OOR/ConferenceCall 2011 03 11

= 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 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!

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
 * ref: World Clock
 * 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


 * In-session chat-room url: http://webconf.soaphub.org/conf/room/oor_20110311


 * 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 [mailto:peter.yim@cim3.com 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.)


 * This session, like all other Ontolog events, is open to the public. Information relating to this session is shared on this wiki page: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_03_04


 * 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

 * Attended:
 * KenBaclawski (co-chair)
 * LeoObrst (can only join 30 minutes into the meeting)
 * TerryLongstreth
 * PeterYim
 * MikeDean
 * TimDarr
 * ToddSchneider (co-chair)
 * ScottFahle (KBSI)
 * JouniTuominen
 * YuriyMilov


 * 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  so that we can reserve enough resources to support everyone's participation. ...
 * ... 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  so that we can reserve enough resources to support everyone's participation. ...


 * Regrets:
 * MatthewHettinger

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: KenBaclawski &amp; MichaelGruninger - Panelists: KenBaclawski+ToddSchneider, AldoGangemi+AlessandroAdamou, JouniTuominen+KimViljanen, EricChan - 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:


 * KenBaclawski takes the chair and welcome everyone
 * review and adopt agenda
 * PeterYim volunteered to keep a record of the proceedings

2. Roll Call:


 * see above

3. Key items for review and discussion today:

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


 * Workshop archives
 * audio archive of the session [ 0:55:52 ; mp3 ; 6.4MB ]


 * 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] PeterYim:.

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

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

proceeedings:
anonymous morphed into TimDarr

TimDarr: this is TimDarr from KBSI joining

PeterYim: Hi Tim ...

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

PeterYim: @Tim - we did post a recording (and the chat transcript, although not much in there) for last weeks' call

TimDarr: I downloaded the audio, but have not listened yet

TimDarr: Which document are we looking at currently?

PeterYim: @Tim - the OORI.java file at: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_03_11#nid2PK8

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"

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

BioPortal can be seamlessly incorporated in the OOR Reference Implementation.

TerryLongstreth: I'd love to see the document that describes the BioPortal architecture and shows where our 'facade' intersects

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

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

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

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

PeterYim: BioPortal architecture - see: http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository_Architecture/From_BioPortal

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

PeterYim: @Tim - access the semwebcentral code repository via link at: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_03_11#nid2POH

PeterYim: or, more directly http://oor.semwebcentral.org/ ... and in fact, http://semwebcentral.org/projects/oor

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

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

YuriyMilov: Sorry, need to go

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

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

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

specifying a collection of match criteria for the metadata, the match criteria being specified using the OMV (or some extension of it).

TimDarr: @Ken - that meets our immediate requirements.

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.

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

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

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

PeterYim: -- 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
 * see developing session page is at OOR/ConferenceCall_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: PeterYim / 2011.03.011-7:00am PST All participants, please review and edit to enhance accuracy and granularity of the documented proceedings.

Resources

 * homepage - OpenOntologyRepository - http://OpenOntologyRepository.org
 * proceedings of our previous meetings
 * OOR/ConferenceCall_2008_01_23
 * OOR/ConferenceCall_2008_02_13
 * OOR/ConferenceCall_2008_03_05
 * OOR/ConferenceCall_2008_03_14
 * OOR/ConferenceCall_2008_03_21
 * OOR/ConferenceCall_2008_04_04
 * OOR/ConferenceCall_2008_04_18
 * OOR/ConferenceCall_2008_05_09
 * OOR/ConferenceCall_2008_05_23
 * OOR/ConferenceCall_2008_06_06
 * OOR/ConferenceCall_2008_06_20
 * OOR/ConferenceCall_2008_07_11
 * OOR/ConferenceCall_2008_07_25
 * OOR/ConferenceCall_2008_08_08
 * OOR/ConferenceCall_2008_08_29
 * OOR/ConferenceCall_2008_09_05
 * OOR/ConferenceCall_2008_09_19
 * OOR/ConferenceCall_2008_10_03
 * OOR/ConferenceCall_2008_10_10
 * OOR/ConferenceCall_2008_10_17
 * OOR/ConferenceCall_2008_11_07
 * OOR/ConferenceCall_2008_11_14
 * OOR/ConferenceCall_2008_12_12
 * OOR/ConferenceCall_2009_01_09
 * OOR/ConferenceCall_2009_01_23
 * OOR/ConferenceCall_2009_02_06
 * OOR/ConferenceCall_2009_03_06
 * OOR/ConferenceCall_2009_03_20
 * OOR/ConferenceCall_2009_04_03
 * OOR/ConferenceCall_2009_05_01
 * OOR/ConferenceCall_2009_05_15
 * OOR/ConferenceCall_2009_05_29
 * OOR/ConferenceCall_2009_06_12
 * OOR/ConferenceCall_2009_06_26
 * OOR/ConferenceCall_2009_07_10
 * OOR/ConferenceCall_2009_07_24
 * OOR/ConferenceCall_2009_08_14
 * OOR/ConferenceCall_2009_09_04
 * OOR/ConferenceCall_2009_09_18
 * OOR/ConferenceCall_2009_10_02
 * OOR/ConferenceCall_2009_11_13
 * OOR/ConferenceCall_2009_12_11
 * OOR/ConferenceCall_2010_01_08
 * OOR/ConferenceCall_2010_01_22
 * OOR/ConferenceCall_2010_02_05
 * OOR/ConferenceCall_2010_03_05
 * OOR/ConferenceCall_2010_03_19
 * OOR/ConferenceCall_2010_04_16
 * OOR/ConferenceCall_2010_04_30
 * OOR/ConferenceCall_2010_05_21
 * OOR/ConferenceCall_2010_06_11
 * OOR/ConferenceCall_2010_07_09
 * OOR/ConferenceCall_2010_07_23
 * OOR/ConferenceCall_2010_08_06
 * OOR/ConferenceCall_2010_08_20
 * OOR/ConferenceCall_2010_09_03
 * OOR/ConferenceCall_2010_10_01
 * OOR/ConferenceCall_2010_10_29
 * OOR/ConferenceCall_2010_12_17
 * OOR/ConferenceCall_2011_01_07
 * OOR/ConferenceCall_2011_01_21
 * OOR/ConferenceCall_2011_02_04
 * OOR/ConferenceCall_2011_02_18
 * OOR Charter - To promote the global use and sharing of ontologies by: 1. establishing a hosted registry-repository; 2. enabling and facilitating open, federated, collaborative ontology repositories; 3. establishing best practices for expressing interoperable ontology and taxonomy work in registry-repositories.
 * "Ontology Repository" Definition - "An ontology repository is a facility where ontologies and related information artifacts can be stored, retrieved and managed"
 * OpenOntologyRepository_Scope - documentation related to this OOR initiative's mission, charter, objectives, goals, terms of reference, definitions, scope, ... etc.
 * OpenOntologyRepository_Requirement - documentation related to the requirements of the "open ontology repository" we are planning to implement through this OOR initiative.
 * OpenOntologyRepository_UseCases
 * OpenOntologyRepository_Approach - documentation related to this OOR initiative's approach, and the process we will be using.
 * OpenOntologyRepository_Architecture - documentation related to the architecture of the "open ontology repository" we are planning to implement through this OOR initiative.
 * OpenOntologyRepository_Plan
 * OOR/ActiveMemberContribution
 * Team mailling list:
 * OOR-Team discussion: [ oor-forum ]''' message archives - http://ontolog.cim3.net/forum/oor-forum/
 * OOR-Users discussion and support: [ oor-users ]''' message archives - http://ontolog.cim3.net/forum/oor-users/
 * Developers mailling list: [ oor-dev ] message archives - http://ontolog.cim3.net/forum/oor-dev/
 * the OOR-IPR mini-series:
 * 2010_09_09 - Thursday: Joint OOR-Ontolog-NCBO-CC-IAOA-OASIS Panel Discussion - "IPR issues in Ontology and the OOR" session-1: an exposition on relevant IPR regimes - Keynote speaker: GeorgeStrawn - Chair: PeterYim - Panelists: JamieClark, JohnWilbanks, BrucePerens - ConferenceCall_2010_09_09
 * 2010_09_16 - Thursday: Joint OOR-Ontolog-NCBO-CC-IAOA-OASIS Panel Discussion - "IPR issues in Ontology and the OOR" session-2: what are the IPR issues relating to open ontology repositories (and ontologies in general)? - Chair: MarkMusen - Panelists: CameronRoss, AlanRector, JohnSowa, BrucePerens, JohnWilbanks, PeterYim - ConferenceCall_2010_09_16
 * 2010_09_30 - Thursday: Joint OOR-Ontolog-NCBO-CC-IAOA-OASIS Panel Discussion - "IPR issues in Ontology and the OOR" session-3: discussion and consensus on licensing arrangements for the OOR Initiative, and positions we might take on related IPR issues - chair: LeoObrst - Panelists: PeterYim, MikeDean, BrucePerens, JamieClark - ConferenceCall_2010_09_30
 * the Joint OOR-OntologySummit2008 Panel Discussions:
 * 2008_02_28 - Thursday: Joint OOR-OntologySummit2008 Panel Discussion: "Ontology Registry and Repository Technology &amp; Infrastructure Landscape" - Co-chairs: LeoObrst &amp; FrankOlken; Panelists: BruceBargmeyer, MikeDean, MarkMusen, FarrukhNajmi &amp; PeterYim - ConferenceCall_2008_02_28
 * 2008_03_27 - Thursday: Joint OOR-OntologySummit2008 Panel Discussion: "An Open Ontology Repository: Rationale, Expectations &amp; Requirements - Session-1" - Chair: LeoObrst &amp; FabianNeuhaus; Panelists: WilliamBug, EvanWallace, JohnLMcCarthy, KenBaclawski, PeterBenson &amp; RexBrooks - ConferenceCall_2008_03_27
 * 2008_04_03 - Thursday: Joint OOR-OntologySummit2008 Panel Discussion: "An Open Ontology Repository: Rationale, Expectations &amp; Requirements - Session-2" - Chair: LeoObrst &amp; FabianNeuhaus; Panelists: DougLenat, DekeSmith, MarciaZeng, DeniseBedford, PatHayes, MalaMehrotra &amp; RobRaskin - ConferenceCall_2008_04_03
 * 2008_04_10 - Thursday: Joint OOR-OntologySummit2008 Panel Discussion: "Developing an Ontology of Ontologies for OOR" - Co-chairs: BarrySmith &amp; MichaelGruninger; Panelists: MichaelGruninger, PeterHaase, NatashaNoy &amp; ElisaKendall - ConferenceCall_2008_04_10
 * the OOR Development panel sessions:
 * 2008_08_22 - Friday: OOR Panel Discussion: "Getting OOR Development Off the Ground: Identifying Synergies &amp; Gaps" (Take-1) - Chair: LeoObrst; Panelists: MikeDean, MarkMusen, LiDing, BruceBargmeyer &amp; BillAndersen - ConferenceCall_2008_08_22
 * 2009_02_19 - Thursday: Joint Ontolog-OOR Panel Discussion: "Getting OOR Development Off the Ground (Take-2): the work begins" - Chair: ToddSchneider; Panelists: MarkMusen, NatashaNoy, MikeDean, PaulBuitelaar / AndreasHarth, MathieuDaquin, KenBaclawski, MichaelGruninger - ConferenceCall_2009_02_19
 * 2009_07_16 - Thursday: Joint Ontolog-OOR Panel Discussion: "Integrated tools for ontology development and management: A field guide to the Stanford technology" - Chair: MarkMusen - Panelists: TaniaTudorache, TimRedmond, NatashaNoy - ConferenceCall_2009_07_16
 * 2009_07_30 - Thursday: Joint Ontolog-OOR Panel Discussion: "BioPortal and related Ontology Repository Implementations and Development" (Take-3) - Chair: NatashaNoy - Panelists: CarlosRueda, PaulAlexander, JohnGraybeal, MikeDean, StephenGranite, AlexGarcia, KenBaclawski - ConferenceCall_2009_07_30
 * 2010_02_19 - Friday: OOR Panel Discussion: "Coordinating our Open Ontology Repository Software Development" - Chair: MikeDean - Panelists: JimChatigny, MichaelGruninger, KenBaclawski, NatashaNoy - OOR/ConferenceCall_2010_02_19
 * 2010_04_01 - Thursday: Joint OOR-Ontolog Panel Session: "OOR Use Cases - Take-3" - Chair: KenBaclawski &amp; ToddSchneider - Panelists: ToddSchneider, MatthewHettinger, KenBaclawski and MaximoGurmendez - ConferenceCall_2010_04_01
 * 2010_09_10 - Friday: Joint SIO-OOR-Ontolog Panel Discussion: "Common Logic (CL) Support for OOR" - Chair: JohnSowa - Panelists: JohnBateman-TillMossakowski, MichaelGruninger, CameronRoss, AdamPease, PatHayes - ConferenceCall_2010_09_10
 * 2010_09_17 - Friday: OOR Panel Discussion - "Getting OOR Development Going - Take-IV" Workshop - Co-chairs: ToddSchneider &amp; MichaelGruninger - Panelists: ToddSchneider, MikeDean, NatashaNoy, ImmanuelNormann, KenBaclawski, MichaelGruninger - OOR/ConferenceCall_2010_09_17
 * 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
 * 2010_11_19 - Friday: OOR Panel Discussion - "(Post-BioPortal fork) OOR Architecture and API - Take-II" - Co-chairs: KenBaclawski &amp; MichaelGruninger - Panelists: KenBaclawski+ToddSchneider, AldoGangemi+AlessandroAdamou, JouniTuominen+KimViljanen, EricChan - OOR/ConferenceCall_2010_11_19
 * 2011_03_04 - Friday: OOR "Architecture &amp; API Specification Development Workshop-I" - Co-chairs: KenBaclawski &amp; ToddSchneider - OOR/ConferenceCall_2011_03_04
 * 2011_03_11 - Friday: OOR - "Architecture &amp; API Specification Development Workshop-II" - Co-chairs: KenBaclawski &amp; ToddSchneider - OOR/ConferenceCall_2011_03_11
 * OntologySummit2008 homepage
 * OntologySummit2008_Communique
 * OntologySummit2008/FaceToFaceAgenda
 * The OOR Project Presentation (delivered at the OntologySummit2008 face-to-face workshop)
 * [ ontology-summit ] discussion archives - http://ontolog.cim3.net/forum/ontology-summit/2008-01/ (~5 months exchanges starting from Jan-2008)
 * Our key content pages:
 * OpenOntologyRepository_Scope
 * OpenOntologyRepository_Organization
 * OpenOntologyRepository_Process
 * OpenOntologyRepository_Policy
 * OpenOntologyRepository_IPR
 * OpenOntologyRepository_Requirement
 * OpenOntologyRepository_UseCases
 * OpenOntologyRepository_Architecture
 * OpenOntologyRepository_Approach
 * OpenOntologyRepository_Roadmap
 * OpenOntologyRepository_Plan
 * OpenOntologyRepository_Funding
 * OpenOntologyRepository_ResearchIssues
 * OpenOntologyRepository_ResearchActivity
 * OpenOntologyRepository_Development
 * OOR Project site at SemWebCentral - http://oor.semwebcentral.org
 * http://semwebcentral.org/scm/?group_id=152 describes SVN access
 * Public sandbox instance of OOR (OOR-sandbox) - http://sandbox.oor.net/ontologies (previously http://oor-01.cim3.net/ontologies)
 * OOR_SandBox
 * NCBO-OOR development documentation - http://www.bioontology.org/wiki/index.php/NCBO-OOR_Development