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OpenOntologyRepository: OOR Infrastructure Workshop - Tue 2011_12_13

Topic: OOR Infrastructure Workshop: "Finalizing the OOR_SandBox upgrade (Dec-2011)"

Session chair: PeterYim

Conference Call Details

  • Date: Tuesday, 13-Dec-2011
  • Start Time: 8:30am PST / 11:30am EST / 5:30pm CET / 16:30 UTC
  • Expected Call Duration: 1.5~2.0 hours
  • Dial-in:
    • Phone (US): +1 (206) 402-0100 (long distance cost will apply)
    • Skype: joinconference
    • when prompted enter PIN: 141184#
  • 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.

Agenda Ideas

  • upgraded OOR_SandBox installation status update
  • technical issues review/discussion
  • customization issues review/discussion
  • planning additional instances of OOR
  • content planning and possible issues review/discussion
  • code contribution planning and possible issues review/discussion
  • Getting us to a stage when we can run a OOR-production box

Attendees

  • Expecting:
    • (please add yourself to the above list if you are a member of OOR community, or, rsvp to <peter.yim@cim3.com>)
  • Regrets:
    • ...

Agenda & Proceedings

Archives:

1. Meeting called to order:

2. Roll Call:

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

3. Key items for review and discussion today

  • upgraded OOR_SandBox installation status update
    • see installation & customization details at: OOR_SandBox_Customization
      • ALL involved: please help maintain this page
    • customised instance now running on ncbo-appliance-xen-0.4 image is now at: http://oor-03.cim3.net
    • MikeDean's has uploaded a couple of ontologies ... things seem to work well
  • technical issues review/discussion
    • still need to resolve "console access" issue befoe moving oor-03 instance to datacenter
    • Mike Dean noted an error when creating a new account (although it did not seem to affect that process.)

... (KenBaclawski and Todd Schneider too, but possibly for different issues.)

  • customization issues review/discussion
    • color - shall we customize (now color changed - no more gradient; need revised logo images) [KenBaclawski to contact AliHashemi]
    • "twitter", "facebook" icons and presence?
    • examples (shadowed labels) in search box, etc. -- customize [KenBaclawski]
    • "categories" - reviewed, slightly updated. [MikeDean will put in place onto "oor-03"]
  • planning additional instances of OOR
    • after oor-03, CIM3 is planning to bring up two more instances (one for dev baseline, and one for socop) ... the devbox will be hosted from the cim3-sm1 location (where Peter has more ready access), and the other two instances will be hosted at the cim3-fmt1 (datacenter) facility
  • content planning and possible issues review/discussion
    • customized "categorization" and more testing need to be in place before we make content drive ... we'll do the latter after we return in Jan-2012
  • code contribution planning and possible issues review/discussion ... (discussion deferred)
  • Getting us to a stage when we can run a OOR-production box ... (discussion deferred)
  • In-session IM chat-transcript:

Peter P. Yim: Welcome to the ...

OOR Infrastructure Workshop - Tue 2011_12_06

Topic: OOR Infrastructure Workshop: "Finalizing the OOR_SandBox upgrade (Dec-2011)"

Session chair: Peter P. Yim

Proceedings:

Todd Schneider: Is the OOR-sandbox URL still the same?

Peter P. Yim: see: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR_SandBox_Customization#nid30R7

Peter P. Yim: [action] Peter to point oor.net - OOR Homepage

Mike Dean: suggest using cname on DNS to redirect

Mike Dean: at the top of the OOR homepage - let's list the various instances of OOR for quick access

Peter P. Yim: see: http://oor-03.cim3.net/

Ken Baclawski: [action] I will look at the i18n customization to see if it supports specifying

a background color.

Ken Baclawski: I will ask Ali to select a suitable background color and texture for the logo.

Mike Dean: [ACTION] (Mike): update categories on new instance

Peter P. Yim: reviewed and updated category list at: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR_SandBox_Customization#nid30RG

Ken Baclawski: [action] Look for non-biomedical terminology and replace example terms with

dublin core or FOAF (social networking) terms.

Peter P. Yim: after oor-03, CIM3 is planning to bring up two more instances (one for dev baseline,

and one for socop)

Peter P. Yim: Peter will keep the devbox at the cim3-sm1 location

Peter P. Yim: the other two instances will be hosted at the cim3-fmt1 facility

Mike Dean: When I created my account (mdean) and clicked Create, I got an error but the account

was created. I recall this happening last time as well. It would be great if others could

also create accounts and report their experiences.

Ken Baclawski: When I try to create a new account I get an internal error. I will check with

Tejas about this.

Peter P. Yim: customized "categorization" and more testing need to be in place before we make content drive

Peter P. Yim: [action] customized "categorization" and more testing in December

Peter P. Yim: when we come back in January, we will start the content drive - starting

from out 2012_01_03 OOR team meeting (first meeting in the year)

Peter P. Yim: Mike Dean and Michael Grüninger both unavailable on Jan-3

Peter P. Yim: [decision] no meeting 2012.01.03 ... first OOR team Meeting of the year 2012.01.10

... Metadata workshop 2012.01.17

Peter P. Yim: all Tuesdays, same time

Peter P. Yim: -- session ended: 9:21am PST --

4. pertinent discussions (below) from previous meetings ... (some material may already be outdated; so, for reference only!)

  • OOR-sandbox, devbox and socop-box status update ... below
    • Peter reported status of the OOR-sandbox install issues, which should be close to being resolved

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

  • 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
  • OOR-sandbox and OOR-devbox status update
  • assessing a strengthened OOR-NCBO collaborative relationship
  • OOR-sandbox and OOR-devbox status update
  • Status and action review: OOR-dev box - http://oor-03.cim3.net
  • Status and action review: SOCoP presentation box - http://socop.oor.net (at BBN?)
  • 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)
  • 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
    • Defense
    • 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) ...
  • code development on an Eclipse IDE for all?
  • Code repository - considering "git" or github?
  • Getting us to a stage when we can run a OOR-production box ... what's still needed, ETA?
    • ...
  • Action planning for "soliciting" content (getting people to upload ontologies)

5. Any Other Business:

  • Michael Grüninger: we will devote the entire next metadata workshop session to the ORWG presentations and discussions ... will re-schedule the financial metadata session with Mike Bennett for a different date.
  • [decision] no meeting 2012.01.03 ... first OOR team Meeting of the year 2012.01.10 ... Metadata workshop 2012.01.17

6. Action items:

7. Schedule Next Meeting & Adjourn:

  • in the mean time, HAPPY HOLIDAYS, Everyone!
  • Call adjourned at: 9:21 am PST

--

notes taken by: Peter P. Yim / 2011.12.13-9:39am PST

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

Resources

  • 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
    • 2011_12_15 - Thursday: Joint IAOA-OOR-Ontolog "Ontologies and Standards" mini-series session-3: "ISO/IEC 24707 Common Logic and IKL" - Co-chairs: Michael Grüninger & John Bateman - ConferenceCall_2011_12_15



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