Ontolog Forum

OpenOntologyRepository: OOR Team Conference Call - Fri 2009-07-10

OpenOntologyRepository team conference call, Fri 2009.07.10, 1.0~1.5 Hr. call starting 12:00pm EDT / 9:00am PDT / 6:00pm CET / 5:00pm GMT / 17:00 UTC

Conference Call Details

  • Date: Friday, July 10, 2009
  • Start Time: 12:00pm EDT / 9:00am PDT / 6:00pm CEST / 5:00pm BST / 16:00 UTC
  • 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 / 0848-414-110
      • UK 0870-738-0765
    • callers from other countries please dial into either one of the US or European numbers
  • 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 above (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

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

  • progress review on planned OOR-related events
  • reports on member activities that are OOR-related
  • ...

Agenda & Proceedings

1. Meeting called to order:

  • review and adopt agenda

2. Roll Call:

3. Status Review and Discussion:

  • Urgent issues:
    • none

Suggested topics to be covered:

  • progress review on planned OOR-related events
    • panel session organization activities updates Jul-16, Jul-30 & Aug-6
  • reports on member activities that are OOR-related
  • Overview on UML diagrams of BioPortal systems
    • see:
    • Todd: UML diagrams generated by "Enterprise Architect" ... will be posting the full set ...
    • Misha: the diagrams are complete; slightly difficult to read now -- some parts not 'relevant' to BioPortal could be removed to make it more readable; with the new update, a lot of changes coming in anyway as an ontology is being used
      • Misha will help provide a list of the 'relevant' subset of classes
    • Benjamin: MDA?
      • ... Todd: probably stick with UML now, and eventually move to CL?
    • Peter / Todd: will add revision level onto the diagrams in the future ... the ones from before, we'll add a date for identification purposes
    • Peter: Misha Dorf suggested a full UML diagram and a highlight diagram ... guess Todd is working on them (haven't heard from him yet)
    • Todd/2009.07.10 - full set of UML diagrams (on BioPortal 2.0) uploaded to the server (as of 2009.06.14)
    • ALL: vote of thanks to Todd
    • Todd: (ref. Misha's suggestion of doinga "highlighted" version with some of the packages removed) think it is better use of time to do another set of diagrams oo the recently updated version of BioPortal (v2.1d) instead
      • Peter: suggest that Todd might ping Misha via the [oor-dev] list to get his advice on when best to grab the new codes for reverse engineering
      • Misha already responded - see:
      • Todd: just downloaded the new BioPortal v2.1d released codes (1016) - will have the UML diagrams by the next call
  • Potential for collaboration with the geospatial ontology folks - Nancy Wiegand / GaryBergCross
    • Nancy: intro; SOCoP - submitting a grant proposal to NSF again; possibility of using OOR for their work
    • Gary: intro - SOCoP secretary; use of ontology repository for interoperability, social aspect of sharing;
    • Mike: welcome the collaboration; probably some additional features needed to support geospatial ontologies
      • Nancy: how much development is expected?
    • K: how much data will be involved .. using
      • Gary: possibly using some USGS data (K: which is already linked to
    • Nancy: supporting data store ... or just ontologies
    • Todd: OOR not supposed to provide data store ... but can consider a extension project to work on
    • Nancy: is the infrastructure stable ... and expected to be around for many years?
      • Mike: the intent is "Yes!"
    • Gary: Nancy is the PI; proposal due in July;
    • K: National Geospatial Symposium ...
    • Ken: already has a grant ... can share some of the language used ... Nancy will contact Ken
      • Ken: will work with Nancy on this offline
    • Ken/2009.07.10 update - I am working with Nancy to supply her some of the language for her proposal
    • Peter: Ontolog has provided Nancy and Gary a "Letter of Collaboration" to NSF - see: the Letter
    • Mike/2009.07.10 - will do "Support Letter" to NSF (for this proposal) on behalf of OOR too (--done! MikeDean/2009.07.20) - see: the Letter
    • Ken: coming from the experience as a review panelist, these letters can help (as well as hurt) a proposal
  • Progress review on planned OOR-related events:
  • Joint OOR-Ontolog Panel sessions ... on deck:
    • panel session on Protege / webProtege / BioPortal / CODS / OOR-sandbox ... and how they work together, now and in the near future ... this is more a OOR user and content providers' session (this would go right before Natasha's's OOR implementers and developers' session) - chair: Mark Musen - date confirmed Thu 16-July-2009
      • panelists will mainly be from Stanford / NCBO
    • panel session on "BioPortal-based ontology repository implementation and development" - chair: Natasha Noy - date confirmed Thu 30-July-2009
    • panel session on "OOR Research Issues" - champion: Ken Baclawski - the date needs to be rescheduled
      • candidate panelists: Michael, Leo->SuzetteStowtenburg, Natasha Noy, Elisa Kendall, Chris Welty, OOR team members from the EU, (and possibly other who were engaged when the OOR initiative first started (ref.).
      • Ken will send out a doodle scheduler on this soon!
    • Ken/2009.07.10 update - session now scheduled for Thu 2009.08.06 - see: ConferenceCall_2009_08_06
    • Peter: noting the huge overlap of panelists (and possibly topics) between the 7/30 & 8/06 sessions ... suggest we try to leverage that to our advantage
      • Ken: I will be looking more for discussions, rather than presentation
        • also, looking for longer term issue rather than more immediate issues
      • Ken, Natasha, Mike and Peter will try to coordinate offline in the organizational effort
  • OOR-related project and activities status updates:
  • Natasha: "Workshop on Collaborative Construction, Management and Linking of Structured Knowledge" proposal for ISWC2009 - proposal went in 2009.05.01
  • OOR sandbox instance - status review -
    • Benjamin: major update - BioPortal v2.1d - to be released on 12-Jun-2009
      • Natasha/2009.06.12 - slightly delayed, release date could now be a couple of week out
    • Peter: hardware for OOR sandbox-2 (and later the production instance of OOR) will be ready fairly soon (next few days).
      • an updated version of the CODS server will also be installed on that hardware cluster
    • Peter/2009.07.10 - hardware is now ready ... once the Stanford / NCBO are back from their International Conference (this week) in Amsterdam
  • OOR Outreach
  • ISWC 2009
    • candidates: A poster on OOR; also presentation as a "Lightning Talk"; BOF meeting
    • Todd, K & Ken will champion and coordinate this group of efforts
      • Ken/2009.7.10: work the poster is in progress
      • Mike: would be great if we could also do a demo ... Ken: we'll submit that (a demo) as part of the proposal.
      • Ken / Mike / Michael: we'll do something to demo Common Logic support too
  • K: I am involved in some of the Obama cyberinfrastructure/security initiatives, and am promoting the use of an OOR
    • Todd: you might consider participating in the NCOIC community too, K.
  • OOR development activities
    • Michael: running into issues with trying to add FOL/CL upload/download onto the BioPortal codebase
      • Michael: issues with inherent binary relationship limitation with the existing OWL implementation (based on Protege)
      • Natasha: BioPortal now supports two backends now - the Protege backend and the LexGrid (OBO/Mayo) backend
      • Pat Cassidy: translate? ... having a CL backend for Protege would be useful
    • Peter: please continue this conversation on the [oor-dev] list
    • K: possibly add another use case for CL
    • Peter/2009.07.10: would love to see Mike's team (or Mike to take the lead on a broader effort) would do a native FOL backend for the OOR
    • Ken/2009.07.10: we need internal interfaces ... modularization ... [Ken, please elaborate ...]
    • Todd/2009.07.10: need to re-emphasize that we should keep a focus on storing and retrieving "stuff" (so far, the focus has been too much on "ontologies") ... need separation of concerns
      • one issue is adaptability
    • Michael/2009.07.10 - we'll get some questions about working on a CL backend onto the [oor-dev] list, and look forward to the Jul-16 & Jul-30 sessions to get some clarification.
    • Bart: anyone interested to collaborate on "ontology mapping" work, especially in the context of the updated release (v2.1d) of OOR?
  • Other Progress updates and Discussions:
  • no discussion
  • Funding and proposals
    • Peter: suggest picking up the effort ... NSF solicitation like INTEROP (07-565) (due 2009.07.23), STCI (PD 06-7231) (due 2009.08.13)
      • Peter: (in the spirit of the encouraged pairwise collaboration) I'll be making proposals to the INTEROP and STCI programs with Mark Musen
      • Ken: I'll look into either INTEROP or STCI to see if we can do something
    • Ken will be in the DC Area Jul-13 for an NIH panel. Ken and K could meet up and do some coordination during that visit
    • Bart: what kind of help can we get (for proposals in Canada)
      • Ken: ping me off-line for some reference on previously submitted proposal
      • Mike: we can provide a "Letter of Collaboration"
  • short term activity and action plans
    • see above

4. New Issues:

5. Any Other Business:

6. Action items:

  • our short-term plan:
    • tasks
    • deliverables
    • Timeline / Milestones:

7. Schedule Next Meeting & Adjourn:

  • Next Meeting:
    • next meeting will be our joint OOR-Ontolog panel session on Thu 2009.07.16 10:30am PDT / 1:30pm EDT - see developing details on: ConferenceCall_2009_07_16
    • next regular team call Fri 2009.07.24 12:00pm ET / 9:00am PT / 16:00 GMT/UTC - see (closer to the time) session page at: OOR/ConferenceCall_2009_07_24
    • Note: earlier resolution: all team members please (if possible) block out Fridays 1.5 Hr starting 12:00pm ET / 9:00am PT / 16:00 GMT/UTC
  • Call adjourned at: 9:59am PDT


notes taken by: Peter P. Yim / 2009.07.10-10:15am PDT

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