OOR/ConferenceCall 2011 09 20

OpenOntologyRepository: Architecture & API Workshop-VIII - Tue 2011_10_11

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

Session Co-chairs: Ken Baclawski & Todd Schneider

Conference Call Details

• Date: Tuesday, 11-Oct-2011
• Start Time: 8:30am PDT / 11:30am EDT / 5:30pm CEST / 4:30pm BST / 15:30 UTC
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Attendees

• Attended:
  • Ken Baclawski (co-chair)
  • Todd Schneider (co-chair)
  • Peter P. Yim

• 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. ...

• Regrets:
  • Mike Dean
  • Terry Longstreth
  • Tim Darr

Agenda Ideas

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

• Discussion on possible adjustments in the OOR architecture and work plans in view of what transpired from last week's Joint NCBO-OOR Team Meeting - ref. OOR/ConferenceCall_2011_09_13

• 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

Abstract

As a result of the two OOR Architecture and API panel sessions back in Oct & Nov-2010, we have been exposed to a large number of architecture and API candidates 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.

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.

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

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-VIII - OOR/ConferenceCall_2011_10_11 (this session)
• 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: 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

Archives:

1. Meeting called to order:

• Ken Baclawski & Todd Schneider took the chair and welcome everyone

• Peter P. Yim volunteered to keep a record of the proceedings

• review and adopt agenda

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

• see above

• ref. proceedings of "Architecture & API Specification Development Workshop-VII" - OOR/ConferenceCall_2011_09_20

• review of agenda

3. Key items for review and discussion today:

• Announcements and Urgent Matters:

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

• Discussion on possible adjustments in the OOR architecture and work plans in view of what transpired from last week's Joint NCBO-OOR Team Meeting - ref. OOR/ConferenceCall_2011_09_13
  • defer the discussion to our next meeting when we will try to invite Ray Fergerson to join us
• Review of action item(s) from the previous meeting(s)
• from 2011.06.17 - Michael Grüninger will examine the OMV to determine which attributes are required and which are optional.
• from 2011.06.17 - Ken Baclawski will send KEEPER (the gatekeeping software) to Todd Schneider who will generate the UML.

• "OOR Architecture & API Specification Development Workshop-VIII:" (Archives)

• 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 Michael Grüninger 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

• chat transcript of this session:

--- Chat transcript begin: ---

Welcome to the OpenOntologyRepository: Architecture & API Workshop-VIII - Tue 2011_10_11

Session co-Chairs: Ken Baclawski & Todd Schneider

see session page at: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_10_11

Proceedings:

Todd Schneider: Here's where we are at, in terms of consensus arrived at from the

previous "OOR Architecture and API" workshops:

0) The interface for searching ontology metadata will consist of a single method

0.a) The method will have a single parameter consisting of a SPARQL query.

0.b) The return value of the method will be a SPARQL result set.

0.c) Metadata will be represented using a named RDF graph.

0.d) Metadata will be based on an extension of OMV.

o The OMV extension may include a notion of domain specification or

topics, represented as text.

0.e) Metadata will be federated, so it is a single named RDF graph, no matter

how many OOR instances there are. pics, represented as text.

0.f) Metadata will be federated, so it is a single named RDF graph, no matter

how many OOR instances there are.

1) Each OOR instance must declare the representation language module it supports.

2) Every OOR shall support RDFS

3) Quality and Gatekeeping. We distinguish between gatekeeping and quality control.

Definition: 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 do not ensure the quality of the ontologies.

3.a) Gatekeeping will vet the metadata associated with an ontology to ensure

entrance criteria are met.

3.b) For each metadata attribute, it will be specified whether it is required

or optional.

3.b.i) It MUST be specified whether the ontology is available (or to be

available in the future).

3.b.ii) The ontology language MUST be specified.

3.b.iii) Other attributes will be handled offline by Michael Gruninger

based on the OMV specification.

3.c) An ontology must satisfy other requirements depending on the ontology

language.

3.d) Syntax checking is always required and the responsibility of the language

module

3.e) Consistency checking is required with some time limit.

3.f) Gatekeeping criteria will include an attribute to indicate whether the

ontology exists or the metadata represents an advertisement.

3.g) The location of the actual ontology is the responsibility of Administration.

3.h) Metadata needs to include an attribute for the 'availability' of the ontology

3.i) 'Location' of the ontology must be provided.

3.j) The representation language of the ontology is a required attribute.

3.k) Michael will provide a preliminary list of required metadata attributes.

3.l) Submission process will be asynchronous

Peter P. Yim: moving us forward ...

Peter P. Yim: now that we have the partitioning (architecturally), we need to adopt a

development platform (say, something like "eclipse"), and start having

team members claim ownership to developing specific modules

Ken Baclawski: Look at http://www.eclipse.org/stp/

Todd Schneider: http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository_Architecture/Candidate03

Peter P. Yim: also (important), please refer to the BioPortal "tab" implementation details

- see: http://palexander.posterous.com/extending-bioportals-rails-ui

Todd Schneider: The 'administration' module is responsible for advertising which

representation languages an instance supports.

Peter P. Yim: All: we might want to partition some of the work to sizes that fit,

say, work by a student in 3-months (which might mean work that takes

an experienced developer a couple of weekends or a month to do)

Todd Schneider: The next Architecture meeting will focus on development platform and work partitioning

Todd Schneider: The next meeting will be on Tue 1 November 2011, same time

Todd Schneider: Homework: learn more about the Eclipse and its capabilities;

Read Paul Alexander's page on tabs

- http://palexander.posterous.com/extending-bioportals-rails-ui

Peter P. Yim: we'll make that (choice of platform and work partitioning) as the main focus of

our next team meeting (Tue 2011.11.01)

Todd Schneider: We need to motivate contributors to provide 'comic' book level descriptions

of their work

Peter P. Yim: -- session ended 9:38am --

--- Chat transcript end: ---

Consensus, Conclusions & Follow-up Actions:

4. Any Other Business:

5. Action items:

6. Schedule Next Meeting & Adjourn:

• Next Meeting:
  • "OOR Metadata Workshop" - Tue 2011.10.18 same time (that's next Tuesday)
  • after that, there will be an joint "Ontology and Standards" session on Thu 2011.10.20 (watch for announcements)
  • no meeting during the week of Oct-24 (as ISWC-2011 will be in session)
  • then we'll be having the next OOR team meeting, same time on Tue 2011.11.01
    • where we will cover the [ items discussed today] .. and, do make sure you have time to look over what's listed as [ homework] too, before the meeting, if possible!

• Call adjourned at: 9:38 am PDT

--

notes taken by: Peter P. Yim / 2011.10.11-10:10am 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: Leo Obrst & Frank Olken; Panelists: Bruce Bargmeyer, Mike Dean, Mark Musen, Farrukh Najmi & Peter P. Yim - ConferenceCall_2008_02_28
  • 2008_03_27 - Thursday: Joint OOR-OntologySummit2008 Panel Discussion: "An Open Ontology Repository: Rationale, Expectations & Requirements - Session-1" - Chair: Leo Obrst & Fabian Neuhaus; Panelists: William Bug, Evan Wallace, JohnLMcCarthy, Ken Baclawski, Peter Benson & Rex Brooks - ConferenceCall_2008_03_27
  • 2008_04_03 - Thursday: Joint OOR-OntologySummit2008 Panel Discussion: "An Open Ontology Repository: Rationale, Expectations & Requirements - Session-2" - Chair: Leo Obrst & Fabian Neuhaus; Panelists: Doug Lenat, Deke Smith, Marcia Zeng, Denise Bedford, Pat Hayes, Mala Mehrotra & Rob Raskin - ConferenceCall_2008_04_03
  • 2008_04_10 - Thursday: Joint OOR-OntologySummit2008 Panel Discussion: "Developing an Ontology of Ontologies for OOR" - Co-chairs: Barry Smith & Michael Grüninger; Panelists: Michael Grüninger, Peter Haase, Natasha Noy & Elisa Kendall - 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: Leo Obrst; Panelists: Mike Dean, Mark Musen, Li Ding, Bruce Bargmeyer & Bill Andersen - 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: Todd Schneider; Panelists: Mark Musen, Natasha Noy, Mike Dean, Paul Buitelaar / Andreas Harth, Mathieu Daquin, Ken Baclawski, Michael Grüninger - 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: Mark Musen - Panelists: Tania Tudorache, Tim Redmond, Natasha Noy - ConferenceCall_2009_07_16
  • 2009_07_30 - Thursday: Joint Ontolog-OOR Panel Discussion: "BioPortal and related Ontology Repository Implementations and Development" (Take-3) - Chair: Natasha Noy - Panelists: Carlos Rueda, Paul Alexander, John Graybeal, Mike Dean, StephenGranite, AlexGarcia, Ken Baclawski - ConferenceCall_2009_07_30
  • 2010_02_19 - Friday: OOR Panel Discussion: "Coordinating our Open Ontology Repository Software Development" - Chair: Mike Dean - Panelists: Jim Chatigny, Michael Grüninger, Ken Baclawski, Natasha Noy - OOR/ConferenceCall_2010_02_19
  • 2010_04_01 - Thursday: Joint OOR-Ontolog Panel Session: "OOR Use Cases - Take-3" - Chair: Ken Baclawski & Todd Schneider - Panelists: Todd Schneider, Matthew Hettinger, Ken Baclawski and Máximo Gurméndez - ConferenceCall_2010_04_01
  • 2010_09_10 - Friday: Joint SIO-OOR-Ontolog Panel Discussion: "Common Logic (CL) Support for OOR" - Chair: John F. Sowa - Panelists: JohnBateman-TillMossakowski, Michael Grüninger, Cameron Ross, Adam Pease, Pat Hayes - ConferenceCall_2010_09_10
  • 2010_09_17 - Friday: OOR Panel Discussion - "Getting OOR Development Going - Take-IV" Workshop - Co-chairs: Todd Schneider & Michael Grüninger - Panelists: Todd Schneider, Mike Dean, Natasha Noy, Immanuel Normann, Ken Baclawski, Michael Grüninger - 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: Ken Baclawski & Michael Grüninger - Panelists: KenBaclawski+ToddSchneider, AldoGangemi+AlessandroAdamou, JouniTuominen+KimViljanen, Eric Chan - OOR/ConferenceCall_2010_11_19
  • 2011_03_04 - Friday: OOR "Architecture & API Specification Development Workshop-I" - Co-chairs: Ken Baclawski & Todd Schneider - OOR/ConferenceCall_2011_03_04
  • 2011_03_11 - Friday: OOR - "Architecture & API Specification Development Workshop-II" - Co-chairs: Ken Baclawski & Todd Schneider - OOR/ConferenceCall_2011_03_11
  • 2011_03_18 - Friday: OOR Metadata Workshop-I - Chair: Michael Grüninger - OOR/ConferenceCall_2011_03_18
  • 2011_03_25 - Friday: OOR - "Architecture & API Specification Development Workshop-III" - Co-chairs: Ken Baclawski & Todd Schneider - OOR/ConferenceCall_2011_03_25
  • 2011_04_22 - Friday: OOR - "Architecture & API Specification Development Workshop-IV" - Co-chairs: Ken Baclawski & Todd Schneider - OOR/ConferenceCall_2011_04_22
  • 2011_05_13 - Friday: OOR Metadata Workshop-II - Chair: Michael Grüninger - OOR/ConferenceCall_2011_05_13
  • 2011_05_20 - Friday: OOR - "Architecture & API Specification Development Workshop-V" - Co-chairs: Ken Baclawski & Todd Schneider - OOR/ConferenceCall_2011_05_20
  • 2011_05_27 - Friday: OOR Metadata Workshop-III - Chair: Michael Grüninger - OOR/ConferenceCall_2011_05_27
  • 2011_06_17 - Friday: OOR - "Architecture & API Specification Development Workshop-VI" - Co-chairs: Ken Baclawski & Todd Schneider - OOR/ConferenceCall_2011_06_17
  • 2011_09_13 - Tuesday: Joint NCBO-OOR Team Meeting - "Kicking-off the Next Phase of Collaboration" - Co-chairs: Ray Fergerson & Peter P. Yim - OOR/ConferenceCall_2011_09_13
  • 2011_09_20 - Tuesday: OOR - "Architecture & API Specification Development Workshop-VII" - Chair: Ken Baclawski - OOR/ConferenceCall_2011_09_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: George Strawn - Chair: Peter P. Yim - Panelists: JamieClark, John Wilbanks, Bruce Perens - 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: Mark Musen - Panelists: Cameron Ross, Alan Rector, John F. Sowa, Bruce Perens, John Wilbanks, Peter P. Yim - 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: Leo Obrst - Panelists: Peter P. Yim, Mike Dean, Bruce Perens, JamieClark - ConferenceCall_2010_09_30
• OntologySummit2008 homepage
  • OntologySummit2008_Communique
  • OntologySummit2008/FaceToFaceAgenda & Proceedings
  • The OOR Project Presentation (delivered at the Ontology Summit 2008 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-02.cim3.net/ontologies)
  • OOR_SandBox
• Development instance of OOR (OOR-dev) - http://oor-01.cim3.net/ - to browse: http://oor-01.cim3.net/ontologies - http://dev.oor.net/
  • OOR_DevBox
  • 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