OOR/ConferenceCall 2012 05 08

= OpenOntologyRepository: Architecture & API Workshop-XII - Tue 2012_05_08 =

Topic: "OOR Architecture & API Workshop-XII: To tab or not to tab"

Session Co-chairs: Professor KenBaclawski & Dr. ToddSchneider

Conference Call Details:

 * Date: Tuesday, 8-May-2012
 * Start Time: 8:30am PDT / 11:30am EDT / 5:30pm CEST / 15:30 UTC
 * ref: World Clock
 * Expected Call Duration: ~1.5 hours


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Attendees:

 * Attended:
 * KenBaclawski (co-chair)
 * ToddSchneider (co-chair)
 * PeterYim
 * MichaelGruninger (need to leave after the first 30 min.)
 * MikeDean
 * MaximoGurmendez


 * Expecting:
 * ... if you are coming to the meeting, please add your name (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 (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 (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:
 * RayFergerson (written input provided ... see below)

Agenda Ideas:

 * Discussion
 * Tabbing: to tab or not to tab
 * understanding where the BioPortal folks come from, in terms of their "tab" architecture for adding/removing functionalities
 * related issues faced by OOR code contributors
 * the OOR team's take and disposition
 * stock items
 * the OOR Architecture
 * the OOR API
 * the Organizing Plan
 * moving from OOR sandbox to OOR production

Session Abstract & Resources:
The main subject for today's session is tabbing. We will be looking into the rationale of the BioPortal team's architectural decision to use "tabs" as the mechanism to add/remove functionality, and how code extensions "plugin" to their exisiting codebase. We will review issues that have been encountered, and attempt to make a disposition on how we shall approach this.

BioPortal "tab" implementation details (provided by PaulAlexander) are at: http://palexander.posterous.com/extending-bioportals-rails-ui

At this "OOR Architecture & API" 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.

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

Here is the status of the strawman architecture: OpenOntologyRepository_Architecture/Candidate03

In addition, there is an API of the core services that was obtained from anearlier implementation 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-XII: To tab or not to tab - OOR/ConferenceCall_2012_05_08  (this session)
 * Architecture & API Specification Development Workshop-XI - OOR/ConferenceCall_2012_03_20
 * Architecture & API Specification Development Workshop-X - OOR/ConferenceCall_2012_01_31
 * Joint NCBO-OOR Session - "OOR Architecture & API Workshop-IX: BioPortal & OOR Synergies" - OOR/ConferenceCall_2011_11_29
 * Architecture & API Specification Development Workshop-VIII - OOR/ConferenceCall_2011_10_11
 * Architecture & API Specification Development Workshop-VII - OOR/ConferenceCall_2011_09_20
 * Kicking-off the Next Phase of OOR-NCBO Collaboration - OOR/ConferenceCall_2011_09_13
 * Architecture & API Specification Development Workshop-VI - OOR/ConferenceCall_2011_06_17
 * Architecture & API Specification Development Workshop-V - OOR/ConferenceCall_2011_05_20
 * 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:
Archives:


 * prepared slides from the co-chairs
 * Audio archive of the session ... [ 1:30:06 ; mp3 ; 10.31 MB ]
 * Chat transcript of the session

1. Meeting called to order:


 * KenBaclawski & ToddSchneider took the chair and welcome everyone


 * PeterYim volunteered to keep a record of the proceedings


 * review and adopt agenda

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


 * see above
 * introduction of new members (as required)
 * review of agenda

3. Key items for review and discussion today:

Protege. The designer of that system suggested it to me. :-) ... The idea is that this mechanism allows the maximum amount of flexibility to end users while providing the minimum amount of coupling to existing software. You can do whatever you want on a tab and it will not affect the rest of the system. You can even replace existing tabs with new ones that do similar things in different ways. It goes a long ways toward making your additions to the system independent of changes to the system that we make. Thus the "forking and merge problem" is almost entirely eliminated.
 * Tabbing: to tab or not to tab ... slides
 * understanding where the BioPortal folks come from ...
 * RayFergerson: Unfortunately I cannot make this meeting. I can provide the background here though for the reasoning about using tabs as a code modification mechanism. ... This idea is inspired by the widely used tab extension mechanism in
 * related issues faced by OOR code contributors
 * the OOR team's take and disposition

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


 * Review of action item(s) from the previous meeting(s)


 * Gatekeeping specifies the a set of minimal requirements that any ontology within the OOR has to meet. The latter are intended to enable the users of the OOR to find quickly ontologies that fit their needs; the criteria are not supposed to ensure the quality of the ontologies.
 * Each OOR instance declares what ontology languages it supports.
 * Every OOR instance MUST support RDFS.
 * This is required because the metadata is expressed in OMV.
 * OMV is written in OWL, but it may be sufficient to require only RDFS. This needs to be investigated.
 * Other ontology languages MAY be supported.
 * For each metadata attribute, it will be specified whether it is required or optional.
 * It MUST be specified whether the ontology is available (or to be available in the future).
 * The ontology language MUST be specified.
 * Other attributes will be handled offline by MichaelGruninger based on the OMV specification.
 * An ontology must satisfy other requirements depending on the ontology language.
 * Syntax checking is always required.
 * Consistency checking is required with some time limit.


 * Proposal for Partition of Components
 * Presentation
 * A minimal presentation module with just search and workflow
 * Browse (already in BioPortal-based sandbox)
 * Search (already in BioPortal-based sandbox)
 * Mapping (already in BioPortal-based sandbox)
 * Recommender (already in BioPortal-based sandbox)
 * Annotator (already in BioPortal-based sandbox)
 * Resource Index (already in BioPortal-based sandbox)
 * Workflow Administration
 * OOR Instance Administration
 * Other windows
 * Workflow
 * Already developed, but needs to be documented
 * Registrar
 * A minimal registrar
 * Find
 * Initially adapt a SPARQL endpoint. Which one?
 * Inference
 * Initially a part of the SPARQL endpoint
 * Other inference engines
 * Persistence
 * Initially adapt 4Store
 * Administration
 * TBD
 * Federation
 * TBD

4. Consensus, Conclusions & Follow-up Actions:

5. Any Other Business:

6. Next Meeting & Adjourn:


 * Upcoming Meetings:
 * 2012_05_15 - no OOR meeting
 * 2012_05_10 & 2012_05_17 - (being staged) "Big Open Data" with NYC, Data.gov, SMW/PSMW & OOR - please mark your calendars and come!
 * 2012_05_22 - OOR-Dev-VIII - Tue 2012.05.22 - Chair: MikeDean
 * 2012_05_29 - OOR-Content-II - Tue 2012.05.29 - Co-chair: MichaelGruninger & MikeDean
 * 2012_06_05 - no OOR meeting, [[SemTech]] will be in session
 * 2012_06_12 - next Regular OOR Team meeting - first Tuesday of the month - OOR/ConferenceCall_2012_06_12


 * Call adjourned at: 10:07 am PDT

-- notes taken by: PeterYim / 2012.05.08-10:07am PDT All participants, please review and edit to enhance accuracy and granularity of the documented proceedings.

Resources

 * Homepage for the Open Ontology Repository Initiative - OpenOntologyRepository - http://OpenOntologyRepository.org or simply http://www.oor.net
 * 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
 * 2011_09_13 - Tuesday: Joint NCBO-OOR Team Meeting - "Kicking-off the Next Phase of Collaboration" - Co-chairs: RayFergerson & PeterYim - OOR/ConferenceCall_2011_09_13
 * 2011_11_29 - Tuesday: Joint NCBO-OOR Session - "OOR Architecture & API Workshop-IX: BioPortal & OOR Synergies" - Co-chairs: KenBaclawski & ToddSchneider - Discussant: RayFergerson - OOR/ConferenceCall_2011_11_29
 * 2012_03_27 - Tuesday: OOR presentation: "Ontohub: an OOR-compliant Repository for Distributed Ontologies" - Chair: TillMossakowski - OOR/ConferenceCall_2012_03_27
 * 2012_03_27 - Tuesday: OOR presentation: "Ontohub: an OOR-compliant Repository for Distributed Ontologies" - Chair: TillMossakowski - OOR/ConferenceCall_2012_03_27


 * 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_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_20 - Friday: OOR - "Architecture & API Specification Development Workshop-V" - Co-chairs: KenBaclawski & ToddSchneider - OOR/ConferenceCall_2011_05_20
 * 2011_06_17 - Friday: OOR - "Architecture & API Specification Development Workshop-VI" - Co-chairs: KenBaclawski & ToddSchneider - OOR/ConferenceCall_2011_06_17
 * 2011_09_20 - Tuesday: OOR - "Architecture & API Specification Development Workshop-VII" - Co-chairs: KenBaclawski & ToddSchneider - OOR/ConferenceCall_2011_09_20
 * 2011_10_11 - Tuesday: OOR - "Architecture & API Specification Development Workshop-VIII" - Co-chairs: KenBaclawski & ToddSchneider - OOR/ConferenceCall_2011_10_11
 * 2012_01_31 - Tuesday: OOR - "Architecture & API Workshop-X" - Co-chairs: ToddSchneider & KenBaclawski - OOR/ConferenceCall_2012_01_31
 * 2012_03_20 - Tuesday: OOR - "Architecture & API Workshop-XI" - Co-chairs: ToddSchneider & KenBaclawski - OOR/ConferenceCall_2012_03_20
 * 2012_05_08 - Tuesday: OOR - "Architecture & API Workshop-XII" - Co-chairs: ToddSchneider & KenBaclawski - OOR/ConferenceCall_2012_05_08
 * 2012_05_08 - Tuesday: OOR - "Architecture & API Workshop-XII" - Co-chairs: ToddSchneider & KenBaclawski - OOR/ConferenceCall_2012_05_08


 * 2011_11_08 - Tuesday: "Getting OOR Development Going - Take-V" Workshop - Chair: MikeDean - "Getting OOR Development going, on Eclipse?" - OOR/ConferenceCall_2011_11_08
 * 2011_11_22 - Tuesday: "Getting OOR Development Going - Take-VI" Workshop - Chair: MikeDean - OOR/ConferenceCall_2011_11_22
 * 2012_02_28 - Tuesday: "Getting OOR Development Going - Take-VII" Workshop - Chair: KenBaclawski - OOR/ConferenceCall_2012_02_28
 * 2012_02_28 - Tuesday: "Getting OOR Development Going - Take-VII" Workshop - Chair: KenBaclawski - OOR/ConferenceCall_2012_02_28


 * 2011_03_18 - Friday: OOR Metadata Workshop-I - Chair: MichaelGruninger - OOR/ConferenceCall_2011_03_18
 * 2011_05_13 - Friday: OOR Metadata Workshop-II - Chair: MichaelGruninger - OOR/ConferenceCall_2011_05_13
 * 2011_05_27 - Friday: OOR Metadata Workshop-III - Chair: MichaelGruninger - OOR/ConferenceCall_2011_05_27
 * 2011_10_18 - Tuesday: OOR Metadata Workshop-IV - Chair: MichaelGruninger - OOR/ConferenceCall_2011_10_18
 * 2012_01_17 - Tuesday: OOR Metadata Workshop-V - Chair: MichaelGruninger - OOR/ConferenceCall_2012_01_17
 * 2012_03_06 - Tuesday: OOR Metadata Workshop-VI - Chair: MichaelGruninger - OOR/ConferenceCall_2012_03_06
 * 2012_04_24 - Tuesday: OOR Metadata Workshop-VII - Chair: MichaelGruninger - OOR/ConferenceCall_2012_04_24
 * 2012_04_24 - Tuesday: OOR Metadata Workshop-VII - Chair: MichaelGruninger - OOR/ConferenceCall_2012_04_24


 * 2011_12_13 - Tuesdayday: OOR Infrastructure Workshop - Chair: PeterYim - OOR/ConferenceCall_2011_12_13
 * 2011_12_13 - Tuesdayday: OOR Infrastructure Workshop - Chair: PeterYim - OOR/ConferenceCall_2011_12_13


 * 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 IAOA-OOR-Ontolog "Ontologies and Standards" mini-series:
 * 2011_10_20 - Thursday: Joint IAOA-OOR-Ontolog "Ontologies and Standards" mini-series session-1: Introducing the ISO NP 17347 "Ontology Integration and Interoperability (OntoIOp)" Standardization Effort - Co-chairs: JohnBateman & MichaelGruninger - ConferenceCall_2011_10_20
 * 2011_11_03 - Thursday: Joint IAOA-OOR-Ontolog "Ontologies and Standards" mini-series session-2: Invited Speaker: ElisaKendall on "Ontology-Related Metadata Standards" - Co-chairs: MichaelGruninger & JohnBateman - ConferenceCall_2011_11_03


 * 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 instances of OOR - http://oor.net
 * OOR_SandBox - http://oor-03.cim3.net - http://sandbox.oor.net/
 * see also: OOR_SandBox_Customization
 * OOR_DevBox - http://oor-05.cim3.net - http://dev.oor.net/
 * a first OOR Test instance - http://oor-06.cim3.net - http://test-00.oor.net/
 * SOCoP_OOR - http://oor-04.cim3.net - http://socop.oor.net/ontologies
 * COLORE_OOR - http://colore.oor.net
 * ORNL-DAAC - http://ornl-daac.oor.net
 * MMI-ORR - http://mmisw.oor.net
 * NCBO - BioPortal
 * BioPortal's [bioontology-support] mailing list - see: https://mailman.stanford.edu/mailman/listinfo/bioontology-support
 * NCBO-OOR development documentation - http://www.bioontology.org/wiki/index.php/NCBO-OOR_Development