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OpenOntologyRepository: "OOR-Ontohub-Gatekeeper API" Hackathon Session - Tue 2013_06_25     (1)

Session Topic: The "OOR-Ontohub-Gatekeeper API" Hackathon     (1A)

Session Co-chairs: TillMossakowski & KenBaclawski     (1B)

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.     (1C)

  • Dial-in:     (1D4)
    • Phone (US): +1 (206) 402-0100 ... (long distance cost may apply)     (1D4A)
    • Skype: joinconference (i.e. make a skype call to the contact with skypeID="joinconference") ... (generally free-of-charge, when connecting from your computer ... ref.)     (1D4B)
      • when prompted enter Conference ID: 141184#     (1D4B1)
      • Unfamiliar with how to do this on Skype? ...     (1D4B2)
        • 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.     (1D4B2A)
      • Can't find Skype Dial pad? ...     (1D4B3)
        • for Windows Skype users: Can't find Skype Dial pad? ... it's under the "Call" dropdown menu as "Show Dial pad"     (1D4B3A)
        • for Linux Skype users: please note that the dial-pad is only available on v4.1 (or later; or on 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.)     (1D4B3B)
  • Discussions and Q & A:     (1D5)
    • Nominally, when a presentation is in progress, the moderator will mute everyone, except for the speaker.     (1D5A)
    • 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.)     (1D5B)
    • 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.)     (1D5C)
    • 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.)     (1D5D)
    • 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").     (1D6A)
    • 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.     (1D6B)
    • thanks to the 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) ... Handy for mobile devices!     (1D6C)
  • Shared-screen support (VNC session), if applicable, will be started 5 minutes before the call at:     (1D7)
    • view-only password: "ontolog"     (1D7A)
    • 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.     (1D7B)
    • 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.     (1D7C)
  • RSVP to appreciated, ... or simply just by adding yourself to the "Expected Attendee" list below (if you are a member of the team.)     (1D9)
  • 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.     (1D11)

Attendees     (1E)

  • Expecting:     (1E2)
    • (please add yourself to the list above if you are a member of the community, or, rsvp to <> with the event title/date and your name and affiliation)     (1E3A)

Agenda Ideas     (1E5)

Resources     (1E6)

Agenda & Proceedings     (1F)

1. Meeting called to order:     (1F5)

2. Roll Call:     (1F10)

3. Key discussion:     (1F13)

4. Prior Discussions:     (1F14)

4.1 Discussion: tactically, what shall we be doing differently in the next 6 to 12 months     (1F15)

... to provide synergies for all.     (1F17)

4.2 Setting the metrics - what does "success" look like     (1F18)

4.3 Action planning for "content drive" (getting people to upload ontologies) ... (deferred discussion of this item)     (1F19)

  • (discussion 2011.05.06):     (1F20)
    • an adopted Architecture & API is definitely crucial, but that's not all     (1F20A)
  • All team members are encouraged to mull over how we can get to that state effectively     (1F21)
    • in particular ... how do we make this a "successful" community-driven, open source project!?     (1F21A)
  • (discussion 2011.08.07) ...     (1F22)
    • ref. IAOA Committee and SIG session at FOIS (2012.07.25) discussion:     (1F22A)
      • IAOA Ontology Registry and Repository Committee to put focus on contents     (1F22A1)
      • getting FOIS papers to be submitted with cited ontologies and their metadata, and have those ontologies hosted on OOR     (1F22A2)
  • 4.6 Getting us to a stage when we can run a OOR-production box ... (deferred discussion of this item)     (1F26)
    • we need a gatekeeping/policy module in place - [KenBaclawski]     (1F26A)
  • 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 ...     (1F27)
    • 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.)     (1F27A)
    • 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     (1F27B)
    • we will make to be an ontology registry, which then links to the ontologies in the actual ontology repository where the ontology is described     (1F27C)
    • 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     (1F27D)
    • after that, we will focus on building up content with each OOR node tackling the domain(s) they are best with     (1F27E)

5. IM Chat Transcript captured during the session     (1G)

see raw transcript here.     (1G1)

(for better clarity, the version below is a re-organized and lightly edited chat-transcript.)     (1G2)

Participants are welcome to make light edits to their own contributions as they see fit.     (1G3)

-- begin in-session chat-transcript --     (1G4)

Chat transcript from room: oor_20130625     (1G5)

2013-06-25 GMT-08:00 [PDT]     (1G6)

[07:01] Peter P. Yim: Welcome to the     (1G7)

OpenOntologyRepository: "OOR-Ontohub-Gatekeeper API" Hackathon Session - Tue 2013_06_25     (1G8)

Session Topic: The "OOR-Ontohub-Gatekeeper API" Hackathon (3TNE)     (1G9)

Session Co-chairs: Till Mossakowski & Ken Baclawski (3TNF)     (1G10)

This is the first of a series of regular activities for the OOR team. The plan is to devote one meeting     (1G11)

a month to intense coding (or other low level development) work.     (1G12)

Attendees: Till Mossakowski (co-chair), Ken Baclawski (co-chair), Bob Smith, Oliver Kutz, Peter P. Yim, ToddSchneider.     (1G14)

Proceedings     (1G15)

[07:11] Ken Baclawski: please point your browsers to the Ontohub-OOR API working document (google-doc)     (1G16)

[07:19] Till Mossakowski: We do not require the API to be minimal, but a minimal set of methods shall be identified.     (1G18)

Derived methods can be implemented in terms of the minimal set; a reference implementation will show how to do this.     (1G19)

[07:20] Till Mossakowski: We will include also the methods from BioPortal not being in the OORService API     (1G20)

[07:21] Till Mossakowski: The API should not be specific to any kind of ontology framework.     (1G21)

[07:26] Till Mossakowski: the method delivering all ontology latest version is take from     (1G22)

[7:31] Till Mossakowski: Ken: what about "latest draft version" vs. "latest released version"?     (1G24)

[7:34] Ken Baclawski: The API should incorporate the branching of a software repository service such as git.     (1G25)

[7:35] Till Mossakowski: we should incorporate some aspects of the git API, involving repositories and branches     (1G26)

[7:36] Till Mossakowski: Peter: ontologies provide a richer structure (classes, attributes, modules) than     (1G27)

files in a file system     (1G28)

[7:42] Ken Baclawski: Each ontology has a URI and it follows linked data principles.     (1G29)

[7:45] Peter P. Yim: ref. consensus from our Jun-18 OOR-Strategy meeting - we will focused on developing     (1G30)

three things (hopefully within the next 3 months): the set of metadata, the API, and some shared thoughts     (1G31)

[7:56] Ken Baclawski: The method for retrieving symbols and sentences should have a filter parameter.     (1G33)

<Ontology name="FamilyBase" logic="OWL2" refname="FamilyBase" relxpath="/">     (1G35)

<Declarations>     (1G36)

<Symbol kind="Class" name="Father">Class Father</Symbol>     (1G37)

<Symbol kind="Class" name="Female">Class Female</Symbol>     (1G38)

<Symbol kind="Class" name="Grandmother">Class Grandmother</Symbol>     (1G39)

<Symbol kind="Class" name="Hybrid">Class Hybrid</Symbol>     (1G40)

<Symbol kind="Class" name="Man">Class Man</Symbol>     (1G41)

<Symbol kind="Class" name="Married">Class Married</Symbol>     (1G42)

<Symbol kind="Class" name="MarriedMother">Class MarriedMother</Symbol>     (1G43)

<Symbol kind="Class" name="Mother">Class Mother</Symbol>     (1G44)

<Symbol kind="Class" name="MotherWithManyChildren>Class MotherWithManyChildren</Symbol>     (1G45)

<Symbol kind="Class" name="MotherWithoutDaughter>Class MotherWithoutDaughter</Symbol>     (1G46)

<Symbol kind="Class" name="Parent>Class Parent</Symbol>     (1G47)

<Symbol kind="Class" name="Person>Class Person</Symbol>     (1G48)

<Symbol kind="Class" name="Wife>Class Wife</Symbol>     (1G49)

<Symbol kind="Class" name="Woman>Class Woman</Symbol>     (1G50)

<Symbol kind="ObjectProperty" name="hasChild>ObjectProperty hasChild</Symbol>     (1G51)

<Symbol kind="ObjectProperty" name="hasHusband>ObjectProperty hasHusband</Symbol>     (1G52)

<Symbol kind="ObjectProperty" name="hasParent>ObjectProperty hasParent</Symbol>     (1G53)

<Symbol kind="Individual" name="clara>NamedIndividual clara</Symbol>     (1G54)

<Symbol kind="Individual" name="john>NamedIndividual john</Symbol>     (1G55)

<Symbol kind="Individual" name="mary>NamedIndividual mary</Symbol>     (1G56)

</Declarations>     (1G57)

<Axiom>Class: Person</Axiom>     (1G59)

<Axiom>Class: Female</Axiom>     (1G60)

<Axiom>Class: Woman     (1G61)

EquivalentTo: Person and Female</Axiom>     (1G62)

<Axiom>Class: Man     (1G63)

EquivalentTo: Person and not Woman</Axiom>     (1G64)

<Axiom>ObjectProperty: hasParent</Axiom>     (1G65)

<Axiom>ObjectProperty: hasChild     (1G66)

InverseOf: hasParent</Axiom>     (1G67)

<Axiom>ObjectProperty: hasHusband</Axiom>     (1G68)

<Axiom>Class: Mother     (1G69)

EquivalentTo: Woman and hasChild some Person</Axiom>     (1G70)

<Axiom>Class: Father     (1G71)

EquivalentTo: Man and hasChild some Person</Axiom>     (1G72)

<Axiom>Class: Parent     (1G73)

EquivalentTo: Father or Mother</Axiom>     (1G74)

<Axiom>Class: Grandmother     (1G75)

EquivalentTo: Mother and hasChild some Parent</Axiom>     (1G76)

EquivalentTo: Mother and hasChild min 3 Thing</Axiom>     (1G78)

EquivalentTo: Mother and hasChild only (not Woman)</Axiom>     (1G80)

<Axiom>Class: Wife     (1G81)

EquivalentTo: Woman and hasHusband some Man</Axiom>     (1G82)

<Axiom>Class: Married</Axiom>     (1G83)

<Axiom>Class: MarriedMother     (1G84)

EquivalentTo: Mother and Married</Axiom>     (1G85)

<Axiom>Class: MarriedMother     (1G86)

SubClassOf: Female and Person</Axiom>     (1G87)

<Axiom>Class: Hybrid     (1G88)

EquivalentTo: Woman and Man</Axiom>     (1G89)

<Axiom>Individual: mary     (1G90)

Types: Mother</Axiom>     (1G91)

<Axiom>Individual: mary     (1G92)

Facts: hasChild john</Axiom>     (1G93)

<Axiom>Individual: john     (1G94)

Types: Father</Axiom>     (1G95)

<Axiom>Individual: john     (1G96)

Facts: hasChild clara</Axiom>     (1G97)

<Axiom>Individual: clara</Axiom>     (1G98)

</Axioms>     (1G99)

</Ontology>     (1G100)

[8:02] Till Mossakowski: We want to have one single method for retrieval, with a lot of parameters for     (1G101)

controlling what is selected/filtered     (1G102)

[8:07] Ken Baclawski: There should be a minimum collection of metrics that every repository instance should provide.     (1G103)

[8:07] Till Mossakowski: metadata includes stored metadata, as well as computed metadata (like metrics)     (1G104)

[8:09] Todd Schneider: The parameters for controlling what is selected/filtered will need to be tied     (1G105)

to 'metadata' maintained by the repository (hence available for individuation).     (1G106)

[8:10] Todd Schneider: I thought we had considered using the 'metadata' as a template (via XSLT or     (1G107)

a similar translation) for filtering.     (1G108)

[8:11] Todd Schneider: Each parameter in the metadata becomes a possible 'filter'.     (1G109)

[8:20] Ken Baclawski: The consensus is to formalize the API in IDL 3.5.     (1G111)

[8:28] Ken Baclawski: Ken will formalize the gatekeeper in IDL.     (1G112)

[8:29] Todd Schneider: I really have to go. Cheers.     (1G113)

[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.     (1G114)

[8:32] Ken Baclawski: Meeting is adjourned.     (1G115)

[8:32] vnc2: very productive session!     (1G116)

[8:32] Peter P. Yim: -- session ended: 8:32am PDT --     (1G117)

-- end in-session chat-transcript --     (1G118)

6. Action items:     (1G119)

7. Any Other Business: ... (deferred to the next meeting)     (1G121)

  • decide if we want to take Aug-2013 off too (like the Ontolog community)     (1G122)
  • we probably want to schedule 2~3 more meetings/events (past Jul-2)     (1G123)

8. Schedule Next Meeting & Adjourn:     (1G124)

notes taken by: Peter P. Yim / 2013.06.25-6:29pm PDT     (1G128)

All participants, please review and edit to enhance accuracy and granularity of the documented proceedings.     (1G129)

Resources     (1H)

  • the Joint IAOA-OOR-Ontolog "Ontologies and Standards" mini-series:     (1H18)

This page has been migrated from the OntologWiki - Click here for original page     (1H27)