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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"

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
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Resources

Agenda & Proceedings

Session Topic: "Getting OOR Development Going - Take-IV"

Abstracts

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.
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 --

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.

  • 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:

http://ontolog.cim3.net/file/work/OOR-Ontolog-Panel/2010-04-01_OOR-Use-Cases-III/QualityAndGatekeepingUseCasesForOOR--KenBaclawski-MaximoGurmendez__20100401.pdf

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 --

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  • Conference Date and Time: 17-Sep-2010 9:06am ~ 11:03pm Pacific Daylight Time
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