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OpenOntologyRepository: Architecture & API Workshop-II - Fri 2011_03_11

Topic: OOR Specification Workshop II - "OOR Architecture & API Specification Development Workshop-II"

Session Co-chairs: KenBaclawski & ToddSchneider

... please note that this meeting will have a hard stop in 1 hour (because there is an Ontology Summit 2011 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!

Conference Call Details

  • Date: Friday, 11-Mar-2011
  • Start Time: 9:00am EST / 6:00am PST / 3:00pm CET / 2:00pm GMT / 14:00 UTC
  • Expected Call Duration: ~1.0 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), if applicable, will be started 5 minutes before the call at: http://vnc2.cim3.net:5800/
    • view-only password: "ontolog"
  • RSVP to peter.yim@cim3.com appreciated, ... or simply just by adding yourself to the "Expected Attendee" list below (if you are a member of the team.)
  • Please note that this session may be recorded, and if so, the audio archive is expected to be made available as open content, along with the proceedings of the call to our community membership and the public at-large under our prevailing open IPR policy.

Attendees

  • Expecting:
    • ... if you are coming to the meeting, 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. ...

Agenda Ideas

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

  • The specifications to be discussed at the meeting are the following (not necessarily discussed in this order):
    • the OOR Architecture
    • the OOR API
    • the Organizing Plan
    • the default development platform

Abstract

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.

The various architectures and APIs for ontology repositories are available at OpenOntologyRepository_Architecture

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.

Here is the straw man architecture: OpenOntologyRepository_Architecture/Candidate03

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

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.

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

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

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

Here is the proposed organizing plan: OpenOntologyRepository_Architecture/GettingOrganized

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

The following are relevant prior meetings:

  • Architecture & API Specification Development Workshop-I - OOR/ConferenceCall_2011_03_04
  • 2011.02.04 discussion
  • 2010_11_19 - Friday: OOR Panel Discussion - "(Post-BioPortal fork) OOR Architecture and API - Take-II" - Co-chairs: Ken Baclawski & Michael Grüninger - Panelists: KenBaclawski+ToddSchneider, AldoGangemi+AlessandroAdamou, JouniTuominen+KimViljanen, Eric Chan - OOR/ConferenceCall_2010_11_19   
  • 2010_10_15 - Friday: OOR Project Team Member Conference Call - discussion on the (post-BioPortal fork) OOR Architecture and API - OOR/ConferenceCall_2010_10_15   

Agenda & Proceedings

1. Meeting called to order:

  • Ken Baclawski takes the chair and welcome everyone
  • review and adopt agenda
  • Peter P. Yim volunteered to keep a record of the proceedings

2. Roll Call:

3. Key items for review and discussion today:

"OOR Architecture & API Specification Development Workshop-II:"

  • ===IM Chat Transcript captured 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 in-session chat-transcript --

[05:57] Peter P. Yim: .

OpenOntologyRepository: Architecture & API Workshop-II - Fri 2011_03_11

Topic: OOR Specification Workshop II - "OOR Architecture & API Specification Development Workshop-II"

Session Co-chairs: Ken Baclawski & Todd Schneider

session page at: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_03_11

proceeedings:

anonymous morphed into Tim Darr

Tim Darr: this is Tim Darr from KBSI joining

Peter P. Yim: Hi Tim ...

Tim Darr: Hello. Sorry I missed last week, but I had a conflict.

Peter P. Yim: @Tim - we did post a recording (and the chat transcript, although not much in there) for

last weeks' call

Tim Darr: I downloaded the audio, but have not listened yet

Tim Darr: Which document are we looking at currently?

Peter P. Yim: @Tim - the OORI.java file at:

http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_03_11#nid2PK8

Peter P. Yim: @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"

Ken Baclawski: 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

BioPortal can be seamlessly incorporated in the OOR Reference Implementation.

Terry Longstreth: I'd love to see the document that describes the BioPortal architecture and shows

where our 'facade' intersects

Todd Schneider: 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

improvements to BioPortal to be incorporated in the OOR Reference Implementation.

Tim Darr: Thanks. Since I missed last week, what is the status of the forked BioPortal code?

Tim Darr: [re. BioPortal] where do I find that location?

Peter P. Yim: BioPortal architecture - see:

http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository_Architecture/From_BioPortal

Tim Darr: Thanks, but where do we get the actual code? cimcentral??

Peter P. Yim: @Tim - access the semwebcentral code repository via link at:

http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_03_11#nid2POH

Peter P. Yim: or, more directly http://oor.semwebcentral.org/ ... and in fact,

http://semwebcentral.org/projects/oor

Mike Dean: @Tim - http://semwebcentral.org/scm/?group_id=152 describes SVN access

Mike Dean: @Tim - it's linked from http://semwebcentral.org/projects/oor

Yuriy Milov: Sorry, need to go

Tim Darr: 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

need, plus we can provide feedback and requirements moving forward.

Ken Baclawski: 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

specifying a collection of match criteria for the metadata, the match criteria being specified using

the OMV (or some extension of it).

Tim Darr: @Ken - that meets our immediate requirements.

Terry Longstreth: 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.

Tim Darr: @Peter - I agree! KBSI has resources available (as long as it is in line with our contract)

Peter P. Yim: 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

session, i.e. our "OOR Architecture-API workshop-III"

Peter P. Yim: -- session ended: 6:59am PST --

-- end of in-session chat-transcript --

4. Any Other Business:

5. Action items:

6. Schedule Next Meeting & Adjourn:

  • Next Meeting:
    • next week we will be having the OOR Metadata workshop on Fri 2011.03.18
    • after that, another Architecture-API workshop session? - (TBD) OOR-Architecture-API workshop (III) team session, Friday, for 1 hours only - Fri 2011.03.25 - 6:00am PST / 9:00am EST (ref. worldclock)
    • Note: earlier resolution: all team members please (if possible) block out Fridays 1.5 Hr
    • ref. our doodle poll (see: http://doodle.com/a2snxkpkd8hhxek4 ), looks like we can settle in on two new meeting times - a 6:00am PT (14:00 UTC) and an 8:30am PT (16:30 UTC) (or something in between) ...
  • Call adjourned at: 6:59 am PST

--

notes taken by: Peter P. Yim / 2011.03.011-7:00am PST

All participants, please review and edit to enhance accuracy and granularity of the documented proceedings.

Resources



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