OOR/ConferenceCall 2010 09 17

= 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 PeterYim 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 [mailto:peter.yim@cim3.com 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:
 * ToddSchneider (co-chair)
 * MichaelGruninger (co-chair)
 * ImmanuelNormann
 * PeterYim
 * CameronRoss
 * KenBaclawski
 * RogerBurkhart
 * AlanRector
 * PaulAlexander
 * Nikkia Anderson (Information International Associates)
 * NatashaNoy
 * SimonSpero
 * TerryLongstreth
 * MishaDorf
 * ElizabethFlorescu
 * FrankOlken
 * YuriyMilov


 * Expecting:
 * JerrySmith
 * MattHettinger
 * ... 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  so that we can reserve enough resources to support everyone's participation. ...
 * ... 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  so that we can reserve enough resources to support everyone's participation. ...


 * Regrets:
 * MikeDean
 * AmandaVizedom (will view/listen asynchronously)
 * BartGajderowicz
 * 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: NatashaNoy - Panelists: CarlosRueda, PaulAlexander, JohnGraybeal, MikeDean, StephenGranite, AlexGarcia, KenBaclawski - 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: ToddSchneider; Panelists: MarkMusen, NatashaNoy, MikeDean, PaulBuitelaar / AndreasHarth, MathieuDaquin, KenBaclawski, MichaelGruninger - ConferenceCall_2009_02_19
 * 2008_08_22 - Friday: OOR Panel Discussion: "Getting OOR Development Off the Ground: Identifying Synergies &amp; Gaps" (Take-1) - Chair: LeoObrst; Panelists: MikeDean, MarkMusen, LiDing, BruceBargmeyer &amp; BillAndersen - 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 OntologySummit2008 - 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  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 - ToddSchneider, PeterYim (for MikeDean), NatashaNoy, ImmanuelNormann, KenBaclawski, MichaelGruninger (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"
 * by ToddSchneider & MichaelGruninger


 * 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.


 * http://ontolog.cim3.net/file/work/OpenOntologyRepository/2010-09-17_OOR-Dev-Take-4/OOR_Development--ToddSchneider_20100917a.png


 * 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 --

PeterYim:.

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 MichaelGruninger (U of Toronto) and Dr. ToddSchneider (Raytheon)

o Dr. ToddSchneider (OOR; Raytheon) - "Getting OOR Development Going - a proposal" o Mr. MikeDean (OOR; Raytheon-BBN) - "The OOR Code Repository" - to be presented by PeterYim on MikeDean's behalf o Dr. NatashaNoy (NCBO; Stanford-BMIR) - "Forking OOR Development: Thoughts from NCBO" o Dr. ImmanuelNormann (Bremen U; BORG) - "More Service Orientation to open Ontology Repositories - HeTS, TNTBase, and OOR" o Professor KenBaclawski (Northeastern U) - "OOR: Architecture and Interfaces" o Dr. AlexanderGarcia (Bremen U BORG) - "The ORATE Contribution" o Professor MichaelGruninger (U of Toronto; IAOA) - "Concerns from the vantage point of COLORE"
 * Panelists:   (2H0V)

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 PaulAlexander

anonymous1 morphed into ToddSchneider

anonymous morphed into Nikkia Anderson

AlanRector: Todd - could you speak louder? thanks

anonymous morphed into ElizabethFlorescu

CameronRoss: +1 OMV

CameronRoss: @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?

SimonSpero: Github (and git in general)++

SimonSpero: But can track svn repository

CameronRoss: @NatashaNoy - Is all BioPortal data stored as triples within MySQL?

PaulAlexander: @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.

CameronRoss: @PaulAlexander - Is the Protege back-end just and XML file, or is it some kind of database?

PaulAlexander: It's a database

PaulAlexander: MySQL with one table per ontology and another table for the metadata

CameronRoss: Thanks

CameronRoss: @All - I think storing general CL in a triple store will be a challenge.

PaulAlexander: 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.

CameronRoss: @PaulAlexander - I wonder if the resource interface could be generalized... if not then supporting unique resource interfaces would be useful.

NatashaNoy: 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.

CameronRoss: @NatashaNoy - Thanks... I tend to agree.

SimonSpero: Q: What do you mean by "SKOS-based"?

NatashaNoy: @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

SimonSpero: @NatashaNoy: So you just want to use it for labeling of ontologies, right?

NatashaNoy: for labeling of ontology concepts, not ontologies themselves

SimonSpero: @NatashaNoy: good - have had a lot of problems with people confusing the word butterfly with butterflies.

NatashaNoy: @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

PaulAlexander: @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).

CameronRoss: @PaulAlexander - The resource difference on the interface tier might be manageable, but representing CL in a triple store would probably be futile.

NatashaNoy: @Paul: MichaelGruninger 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

PaulAlexander: @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.

NatashaNoy: 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?)

CameronRoss: @NatashaNoy - I guess it depends on the CL theories you're considering, but in general, I believe so.

SimonSpero: @ImmanuelNormann: Does using a version control repository that deals in files make properly tracking provenance of assertions harder?

SimonSpero: @NastashaNoy: As long as you ignore the SKOS support for of Non-Transitive hierarchical relations which was forced in due to butterfly/"butterfly" confusions

NatashaNoy: @Simon: not sure i understand

SimonSpero: @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

NatashaNoy: Simon: Sorry, still confused. What is the relationship between concepts A, B, and C in your example

SimonSpero: A broader B, B broader C

NatashaNoy: There are two "broader" properties in SKOS: one is transitive, one is not

CameronRoss: @Immanuel - The general architecture I think you're proposing sounds very familiar to JohnSowa's Flexible Modular Framework for Intelligent Systems.

SimonSpero: @Natasha: yes - that was a bug introduced after the SMEs left

NatashaNoy: @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?

SimonSpero: @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.

SimonSpero: @Natasha: can take off line

SimonSpero: 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)

AlanRector: Apologies - I must go to catch a train

CameronRoss: @All - If we're talking about platform independence, then we should focus on the specification... +1

CameronRoss: @Ken - Are the non-functional requirements documented beyond the 2008 communique?

ImmanuelNormann: 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

ToddSchneider: Cameron, there has been little additional work on the requirements.

anonymous morphed into FrankOlken

FrankOlken: Hi

PeterYim: @Ken - ref. your slide#14 - the link to the "OOR Interface" doesn't seem to be active ... please advise what the URL should be

KenBaclawski: Here is the link to the OOR Interface page: http://www.ccs.neu.edu/home/kenb/oor/index.html

CameronRoss: Re: CL - The BioPortal presentation tier, interface tier and persistence tier all require 'thought' for CL.

KenBaclawski: @Cameron I believe that they have, but I don't recall what the link is. Perhaps Peter could find this?

PeterYim: @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

PeterYim: Key content pages for OOR are listed at: http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository#nid293Q

CameronRoss: @PeterYim - Thanks Peter.

SimonSpero: Isn't that orthogonal to federation?

PeterYim: @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)

SimonSpero: @PeterYim: (adding context) Isn't the issue of handling CL and OWL separate from federation (which is more a distributed architecture)

NatashaNoy: sorry, will have to sign off in a couple of minutes

PeterYim: @Todd and All - ref. an earlier presentation by KenBaclawski and MaximoGurmendez 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: http://ontolog.cim3.net/file/work/OOR-Ontolog-Panel/2010-04-01_OOR-Use-Cases-III/QualityAndGatekeepingUseCasesForOOR--KenBaclawski-MaximoGurmendez__20100401.pdf

ToddSchneider: All, I'll need to leave this meeting at 13:45 EDT. Thanks to all presenters. Let's press on.

TerryLongstreth: on provenance- not all artifacts will be necessarily be generated by individuals. Provenance tracking should include provisions for stowing identifiers for automated functions.

SimonSpero: [May I comment on the meta first]

SimonSpero: [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

SimonSpero: [Which protege?]

SimonSpero: [reference to frame based]

SimonSpero: Q: Is there a BioPortal git repository right now, or is this currently proposed?

PaulAlexander: @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).

PaulAlexander: Re: Git. We would definitely love comments if people have opinions.

SimonSpero: Paul: git svn fetch works reasonably well

PaulAlexander: @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.

TerryLongstreth: new term for me - 'git'. Can you explain or provide a URL?

SimonSpero: git svn dcommit

SimonSpero: @Paul: also git svn commit-diff and git patch

PaulAlexander: 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

TerryLongstreth: Thanks. Source code control is very complicated when your managing individual items (concepts, data elements...

TerryLongstreth: c/your/you're/

PeterYim: can't hear you any more Immanuel

ImmanuelNormann: I lost telephone connection - don't know why - sorry

ImmanuelNormann: 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!

CameronRoss: @Ken - What exactly is "the issue"... to be clear?

KenBaclawski: @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.

CameronRoss: @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.

CameronRoss: @Ken - Shouldn't we start with the "API" and not the implementation?

KenBaclawski: @Cameron - Yes, I think the discourse should be at the architecture and API level for now.

CameronRoss: @Ken - Great! I couldn't agree more.

SimonSpero: [Quick compare/contrast use case: https://www.nescent.org/sites/hive/Main_Page]

PeterYim: @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"

KenBaclawski: @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.

PeterYim: Please continue the conversation on the [oor-forum] & [oor-dev] list ... and come to the next (and future) OOR-team meeting

SimonSpero: Good bye and good yomtov

YuriyMilov: Thanks, bye

PeterYim: -- 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 
 * (if you are not yet subscribed) you may subscribe yourself to the [ oor-forum ] listserv listserv, by sending a blank email to  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