OOR Panel Discussion: "Getting OOR Development Going - Take-IV" - Fri 17-Sep-2010    (2H0S)

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.    (2H0T)

Conference Call Details:    (2H1A)

Attendees:    (2H29)

Resources    (2H2N)

Agenda & Proceedings:    (2H31)

Session Topic: "Getting OOR Development Going - Take-IV"    (2H32)

Abstracts:    (2H38)

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.    (2H3B)

http://ontolog.cim3.net/file/work/OpenOntologyRepository/2010-09-17_OOR-Dev-Take-4/OOR_Development--ToddSchneider_20100917a.png    (2H3C)

Figure 1: A Concept Map on OOR Development    (2H3D)

Transcript of the online chat during the session:    (2H3X)

 see raw transcript here.    (2H3Y)
 (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.    (2H3Z)
    -- begin of chat session --    (2H40)
	PeterYim: .    (2I48)
	Welcome to the OOR Panel Discussion: "Getting OOR Development Going - Take-IV" - Fri 17-Sep-2010    (2I49)
	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.    (2I4A)
	* Co-chairs: Professor MichaelGruninger (U of Toronto) and Dr. ToddSchneider (Raytheon)    (2I4B)
	* Panelists:    (2H0V)
	  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"    (2I4C)
	Please refer to details on the session page
	at: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2010_09_17    (2I4D)
	anonymous morphed into PaulAlexander    (2I4E)
	anonymous1 morphed into ToddSchneider    (2I4F)
	anonymous morphed into Nikkia Anderson    (2I4G)
	AlanRector: Todd - could you speak louder? thanks    (2I4H)
	anonymous morphed into ElizabethFlorescu    (2I4I)
	CameronRoss: +1 OMV    (2I4J)
	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?    (2I4K)
	SimonSpero: Github (and git in general)++    (2I4L)
	SimonSpero: But can track svn repository    (2I4M)
	CameronRoss: @NatashaNoy - Is all BioPortal data stored as triples within MySQL?    (2I4N)
	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.    (2I4O)
	CameronRoss: @PaulAlexander - Is the Protege back-end just and XML file, or is it some kind of 
	database?    (2I4P)
	PaulAlexander: It's a database    (2I4Q)
	PaulAlexander: MySQL with one table per ontology and another table for the metadata    (2I4R)
	CameronRoss: Thanks    (2I4S)
	CameronRoss: @All - I think storing general CL in a triple store will be a challenge.    (2I4T)
	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.    (2I4U)
	CameronRoss: @PaulAlexander - I wonder if the resource interface could be generalized... if not then 
	supporting unique resource interfaces would be useful.    (2I4V)
	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.    (2I4W)
	CameronRoss: @NatashaNoy - Thanks... I tend to agree.    (2I4X)
	SimonSpero: Q: What do you mean by "SKOS-based"?    (2I4Y)
	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    (2I4Z)
	SimonSpero: @NatashaNoy: So you just want to use it for labeling of ontologies, right?    (2I50)
	NatashaNoy: for labeling of ontology concepts, not ontologies themselves    (2I51)
	SimonSpero: @NatashaNoy: good - have had a lot of problems with people confusing the word 
	butterfly with butterflies.    (2I52)
	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    (2I53)
	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).    (2I54)
	CameronRoss: @PaulAlexander - The resource difference on the interface tier might be manageable, but 
	representing CL in a triple store would probably be futile.    (2I55)
	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    (2I56)
	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.    (2I57)
	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?)    (2I58)
	CameronRoss: @NatashaNoy - I guess it depends on the CL theories you're considering, but in general, 
	I believe so.    (2I59)
	SimonSpero: @ImmanuelNormann: Does using a version control repository that deals in files make 
	properly tracking provenance of assertions harder?    (2I5A)
	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    (2I5B)
	NatashaNoy: @Simon: not sure i understand    (2I5C)
	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    (2I5D)
	NatashaNoy: Simon: Sorry, still confused. What is the relationship between concepts A, B, and C in 
	your example    (2I5E)
	SimonSpero: A broader B , B broader C    (2I5F)
	NatashaNoy: There are two "broader" properties in SKOS: one is transitive, one is not    (2I5G)
	CameronRoss: @Immanuel - The general architecture I think you're proposing sounds very familiar to 
	JohnSowa's Flexible Modular Framework for Intelligent Systems.    (2I5H)
	SimonSpero: @Natasha: yes - that was a bug introduced after the SMEs left    (2I5I)
	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?    (2I5J)
	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.    (2I5K)
	SimonSpero: @Natasha: can take off line    (2I5L)
	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)    (2I5M)
	AlanRector: Apologies - I must go to catch a train    (2I5N)
	CameronRoss: @All - If we're talking about platform independence, then we should focus on the 
	specification... +1    (2I5O)
	CameronRoss: @Ken - Are the non-functional requirements documented beyond the 2008 communique?    (2I5P)
	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    (2I5Q)
	ToddSchneider: Cameron, there has been little additional work on the requirements.    (2I5R)
	anonymous morphed into FrankOlken    (2I5S)
	FrankOlken: Hi    (2I5T)
	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    (2I5U)
	KenBaclawski: Here is the link to the OOR Interface page: 
	http://www.ccs.neu.edu/home/kenb/oor/index.html    (2I5V)
	CameronRoss: Re: CL - The BioPortal presentation tier, interface tier and persistence tier all 
	require 'thought' for CL.    (2I5W)
	KenBaclawski: @Cameron I believe that they have, but I don't recall what the link is. Perhaps Peter 
	could find this?    (2I5X)
	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    (2I5Y)
	PeterYim: Key content pages for OOR are listed at: 
	http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository#nid293Q    (2I5Z)
	CameronRoss: @PeterYim - Thanks Peter.    (2I60)
	SimonSpero: Isn't that orthogonal to federation?    (2I61)
	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)    (2I62)
	SimonSpero: @PeterYim: (adding context) Isn't the issue of handling CL and OWL separate from 
	federation (which is more a distributed architecture)    (2I63)
	NatashaNoy: sorry, will have to sign off in a couple of minutes    (2I64)
	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    (2I65)
	ToddSchneider: All, I'll need to leave this meeting at 13:45 EDT. Thanks to all presenters. Let's 
	press on.    (2I66)
	TerryLongstreth: on provenance- not all artifacts will be necessarily be generated by individuals. 
	Provenance tracking should include provisions for stowing identifiers for automated functions.    (2I67)
	SimonSpero: [May I comment on the meta first]    (2I68)
	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    (2I69)
	SimonSpero: [Which protege?]    (2I6A)
	SimonSpero: [reference to frame based]    (2I6B)
	SimonSpero: Q: Is there a BioPortal git repository right now, or is this currently proposed?    (2I6C)
	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).    (2I6D)
	PaulAlexander: Re: Git. We would definitely love comments if people have opinions.    (2I6E)
	SimonSpero: Paul: git svn fetch works reasonably well    (2I6F)
	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.    (2I6G)
	TerryLongstreth: new term for me - 'git'. Can you explain or provide a URL?    (2I6H)
	SimonSpero: git svn dcommit    (2I6I)
	SimonSpero: @Paul: also git svn commit-diff and git patch    (2I6J)
	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    (2I6K)
	TerryLongstreth: Thanks. Source code control is very complicated when your managing individual items 
	(concepts, data elements...    (2I6L)
	TerryLongstreth: c/your/you're/    (2I6M)
	PeterYim: can't hear you any more Immanuel    (2I6N)
	ImmanuelNormann: I lost telephone connection - don't know why - sorry    (2I6O)
	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!    (2I6P)
	CameronRoss: @Ken - What exactly is "the issue"... to be clear?    (2I6Q)
	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.    (2I6R)
	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.    (2I6S)
	CameronRoss: @Ken - Shouldn't we start with the "API" and not the implementation?    (2I6T)
	KenBaclawski: @Cameron - Yes, I think the discourse should be at the architecture and API level for now.    (2I6U)
	CameronRoss: @Ken - Great! I couldn't agree more.    (2I6V)
	SimonSpero: [Quick compare/contrast use case: https://www.nescent.org/sites/hive/Main_Page]    (2I6W)
	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"    (2I6X)
	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.    (2I6Y)
	PeterYim: Please continue the conversation on the [oor-forum] & [oor-dev] list ... and come to the 
	next (and future) OOR-team meeting    (2I6Z)
	SimonSpero: Good bye and good yomtov    (2I70)
	YuriyMilov: Thanks, bye    (2I71)
	PeterYim: -- session ended: 11:03am PDT --    (2I72)
    -- end of chat session --    (2H41)

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