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OpenOntologyRepository: OOR Team Conference Call - Fri 2010-10-15

We will be discussing the (post-BioPortal fork) OOR Architecture and the adoption of an API. ... See detailed agenda below. Please refer also to the notes from the last regular meeting at: OOR/ConferenceCall 2010_10_01 and the two recent panel sessions:

... note, in particular, the start time of this meeting is three hours earlier than before (9:00am, rather than 12:00noon EDT)

==Archives==

Conference Call Details

  • Date: Friday, 15-Oct-2010
  • Start Time: 9:00am EDT / 6:00am PDT / 3:00pm CEST / 2:00pm BST / 13:00 UTC
  • Expected Call Duration: 1.5~2.0 hours
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  • For those who cannot join us, or who have further questions or remarks on the summit topic and content, please post them to the [ oor-forum ] listserv so that everyone in the community can benefit from the discourse.
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  • 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. ...

Resources

Agenda Ideas

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

  • discussion on OOR Architecture and API
  • ...

Agenda & Proceedings

1. Peter P. Yim takes the chair and welcomes everyone.

2. Roll call and review of agenda

3. Discussion:

  • an update on the OOR-IPR policy

Pertinent Questions We Will be Asking

  • Key requirements of the new OOR architecture? (very brief ... this can take over the whole session otherwise!)
  • Who are the immediate software contributors that we will need to accommodate?
  • Enumerating our options and candidate architectural approaches (1 slide (max. 2) from anyone who has a proposal.)
  • interim consensus on key tenets of the OOR architecture? ... delegate to a small team to work this offline?
  • Suggestions towards defining an API (1 to 2 slides from anyone who has a proposal.)
  • interim OOR API-related consensus? ... delegate to a small team to work this offline?
  • Recommended development platform ... consensus

4. Review of Immediate next steps and action items.

5. Any other business

6. Discussion on future regular meeting time

7. Adjourn

Transcript of the online chat during the session

see raw transcript here in the mean time.

(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 OpenOntologyRepository: OOR Team Conference Call - Fri 2010-10-15

.

Peter P. Yim: session page is at: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2010_10_15

Peter P. Yim: .

anonymous morphed into JouniTuominen

Ken Baclawski: Here is the architecture diagram we propose (as presented on 17-Sep-2010):

OOR-Architecture--KenBaclawski_20100917.png

Ken Baclawski: This is the current OOR API (in Java) based on BioPortal:

http://ontolog.cim3.net/work/OpenOntologyRepository/2010-09-17_OOR-Dev-Take-4/OOR-API--KenBaclawski_20100917.java

Peter P. Yim: all new contributions to the OOR software (except for existing non-BSD contributions that

will, hopefully, be migrated over), as well as content (i.e. ontologies) uploaded to the public

instance of the production OOR, operated by the OOR-team, will be made under the "Simplified

(2-clause) BSD License" - see: http://opensource.org/licenses/bsd-license.php

Peter P. Yim: Let's step through the questions we need to address at this session (below)

Peter P. Yim: == Key requirements of the new OOR architecture? ==

Michael Grüninger: support for multiple ontology specification languages

Peter P. Yim: I think it must accommodate both the existing codebase (BioPortal) and new contributions

Ken Baclawski: The use cases are certainly important. The posted architecture is based on the use

cases.

Michael Grüninger: services of the OOR should be independent of the ontology specification language

Till Mossakowski: It should be flexible enough in order to easily integrate new formats and services

Peter P. Yim: as per OntologySummit2008_Communique ... we want to be on a Service Oriented Architecture

Michael Grüninger: support for ontology metdata

Peter P. Yim: metadata should be an extension of OMV too

Peter P. Yim: robustness, scalability, etc. for the repository is definitely important

Yuriy Milov: Java based ... I agree to discuss the Java implementation later (as a recommendation,

when we come to the choice of platform discussion (as Peter P. Yim suggests)

Peter P. Yim: == Who are the immediate software contributors that we will need to accommodate? ==

Peter P. Yim: NCBO / BioPortal

Ken Baclawski: My team at Northeastern University (NEU)

Michael Grüninger: Cameron Ross is leading the architectural design of COLORE

Till Mossakowski: at Bremen, we have a BioPortal clone and the Hets system

Till Mossakowski: the BioPortal clone is at http://ontologies.informatik.uni-bremen.de/ (which is

AlexGarcia has been working on)

Till Mossakowski: We might want to use tntbase.org (but we have close contact to them)

Mike Dean: contributions from Raytheon-BBN

Peter P. Yim: NeOn project? .... (of course, OMV is from the NeOn project, and that is definitely in)

Peter P. Yim: ref. NeOn involvement I will continue the conversations with Aldo Gangemi, Mathieu Daquin,

Andreas Harth and Enrico Motta to solicit their involvement

JouniTuominen: ONKI ontology service http://www.onki.fi, project page

http://www.seco.tkk.fi/services/onki/

Bart Gajderowicz: My contribution would be library development

Bart Gajderowicz: so code part

Bart Gajderowicz: As part of my thesis, I have been working on ontology matching, and have developed

an application, which I would like to contribute to the OOR architecture

Peter P. Yim: == Enumerating our options and candidate architectural approaches ==

Till Mossakowski: slide no. 7 of Immanuel's presentation

http://ontolog.cim3.net/file/work/OpenOntologyRepository/2010-09-17_OOR-Dev-Take-4/SOA-for-OOR--ImmanuelNormann_20100917.pdf

Yuriy Milov: Is Google's AppEngine an appropriate platform? I'd like to add some stuff from there

Till Mossakowski: I think a good thing is define a RESTful interface of services. We have implemented

one for Hets, see http://trac.informatik.uni-bremen.de:8080/hets/wiki/RESTfulInterface . I am not

meaning to use this one, but just want to give an idea of what a RESTful interface is.

Peter P. Yim: ref. BioPortal high level architecture -

http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository_Architecture#nid2J32

Ken Baclawski: I have posted an architecture which is based on the use cases, but I am open to

suggestions especially concerning how to accommodate multiple specification languages for

ontologies.

JouniTuominen: +1 for RESTful interface. We have developed LOOS API (Linked Open Ontology Services,

in spirit of LOD) for ONKI, see http://www.yso.fi/onkirest . Actually the intefrace it's not that

RESTful, more like a method-based HTTP API

Ken Baclawski: @Till - Concerning the slide in Immanuel's presentation, this is not an SOA

architecture diagram. In fact the entire diagram is just two diagrams: the GUI and the core

services.

Ken Baclawski: @Till - I have the experience of developing web services for a military contract, and

SOAP/WSDL was much easier to develop than REST.

Till Mossakowski: We have a bit of experience with SOAP, but have not implemented one project with

both REST and SOAP.

Ken Baclawski: The current trend in SOA is for REST and SOAP to converge, so the distinction may

disappear.

Till Mossakowski: Can WSDL be used together with either of them?

Ken Baclawski: Yes, it is possible for a single service to support both SOAP and REST at the same

time.

Ken Baclawski: In my previous post about Immanual's presentation, I mean the diagram is two

components, not two diagrams.

Michael Grüninger: Architecture for COLORE can be found in slide 5 in the presentation at

http://ontolog.cim3.net/file/work/OpenOntologyRepository/2010-09-10_CL-support-for-OOR/An-OOR-Implementation-for-COLORE--CameronRoss_20100910.pdf

Yuriy Milov:

http://www.memo.in.th/wp-content/uploads/2010/09/Service-Oriented-Cloud-Computing-Architecture.pptx

Yuriy Milov: SOCCA supports easy application migration from one cloud to another and service

redeployment to different clouds by separating the roles of service logic provider and service

hosting/cloud providers. It promotes an open platform on which open standards, ontology are

embraced.

Peter P. Yim: == decision: let's delegate the workout of architectural details to a committee ==

Peter P. Yim: the committee is to run with an open transparent process, and will keep all of us in synch

Peter P. Yim: committee meetings to be announced so others can join as observers

Peter P. Yim: only code contributors will participate in making the final decisions ... other

architectural suggestions will only be provided as references to the committee

Peter P. Yim: the precepts agreed earlier as "Key requirements of the new OOR architecture" will drive

the committee's work and decisions

Peter P. Yim: on the committee: rep from NCBO, NEU, UToronto, Bremen, Raytheon-BBN, NeOn ... (to be

decided) ONKI, Yuriy Milov, ... (BartGajderowicz agreed that he will just observe and work with what

comes out of the committee)

Peter P. Yim: Architecture Committee will work up a architecture first ... and then develop the API

Peter P. Yim: each party in the committee to nominate their committee member ... Peter to contact those

who are not here today

Peter P. Yim: we will defer discussion on development platform

Peter P. Yim: we will continue to discuss regular meeting times on the [oor-forum] list ... please

provide input into the doodle poll if you haven't already - goto: http://doodle.com/a2snxkpkd8hhxek4

Peter P. Yim: as discussed previously, this is almost about time we start this - have alternate Friday

OOR team meetings - one for OOR high level issues, content, admin etc., and the other for deep-water

technical meetings.

Peter P. Yim: ALL: agreed ... we can possibly even have alternate (Friday) start-times for each of these

meeting sets

Peter P. Yim: thanks everyone ... very productive meeting indeed!

Peter P. Yim: -- session ended 8:10am PDT --

Peter P. Yim: The unedited chat-transcript is now online ... I will be posting the audio archive and a

lightly edited (and re-organized) version of the chat transcript (for clarity and better

intelligibility) later.

-- end of chat session --

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: 15-Oct-2010 6:12~8:10 am Pacific Daylight Time
  • Duration of Recording: 1 Hour 48 Minutes
  • Recording File Size: 12.3 MB (in mp3 format)
  • suggestion: its best that you listen to the session while having the viewgraphs 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.)

Proposed Architectural Approaches

MikeDean_proposed-OOR-modules_2080606b.png
  • NCBO-BioPortal - ref. BioPortal-Proposed-Architecture-Technology-Stack-Diagram-4 dated 2010-07-24
NCBO_BioPortal-ProposedArchitecture-DetailedHighLevel_20100724b.jpg
  • KenBaclawski (NEU) - ref. Ken Baclawski 2010-09-17 presentation slide#10
NEU_proposed-OOR-Architecture--KenBaclawski_20100917b.png
Bremen_proposed-SOA-for-OOR_20100917c.png
CameronRoss-UToronto_COLORE-System-Architecture_20100910b.png



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