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OpenOntologyRepository: "OOR-Ontohub-Gatekeeper API" Hackathon Session - Tue 2013_06_25

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

Session Co-chairs: TillMossakowski & KenBaclawski

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.

Conference Call Details

  • Date: Tuesday, 25-Jun-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

  • finish defining the OOR-Ontohub API
  • start defining the OOR-Gatekeeper requirements and then the API
  • set deliverables and due dates
  • ... (add yours)

Resources

Agenda & Proceedings

Archives:

1. Meeting called to order:

  • Till Mossakowski & Ken Baclawski took the chair and welcome everyone
  • Ken Baclawski 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:

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
    • explore how we might possibly leverage

... 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_20130625

2013-06-25 GMT-08:00 [PDT]

[07:01] Peter P. Yim: Welcome to the

OpenOntologyRepository: "OOR-Ontohub-Gatekeeper API" Hackathon Session - Tue 2013_06_25

Session Topic: The "OOR-Ontohub-Gatekeeper API" Hackathon (3TNE)

Session Co-chairs: Till Mossakowski & Ken Baclawski (3TNF)

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_06_25

Attendees: Till Mossakowski (co-chair), Ken Baclawski (co-chair), Bob Smith, Oliver Kutz, Peter P. Yim, ToddSchneider.

Proceedings

[07:11] Ken Baclawski: please point your browsers to the Ontohub-OOR API working document (google-doc)

- at: http://tinyurl.com/onto-arch

[07:19] Till Mossakowski: We do not require the API to be minimal, but a minimal set of methods shall be identified.

Derived methods can be implemented in terms of the minimal set; a reference implementation will show how to do this.

[07:20] Till Mossakowski: We will include also the methods from BioPortal not being in the OORService API

[07:21] Till Mossakowski: The API should not be specific to any kind of ontology framework.

[07:26] Till Mossakowski: the method delivering all ontology latest version is take from

the BioPortal API: http://www.bioontology.org/wiki/index.php/BioPortal_REST_services

[7:31] Till Mossakowski: Ken: what about "latest draft version" vs. "latest released version"?

[7:34] Ken Baclawski: The API should incorporate the branching of a software repository service such as git.

[7:35] Till Mossakowski: we should incorporate some aspects of the git API, involving repositories and branches

[7:36] Till Mossakowski: Peter: ontologies provide a richer structure (classes, attributes, modules) than

files in a file system

[7:42] Ken Baclawski: Each ontology has a URI and it follows linked data principles.

[7:45] Peter P. Yim: ref. consensus from our Jun-18 OOR-Strategy meeting - we will focused on developing

three things (hopefully within the next 3 months): the set of metadata, the API, and some shared thoughts

on the UI - see: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2013_06_18#nid3UE6

[7:56] Ken Baclawski: The method for retrieving symbols and sentences should have a filter parameter.

[7:56] Till Mossakowski:

<Ontology name="FamilyBase" logic="OWL2" refname="FamilyBase" relxpath="/">

<Declarations>

<Symbol kind="Class" name="Father">Class Father</Symbol>

<Symbol kind="Class" name="Female">Class Female</Symbol>

<Symbol kind="Class" name="Grandmother">Class Grandmother</Symbol>

<Symbol kind="Class" name="Hybrid">Class Hybrid</Symbol>

<Symbol kind="Class" name="Man">Class Man</Symbol>

<Symbol kind="Class" name="Married">Class Married</Symbol>

<Symbol kind="Class" name="MarriedMother">Class MarriedMother</Symbol>

<Symbol kind="Class" name="Mother">Class Mother</Symbol>

<Symbol kind="Class" name="MotherWithManyChildren>Class MotherWithManyChildren</Symbol>

<Symbol kind="Class" name="MotherWithoutDaughter>Class MotherWithoutDaughter</Symbol>

<Symbol kind="Class" name="Parent>Class Parent</Symbol>

<Symbol kind="Class" name="Person>Class Person</Symbol>

<Symbol kind="Class" name="Wife>Class Wife</Symbol>

<Symbol kind="Class" name="Woman>Class Woman</Symbol>

<Symbol kind="ObjectProperty" name="hasChild>ObjectProperty hasChild</Symbol>

<Symbol kind="ObjectProperty" name="hasHusband>ObjectProperty hasHusband</Symbol>

<Symbol kind="ObjectProperty" name="hasParent>ObjectProperty hasParent</Symbol>

<Symbol kind="Individual" name="clara>NamedIndividual clara</Symbol>

<Symbol kind="Individual" name="john>NamedIndividual john</Symbol>

<Symbol kind="Individual" name="mary>NamedIndividual mary</Symbol>

</Declarations>

<Axioms>

<Axiom>Class: Person</Axiom>

<Axiom>Class: Female</Axiom>

<Axiom>Class: Woman

EquivalentTo: Person and Female</Axiom>

<Axiom>Class: Man

EquivalentTo: Person and not Woman</Axiom>

<Axiom>ObjectProperty: hasParent</Axiom>

<Axiom>ObjectProperty: hasChild

InverseOf: hasParent</Axiom>

<Axiom>ObjectProperty: hasHusband</Axiom>

<Axiom>Class: Mother

EquivalentTo: Woman and hasChild some Person</Axiom>

<Axiom>Class: Father

EquivalentTo: Man and hasChild some Person</Axiom>

<Axiom>Class: Parent

EquivalentTo: Father or Mother</Axiom>

<Axiom>Class: Grandmother

EquivalentTo: Mother and hasChild some Parent</Axiom>

<Axiom>Class: MotherWithManyChildren

EquivalentTo: Mother and hasChild min 3 Thing</Axiom>

<Axiom>Class: MotherWithoutDaughter

EquivalentTo: Mother and hasChild only (not Woman)</Axiom>

<Axiom>Class: Wife

EquivalentTo: Woman and hasHusband some Man</Axiom>

<Axiom>Class: Married</Axiom>

<Axiom>Class: MarriedMother

EquivalentTo: Mother and Married</Axiom>

<Axiom>Class: MarriedMother

SubClassOf: Female and Person</Axiom>

<Axiom>Class: Hybrid

EquivalentTo: Woman and Man</Axiom>

<Axiom>Individual: mary

Types: Mother</Axiom>

<Axiom>Individual: mary

Facts: hasChild john</Axiom>

<Axiom>Individual: john

Types: Father</Axiom>

<Axiom>Individual: john

Facts: hasChild clara</Axiom>

<Axiom>Individual: clara</Axiom>

</Axioms>

</Ontology>

[8:02] Till Mossakowski: We want to have one single method for retrieval, with a lot of parameters for

controlling what is selected/filtered

[8:07] Ken Baclawski: There should be a minimum collection of metrics that every repository instance should provide.

[8:07] Till Mossakowski: metadata includes stored metadata, as well as computed metadata (like metrics)

[8:09] Todd Schneider: The parameters for controlling what is selected/filtered will need to be tied

to 'metadata' maintained by the repository (hence available for individuation).

[8:10] Todd Schneider: I thought we had considered using the 'metadata' as a template (via XSLT or

a similar translation) for filtering.

[8:11] Todd Schneider: Each parameter in the metadata becomes a possible 'filter'.

[8:12] Till Mossakowski: OMG IDL 3.5 (tmp link): http://www.informatik.uni-bremen.de/~till/OMG-IDL-3.5-ptc-13-02-02.pdf

[8:20] Ken Baclawski: The consensus is to formalize the API in IDL 3.5.

[8:28] Ken Baclawski: Ken will formalize the gatekeeper in IDL.

[8:29] Todd Schneider: I really have to go. Cheers.

[8:31] Ken Baclawski: Next hackathon session is on July 16 at the same time, same topic. Till and Ken will be providing their IDL documents.

[8:32] Ken Baclawski: Meeting is adjourned.

[8:32] vnc2: very productive session!

[8:32] Peter P. Yim: -- session ended: 8:32am PDT --

-- end in-session chat-transcript --

6. Action items:

  • 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

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

  • decide if we want to take Aug-2013 off too (like the Ontolog community)
  • we probably want to schedule 2~3 more meetings/events (past Jul-2)

8. Schedule Next Meeting & Adjourn:

  • Next Meetings:
    • next Meeting Tue 2013.07.02 - OOR Metadata Workshop-VIII: "Metadata in Ontology Mapping" with FIBO as our use case - co-chairs: Michael Grüninger & Mike Bennett
    • next OOR-Hackathon (n.02) - Tue 2013.07.16 - Co-chair: Ken Baclawski & Till Mossakowski
    • ... please mark your calendars and make sure you can come!
  • Call adjourned at: 8:32 am PDT

--

notes taken by: Peter P. Yim / 2013.06.25-6:29pm 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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