OpenOntologyRepository: Architecture & API Workshop-II - Fri 2011_03_11    (2PIR)

Topic: OOR Specification Workshop II - "OOR Architecture & API Specification Development Workshop-II"    (2PIS)

Session Co-chairs: KenBaclawski & ToddSchneider    (2PIT)

... please note that this meeting will have a hard stop in 1 hour (because there is an OntologySummit2011 organizing committee meeting coming up next that a few of us are involved in. Therefore, this meeting will start promptly. Please try to call in a few minutes before the scheduled start time!    (2PQ2)

Conference Call Details:    (2PIU)

Attendees    (2PJJ)

Agenda Ideas:    (2PJU)

please insert any additional items below (along with your name for follow-up purposes)    (2PJV)

Abstract:    (2PK1)

As a result of the two OOR Architecture and API panel sessions, we have seen a large number of architectures and APIs for ontology repositories. We have had requirements for the OOR, at least in broad outline form, since the Ontology Summit 2008. We have been running an OOR sandbox based on BioPortal. Most recently, we have forked from the BioPortal code base with the intention of proceeding separately with the development of a reference implementation.    (2PK2)

The various architectures and APIs for ontology repositories are available at OpenOntologyRepository_Architecture    (2PK3)

At this meeting we begin the process of producing the actual OOR specification. It will be run as a workshop where the straw man proposal will be discussed and modified as needed.    (2PK4)

Here is the straw man architecture: OpenOntologyRepository_Architecture/Candidate03    (2PK5)

The workflow component is explained in http://www.ccs.neu.edu/home/kenb/oor/workflow.pdf and the API is in http://www.ccs.neu.edu/home/kenb/oor/workflowAPI.pdf    (2PQH)

In addition, there is an API of the core services that was obtained from BioPortal, which is not entirely compatible with the straw man architecture, but furnishes a starting point. This API will also be discussed and modified as needed.    (2PK6)

Here is the API expressed in WSDL: http://www.ccs.neu.edu/home/kenb/oor/OORService.wsdl    (2PK7)

Here is the API expressed in Java: http://www.ccs.neu.edu/home/kenb/oor/OORI.java    (2PK8)

Finally, we need to agree on a plan for completing the development of the specification.    (2PK9)

Here is the proposed organizing plan: OpenOntologyRepository_Architecture/GettingOrganized    (2PKA)

We encourage all to up date your candidate contributions to ensure your ideas are known and understood.    (2PKB)

The following are relevant prior meetings:    (2PKC)

Agenda & Proceedings    (2PKH)

1. Meeting called to order:    (2PKI)

2. Roll Call:    (2PKM)

3. Key items for review and discussion today:    (2PKO)

"OOR Architecture & API Specification Development Workshop-II:"    (2PKP)

 see raw transcript here.    (2PW5)
 (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.    (2PW6)
 -- begin in-session chat-transcript --    (2PW7)
	[05:57] PeterYim: .    (2PV1)
	OpenOntologyRepository: Architecture & API Workshop-II - Fri 2011_03_11    (2PV2)
	Topic: OOR Specification Workshop II - "OOR Architecture & API Specification Development Workshop-II"    (2PV3)
	Session Co-chairs: KenBaclawski & ToddSchneider    (2PV4)
	session page at: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_03_11    (2PV5)
	 == proceeedings: ==    (2PV6)
	anonymous morphed into TimDarr    (2PV7)
	TimDarr: this is TimDarr from KBSI joining    (2PV8)
	PeterYim: Hi Tim ...    (2PV9)
	TimDarr: Hello. Sorry I missed last week, but I had a conflict.    (2PVA)
	PeterYim: @Tim - we did post a recording (and the chat transcript, although not much in there) for 
	last weeks' call    (2PVB)
	TimDarr: I downloaded the audio, but have not listened yet    (2PVC)
	TimDarr: Which document are we looking at currently?    (2PVD)
	PeterYim: @Tim - the OORI.java file at: 
	http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_03_11#nid2PK8    (2PVE)
	PeterYim: @Tim - during the session, we will generally refer to that as "purple number 2PK8" ... 
	which is what you can get to if you search on the session page for the string "2PK8"    (2PVF)
	KenBaclawski: The guiding principle we will use is to introduce a facade that exposes the OOR API 
	and uses the BioPortal API internally. This ensures that any improvements to    (2PVG)
	BioPortal can be seamlessly incorporated in the OOR Reference Implementation.    (2PVH)
	TerryLongstreth: I'd love to see the document that describes the BioPortal architecture and shows 
	where our 'facade' intersects    (2PVI)
	ToddSchneider: Suggested modification: An OOR guiding principle: we will provide a facade that 
	exposes the OOR API and can be coupled to the BioPortal API. This will allow for    (2PVJ)
	improvements to BioPortal to be incorporated in the OOR Reference Implementation.    (2PVK)
	TimDarr: Thanks. Since I missed last week, what is the status of the forked BioPortal code?    (2PVL)
	TimDarr: [re. BioPortal] where do I find that location?    (2PVM)
	PeterYim: BioPortal architecture - see: 
	http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository_Architecture/From_BioPortal    (2PVN)
	TimDarr: Thanks, but where do we get the actual code? cimcentral??    (2PVO)
	PeterYim: @Tim - access the semwebcentral code repository via link at: 
	http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_03_11#nid2POH    (2PVP)
	PeterYim: or, more directly http://oor.semwebcentral.org/ ... and in fact, 
	http://semwebcentral.org/projects/oor    (2PVQ)
	MikeDean: @Tim - http://semwebcentral.org/scm/?group_id=152 describes SVN access    (2PVR)
	MikeDean: @Tim - it's linked from http://semwebcentral.org/projects/oor    (2PVS)
	YuriyMilov: Sorry, need to go    (2PVT)
	TimDarr: Thanks, Mike! You should get a request to join from Scott Fahle at KBSI. We are very 
	interested in contributing. It seems like BioPortal has the default capabilities that we    (2PVU)
	need, plus we can provide feedback and requirements moving forward.    (2PVV)
	KenBaclawski: The consensus is to have a single searchOntologyMetadata method that has a single 
	parameter, the query, and returns a list of matching ontologies. One is basically    (2PVW)
	specifying a collection of match criteria for the metadata, the match criteria being specified using 
	the OMV (or some extension of it).    (2PVX)
	TimDarr: @Ken - that meets our immediate requirements.    (2PVY)
	TerryLongstreth: Thoughts on admin and workflow, for consideration: Administration : functions with 
	special privileges, rules and workflow Admin would be tailored by instances, but should include a 
	correlated set of common functions for protections of the content across the federation Admin is a 
	distinguished type of workflow, as is find, inference, persistence, etc So Workflow is the enabling 
	meta-language as well as a standard mechanism for scheduling functions in the system.    (2PVZ)
	TimDarr: @Peter - I agree! KBSI has resources available (as long as it is in line with our contract)    (2PW0)
	PeterYim: next week (Fri Mar-18) is session OOR Metadata (MichaelGruninger) ... therefore, next 
	Architecture-API workshop - Fri 3/25 same time ... we will focus on workflow at that    (2PW1)
	session, i.e. our "OOR Architecture-API workshop-III"    (2PW2)
	PeterYim: -- session ended: 6:59am PST --    (2PW3)
 -- end of in-session chat-transcript --    (2PW8)

4. Any Other Business:    (2PKS)

5. Action items:    (2PKT)

6. Schedule Next Meeting & Adjourn:    (2PKU)

 --
 notes taken by: PeterYim / 2011.03.011-7:00am PST
 All participants, please review and edit to enhance accuracy and granularity of the documented proceedings.    (2PL2)

Resources    (2PL3)