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OpenOntologyRepository: OOR "Hackathon" Session (n.03) - Tue 2013_07_30

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

Session Co-chairs: TillMossakowski & KenBaclawski

This is the 3rd 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, 30-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
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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

  • review and finish defining the OOR-Ontohub-Gatekeeper API
  • start setting up requirements on the handling of ontology categorization and ontology metadata
  • set deliverables, due dates and follow-up action plans
  • decide on future sessions ... possibly an open session on ontology categorization
  • ... (add yours)

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:

  • 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 Review of previous meetings' decision and action items

  • 2013.06.18: we agreed to focus on developing three things (hopefully within the next 3 months): the set of metadata, the API, and some shared thoughts on the UI (ref.)
  • 2013.06.25: we reached consensus that we will be formalizing the API as discussed using the (OMG) Interface Definition Language (IDL) (v3.5)

3.2 work for this hackathon session

  • review and finish defining the OOR-Ontohub-Gatekeeper API
  • start setting up requirements on the handling of ontology categorization and ontology metadata
  • set deliverables, due dates and follow-up action plans
  • decide on future sessions ... possibly an open session on ontology categorization

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.

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_20130730

2013-07-30 GMT-08:00 [PDT]

[6:56] Peter P. Yim: Welcome to the

OpenOntologyRepository: OOR Hackathon Session n.03 - Tue 2013_07_30

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

Session Co-chairs: Till Mossakowski & Ken Baclawski

This is the first of 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.

session page: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2013_07_30

Attendees: Till Mossakowski (co-chair), Ken Baclawski (co-chair), Aleksandra Sojic, DanielCoutoVale, Michael Grüninger, Peter P. Yim, Todd Schneider

Proceedings

[7:02] Peter P. Yim: Till: Daniel and Aleksandra are on the same voice line with me

[7:02] Peter P. Yim: Michael: I need to leave in an hour

[7:04] Peter P. Yim: == Till: let's start with the IDL interface

[7:04] Till Mossakowski: https://github.com/ontohub/OOR_Ontohub_API/blob/master/src/Ontology.idl

[7:05] Peter P. Yim: Till: Daniel has completely revised the interface (API)

[7:08] Michael Grüninger: my github id is gruninger

[7:09] Till Mossakowski: OK, have added you

[7:10] Peter P. Yim: Till: API needs to be compatible with OMV - ref. http://ontolog.cim3.net/cgi-bin/wiki.pl?OMV

[7:18] Till Mossakowski: TODO: links, covering both ontology alignments, as well as the relation between an OWL version

and the CL version of an ontology

[7:21] Till Mossakowski: an initial ontology of links can be found at https://github.com/ontohub/ontohub/blob/master/syntax/dol-rdf.omn

[7:29] Till Mossakowski: [consensus] links are a fundamental notion, hardwired into the API. But the properties of links

are expressed using a meta ontology.

[7:30] Peter P. Yim: == Gatekeeper API discussion

[7:31] Till Mossakowski: [consensus] gatekeeper is included, but modified in that it is about access of users to repositories

(the latter in turn contain ontologies)

[7:32] Peter P. Yim: == Till: discussing the meta-ontology on categories

[7:33] Peter P. Yim: ... Aleksandra explains her work

[7:33] Till Mossakowski: please find the latest version at https://github.com/ontohub/OOR_Ontohub_API/blob/master/Domain_fields.owl

[7:33] Till Mossakowski: raw version for Protégé: https://raw.github.com/ontohub/OOR_Ontohub_API/master/Domain_fields.owl

[7:45] Peter P. Yim: Till: this is a meta-ontology on subjects only

[7:46] Peter P. Yim: Ken / Michael: ref. dimensions identified in Ontology Summit 2007 - see: http://ontolog.cim3.net/cgi-bin/wiki.pl?OntologySummit2007_Framework_Session#nid10HH

[7:50] Todd Schneider: Why can't the 'categories' of ontology subject be instances of a class 'category' and thus the range of 'hasSubject'?

[7:55] Peter P. Yim: at the OOR level, maybe we want to "under-specify" ... and leave it to the domain-specific

Ontology Repositories (open or otherwise) to define their own categorization

[7:58] Ken Baclawski: The ontology classification should be a distributed ontology in several senses of "distributed".

[7:59] Till Mossakowski: However, all these meta ontologies should be properly aligned, such that they form a

distributed ontology, which can also (using DOL's combine construct) by combined into one big meta ontology.

[8:00] Till Mossakowski: This lifts federation among ontology repositories to the level of meta ontologies, which also

need to be federated and aligned.

[8:01] Aleksandra Sojic: The first version of the Domain-fields-ontology ( https://raw.github.com/ontohub/OOR_Ontohub_API/master/Domain_fields.owl )

provides a meta-classification that according to the domain subjects distributes domain-ontologies into the domain-specific

classes. The first version (respecting the specification of the International Standard Classification of Education (ISCED))

consists of 102 classes. The revised version, extended with biological and medical categories consists of 225 classes.

[8:01] Till Mossakowski: Michael: we should work in a bottom up way, looking at existing meta classifications for ontologies.

[8:03] Till Mossakowski: Michael: we should not freeze things in advance

[8:02] Peter P. Yim: @Aleksandra & Till - ref. the categorization proposed earlier by Mike Dean - http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR_SandBox_Customization#nid30RG

- would this categorization be a subset of the "Domain_fields.owl" ontology now?

[8:04] Till Mossakowski: @Peter: no, it is not (yet)

[7:58] Till Mossakowski: [consensus] OOR and Ontohub should only have a coarse-grained meta-ontology for subject classification.

Different communities will have more specific OOR / Ontohub instances, with more specialized meta ontologies.

The latter should be maintained by these specialized communities.

[8:07] Till Mossakowski: for Ontohub, we plan that the user can add new categories on-the-fly. This is a bit like tagging.

However, we want to force the user to place the new category at some position in the class tree of the meta ontology.

[8:07] Till Mossakowski: This new category can then later be accepted, modified or rejected by the maintainer of the meta ontology.

[8:09] Peter P. Yim: I suspect we are having the same discussion that the schema.org people were having! :)

[8:09] Todd Schneider: Good suggestion

[8:12] Peter P. Yim: ... [on further discussion, adopting schema.org doesn't seem very appropriate] point well taken;

we can't just adopt schema.org ... their scope and use case is very different from ours

[8:15] Todd Schneider: Bottom up is not necessarily bad, only when it's unconstrained.

[8:16] Todd Schneider: Have to go. Cheers.

[8:24] Till Mossakowski: Peter: we have agreed on 1) API, 2) metadata, 3) UI. We can discuss all three points.

[8:25] Till Mossakowski: UI=user interface

[8:27] Till Mossakowski: we agreed on having three topics 1) API, 2) metadata, 3) UI

[8:37] Peter P. Yim: to be exact ... we have agreed *to focus on* three topics 1) API, 2) metadata, 3) UI ... and try to complete

work on them in 3 months - ref. 2013.06.18 discussion: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2013_06_18#nid3UE6

[8:28] Till Mossakowski: in detail, we have more agreement on API than on metadata than on UI

[8:30] Peter P. Yim: we will align our (OOR team) thoughts on categorization at the Sep.10 OOR meeting (internally) ... then

schedule a community session, on Tue Sep.24, to get input and buy-in from other major domain communities (like BioPortal,

Geospatial, Standards, etc.)

... [action] ALL: please start thinking who we should be inviting over to that 9/24 session

[8:32] Peter P. Yim: [action] we will start a wiki page for the categories meta-ontology ... to capture developing work, and

help prepare for the Sep-24 community session

[8:38] Peter P. Yim: next meeting - Tue 2013.09.03 - 7:00am PDT / 10:00am EDT / 4:00pm CEST / 3:00pm BST / 1400 UTC - regular

OOR Team (admin & planning) session

[8:38] Peter P. Yim: talk to you all then! Have a wonderful summer holiday in August!

[8:39] Peter P. Yim: very productive session!

[8:39] Peter P. Yim: -- session ended: 8:37am PDT --

-- end in-session chat-transcript --

6. Action items:

  • ...

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 2013.09.24 - 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:

  • no OOR meeting in the month of August, 2013 - Enjoy the Summer, Everyone!
  • next Meeting - Tue 2013.09.03 - Regular OOR Team planning and admin monthly meeting
  • then we'll have - Tue 2013.09.10 - OOR-hackathon n.04 - Co-chairs: Ken Baclawski & Till Mossakowski
  • also scheduled: Tue 2013.09.24 - OOR community session on "Meta-Ontology for Ontology Categories"
  • 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: 8:37 am PDT

--

notes taken by: Peter P. Yim / 2013.07.30-9:59am 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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