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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 Ken Baclawski & Dr. ToddSchneider

Conference Call Details

  • Date: Tuesday, 8-May-2012
  • Start Time: 8:30am PDT / 11:30am EDT / 5:30pm CEST / 15:30 UTC
  • Expected Call Duration: ~1.5 hours
  • Dial-in:
    • Phone (US): +1 (206) 402-0100 (long distance cost may apply)
      • ... [ backup nbr: (415) 671-4335 ]
    • Skype: joinconference ... free-of-charge if you connect through skype from your computer/device with an Internet connection)
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    • Nominally, when a presentation is in progress, the moderator will mute everyone, except for the speaker.
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  • RSVP to appreciated, ... or simply just by adding yourself to the "Expected Attendee" list below (if you are a member of the team.)
  • 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.


  • 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. ...

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:

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.

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:

Agenda & Proceedings


1. Meeting called to order:

  • 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
  • introduction of new members (as required)
  • review of agenda

3. Key items for review and discussion today:

  • Tabbing: to tab or not to tab ... slides
    • understanding where the BioPortal folks come from ...
      • Ray Fergerson: 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

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.

    • 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 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

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,, SMW/PSMW & OOR - please mark your calendars and come!
    • 2012_05_22 - OOR-Dev-VIII - Tue 2012.05.22 - Chair: Mike Dean
    • 2012_05_29 - OOR-Content-II - Tue 2012.05.29 - Co-chair: Michael Grüninger & Mike Dean
    • 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: Peter P. Yim / 2012.05.08-10:07am PDT

All participants, please review and edit to enhance accuracy and granularity of the documented proceedings.


  • 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
  • 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: John Bateman & Michael Grüninger - ConferenceCall_2011_10_20
    • 2011_11_03 - Thursday: Joint IAOA-OOR-Ontolog "Ontologies and Standards" mini-series session-2: Invited Speaker: Elisa Kendall on "Ontology-Related Metadata Standards" - Co-chairs: Michael Grüninger & John Bateman - ConferenceCall_2011_11_03