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OpenOntologyRepository: OOR Infrastructure Meeting - Tue 2013_11_12

Topic: OOR Infrastructure Discussion: "SOCoP-OOR and related issues"

Co-chairs: KenBaclawski, Mike Dean & TillMossakowski

Conference Call Details

  • Date: Tuesday, 12-Nov-2013
  • Start 7:00am PST / 10:00am EST / 4:00pm CET / 1500 GMT/UTC
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  • 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

Agenda & Proceedings

Archives:

1. Meeting called to order:

  • Urgent items or quick announcements

1.1 Roll Call:

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

2. Key discussion:

2.1 Discuss SOCoP-OOR and related issues

2.2 Scheduling of upcoming OOR Events

  • more OOR session plans ... from now through first half of Jan-2014.

see also 3.2 below : http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2013_11_12#nid40UY

most of the content below are inherited from the previous call(s), and will be edited/updated as this meeting progresses ...

  • 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 encourage 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
    • initially (prior to federation mechanisms being in place) 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, and put in a concerted effort towards OOR adoption
  • current SOCoP-OOR issues
    • and discussion on hosting/maintenance of OOR instances
  • action plans - medium/long term
    • collaboration and synergies with IAOA
    • keeping OOR relevant
    • ... and invigorated

3.2 scheduling of OOR Events

  • Events planned/scheduled so far ...
    • the regular (monthly) OOR Team meeting for planning and admin discussions - 1st Tuesday of each month
    • the monthly Hackathon sessions - 2nd Tuesday of each month
    • a session on "common UI for OOR instances" ...?
    • (periodic) workshop on metadata
    • (periodic) session on architecture
    • (periodic) session on strategy and tactics
  • 3.3 Member activities updates - Review: members and OOR-related activities (list from 2013.05.21) ... (deferred discussion of this item)
    • OOR-sandbox status
    • code repository status
    • NCBO - BioPortal updates
    • NEU - Gatekeeper, ...
    • Raytheon-BBN - federation, ...
    • UToronto - COLORE
      • Ryerson (see above: Bart Gajderowicz has joined MichaelGruninger's team at U of Toronto soon)
    • Bremen - Ontohub
    • Mathet
    • SOCoP_INTEROP - SOCoP-OOR
    • DataONE
    • NeOn (KMi and STL)
    • ONKI
    • KBSI
    • MMI
    • Use Cases
    • Architecture
    • API
    • Metadata
    • Gatekeeping
    • production OOR instance
    • SIO
    • ICOM / DERI
    • content drive
    • Funding

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]

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_20131112

2013-11-12 GMT-08:00 [PST]

[6:55] Peter P. Yim: Welcome to the

OpenOntologyRepository: OOR Infrastructure Meeting - Tue 2013_11_12

Topic: OOR Infrastructure Discussion: "SOCoP-OOR and related issues"

Co-chairs: Ken Baclawski, Mike Dean & Till Mossakowski

session page: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2013_11_12

Attendees: Ken Baclawski (co-chair), Mike Dean (co-chair), Till Mossakowski (co-chair),

Aleksandra Sojic, Dalia Varanka, GaryBergCross, Oliver Kutz, Peter P. Yim (scribe), Todd Schneider, and

Nancy Wiegand (on voice only; not in chat-room)

Proceedings:

[7:00] List of members: Ken Baclawski, Oliver Kutz, Peter P. Yim, Till Mossakowski

[7:01] Peter P. Yim: Till: needs to leave in 30 minutes;

[7:01] Peter P. Yim: Ken: need to leave in an hour too

[7:04] Peter P. Yim: == Ken Baclawski, Mike Dean & Till Mossakowski starts the meeting ...

[7:06] Peter P. Yim: access to various OOR instances & SOCoP-OOR - see: http://oor.net/index1.html &

http://socop.oor.net/ontologies

[7:11] Peter P. Yim: so far, we don't know what caused the Oct-22 SOCoP-OOR crashing (and another

subsequent crash after rebooting)

[7:14] GaryBergCross: Note that Stephen M Richard from Arizona loaded IUGS CGI Consolidation Degree

Term Vocabulary (consoldeg) in Pct. Also Simon Cox loaded his O & M ontology in Sept and got a

parsing error. These are people that I talked to about the OOR and so they tried to load things to

test it out.

[7:25] Mike Dean: The BioPortal version used for SOCoP still uses Protege 3 code. If you get a

loading error, try loading the ontology into Protege 3.

[7:09] GaryBergCross: @Peter, Does your retirement mean that CIM3 will no longer be involved?

[7:14] Peter P. Yim: @Gary - I am just starting to plan that (and is just giving people ample notice)

... nothing is assumed yet, and it is not happening in, at least, another 6 (or 12) months

[7:14] Till Mossakowski: (imported content of) BioPortal at Ontohub:

http://develop.ontohub.org/bioportal

[7:17] Peter P. Yim: Till: we have imported all the BioPortal ontologies onto Ontohub already; we can do

that for the SOCoP-OOR content as well

[7:18] Peter P. Yim: Till: we plan to run multiple instances of Ontohub ... look under the

Repositories" tab - at http://develop.ontohub.org/repositories

[7:19] Till Mossakowski: Note that there are multiple repositories *within* one instance of Ontohub

[7:20] Till Mossakowski: Is the BioPortal API available also for the SOCoP instance?

[7:26] Till Mossakowski: The BioPortal API is available under

http://rest.bioontology.org/bioportal/ontologies?apikey=YourAPIKey .

How do I translate this into socop.oor.net ?

[7:28] Peter P. Yim: [action] Ken: I'll get back to you, Till

[7:30] GaryBergCross: Till Would your propose running the SOCoP repository as a separate instance?

[7:30] Till Mossakowski: sorry, have to leave now

[7:31] Peter P. Yim: question for the SOCoP principals - are you in touch with the ESIP people?

[7:30] GaryBergCross: No I haven't been in touch with Peter Fox.

[7:32] Peter P. Yim: Ref: http://ontolog.cim3.net/forum/socop-forum/2013-05/msg00005.html#nid07

[7:32] Peter P. Yim: ESIP = Earth Science International Partners

[7:33] Peter P. Yim: ESIP-Portal = the Federation of Earth Science Information Partnerss ESIP-Portal.

ESIP-Portal is a customized version of the National Center for Biomedical Ontologys BioPortal

application, and is used for accessing and sharing Earth Science ontologies. This is run by

Foundation for Earth Science

[7:33] Peter P. Yim: see: http://semanticportal.esipfed.org/ontologies

[7:40] Peter P. Yim: [answering question from Nancy on "what is the focus and scope of Ontohob" ...

(Till lready left the meeting)] as far as I undestand, one main focus of Ontohub is to implement

OntoIOp (Ontology, Model and Specification Integration and Interoperability) - see:

http://ontoiop.org (or http://ontolog.cim3.net/cgi-bin/wiki.pl?OntoIOp )

[7:44] Peter P. Yim: [action] GaryBergCross to work with MikDean (offline) to get access to the

SOCoP-OOR admin interface

[7:45] Peter P. Yim: [action] Ken will work with Till to mirror the SOCoP-OOR content over to Ontohub

[7:48] Peter P. Yim: Nancy Wiegand / GaryBergCross: @Ken, @Till - please do not move "WisLandUseCodes (WisLandUseCodes)"

(Nancy: don't want to go public with this yet) and "Observations and Measurements (OM)" (Gary: not while

it still has parsing error)

[7:47] Ken Baclawski: [ follow-up on [7:14] GaryBergCross' comment on SimonCox's parsing error:

validator error messages regarding the version of "Observations and Measurements (OM)" on the

SOCoP-OOR now ] Detailed report

Use of non-absolute IRI

<http://def.seegrid.csiro.au/isotc211/iso19150-2/2012/gml#noPropertyType> Domain <_:genid634989>

[in ontology OntologyID(OntologyIRI() VersionIRI())]

Use of non-absolute IRI

<http://def.seegrid.csiro.au/isotc211/iso19150-2/2012/gml#byValuePropertyType> Domain <_:genid635005>

[in ontology OntologyID(OntologyIRI() VersionIRI())]

Use of non-absolute IRI

<http://def.seegrid.csiro.au/isotc211/iso19150-2/2012/gml#isCollection> Domain <_:genid635011>

[in ontology OntologyID(OntologyIRI() VersionIRI())]

[7:47] Ken Baclawski: These are the errors reported by OWL Validator.

[7:56] Ken Baclawski: I checked IUGS CGI Lithology ontology with OWL Validator and it is valid, so it

should not have a problem at OntoHub.

[7:53] Peter P. Yim: still need to address the IPR issues, and gatekeeper to enforce the OOR-IPR Policy

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

[7:58] Peter P. Yim: as a reference COLORE is now using: http://code.google.com/p/colore/ - Code

license: Apache License 2.0 ; Content license: Creative Commons 3.0 BY-SA

[7:58] Peter P. Yim: Ontohub, I believe, is on AGPL (for code)

[7:59] Peter P. Yim: I am negotiating with both Michael Grüninger and Till Mossakowski about the

possibility of changing their licenses to align with the OOR-IPR Policy

[8:00] Peter P. Yim: BioPortal has changed (from a Mozilla License) to be a fully OOR-IPR Policy

compliant set of licenses

[8:04] Peter P. Yim: from the outset (2008 Ontology Summit), the OOR Initiative does support both "open"

and "non-open" content ... so, we *need to be clear*

[8:08] Mike Dean: OOR should be able to (optionally) accommodate ontologies with different IPR rights

within a single repository.

[8:07] GaryBergCross: Mike...Nancy... We will have to address some of these issues/lessons learned

about maintenance and porting in our NSF report.

[8:13] GaryBergCross: Mike, Nancy et al., do you think that NSF would have any issues with some of

the products of their supported work going overseas???

[8:08] Peter P. Yim: Aleksandra: we will have the option on Ontohub to support ontologies that can be

openly accessed, and ones with "limited access" ... that should be in place in a week or two ...

this is part of the preparation for the FOIS competition too

[8:11] GaryBergCross: @Aleksandra This model of different domains for ontologies sounds very useful

and would accommodate a place for our geospatial topics.

[8:13] GaryBergCross: One question if we port our ontologies there would be how to help develop,

manage and administer our part - or would OntoHub assume all of these duties....

[8:23] Peter P. Yim: something else to think about: implementing the next ncbo-vm release

(triple-store-based; probably in the next month or so) on the Amazon cloud ... we should see whether

we can round up the resources to do it

[8:26] GaryBergCross: Peter / Mike when do you think the SOCoP OOR would go away do to lack of funding?

[8:27] GaryBergCross: I won't have time till December to consider some new work..

[8:28] Peter P. Yim: @Gary - if SOCoP-OOR is going away, it is not for lack of funding

(it is "not funded" already!)

[8:28] Peter P. Yim: good meeting!

[8:29] Mike Dean: Thanks everyone!

[8:55] Aleksandra Sojic: [in response to Nancy's question on whether Ontohub will be available and

stable while the team is still developing that infrastructure] an important point regarding

stability of Ontohub. Since Ontohub is built on a git structure, it has separate branches for

development and staging. So, nothing is submitted to the staging (and master, i.e. visible website)

unless it is stable to be merged to it. In that way, while the development is taking place on

develop.ontohub.org, the UI on the main page is always stable.

[8:29] Peter P. Yim: [action] Peter will follow-up with Ken & Till ref. the focus of next Tuesday's

OOR-Hackathon (n.05 - Tue 2013.11.19)

[8:30] Peter P. Yim: -- session ended: 8:29am PST --

-- end in-session chat-transcript --

6. Action items:

  • [7:44] GaryBergCross to work with MikDean (offline) to get access to the SOCoP-OOR admin interface
  • [7:28] Ken will get back to Till about the access to the socop-oor API

(Nancy: don't want to go public with this yet) and "Observations and Measurements (OM)" (Gary: while it still has parsing error)

  • [8:29] Peter will follow-up with Ken & Till ref. the focus of next Tuesday's OOR-Hackathon (n.05 - Tue 2013.11.19)

7. Any Other Business:

  • ...

8. Schedule Next Meeting & Adjourn:

  • Next Meetings:
    • Next Tuesday: Tue 2013_11_12 - OOR Hackathon n.05 - topic? - co-chairs: Till Mossakowski & Ken Baclawski
    • also, see above
    • ... please mark your calendars and make sure you can come!
  • Call adjourned at: 8:29 am PST

--

notes taken by: Peter P. Yim / 2013.11.12-8:33am 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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