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OpenOntologyRepository: Architecture & API Workshop-X - Tue 2012_01_31     (1)

Topic: "OOR Architecture & API Specification Development Workshop-X"     (1A)

Session Co-chairs: Dr. Todd Schneider & Professor KenBaclawski     (1B)

  • Shared-screen support (VNC session), if applicable, will be started 5 minutes before the call at:     (1C5)
    • view-only password: "ontolog"     (1C5A)
    • 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.     (1C5B)
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    • 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!     (1C6C)
  • Discussions and Q & A:     (1C7)
    • Nominally, when a presentation is in progress, the moderator will mute everyone, except for the speaker.     (1C7A)
    • 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.)     (1C7B)
    • 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.)     (1C7C)
    • 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.)     (1C7D)
  • RSVP to appreciated, ... or simply just by adding yourself to the "Expected Attendee" list below (if you are a member of the team.)     (1C9)
  • 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.     (1C11)

Attendees     (1E)

  • Expecting:     (1E2)
    • ... if you are coming to the meeting, please add your name above (plus your affiliation, if you aren't already a member of the community) above, or e-mail <> so that we can reserve enough resources to support everyone's participation. ...     (1E3A)

Session Abstract & Resources     (1E5)

With this workshop we'll start reviewing the BioPortal build 3253 source code (from November 2011) to see how it fits into the current OOR (draft) architecture and identify changes or additions that need to made to the source code or the architecture.     (1E5A)

The review will be based on an HTML report from the Enterprise Architect (EA) UML model of the (reverse engineered) BioPortal source code build 3253 (circa November 2011).     (1E5B)

In addition, there is an API of the core services that was obtained from anearlier implementation BioPortal, which is not entirely compatible with the straw man architecture, but furnishes a starting point. This API will also be discussed and modified as needed.     (1E5E)

Finally, we need to agree on a plan for completing the development of the specification.     (1E5H)

We encourage all participants to update your candidate contributions to ensure your ideas are known and understood.     (1E5J)

The following are relevant prior meetings:     (1E5K)

Agenda Ideas     (1F)

code build 3253 (circa November 2011)     (1F2)

Agenda & Proceedings     (1G)

1. Meeting called to order:     (1G4)

2. Roll Call & Adoption of last meeting's minutes:     (1G8)

3. Key items for review and discussion today:     (1G12)

  • status review of our infrastructure and development resources and platform     (1G16)

... items below are mostly from the previous workshop, and will be updated as this session progresses.     (1G17)

  • Gatekeeping specifies the a set of minimal requirements that any ontology within the OOR has to meet. The latter are intended to enable the users of the OOR to find quickly ontologies that fit their needs; the criteria are not supposed to ensure the quality of the ontologies.     (1G22)

--- Chat transcript begin: ---     (1G25)

OpenOntologyRepository: Architecture & API Workshop-X - Tue 2012_01_31     (2)

Topic: "OOR Architecture & API Specification Development Workshop-X"     (2A)

Session Co-chairs: Dr. Todd Schneider & Professor Ken Baclawski     (2B)

Conference Call Details:     (2C)

  • Start Time: 8:30am PST / 11:30am EST / 5:30pm CET / 16:30 UTC     (2E)

Can't find Skype Dial pad? ... it's under the "Call" dropdown menu as "Show Dial pad"     (2H)

Proceedings:     (2J)

Todd / Ken: ref. MikeDean's question: "are javadoc's available?" ... answer: seemingly "no!"     (2J6)

Peter P. Yim: [consensus] our approach toward code contribution (/extension from the BioPortal codebase):     (2J7)

(a) KenBaclawski-ToddSchneider to focus on "gatekeeping";     (2J8)

(b) Mike Dean on "federation", and     (2J9)

(c) Michael Grüninger on "metadata" then "mapping"     (2J10)

Todd Schneider: Action Plan: Michael and his team will focus on metadata (and then mapping); Mike Dean will focus on federation capabilities; Ken and Todd will focus on workflow     (2J11)

Mike Dean: like idea of an OOR service layer that includes OOR-specific services (e.g. Find) and     (2J12)

can be easily adapted to new BioPortal releases     (2J13)

Peter P. Yim: as far as ncbo-RayFergerson is concerned, he'd appreciate all code extensions to be implemented on "tabs"     (2J14)

Mike Dean: it's easy to add new tabs to the UI     (2J15)

Todd Schneider: The three 'action items' will have there own tabs: adjuncts to the current BioPortal UI     (2J17)

Todd Schneider: Need to find out if BioPortal data model supports 'location' (i.e., repository location/id) information     (2J18)

Todd Schneider: How will access control across federates be handled?     (2J19)

Todd Schneider: There may be additional fields from OMV that OOR will need.     (2J20)

Todd Schneider: Can the OMV interface be generated dynamically from the OMV ontology? This may break some existing BioPortal code.     (2J21)

Todd Schneider: Each of items of the 'action plan' will be added as a new tab (on the current UI).     (2J22)

Todd Schneider: The federation tab will be labeled 'Federation' (this may only be visible to administrators);     (2J23)

The workflow tab will initially expose the uploading capability of the gatekeeper functionality.     (2J24)

Other gatekeeper capabilities/functionalities will be exposed on other tabs.     (2J25)

Todd Schneider: Another action item is to agree on tab labels for the 'upload' and 'metadata' tabs.     (2J26)

Peter P. Yim: [action] targeting this - Mike, Ken & Michael will all try to have a prototype tab     (2J27)

(even just a "hello world" tab) done by our next workshop     (2J28)

Ken Baclawski: Subject: [oor-dev] Problem with extending the UI     (2J29)

I am trying to extend the BioPortal Rails UI on oor-03 using     (2J30)

It seems one must use     (2J32)

cd [[OOR/ConferenceCall_2012_01_31/srv/ncbo/rails/BioPortal/current]]     (2J33)

rather than     (2J34)

cd [[OOR/ConferenceCall_2012_01_31/var/rails/BioPortal/current]]     (2J35)

There is a script/generate, but when I try running it, I get     (2J36)

/usr/bin/env: ruby: No such file or directory     (2J37)

Does anyone have some idea of how this can be fixed?     (2J38)

Peter P. Yim: Mike Dean gave a brief report on the SOCoP-OOR at the INTEROP NSF PI meeting     (2J41)

Todd Schneider: Can we pose a question to BioPortal to see if they would be open to moving     (2J42)

the 'Submit New Ontology' functionality to a new tab, called 'Submit'?     (2J43)

Ken Baclawski: I will continue to find out how to fix the captcha feature. Until it is fixed, captcha is off.     (2J45)

Peter P. Yim: who is anonymous?     (2J46)

Peter P. Yim: let's talk about the next workshops at next Tuesday's regular OOR team meeting     (2J47)

Peter P. Yim: Mike Dean: I'll probably be missing next week's meeting, because i'll be traveling     (2J48)

Peter P. Yim: good meeting ... got a lot done ... bye!     (2J49)

Peter P. Yim: -- session ended: 10:14am PST --     (2J50)

--- Chat transcript end: ---     (2J51)

Consensus, Conclusions & Follow-up Actions:     (2J52)

4. Any Other Business:     (2J53)

5. Action items:     (2J54)

6. Schedule Next Meeting & Adjourn:     (2J55)

notes taken by: Peter P. Yim / 2012.01.31-11:01am PST     (2J59)

All participants, please review and edit to enhance accuracy and granularity of the documented proceedings.     (2J60)

Resources     (2K)

  • the Joint IAOA-OOR-Ontolog "Ontologies and Standards" mini-series:     (2K13)
    • 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     (2K13A)
    • 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     (2K13B)
    • 2011_12_15 - Thursday: Joint IAOA-OOR-Ontolog "Ontologies and Standards" mini-series session-3: "ISO/IEC 24707 Common Logic and IKL" - Co-chairs: Michael Grüninger & John Bateman - ConferenceCall_2011_12_15     (2K13C)

This page has been migrated from the OntologWiki - Click here for original page     (2K20)