality being described generalizes
across all kinds of Repositories of Semantic data (not just repositories of Ontologies)
Alan Rector: Apologies - I must go to catch a train
Cameron Ross: @All - If we're talking about platform independence, then we should focus on the
specification... +1
Cameron Ross: @Ken - Are the non-functional requirements documented beyond the 2008 communique?
Immanuel Normann: I absolutely agree with Cameron: we should focus on the specification ... and
consider the BioPortal of one possible instance, satisfying this spacification to a certain extend
Todd Schneider: Cameron, there has been little additional work on the requirements.
anonymous morphed into Frank Olken
Frank Olken: Hi
Peter P. Yim: @Ken - ref. your slide#14 - the link to the "OOR Interface" doesn't seem to be active ...
please advise what the URL should be
Ken Baclawski: Here is the link to the OOR Interface page:
http://www.ccs.neu.edu/home/kenb/oor/index.html
Cameron Ross: Re: CL - The BioPortal presentation tier, interface tier and persistence tier all
require 'thought' for CL.
Ken Baclawski: @Cameron I believe that they have, but I don't recall what the link is. Perhaps Peter
could find this?
Peter P. Yim: @Cameron & Ken - ref. the question on non-functional requirements - the slides from Todd
and Ken today are good ... some of those may also have been captured into the "OOR_Requirement" page
at: http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository_Requirement
Peter P. Yim: Key content pages for OOR are listed at:
http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository#nid293Q
Cameron Ross: @PeterYim - Thanks Peter.
Simon Spero: Isn't that orthogonal to federation?
Peter P. Yim: @Simon - this conversation is going to be archived ... therefore, please provide some
context when making a comment (otherwise it will not mean much to someone going through the archives)
Simon Spero: @PeterYim: (adding context) Isn't the issue of handling CL and OWL separate from
federation (which is more a distributed architecture)
Natasha Noy: sorry, will have to sign off in a couple of minutes
Peter P. Yim: @Todd and All - ref. an earlier presentation by Ken Baclawski and Máximo Gurméndez of NEU on
Quality and Gatekeeping Use Cases for the OOR at:
http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2010_04_01 ... their slides are at:
Todd Schneider: All, I'll need to leave this meeting at 13:45 EDT. Thanks to all presenters. Let's
press on.
Terry Longstreth: on provenance- not all artifacts will be necessarily be generated by individuals.
Provenance tracking should include provisions for stowing identifiers for automated functions.
Simon Spero: [May I comment on the meta first]
Simon Spero: [on the multiple view problem the issue comes up when different viewers have different
sets of people who are willing to view for example Wiki/DBPedia timeliness v. reliability issues
Simon Spero: [Which protege?]
Simon Spero: [reference to frame based]
Simon Spero: Q: Is there a BioPortal git repository right now, or is this currently proposed?
Paul Alexander: @Simon: We're exploring migrating to Git, especially if there is a broader community
interested in participating using some of the tools out there that would seemingly enable easier
community development (like GitHub).
Paul Alexander: Re: Git. We would definitely love comments if people have opinions.
Simon Spero: Paul: git svn fetch works reasonably well
Paul Alexander: @Simon: One of the reasons we're considering switching is so we can more easily roll
changes that are being made back into our master repository. I don't think the svn-git conversion
would help us there.
Terry Longstreth: new term for me - 'git'. Can you explain or provide a URL?
Simon Spero: git svn dcommit
Simon Spero: @Paul: also git svn commit-diff and git patch
Paul Alexander: Git is one of a number of solutions for a new paradigm for source control management
where the code gets distributed rather than centralized in a single repository. Similar to SVN but
not centralized. http://en.wikipedia.org/wiki/Distributed_revision_control
Terry Longstreth: Thanks. Source code control is very complicated when your managing individual items
(concepts, data elements...
Terry Longstreth: c/your/you're/
Peter P. Yim: can't hear you any more Immanuel
Immanuel Normann: I lost telephone connection - don't know why - sorry
Immanuel Normann: My telephone seems to be broken - I will put my comments on the OOR mailing list -
and leave the session now. Thanks and good bye!
Cameron Ross: @Ken - What exactly is "the issue"... to be clear?
Ken Baclawski: @Cameron regarding "the issue". I see the issue as being whether the fork should
remain consistent with the BioPortal code base or should we diverge so that we would not be able to
remain consistent with their code base.
Cameron Ross: @All - I agree with Immanuel. We could really use Use Cases that describe the reasoning
related functionalities, as this is the part that seems to have more uncertainty associated with it.
Cameron Ross: @Ken - Shouldn't we start with the "API" and not the implementation?
Ken Baclawski: @Cameron - Yes, I think the discourse should be at the architecture and API level for now.
Cameron Ross: @Ken - Great! I couldn't agree more.
Simon Spero: [Quick compare/contrast use case: https://www.nescent.org/sites/hive/Main_Page]
Peter P. Yim: @Ken - ref. the comment about robustness - it *is* an objective of the OOR initiative to
provide (at least one instance of a) robust OOR ... therefore, we (the OOR-team) are not deferring
that to "commercial enterprises"
Ken Baclawski: @Peter re: robustness. I misspoke. The reference implementation must be robust. My
intention was to distinguish a reference implementation which has only the required functionality
from an "industrial-strength" implementation which has much more. In other words, the reference
implementation is only a starting point for other groups, whether they are open source or
commercial.
Peter P. Yim: Please continue the conversation on the [oor-forum] & [oor-dev] list ... and come to the
next (and future) OOR-team meeting
Simon Spero: Good bye and good yomtov
Yuriy Milov: Thanks, bye
Peter P. Yim: -- session ended: 11:03am PDT --
-- end of chat session --
- Further Question & Remarks - please post them to the [ oor-forum ] listserv
- if you are already subscribed, post to <oor-forum [at] ontolog.cim3.net>
- (if you are not yet subscribed) you may subscribe yourself to the [ oor-forum ] listserv listserv, by sending a blank email to <oor-forum-join [at] ontolog.cim3.net> from your subscribing email address, and then follow the instructions you receive back from the mailing list system.
Audio Recording of this Session
- To download the audio recording of the session, click here
- the playback of the audio files require the proper setup, and an MP3 compatible player on your computer.
- Conference Date and Time: 17-Sep-2010 9:06am ~ 11:03pm Pacific Daylight Time
- Duration of Recording: 1 Hour 52 Minutes
- Recording File Size: 12.8 MB (in mp3 format)
- suggestion: its best that you listen to the session while having the presentation opened in front of you. You'll be prompted to advance slides by the speaker.
- 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)
- 1. Dial in with a phone: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2010_09_17#nid2H1F
- 2. Open chat in a new browser window: http://webconf.soaphub.org/conf/room/ontolog_20100917
- 3. Download presentations for each speaker here: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2010_09_17#nid2H15
- or, 3.1 access our shared-screen vnc server, if you are not behind a corporate firewall