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OpenOntologyRepository: OOR "Hackathon" Session (n.02) - Tue 2013_07_16

Session Topic: The "OOR-Ontohub-Gatekeeper API - II" Hackathon

Session Co-chairs: KenBaclawski & TillMossakowski

This is the 2nd session in a series of regular "hackathon" 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, 16-Jul-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 ]
      • when prompted enter Conference ID: 141184#
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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.
      • 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"
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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.)
    • we will usually save all questions and discussions till after all presentations are through. You are encouraged to jot down questions onto the chat-area in the mean time (that way, they get documented; and you might even get some answers in the interim, through the chat.)
    • During the Q&A / discussion segment (when everyone is muted), If you want to speak or have questions or remarks to make, please raise your hand (virtually) by clicking on the "hand button" (lower right) on the chat session page. You may speak when acknowledged by the session moderator (again, press "*7" on your phone to un-mute). Test your voice and introduce yourself first before proceeding with your remarks, please. (Please remember to click on the "hand button" again (to lower your hand) and press "*6" on your phone to mute yourself after you are done speaking.)
  • In-session chat-room url: http://webconf.soaphub.org/conf/room/oor_20130716
    • 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_20130716@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

  • finish defining the OOR-Ontohub API
  • defining the OOR-Gatekeeper requirements and then the API
  • set deliverables, due dates and follow-up action plans
  • decide on agenda for the next 2 meeting Jul-23 & Jul-30 (before we take a break in Aug-2013)
  • ... (add yours)

Resources

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 last meeting's decision and action items

  • 2013.06.25: we reached consensus that we will be formalizing the API as discussed using the (OMG) Interface Definition Language (IDL) (v3.5)
    • Till Mossakowski will work on formalizing the API agreed on (ref.)
    • Ken Baclawski will work on the OOR-Gatekeeper API (also using IDL)
    • Till & Ken will have these ready by the next hackathon session - scheduled for Tue 2013.07.16

3.2 work for this hackathon session

  • finish defining the OOR-Ontohub API
  • defining the OOR-Gatekeeper requirements and then the API
  • set deliverables, due dates and follow-up action plans

3.3 scheduling ... (ref. "7. Any Other Business" below)

  • decide on agenda for the next 2 meeting Jul-23 & Jul-30 (before we take a break in Aug-2013) ... and then Sep-3 and Sep-10

4. Prior Discussions:

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.

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_20130716

2013-07-16 GMT-08:00 [PDT]

[6:59] Peter P. Yim: Welcome to the

OOR "Hackathon" Session (n.02) - Tue 2013_07_16

  • Session Topic: The "OOR-Ontohub-Gatekeeper API - II" Hackathon

Attendees: Ken Baclawski (co-chair), Till Mossakowski (co-chair), Aleksandra Sojic, DanielCoutoVale,

Mike Bennett, Oliver Kutz, Peter P. Yim (scribe), ToddSchneider.

Proceedings

[7:03] anonymous morphed into Aleksandra Sojic

[7:02] Peter P. Yim: Till: ref.

http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2013_07_16#nid3VKT -

https://github.com/ontohub/ontohub/blob/specifying179_formalizing_ontology_repository_service/api/ontology.idl

[7:13] Ken Baclawski: The idlj compiler converts from IDL to Java. It is a standard tool in any Java

Development Kit (jdk) so if you have Java installed you should also have idlj.

[7:15] Ken Baclawski: The idlj compiler is handy for checking the IDL syntax. I used idlj to convert

an IDL to Java, and then it is relatively easy to convert to WSDL.

[7:09] Till Mossakowski: [action] we will set up a new github repository, only for the API

[7:07] Ken Baclawski: My GitHub name is "baclawski."

[7:15] Peter P. Yim: when this OOR-API github instance is up, please subscribe me too - my github

username is "yimpp"

[7:23] Till Mossakowski: [action-completed] new repository at

https://github.com/ontohub/OOR_Ontohub_API ... both Ken and Peter are subscribed now

[7:11] Todd Schneider: What happened to the use of instances of the metadata ontology as the function

parameter?

[7:30] Todd Schneider: The API for 'selecting' is effectively a query mechanism, the front end to the

user. The other side of this is the 'retrieving' of the requested or queried data. For the front end

of selecting or querying for ontologies (or metadata about them) use of an instance of the metadata

ontology should be used as the single parameter for the 'select' method. The particular parameters

of interest would be represented by non-null values (in the ontology instance). This simplifies the

API and overall architecture (but moves complexity to the parsing of the ontology instance). The

retrieval (or return values) of the 'selected' results would make use of federate identifiers.

[7:35] Till Mossakowski: @Todd: the single parameter should be a struct

[7:39] Till Mossakowski: add-on to Todd's message: the user should be able to select whether the

method call should just deliver ids (compact representation) or all the metadata (say, as an XML

tree), or even the whole ontology/ies (can become very large)

[7:42] Todd Schneider: Till, good point about a parameter to specify return value(s).

[7:42] Till Mossakowski: IDL methods are synchronous by default. If the execution of a method takes

very long, it should be made asynchronous (keyword: oneway).

[7:33] Ken Baclawski: I have posted the Gatekeeper API in gatekeeper.idl. This is accepted by idlj.

[7:44] Peter P. Yim: Till+Ken: now online at github:

... OOR_Ontohub API - https://github.com/ontohub/OOR_Ontohub_API/blob/master/ontology.idl ... and,

... OOR_Gatekeeper API - https://github.com/ontohub/OOR_Ontohub_API/blob/master/gatekeeper.idl

[7:47] Till Mossakowski: Daniel will work on a new iteration of the API, and test it with idlj. He

will also integrate the gatekeeper API as a module. Once this iteration is there, Daniel will send a

mail, and others can contribute through github.

[7:47] Peter P. Yim: [consensus] we will leave these two API's as separate modules - OOR-Ontohub-API and

OOR-Gatekeeper-API

[7:48] Peter P. Yim: (for the lower level development work) we should use the [oor-dev] mailing list

[7:48] DanielCoutoVale: my e-mail is danielvale [at] uni-bremen.de

[7:49] Peter P. Yim: [action] I will subscribe everyone present at today's session to the [oor-dev] list

(in case he/she isn't yet)

[7:50] List of members: Aleksandra Sojic, DanielCoutoVale, Ken Baclawski, Mike Bennett, Oliver Kutz,

Peter P. Yim, Till Mossakowski, Todd Schneider

[7:49] Peter P. Yim: ^[action-completed] ... done subscribing everyone here onto the [oor-dev] list!

[8:04] Todd Schneider: Sorry; Have to go. Thank you.

[8:01] Till Mossakowski: we just need to start with the "upper level" of the classification.

People can later add finer distinctions. The classification system should be itself an OWL ontology,

hosted at OOR-Ontohub.

[7:53] Ken Baclawski: Another source of ontology classification (or perhaps properties of an

ontology) is the Ontology Summit 2007 http://ontolog.cim3.net/cgi-bin/wiki.pl?OntologySummit2007

[7:57] Till Mossakowski: United Nations Standard Products and Services Code: http://www.unspsc.org/

[8:03] Peter P. Yim: @Ken - UNSPSC codeset can be downloaded at: http://www.unspsc.org/codeset-downloads

... (generally cost $100) the pdf's are free

[8:06] Mike Bennett: Prescriptive v Descriptive ontologies

[8:07] Till Mossakowski: follow up to Ken/2007 summit: ontologies may be classified as descriptive or prescriptive

[8:07] Mike Bennett: (that is extensional v intensional definitions in the ontology)

[8:08] TillMossakowski-KenBaclawski: The Ontology Summit 2007 Communique is

at: http://ontolog.cim3.net/cgi-bin/wiki.pl?OntologySummit2007_Communique

[8:11] Peter P. Yim: upcoming meetings: OOR-hackathon n.03 - Tue Jul-30 ... break in Aug-2013

... OOR-hackathon n.04 - Tue Sep-10

[8:11] Peter P. Yim: we will use the second Tuesday of each month for the OOR-hackathon activities

[8:11] Peter P. Yim: same regular start-time: 7:00am PDT / 10:00am EDT / 4:00pm CEST / 3:00pm BST / 1400 UTC

[8:12] Peter P. Yim: great session ... covered a lot of grounds!

[8:12] Peter P. Yim: -- session ended: 8:11am PDT --

-- end in-session chat-transcript --

6. Action items:

  • ...

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

  • we probably want to schedule a few more meetings/events - Tuesdays: Jul-23, Jul-30, Sep-3, Sep-10, 2013
    • note that we have decided to take Aug-2013 off (like the Ontolog community) so no meeting or event will be scheduled for that month

8. Schedule Next Meeting & Adjourn:

  • no meeting on Tue 2013.07.23 (unless otherwise notified)
  • next Meeting - Tue 2013.07.30 - OOR-hackathon n.03 - Co-chairs: Till Mossakowski & Ken Baclawski
  • after that we will take a break in Aug-2013 (no meetings/events will be scheduled)
  • and we come back to our Sep-2013 OOR Team regular monthly confcall (for admin/planning ) on Tue 2013.09.03
  • 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: 8:11 am PDT

--

notes taken by: Peter P. Yim / 2013.07.16-8:36am 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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