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OpenOntologyRepository: "OOR-Ontohub-Gatekeeper API" Hackathon Session - IV - Tue 2013_09_10

Session Topic: OOR-Ontohub-Gatekeeper API Hackathon-IV - Alignment

Session Co-chairs: KenBaclawski & TillMossakowski

This is the 4th session in a series of regular activities for the OOR team. The plan is to devote one meeting a month to intense coding (or other low level development) work.

Conference Call Details

  • Date: Tuesday, 10-Sep-2013
  • Start Time: 7:00am PDT / 10:00am EDT / 4:00pm CEST / 3:00pm BST / 1400 UTC
  • Expected Call Duration: 1.5~2.0 hours
  • Dial-in:
    • Phone (US): +1 (206) 402-0100 ... (long distance cost may apply)
      • ... [ backup nbr: (415) 671-4335 ]
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      • when prompted enter Conference ID: 141184#
      • Unfamiliar with how to do this on Skype? ...
        • Add the contact "joinconference" to your skype contact list first. To participate in the teleconference, make a skype call to "joinconference", then open the dial pad (see platform-specific instructions below) and enter the Conference ID: 141184# when prompted.
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  • 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.)
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  • In-session chat-room url: http://webconf.soaphub.org/conf/room/oor_20130910
    • 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 soaphub.org 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) oor_20130910@soaphub.org ... Handy for mobile devices!
  • Shared-screen support (VNC session), if applicable, will be started 5 minutes before the call at: http://vnc2.cim3.net:5800/
    • 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 download the [ slides] (where applicable) and running them locally. The speaker(s) will prompt you to advance the slides during the talk.
  • 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:
    • ...
    • (please add yourself to the list above if you are a member of the community, or, rsvp to <peter.yim@cim3.com> with the event title/date and your name and affiliation)

Agenda Ideas

  • review and finish defining the OOR-Ontohub-Gatekeeper API
  • discussion, deliberation and implement features addressing alignment issues
  • set deliverables, due dates and follow-up action plans
  • ... (add yours)
  • ... Ken Baclawski & Till Mossakowski will be providing further details

In-session Resources

OntologySummit2013_Hackathon_Clinics_Ontohub_OOR_OOPS_Integration HC-07]) - http://ontolog.cim3.net/file/work/OpenOntologyRepository/OOR-Architecture/OOR-API/OOR-Ontohub-API_wip-snapshot_20130430c.pdf (ref.)

Agenda & Proceedings

Archives:

1. Meeting called to order:

  • Ken Baclawski & Till Mossakowski took the chair and welcome everyone
  • Peter P. Yim volunteered to collate the notes, but urged everyone to capture their thoughts and document them on the chat board, as usual.
  • review and adopt agenda
  • Urgent items or quick announcements

2. Roll Call:

  • welcome and intro of new member(s) (if applicable)

3. Key discussion:

3.1 Review of previous meetings' decision and action items

3.2 work for this hackathon session

  • review and finish defining the OOR-Ontohub-Gatekeeper API
  • discussion, deliberation and implement features addressing alignment issues
  • set deliverables, due dates and follow-up action plans
  • ... Ken Baclawski & Till Mossakowski will be providing further details

4. Prior Discussions: ... for reference only!

4.1 Discussion: tactically, what shall we be doing differently in the next 6 to 12 months

  • Focused discussion on the tactics and action plans that will help put the recently refined OOR Strategy in place

... to provide synergies for all - please join this Thursday's ONTOLOG Community Planning Session: Event Scheduling for the Rest of 2013: ConferenceCall_2013_09_12

4.2 Setting the metrics - what does "success" look like

4.3 Action planning for "content drive" (getting people to upload ontologies) ... (deferred discussion of this item)

  • (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 2011.08.07) ...
    • ref. IAOA Committee and SIG session at FOIS (2012.07.25) discussion:
      • IAOA Ontology Registry and Repository Committee to put focus on contents
      • getting FOIS papers to be submitted with cited ontologies and their metadata, and have those ontologies hosted on OOR
  • 4.5 OOR instances OOR: status update and coordination ... (deferred discussion of this item)
  • OOR: sandbox, devbox, test-instance, socop, colore, ontohub, ornl-daac, mmi-orr, new ncbo-appliance, ... status update and coordination
  • 4.6 Getting us to a stage when we can run a OOR-production box ... (deferred discussion of this item)
    • we need a gatekeeping/policy module in place - [KenBaclawski]
  • 4.7 Renewed OOR tactics (as agreed during the 2013.06.18 meeting) - there is general consensus we would change to a more bottom-up approach (rather than the "top-down" approach we have been taking ...
    • we will allow each oor node project to develop (colore, ontohub, socop, oor public instance, etc.) on their own, and coordinate the "team" effort through the use of a shared set of metadata, API and the UI (e.g. how people download (or even upload) ontologies, etc.)
    • The key is to ensure that each of the ontology repository projects in OOR are interoperable from the software perspective, uniform in the GUI, and they use a shared approach to ontology metadata
    • we will make oor.net to be an ontology registry, which then links to the ontologies in the actual ontology repository where the ontology is described
    • actions will be focused on developing three things (hopefully within the next 3 months): the set of metadata, the API, and some shared thoughts on the UI
    • after that, we will focus on building up content with each OOR node tackling the domain(s) they are best with

5. IM Chat Transcript captured during the session

see raw transcript here.

(for better clarity, the version below is a re-organized and lightly edited chat-transcript.)

Participants are welcome to make light edits to their own contributions as they see fit.

-- begin in-session chat-transcript --

Chat transcript from room: oor_20130910

2013-09-10 GMT-08:00

[6:53] Peter P. Yim: Welcome to the

OpenOntologyRepository: "OOR-Ontohub-Gatekeeper API" Hackathon Session - Tue 2013_09_10

Session Topic: OOR-Ontohub-Gatekeeper API Hackathon-IV - Alignment

Session Co-chairs: Ken Baclawski & Till Mossakowski

This is the 4th of the series of regular activities for the OOR team. The plan is to devote one meeting a month to

intense coding (or other low level development) work.

session page: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2013_09_10

Attendees: Ken Baclawski (co-chair), Till Mossakowski (co-chair), Bob Smith, Michael Grüninger, Peter P. Yim (scribe), DanielCoutoVale.

Proceedings

[7:06] Peter P. Yim: == session starts ...

[7:06] List of members: Bob Smith, Ken Baclawski, Michael Grüninger, Peter P. Yim, Till Mossakowski

[7:07] Peter P. Yim: Till: updated/current version of API (by Daniel) is at: https://github.com/ontohub/OOR_Ontohub_API/commits/master/src/Ontology.idl

[7:09] Peter P. Yim: Till showed us how to do a diff on github: just goto History, then click on the hexadecimal version-ID

[7:15] Peter P. Yim: from the source comments: # TODO: also include the gatekeeper API, BUT: users should have access to repositories (not ontologies - they belong to repositories)

[7:16] Peter P. Yim: Till / Peter: hopefully, this "Alignment" exercise is our last (OOR) internal step before we are in

a position to "publish" this API to the broader ontology community

[7:20] Ken Baclawski: The Item in gatekeeper should be changed to Repository to make it consistent with the Ontology.idl.

[7:21] Till Mossakowski: ... and then it can be imported in Ontology.idl

[7:21] Peter P. Yim: ref. BioPortal Interface Tier - see: http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository_Architecture/From_BioPortal#nid2MT0

[7:22] Peter P. Yim: Question: are we handling access control and authentication via the Gatekeeper or via the BioPortal interface?

[7:24] Ken Baclawski: The gatekeeper.idl is not concerned with access control and authentication but rather with

roles and responsibilities of a user.

[7:53] Peter P. Yim: Till: github is closed sourced

[8:00] Michael Grüninger: I need to leave now -- sorry, I double-booked meetings

[8:00] Peter P. Yim: bye, Michael!

[8:03] Ken Baclawski: I will send the existing gatekeeper prototype to Till. It is based on existing business process software.

I also have a paper that explains the gatekeeper. Unfortunately, I was unable to modify the gatekeeper so that it could be

integrated with the OOR.

[8:05] Ken Baclawski: We will look for existing software that could be used for gatekeeping/workflow.

[8:08] DanielCoutoVale: I'm connecting to the conference now! Need to make contact with Ken ref. preparation of the Sep-17 session

[8:10] Peter P. Yim: Hi Daniel ... we are about done NOW

[8:11] Ken Baclawski: My email is Ken [at] Baclawski.com

[8:14] Peter P. Yim: next hackethon session will be on Oct-15 - OOR Hackathon n.05 Tue 2013.10.15 ... (there is a possibility that

Till will be teaching at this hour; if so, we will consider moving the regular Tuesday OOR confcall time to accommodate it.)

[8:14] Peter P. Yim: -- session ended: 8:12am PDT --

-- end in-session chat-transcript --

6. Action items:

  • (see above)

7. Any Other Business: ... (deferred to the next meeting)

  • we have decided to host a community session to collect input, discuss, and gain consensus on the approach towards the "Meta-Ontology for Ontology Categories" - this is now scheduled for Tue 2013.10.08 - start-time: 7:00am PDT / 10:00am EDT / 4:00pm CEST / 3:00pm BST / 1400 UTC
    • we hope stewards of current and developing ontology repositories (folks from BioPortal, SOCoP-OOR, COLORE, Ontohub, and various OOR nodes ... and other domain ontology repositories, like, for Standards, space-portal, etc. )

8. Schedule Next Meeting & Adjourn:

  • next Meeting - Tue 2013.09.17 - OOR Common UI - chair: Ken Baclawski ... with opening brief from DanielCouteVale
  • after that we'll have ...
    • Tue 2013.10.01 - regular (monthly) OOR Team planning & admin meeting
    • Tue 2013.10.08 - "Meta-Ontology for Ontology Categories" - co-chairs: Till Mossakowski & Michael Grüninger
      • ... We hope stewards of current and developing ontology repositories (folks from BioPortal, SOCoP-OOR, COLORE, Ontohub, and various OOR nodes ... and other domain ontology repositories, like, for Standards, SpacePortal, Financial Industry, etc.) will join us in this session, share their thoughts and help develop a consensus.
  • please also join this Thursday's ONTOLOG Community Planning Session: Event Scheduling for the Rest of 2013: ConferenceCall_2013_09_12
  • regular meeting start-times will be: 7:00am PDT / 10:00am EDT / 4:00pm CEST / 3:00pm BST / 1400 UTC
  • 1st Tuesdays of each month will be for OOR team regular monthly confcall - for admin/planning
  • 2nd Tuesdays of each month will be for OOR-hackathon
  • ... please mark your calendars and make sure you can come!
  • Call adjourned at: 8:12 am PDT

--

notes taken by: Peter P. Yim / 2013.09.10-11:26am PDT

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

Resources

  • 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
    • 2012_07_17 - Tuesday: Joint IAOA-OOR-Ontolog "Ontologies and Standards" mini-series session-3: "Standardisation Coordination and Ontology Repositories" - Co-chairs: Michael Grüninger & John Bateman - ConferenceCall_2012_07_17
    • 2012_09_20 - Thursday: Joint IAOA-OOR-Ontolog "Ontologies and Standards" mini-series session-4: "Common Logic" - Co-chairs: Michael Grüninger & John Bateman - ConferenceCall_2012_09_20
  • 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



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