OOR/ConferenceCall 2011 05 20

= OpenOntologyRepository: Architecture & API Workshop-V - Fri 2011_05_20 =

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

Session Co-chairs: KenBaclawski & ToddSchneider

Conference Call Details:

 * Date: Friday, 20-May-2011
 * Start Time: 9:00pm EDT / 6:00am PDT / 3:00pm CEST / 2:00pm BST / 13:00 UTC
 * ref: World Clock
 * Expected Call Duration: 1.0~1.5 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


 * 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_05_20


 * 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
 * PeterYim
 * MikeDean
 * MichaelGruninger
 * ToddSchneider (co-chair)


 * Expecting:


 * Regrets:
 * MattHettinger

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


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


 * ToddSchneider: - agenda to include:
 * 0) Adopting (formally) the work from the last workshop, modulo any discussion/modifications entered on the wiki page.
 * 1) Resolve / Finalize the first method proposed
 * http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository_Architecture#nid2Q6G ... and,
 * http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository_Architecture#nid2Q65
 * 2) Starting with the Registrar, as identified in your use cases, specify the functions to support that role starting with the use cases.
 * Thereafter, move on to Accreditor, Steward, Process Manager, and Submitter.
 * For each of the roles we also have to keep in mind any coupling to representation languages (relative to the actions taken).


 * PeterYim: we should really try to get into a position whereby people can start contributing code ASAP!

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 series of meetings, we are going through 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

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 participants to update your candidate contributions to ensure your ideas are known and understood.

The following are relevant prior meetings:


 * Architecture & API Specification Development Workshop-IV - OOR/ConferenceCall_2011_04_22
 * Architecture & API Specification Development Workshop-III - OOR/ConferenceCall_2011_03_25
 * Architecture & API Specification Development Workshop-II - OOR/ConferenceCall_2011_03_11
 * 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 & 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 & ToddSchneider takes the chair and welcome everyone
 * review and adopt agenda
 * PeterYim volunteered to keep a record of the proceedings

2. Roll Call & Adoption of last meeting's minutes:


 * see above


 * minutes of the last meeting adopted, as captured in the proceedings on the session page at: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_03_25


 * Announcements:
 * OOR Logo candidates - first round polling results:
 * 13 participants entered 35 votes all together, and candidates "Hashemi-4" and "Hashemi-c" were selected as finalists, each with 6 votes (behind that, were "Milov-1 with 4, and "Ding-1" and "Hashemi-a" with 3 votes each.)
 * Peter will post results to the [oor-forum] list, the community has one week to make suggestions to the candidate logo designer (AliHashemi in this case) so he can prepare the finalists designs for the final selection
 * MikeDean: BioPortal v3.0 released yesterday - ref.
 * PeterYim: webProtege beta was also release a few days ago, which allows ontologies on BioPortal to be edited through webProtege - ref.

3. Key items for review and discussion today:


 * "OOR Architecture & API Specification Development Workshop-V:" (Archives)


 * audio archive of the session [ [ 1:09:36 ; mp3 ; 8.0 MB ] ]


 * chat transcript of the session

3.0) Adopting (formally) the work from the last workshop, modulo any discussion/modifications entered on the wiki page.

3.1) Resolve / Finalize the first method proposed


 * http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository_Architecture#nid2Q6G ... and,
 * http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository_Architecture#nid2Q65

... items below are mostly from the previous workshop, and will be updated as this session progresses.

3.2) Starting with the Registrar, as identified in your use cases, specify the functions to support that role starting with the use cases. Thereafter, move on to Accreditor, Steward, Process Manager, and Submitter. ... For each of the roles we also have to keep in mind any coupling to representation languages (relative to the actions taken).

3.3) Discussed today (2011.05.20)


 * we should organize a workshop between the BioPortal team and the OOR team to learn about their latest progress and see how our work could be complementary and synergistic -- Ken will make the invitation


 * the current BioPortal UI is "uniform" in the sense that everyone has access to every screen. Since OOR users will have different roles, we will adopt a "role-based" UI


 * Security v. Gatekeeping - see: chat discussion


 * on MichaelGruninger's suggestion, we should invite ElisaKendall or EvanWallace to come give us a talk on ISO 19763 -- Michael will make the invitation
 * plan is to feature it as part of a IAOA-OOR-Ontolog joint event (series)
 * a Thursday+Friday combo - Overview + Drill-down (Michael will try for Jun 9 & 10)

Consensus, Conclusions & Follow-up Actions:


 * The interface for searching ontology metadata will consist of a single method:
 * The method will be called find.
 * The method will have a single parameter consisting of a SPARQL query.
 * The return value of the method will be a SPARQL result set.
 * Metadata will be represented using a named RDF graph.
 * The metadata RDF graph will use the following name: http://metadata.oor.net
 * Metadata will be based on an extension of OMV.
 * The OMV extension may include a notion of domain specification or topics, represented as text.
 * Metadata will be federated, so it is a single named RDF graph, no matter how many OOR instances there are.

-- begin in-session chat-transcript --

PeterYim: Welcome to the

OpenOntologyRepository: Architecture & API Workshop-V - Fri 2011_05_20

Session Co-chairs: KenBaclawski & ToddSchneider

Ref. details at: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_05_20

anonymous2 morphed into MichaelGruninger

anonymous morphed into MikeDean

KenBaclawski: The current UI is "uniform" in the sense that everyone has access to every screen. Since OOR users will have different roles, would it make sense to change this design?

KenBaclawski: Should security rules and gatekeeping rules be done together? This integrates the workflow with security.

ToddSchneider: Depends on what gatekeeping means?

ToddSchneider: Gatekeeping - The Gatekeeping component shall be responsible for enforcing role based behaviors which include access control; Behaviors will be represented as rules

PeterYim: ref. "Quality and Gatekeeping" on the OntologySummmit2008_Communique - http://ontolog.cim3.net/cgi-bin/wiki.pl?OntologySummit2008_Communique#nid1GV5

MichaelGruninger: There is some ambiguity in the terms within the architecture (such as Gatekeeping and Administration). For each of these terms we should explicitly specify the functionalities that correspond to the component within the architecture.

-- 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-III" on Fri 2011.05.27
 * see developing session page is at OOR/ConferenceCall_2011_05_27
 * Fri 2011.05.27 - 9:00pm EDT / 6:00am PDT / 3:00pm CEST / 2:00pm BST / 13:00 UTC (ref. worldclock)
 * after that: we'll have a regular OOR-team meeting on Fri 2011.06.03 and "Architecture-API Workshop-VI" on Fri 2011.06.10
 * 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: 7:12 am PDT

-- notes taken by: PeterYim / 2011.05.27-7:18am PDT All participants, please review and edit to enhance accuracy and granularity of the documented proceedings.

Resources

 * homepage - OpenOntologyRepository - http://OpenOntologyRepository.org
 * 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"
 * 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/
 * proceedings of our previous meetings, panel discussions and workshops
 * the Joint OOR-OntologySummit2008 Panel Discussions:
 * 2008_02_28 - Thursday: Joint OOR-OntologySummit2008 Panel Discussion: "Ontology Registry and Repository Technology & Infrastructure Landscape" - Co-chairs: LeoObrst & FrankOlken; Panelists: BruceBargmeyer, MikeDean, MarkMusen, FarrukhNajmi & PeterYim - ConferenceCall_2008_02_28
 * 2008_03_27 - Thursday: Joint OOR-OntologySummit2008 Panel Discussion: "An Open Ontology Repository: Rationale, Expectations & Requirements - Session-1" - Chair: LeoObrst & FabianNeuhaus; Panelists: WilliamBug, EvanWallace, JohnLMcCarthy, KenBaclawski, PeterBenson & RexBrooks - ConferenceCall_2008_03_27
 * 2008_04_03 - Thursday: Joint OOR-OntologySummit2008 Panel Discussion: "An Open Ontology Repository: Rationale, Expectations & Requirements - Session-2" - Chair: LeoObrst & FabianNeuhaus; Panelists: DougLenat, DekeSmith, MarciaZeng, DeniseBedford, PatHayes, MalaMehrotra & RobRaskin - ConferenceCall_2008_04_03
 * 2008_04_10 - Thursday: Joint OOR-OntologySummit2008 Panel Discussion: "Developing an Ontology of Ontologies for OOR" - Co-chairs: BarrySmith & MichaelGruninger; Panelists: MichaelGruninger, PeterHaase, NatashaNoy & 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 & Gaps" (Take-1) - Chair: LeoObrst; Panelists: MikeDean, MarkMusen, LiDing, BruceBargmeyer & 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 & 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 & 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 & MichaelGruninger - Panelists: KenBaclawski+ToddSchneider, AldoGangemi+AlessandroAdamou, JouniTuominen+KimViljanen, EricChan - OOR/ConferenceCall_2010_11_19
 * 2011_03_04 - Friday: OOR "Architecture & API Specification Development Workshop-I" - Co-chairs: KenBaclawski & ToddSchneider - OOR/ConferenceCall_2011_03_04
 * 2011_03_11 - Friday: OOR - "Architecture & API Specification Development Workshop-II" - Co-chairs: KenBaclawski & ToddSchneider - OOR/ConferenceCall_2011_03_11
 * 2011_03_18 - Friday: OOR Metadata Workshop-I - Chair: MichaelGruninger - OOR/ConferenceCall_2011_03_18
 * 2011_03_25 - Friday: OOR - "Architecture & API Specification Development Workshop-III" - Co-chairs: KenBaclawski & ToddSchneider - OOR/ConferenceCall_2011_03_25
 * 2011_04_22 - Friday: OOR - "Architecture & API Specification Development Workshop-IV" - Co-chairs: KenBaclawski & ToddSchneider - OOR/ConferenceCall_2011_04_22
 * 2011_05_13 - Friday: OOR Metadata Workshop-II - Chair: MichaelGruninger - OOR/ConferenceCall_2011_05_13
 * 2011_05_20 - Friday: OOR - "Architecture & API Specification Development Workshop-V" - Co-chairs: KenBaclawski & ToddSchneider - OOR/ConferenceCall_2011_05_20
 * 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
 * OntologySummit2008 homepage
 * OntologySummit2008_Communique
 * OntologySummit2008/FaceToFaceAgenda & Proceedings
 * 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
 * OpenOntologyRepository_Metadata
 * OOR/ActiveMemberContribution
 * OOR Project site at SemWebCentral - http://oor.semwebcentral.org
 * Public sandbox instance of OOR (OOR-sandbox) - http://sandbox.oor.net/ontologies (previously http://oor-01.cim3.net/ontologies)
 * OOR_SandBox
 * NCBO - BioPortal
 * NCBO-OOR development documentation - http://www.bioontology.org/wiki/index.php/NCBO-OOR_Development