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OpenOntologyRepository: OOR Team Conference Call - Tue 2011_09_06

This is a regular OOR Team meeting. Do pay special attention to the time of the call, as this is the first session on the newly adopted meeting slot (where we moved the Fridays starting 6:00am PDT / 9:00am EDT / 3:00pm CEST to Tuesdays starting at 8:30am PDT / 11:30am EDT / 5:30pm CEST.)

... please refer to proceedings from the last team meeting at OOR/ConferenceCall_2011_08_05

Conference Call Details

  • Date: Tuesday, 6-Sep-2011
  • Start Time: 8:30am PDT / 11:30am EDT / 5:30pm CEST / 4:30pm BST / 15:30 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
      • UK 0844-581-9148
    • callers from other countries please dial into either one of the US or European numbers
  • RSVP to peter.yim@cim3.com 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.

Attendees

  • 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. ...

Agenda Ideas

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

Agenda & Proceedings

Archives:

1. Meeting called to order:

  • Mike Dean takes the chair and welcome everyone
  • review and adopt agenda
  • Peter P. Yim volunteered to take notes

2. Roll Call:

  • welcome and intro of new member(s) (as needed)

3. Status Review and Discussion:

4. Key items for review and discussion today

Mike Dean: Issues/questions for next week's joint meeting

Terry Longstreth: I will plan to attend next Tuesday

Mike Bennett: I probably won't make it a I sometimes have a conflict at this time now.

Mike Bennett: Modularity of ontologies - any requirements / constraints on this?

Terry Longstreth: Old business I know but: status/influence of Metadata repository standard (ISO 19763)

and New work item 17347?

Peter P. Yim: @Terry - Michael Grüninger and John Bateman is working rolling out a joint

IAOA-OOR-Ontolog mini-series on "Ontology Standards" - a session on ISO 19763 is

one of the first ones they'll be featuring. As for ISO 17347, that is very new

(just got adopted as a NWI (new work item)during the ISO meeting in Seoul, Korea

this June - see: http://ontolog.cim3.net/cgi-bin/wiki.pl?OntoIOp - I will email

you SueEllenWright's contact, she is the ISO/TC37/SC3 chair, where this work is

going to take place.

Mike Dean: Like Mike Bennett, support for ontologies consisting of multiple modules/files

(e.g. NASA SWEET has 200 modules)

Mike Dean: How best to support a larger category hierarchy, user-defined categories, etc.

Mike Bennett: Standardized use of element-level metadata i.e. the emerging consensus on what terms to

use from DC, SKOS and so on; when and whether to add additional element metadata

Mike Bennett: Consensus on how precisely to use OWL Annotation Properties for additional

element-level metadata (provenance, labeling, additional logical information etc,)

Mike Dean: Plans for federation

Ken Baclawski: Naming is always a big problem for federated systems. BioPortal assigns database

identifiers which is fine for a centralized repository but does not work well for

a federated system. We need a more flexible mechanism for assigning names/identifiers.

Ken Baclawski: Distributed reasoning capability: reasoning with a combination of ontologies that

are not all stored at the same site.

Peter P. Yim: now that we are "branching" instead of "forking" ... since Natasha Noy told us that NCBO

was thinking of moving their code repository to git (github, maybe?), we may want to

explore how we can best working off a shared repository to facilitate cross-contributions

in the future.

Peter P. Yim: how can we best handle support issues ... need support from the BioPortal team

- Ray Fergerson, Trish Whetzel, Paul Alexander, Natasha Noy, et al.

      • Peter: also (for later) should we explore running a shared eclipse development environment for the community?
  • planning and coordination on other upcoming OOR events ... (discussion postponed)

... Notes below are from previous meeting(s), and will be updated as this meeting progresses.

  • status update on the OOR Logo quest
    • Peter: I'm behind on getting the voting mechanism in place, will work on it within this coming week
    • will allow multiple votes from each voter, to be split between their choices
  • Review status: the upgraded OOR_SandBox - http://sandbox.oor.net/ontologies
    • for now certain behaviors seem strange - Ken and Mike will look into the issues
      • Ken: a lot of it is with the disabling of some hard coded portions (like the swf codes) now
    • "visualize" not working now ... Ken will try re-enabling access to U of Victoria (which serves the visualization)
  • updating "categories"
    • Peter: the ICOM people suggests adding the categories of "standards" and "collaboration" (the latter probably belongs under "Cultural"
    • Mike: something like Dublin Core should go under "metadata" - we are adding this category, "process" too
    • discussed - see updated "category" list at: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_08_05#nid2W6B
    • one can select multiple categories by doing a "ctrl-click" (or "cmd" for Mac users)
    • Ken: the software stores "categories" in an OMV ontology, and support a hierarchy of nested categories
      • Mike: there is a GUI interface for adding categories
    • All: we probably want to leave it simple (one level) and support "addition of categories" on demand
    • Todd: For some categories, e.g., science, subcategories will be needed. Since the provided listing is linear, subcategories could be listed as pairs or triples: Science, Science - Biology, Science-Physics, Science-Physics-Gravitation, etc.
    • Leo: we might consider adopting some standard categorization, like what the Library of Congress has put out (maybe not the entire hierarchy, but only the very upper level(s)
  • soliciting content (ask people to upload their ontologies again)
    • we will put out a note to [oor-forum] when we are ready ... i.e.
      • updated categories are up
      • we clearly know what we'll be doing ref. the dual-track approach (see discussion below)
  • Discussion: the newly adopted dual-track OOR approach
    • action planning
      • we run (for now) 2 instances - a sandbox instance[1] on the OOR-01 vm, and an experimental instance[2] on the OOR-02 vm
        • [1] this will be a straight forward, and updated BioPortal code install, with customization only for: the logo, the IP / License statement, categories.
        • [2] this will be the instance we use to continue the current work of further development in Architecture, API, metadata, CL support, etc.
        • consensus: both instances would use the same database (so ontologies uploaded are accessible by both instances, and are obviously "in sync" ... saving us the need to "import" as we ad discussed at the last meeting)
      • Peter: the next things to push is to have "gatekeeping" in place so we can stand up a "production" OOR
    • scheduling meeting with the NCBO team
      • candidate dates Sep-20 or 27 Tuesdays 8:30am PT ... Peter will ping Mark Musen et al.
  • OOR or joint OOR events planning, for the Fall and beyond
  • Revisiting regular meeting time (day-of-week, and starting-time)

(unless specifically addressed) items below are from the previous meeting(s) and will be updated as we proceed with this meeting.

  • Status and action review: upgrade to OOR-sandbox - http://oor-01.cim3.net or http://sandbox.oor.net
    • workplan (from previous calls):
      • update codebase to appropriate oor install code
        • customize banner/logo
        • customize IPR statement
        • re-establish categories - ref. MikeDean's input
        • other?
      • installation - ETA of updated OOR (v ? )
    • prepare vm image
      • vm image available for download - ETA
    • Tim Darr offer to help, some from his team of 8~10 people might get involved, most of the necessary skill sets in java programming, linux sysadmin, vmware, etc. are available
    • (from 2011.05.06) ref input from Paul Alexander, BioPortal is now delivered as an "appliance" - in a vm image
      • the NCBO folks uses the VMware platform for their virtual machine
      • we are currently using (at CIM3) Xen virtual machine for the OOR-sandbox
      • Mike Dean: there are utilities that help convert between VMware and Xen vm images
    • Anyhow, we need to install from the code - code from the semwebcentral oor code repository
    • it is suggested that a conf call between us and the Stanford folks (with, say, Tejas Parikh, Ken Baclawski, Mike Dean with Paul Alexander, AlexSkrenchuk, ...) be done ASAP so that we can learn from them they key changes in the recent versions and how the installation is different now [ Ken will arrange ]
  • Category list (based on MikeDean's list): (updated 2011.08.05)
    • Upper Ontologies
    • Standards (for example, Measurement)
    • Science (for example, Biomedical)
    • Financial
    • Government
    • Cultural (for example, Social Networking, People)
    • Geospatial
    • Commercial
    • Literature
    • Technology
    • Provenance
    • Defence
    • Metadata (for example, OMV, Dublin Core)
    • Process (for example, PSL)
    • Other
  • Getting us to a stage when members can contribute code ... how, ETA?
    • (discussion 2011.05.06):
      • an adopted Architecture & API is definitely crucial, but that's not all
    • All team members are encouraged to mull over how we can get to that state effectively
      • in particular ... how do we make this a "successful" community-driven, open source project!?
    • (discussion 2011.06.03) ...
  • getting the OOR code repository at semwebcentral started (for real!) - http://oor.semwebcentral.org/
    • OOR_SandBox - http://sandbox.oor.net/ontologies (previously http://oor-01.cim3.net/ontologies)
    • OOR code-repository and re-assessing the 'fork' (what does that mean?) [MikeDean, Ken Baclawski, et al.]
    • categories - ref. MikeDean's msg - http://ontolog.cim3.net/forum/oor-dev/2011-02/msg00012.html
    • 2011.02.18: *Important Note* - we will start afresh on the OOR sandbox content (i.e. uploaded ontologies) after the update install - everyone who has uploaded ontologies so far should note
      • those who are "using" the OOR sandbox content now, should note down the ontologies they need, and may need to contact the authors to upload them again if they don't show up. (presumably, those content relating to biomedicine, previously federated from BioPortal, will not be there any more, at least not automatically.) Also, links to ontologies or elements within ontologies established previously will no longer be valid after the content gets re-populated - Ken will make a post about this on [oor-forum]
    • workplan:
      • update codebase to appropriate oor install code
        • The consensus is that we should use a uniform language in each component to make it easier for people to contribute code and add extensions.
        • customize banner/logo
        • customize IPR statement
        • re-establish categories - ref. MikeDean's input
        • other?
      • installation - ETA of updated OOR (v ? )
    • prepare vm image
      • vm image available for download - ETA
    • Tim Darr offer to help, some from his team of 8~10 people might get involved, most of the necessary skill sets in java programming, linux sysadmin, vmware, etc. are available
  • Getting us to a stage when we can run a OOR-production box ... what's still needed, ETA?
    • (discussion 2011.06.03) ...
  • Soliciting content (getting people to upload ontologies)
  • staged events planning
    • Architecture & API - VII workshop - Fri 2011.07.29 ... afterwards?
    • Metadata - IV workshop - to be scheduled - date?
    • Joint IAOA-OOR-Ontolog "Ontology and Standards" mini-series
      • ISO 19763 with Elisa Kendall and Evan Wallace - to be scheduled [MichaelGruninger]
      • ISO NP 17347 "Ontology Integration and Interoperability (OntoIOp)" - to be scheduled [JohnBateman]
      • ... more
    • updates and plans on BioPortal; what does that mean for OOR - date? - [KenBaclawski]
    • OOR Metadata-IV workshop - ? - Chair: Michael Grüninger
    • Fact Guru incorporation & integration?
    • more on SIO ...?
  • new activities planning

4. Member activities updates:

  • Review: members and OOR-related activities
    • OOR-sandbox status
    • code repository status
    • NCBO
    • NEU
    • Raytheon-BBN
    • Bremen
    • UToronto
    • Ryerson
    • Mathet
    • SOCoP_INTEROP
    • DataONE
    • NeOn (KMi and STL)
    • ONKI

they'd like to see

    • KBSI
    • MMI
    • Use Cases
    • Architecture
    • API
    • Gatekeeping
    • production OOR instance
    • SIO
    • Funding
    • ICOM / DERI

5. Funding progress:

6. Any Other Business:

7. Action items:

8. Schedule Next Meeting & Adjourn:

  • Next Meeting:
    • do we break for the rest of August? ... seems like a lot of people are either on vacation or traveling (our friends from Europe, especially)
      • consensus: let's take a break for the rest of August
    • revisiting the regular meeting date/time - Fridays 6:00am PDT still good for everyone?
      • let's move our weekly meetings to Tuesdays 11:30am ET / 8:30am PT / 5:30pm CET ... Peter will send a message to [oor-forum] to see if there are huge
    • the next "Architecture & API - VII" workshop (championed by Ken Baclawski & ToddSchneider) is going to be Tue Sep-13
    • next regular OOR-team meeting will be (first Tue of Sep.) on Tue 2011.09.06 - 11:30am EDT / 8:30am PDT / 5:30pm CEST / 15:30 UTC - ref. worldclock (note: that Monday is Labor Day in the US)
    • Note: earlier resolution: all team members please (if possible) block out Fridays 1.5 Hr
    • ref. our doodle poll (see: http://doodle.com/a2snxkpkd8hhxek4 ), looks like we can settle in on two new meeting times - a 6:00am PT (14:00 UTC) and an 8:30am PT (16:30 UTC) (or something in between) ...
    • [decision/2011.04.01] we will have an OOR team admin-planning meeting first Friday of every month; and use the other Fridays for workshops to move work forward
  • Call adjourned at: 9:33 am PDT

--

notes taken by: Peter P. Yim / 2011.09.06-9:35am PDT

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

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