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OpenOntologyRepository: Architecture & API Workshop-XI - Tue 2012_03_20

Attention! ... Please note start-time of the meeting, timing these couple of weeks is fairly tricky (especially for non-US participants) - as North America has gone into daylight saving time, Europe hasn't, and a lot of Asian countries don't do daylight saving at all!

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

Session Co-chairs: Professor Ken Baclawski & Dr. ToddSchneider

Conference Call Details

  • Date: Tuesday, 20-Mar-2012
  • Start Time: 8:30am PDT / 11:30am EDT / 4:30pm CET / 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)
    • when prompted enter PIN: 141184#
  • Shared-screen support (VNC session), if applicable, will be started 5 minutes before the call at:
    • view-only password: "ontolog"
    • if you plan to be logging into this shared-screen option (which the speaker may be navigating), and you are not familiar with the process, please try to call in 5 minutes before the start of the session so that we can work out the connection logistics. Help on this will generally not be available once the presentation starts.
    • people behind corporate firewalls may have difficulty accessing this. If that is the case, please point your browser directly to the [ presentation(s)] (where applicable) and running them locally. The speaker(s) will prompt you to advance the slides during the talk.
  • In-session chat-room url:
    • instructions: once you got access to the page, click on the "settings" button, and identify yourself (by modifying the Name field from "anonymous" to your real name, like "JaneDoe").
    • You can indicate that you want to ask a question verbally by clicking on the "hand" button, and wait for the moderator to call on you; or, type and send your question into the chat window at the bottom of the screen.
    • thanks to the folks, one can now use a jabber/xmpp client (e.g. gtalk) to join this chatroom. Just add the room as a buddy - (in our case here) ... Handy for mobile devices!
  • Discussions and Q & A:
    • Nominally, when a presentation is in progress, the moderator will mute everyone, except for the speaker.
    • To un-mute, press "*7" ... To mute, press "*6" (please mute your phone, especially if you are in a noisy surrounding, or if you are introducing noise, echoes, etc. into the conference line.)
    • we will usually save all questions and discussions till after all presentations are through. You are encouraged to jot down questions onto the chat-area in the mean time (that way, they get documented; and you might even get some answers in the interim, through the chat.)
    • During the Q&A / discussion segment (when everyone is muted), If you want to speak or have questions or remarks to make, please raise your hand (virtually) by clicking on the "hand button" (lower right) on the chat session page. You may speak when acknowledged by the session moderator (again, press "*7" on your phone to un-mute). Test your voice and introduce yourself first before proceeding with your remarks, please. (Please remember to click on the "hand button" again (to lower your hand) and press "*6" on your phone to mute yourself after you are done speaking.)
  • 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. ...

Session Abstract & Resources

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 Ideas

  • Discussion
    • the OOR Architecture
    • the OOR API
    • the Organizing Plan
    • moving from OOR sandbox to OOR production

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:

  • Announcements and Urgent Matters:
    • ...

... 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)
  • "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

Consensus, Conclusions & Follow-up Actions:

  • Ken Baclawski: To deal with visualization of other ontology languages, there should be a visualization mapping mechanism (e.g., an automated way to extract the concepts and relationships from the ontology) that can use the existing visualization software or a visualization plugin capability that allows one to introduce an entirely new visualization.

4. Any Other Business:

5. Action items:

6. Schedule Next Meeting & Adjourn:

  • Next Meeting:
    • we will hear from the Bremen folks on their recent "Ontohub" development effort - [ Tue 2012.03.27 ]
    • next regular OOR team meeting next week - Tue 2012.04.03 same time - [ Tue 2012.04.03 ]
      • Mike Dean: I'll probably have to miss that meeting, as I will be traveling.
    • we'll plan other events at that meeting
  • Call adjourned at: 9:31 am PDT


notes taken by: Peter P. Yim / 2012.03.20-11:47am 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