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OpenOntologyRepository: OOR Code Development Workshop (n.10) - Tue 2013_12_10

Topic: Ontohub at OOR: Should the OOR code be based on Ontohub?

Session Co-Chairs: TillMossakowski and KenBaclawski

Conference Call Details

  • Date: Tuesday, 10-Dec-2013
  • Start 7:00am PST / 10:00am EST / 4:00pm CET / 1500 GMT/UTC
  • Expected Call Duration: 1.0~1.5 hours
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  • In-session chat-room url: http://webconf.soaphub.org/conf/room/oor_20131210
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  • 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

  • This will be a general discussion in which Till Mossakowski will give a brief introduction.
  • The panel will consist of Till Mossakowski, Ken Baclawski, ...
  • The OntoHub source code is available for downloading and installation.
  • The following are some of the issues that should be discussed:
    • Are the installation instructions current?
    • What configuration files must be created/updated for installation?
    • What customizations are supported?
    • Will the customizations be compatible with new versions of OntoHub?
    • Are there any issues with versions of required software, such as Ruby and Tomcat?
    • Is a virtual machine image available?
    • Add additional issues here.
  • Announcement of the Ontology Summit 2014 and discussion of the impact on the OOR meeting schedule.

In-session Resources

Agenda & Proceedings

Archives:

1. Meeting called to order:

  • Till Mossakowski & Ken Baclawski 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 Briefing: Till Mossakowski ... (slides)

3.2 Open discussion: "Should the OOR code be based on Ontohub?"

  • The following are some of the issues that should be discussed:
    • Are the installation instructions current?
    • What configuration files must be created/updated for installation?
    • What customizations are supported?
    • Will the customizations be compatible with new versions of OntoHub?
    • Are there any issues with versions of required software, such as Ruby and Tomcat?
    • Is a virtual machine image available?
    • ... more

4. 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_20131210

2013-12-10 GMT-08:00 [PST]

[7:00] Peter P. Yim: Welcome to the

OpenOntologyRepository: OOR Code Development Workshop (n.10) - Tue 2013_12_10

Topic: Ontohub at OOR: : Should the OOR code be based on Ontohub?

Session Co-Chairs: Till Mossakowski and Ken Baclawski

Logistics:

  • (if you haven't already done so) please click on "settings" (top center) and morph from "anonymous" to your RealName
  • Mute control (phone keypad): *7 to un-mute ... *6 to mute
    • you may connect to (the skypeID) "joinconference" whether or not it indicates that it is online

(i.e. even if it says it is "offline," you should still be able to connect to it.)

    • if you are using skype and the connection to "joinconference" is not holding up, try using (your favorite POTS or

VoIP line, etc.) either your phone, skype-out or google-voice and call the US dial-in number: +1 (206) 402-0100

... when prompted enter Conference ID: 141184#

    • Can't find Skype Dial pad?
      • for Windows Skype users: Can't find Skype Dial pad? ... it's under the "Call" dropdown menu as "Show Dial pad"
      • for Linux Skype users: if the dialpad button is not shown in the call window you need to press the "d" hotkey to enable it

Attendees: Till Mossakowski (co-chair), Ken Baclawski (co-chair), Aleksandra Sojic, Michael Grüninger, Oliver Kutz, Paul Alexander, Peter P. Yim (scribe).

Proceedings

[7:03] anonymous morphed into Paul Alexander

[7:06] Peter P. Yim: == Till Mossakowski and Ken Baclawski starts the session

[7:07] Peter P. Yim: == Till makes presentation on Ontohub - see slides

at: http://ontolog.cim3.net/file/work/OpenOntologyRepository/OOR-dev/ontohub-at-OOR--TillMossakowski_20131210.pdf

[7:25] Till Mossakowski: (in response to question from Ken on the availability of the installation instructions)

see: http://wiki.ontohub.org/index.php/Installation

[7:29] Peter P. Yim: Till: federation will be a feature in the future ... for now, mirroring of git instances is supported

[7:53] Peter P. Yim: I strongly urge a healthy dialog between the Ontohub / OOR team and the (BioPortal) team ... especially towards setting up

an agenda to interface, integrate and federating content of repositories based on these two code-bases in the future

[7:55] Till Mossakowski: Paul: rack is the useful level for speaking with BioPortal.

[7:56] Till Mossakowski: Paul: the triple store is not recommended as a production-level interface. It is more for simple SparQL queries.

[7:57] Till Mossakowski: Paul: The API is being moved to a new version, and it is highly optimized.

[7:58] Till Mossakowski: Paul: some rack middleware (run on both systems) could provide a common interface to program against internally

[7:59] Till Mossakowski: Paul: this would be a more fine-grained integration than just the REST API

[8:00] Till Mossakowski: on the other hand, the RESTful API is already there and requires no extra programming

[8:02] Till Mossakowski: Paul: the API should only give you ontologies that don't have legal issues

[8:02] Peter P. Yim: Paul: access to IPR encumbered content from BioPortal will not be supported through the API

[8:03] Paul Alexander: BioPortal v4.0 REST service: http://data.bioontology.org/

[8:07] Paul Alexander: BioPortal v4.0 Documentation: http://data.bioontology.org/documentation

[8:07] Paul Alexander: BioPortal v4.0 REST API Ruby client: https://github.com/ncbo/ontologies_api_ruby_client

[8:01] Peter P. Yim: would it be possible to schedule, say, quarterly session to align API's and other pertinent issues

(integration, federation, etc.) between the two teams?

[8:15] Peter P. Yim: where do we stand on implementing the mandatory capture of ontology metadata when content is uploaded

... and "gatekeeping" in general

[8:20] Peter P. Yim: I am also concerned that, while both the OOR software license (Simplified BSD)[1] and the Ontohub software license (AGPL)[2]

are open source, the former (Simplified BSD) is a "gift" License, and the latter (AGPL) is a "reciprocal" license. I hope they can be aligned

... [1] see: http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository_IPR#nid2L0S

... [2] ref.: http://en.wikipedia.org/wiki/Affero_General_Public_License

[8:20] Till Mossakowski: anyone who would want to commercialize the Ontohub software are welcome to talk to us.

[8:20] Peter P. Yim: @Till, I will try to talk to you offline (as I do hope the original spirit of the IPR Policy is maintained.)

[8:23] Till Mossakowski: Michael, please see https://github.com/ontohub/ontohub/issues/486

[8:24] Till Mossakowski: this is about the tree view of repositories in Ontohub

[8:25] Peter P. Yim: to allow team members to support Ontology Summit 2014, the OOR regular meetings will be paused between now and the

end of the Summit. Therefore, the next regular OOR meeting will be in may 2104.

[8:26] Peter P. Yim: hope Ontohub has a strong representation in the Ontology Summit 2014 organizing team (Oliver?)

[8:26] Peter P. Yim: -- session ended: 8:26am PST --

-- end in-session chat-transcript --

5. Action items:

  • ...

6. Any Other Business:

  • Note that we will break for the year, and start to focus the OOR team's effort to support OntologySummit2014.
  • Regular OOR meeting will resume after Ontology Summit 2014 is over.

7. Schedule Next Meeting & Adjourn:

  • next Meeting, probably some time in may, 2014 ... in the mean time,
  • Call adjourned at: 8:24 am PST

--

notes taken by: Peter P. Yim / 2013.12.10-12:29pm PST

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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