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OpenOntologyRepository: OOR Team Conference Call - Tue 2013_02_05

This is a regular monthly OOR Team meeting. Besides covering the nominal team status review and planning, we will continue to explore how the OOR initiative can leverage on the Ontology Summit 2013, which will be in session now (and over the next 3 months or so,) and produce something synergistic to both programs during this period. We will pick up from where we left off at OOR/ConferenceCall_2013_01_15 and the Software for Ontology Evaluation exploratory meeting of Fri 2013.01.25.

Conference Call Details

  • Date: Tuesday, 5-Feb-2013
  • Start Time: 7:30am PST / 10:30am EST / 4:30pm CET / 15:30 GMT/UTC
  • Expected Call Duration: ~1.5 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#
    • Skype: joinconference (i.e. make a skype call to the contact with skypeID="joinconference") ... (generally free-of-charge, when connecting from your computer)
      • 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"
        • for Linux Skype users: please note that the dial-pad is only available on v4.1 (or later or the earlier Skype versions 2.x,) if the dialpad button is not shown in the call window you need to press the "d" hotkey to enable it. ... (ref.)
  • In-session chat-room url: http://webconf.soaphub.org/conf/room/oor_20130205
    • 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_20130205@soaphub.org ... Handy for mobile devices!
  • 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.)
  • 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

  • supporting and leveraging Ontology Summit 2013
    • specifically: how do we leverage Track-D ("Software Environments for Evaluating Ontologies") and the Symposium, where a "survey", a "hackathon" and various "clinics" may be featured
  • regular OOR team status review
  • plan, confirm and make additions to the OOR event calendar
  • ... (add yours)

Agenda & Proceedings

OOR Meeting Archives: (OntologySummit2013 hackathon-clinic wip archives)

1. Meeting called to order:

  • Peter P. Yim 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

2. Roll Call:

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

most of the content below are inherited from the previous call(s); since we did not follow the regular OOR monthly meeting agenda this time, only the discussions captured in the chat-transcript will be most relevant ...

3. Key discussion:

  • 3.1 Team priority: Review and update our "Most Critical Task(s) At Hand" list
    • ref. http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository#nid17YH
    • consider adding to the list work that address the two focused areas identified in the recent strategic planning discussion
      • developing reference practices, and the technology involved, to support OOR-augmented OntologyBasedStandards
      • developing a reference practice, and the technology involved, to support an OOR-augmented "big data" application (such as "tackling research data" ref.)
    • review proposed modifications, as drafted by Mike Dean (ref. discussion at the last call, 2012.12.04)
  • 3.2 Announcements & Reports
  • Various members making brief reports on relevant events and activities
      • during our 2012.12.11 discussion we decided we will not be doing standalone OOR meetings, but will be merging the OOR discourse into OntologySummit2013-related discussions/sessions, while the Summit is in session. We said we will try to figure this out a bit more as the Summit program becomes clearer (which would be now).
      • see:
    • ...
  • 3.3 Key discussion this meeting: "supporting and leveraging OntologySummit2013"
    • specifically: how do we leverage Track-D ("Software Environments for Evaluating Ontologies") and the Symposium, where a "survey", a "hackathon" and various "clinics" may be featured
    • ref. Ontology Summit 2013 Tracks structure & Master Calendar
    • thoughts and suggestions ...
  • 3.4 upcoming activities / virtual-session planning
    • Scheduled:
    • To be scheduled:
      • OOR Architecture & API Workshop-XV - Co-chairs: Ken Baclawski & Todd Schneider
      • OOR Infrastructure-II - Chair: Peter P. Yim - pending: possibly after our next update on the ncbo-appliance vm
      • need to be rescheduled: 2012_10_23 - Tuesday: "Getting OOR Development Going - Take-IX" Workshop - Chair: Mike Dean & Michael Grüninger
        • Michael will try to engage Till Mossakowski, and hopefully, through this session, start getting more integration between the Ontohub and the OOR activities
      • ...
  • 3.5 Member activities updates - Review: members and OOR-related activities (2012.07.10) ... (deferred discussion of this item)
    • OOR-sandbox status
    • code repository status
    • NCBO - BioPortal updates
    • NEU - Gatekeeper, ...
    • Raytheon-BBN - federation, ...
    • UToronto - COLORE
    • Bremen - Ontohub
    • Ryerson
    • Mathet
    • SOCoP_INTEROP - SOCoP-OOR
    • DataONE
    • NeOn (KMi and STL)
    • ONKI
    • KBSI
    • MMI
    • Use Cases
    • Architecture
    • API
    • Gatekeeping
    • production OOR instance
    • SIO
    • ICOM / DERI
    • content drive
    • Funding

4. References:

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]

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 --

[07:30] Peter P. Yim: Welcome to the

OpenOntologyRepository: OOR Team Conference Call - Tue 2013_02_05

session page: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2013_02_05

Attendees: Peter P. Yim (chair), Ken Baclawski, Maria Poveda, Mike Dean, Mike Denny, Oliver Kutz,

Till Mossakowski, Yuriy Milov

Proceedings:

[07:25] anonymous morphed into Maria Poveda

[07:27] anonymous morphed into Mike Denny

[07:28] anonymous morphed into Yuriy Milov

[07:35] Maria Poveda: xd plugin

[07:35] Maria Poveda: (ref. contacts for earlier NeOn project work) valentina presutti

[07:35] Maria Poveda: aldo gangemi

[07:36] Maria Poveda: Here you can find the plugins developed during NeOn

[07:36] Maria Poveda: http://neon-toolkit.org/wiki/Neon_Plugins

[07:37] Peter P. Yim: -- session started: 7:37am PST --

[07:55] Till Mossakowski: I am also here

[07:55] Peter P. Yim: Hi Till

[07:55] Till Mossakowski: Hi Peter

[07:56] Till Mossakowski: I just stayed in the room of my previous meeting ... still a bit noisy

here...

[08:00] Till Mossakowski: Mike Dean is happy to focus on the ontology clinic idea

[08:01] Peter P. Yim: three ideas being tossed around (at the Ontology Summit 2013 organizing committee):

hackathon (coding), "ontology clinic", "application clinic"

[08:15] Maria Poveda: @Peter, could you write a very brief description of "ontology clinic" and

application clinic? I think I'm misunderstanding something. Maybe after the meeting in the

proceedings.

[08:20] Peter P. Yim: @Maria and All: with the "ontology clinic" - we send (a) ontologies to be

evaluated through the "tool", study the results and see how the ontology may be improved, and (b)

gold standard ontology through the "tool", study the results and see how the "tool" (the ontology

too, possibly) may be improved

[08:40] Peter P. Yim: @Maria and All: with the "application clinic" - we (a small team) work with a (one

or more) user community that has a real need to evaluate ontology, the clinic exercise helps the

user evaluate what ontologies are most suitable for them, etc.

[08:22] Maria Poveda: thank

[08:01] Peter P. Yim: @ALL: please capture your ideas for the "hackathon/clinic" activity which you (or

the team of people you can bring to the table) would want to focus on

[08:06] Maria Poveda: [another relevant tool - Eyeball: a library and command-line tool for checking

RDF and OWL models for various common problems] see: http://jena.sourceforge.net/Eyeball/full.html

[08:07] Ken Baclawski: It would be useful to integrate any evaluation tools into the OOR

architecture. This would involve agreeing on a common web services API.

[08:08] Maria Poveda: sorry, I am not familiar with the OOR architecture

[08:11] Till Mossakowski: @Maria: for the OOR architecture, see

http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository_Architecture/Candidate03

[08:11] Maria Poveda: thanks

[08:10] Till Mossakowski: sorry, can you post a link to "oops" ?

[08:10] Maria Poveda: http://www.oeg-upm.net/oops/

[08:10] Peter P. Yim: @Till: re: OOPS! - see also:

http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2013_01_31#nid3L73

[08:11] Ken Baclawski: The result of evaluations should be in a common ontology so that the output of

evaluations would be interoperable. While I developed an ontology for this 10 years ago, it would

need to be updated and extended to handle other kinds of evaluations. This is an ontology

development effort, not a code development effort.

[08:12] Mike Dean: Hackathon idea: access OOPS web services from OOR

[08:14] Maria Poveda: @Mike I'll let you know, maybe tomorrow, when you can use the web services

[8:24] Peter P. Yim: (answering MikeDenny's question about tools to support our survey) we have, at our

disposal, (a) Perseus Survey Solution, (b) Survey Monkey, (c) Lime Survey, (d) using Semantic Forms

etc. on Purple Semantic MediaWiki (psmw), plus soliciting input via the mailing list(s), wiki,

during panel sessions (collect input into the chat-room), etc. ... I would prefer (d) if we can get

the resources and people with the skill-set to support us on that.

[08:15] Till Mossakowski: Peter: Ontolog is being moved to purple semantic MediaWiki (psmw)

[08:17] Peter P. Yim: @Till & All - ref. Ontolog moving its wiki platform to OntologPSMW - see:

http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2012_12_19

[08:25] Till Mossakowski: http://en.wikipedia.org/wiki/LimeSurvey

[09:11] Peter P. Yim: (ref. survey tools at our disposal) our instance of Lime Survey - ref.

http://project.cim3.net/survey & http://ontolog.cim3.net/cgi-bin/wiki.pl?OntologySummit2012#nid39VK

[08:37] Mike Denny: Is there a link to Ontohub?

[08:37] Oliver Kutz: http://ontohub.org

[08:38] Yuriy Milov: I think if it is possible to make a "mobile ontologies store" (similar to Google

Play) to have a convenient search and quick test env. for similar ontologies mobile platforms

[08:39] Yuriy Milov: sorry, have to go

[08:41] Maria Poveda: sorry, there is a meeting in my office, my idea about what you say about

evaluation competition: could we use that result to identify which tools complement others?

[08:41] Maria Poveda: I mean there are several aspects to evaluate, and as a user I would like to

combine several tools to evaluate my ontology

[08:41] Maria Poveda: sorry

[08:42] Maria Poveda: could you repeat last part?

[08:43] Maria Poveda: please write in the chat

[08:43] Maria Poveda: there is a meeting here as well

[08:43] Maria Poveda: I'm a bit lost

[08:44] Maria Poveda: of course, OOPS will be more useful integrated in other tools

[08:44] Maria Poveda: for example ontology editors

[08:44] Peter P. Yim: note discussion and relevant dates from our last meeting (Fri 2013.01.25):

http://ontolog.cim3.net/cgi-bin/wiki.pl?OntologySummit2013_Software_Environments_For_Evaluating_Onto

logies_CommunityInput#nid3L8N

[08:44] Till Mossakowski: OBO is an ontology language used in the biomedical community. It can be

translated to OWL, thus OOPS could be used for OBO as well.

[08:46] Till Mossakowski: However, for first-order ontologies, a first-order analogon of OOPS would

be needed. Probably, it would not be of much use to project a first-order ontology to OWL, thereby

losing information, and then sending it to OOPS. But I am not entirely sure.

[08:45] Till Mossakowski: We could also integrate OOPS with Ontohub, i.e. such that any ontology

uploaded to Ontohub can be checked with OOPS.

[08:46] Maria Poveda: You can use web services soon while we think how to proceed for sharing the

code

[08:46] Till Mossakowski: @Maria: good, we will be happy to do so.

[08:48] Till Mossakowski: The Ontology Summit could also be used for evaluation of ontology evaluation

tools, identify their weaknesses and strengths, and collect suggestions for improvements and further

developments

[08:49] Peter P. Yim: coming up ... Thu 2013.02.21 - session-06 - Synthesis-I; proposed Communique

Outline; present how we frame the "hackathon/clinics"

[08:52] Peter P. Yim: [action] let use the [ontolog-dev] mailing list to continue to explore and further

fine tune our thought so we can articulate it on the Feb-21 session - Mike Dean will do the

presentation on behalf of this team

[08:52] Ken Baclawski: I have to leave.

[08:55] Peter P. Yim: [action] Peter to add Maria, Mari Carmen, Oliver and Till to both the

[ontolog-dev] and [oor-dev] and [oor-forum] lists

[09:01] Peter P. Yim: no meeting on Feb-8 (Fri) nor Feb-12 (Tue) ... we will work asynchronously (via

the [ontolog-dev] list) ... will explore date for next meeting on the list (possibly Tue Feb-19)

which will be right before the Feb-21 presentation

[09:01] Peter P. Yim: -- session ended 8:59am PST --

[10:22] List of attendees: Ken Baclawski, Maria Poveda, Mike Dean, Mike Denny, Oliver Kutz,

Peter P. Yim, Till Mossakowski, Yuriy Milov, anonymous

-- end in-session chat-transcript --

6. (Other) Action items:

  • ...

7. Any Other Business:

  • ...

8. Schedule Next Meeting & Adjourn:

  • Next Meetings:
    • To be decided (no meetings on Fri 2013_02_15 or Tue 2013.02.12) ... in the mean time, work to be transacted asynchronously on [ontolog-dev] mailing list
      • during our 2012.12.11 discussion we decided we will not be doing standalone OOR meetings, but will be merging the OOR discourse into OntologySummit2013-related discussions/sessions, while the Summit is in session.
      • in view of MichaelGruninger's teaching schedule conflict this term, we need to set up a different meeting time for this call, at least for the next few months ...
      • Michael: the only possibility is a later time on Tuesday
      • also ref. the earlier doodle poll we conducted - http://www.doodle.com/55wawkczhiuteyze
        • note: we have decided, earlier, to move the start earlier by one hour (just like today's and the last meeting) - future OOR meetings will continue to start at: 7:30am PST / 10:30am EST / 4:30pm CET / 15:30 GMT/UTC
    • ... please mark your calendars and come!
  • Call adjourned at: 8.59 am PST

--

notes taken by: Peter P. Yim / 2013.01.15-20.39pm 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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