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OpenOntologyRepository: Architecture & API Workshop-X - Tue 2012_01_31

Topic: "OOR Architecture & API Specification Development Workshop-X"

Session Co-chairs: Dr. Todd Schneider & Professor KenBaclawski

Conference Call Details

  • Date: Tuesday, 31-Jan-2012
  • Start Time: 8:30am PST / 11:30am EST / 5:30pm CET / 16:30 UTC
  • Expected Call Duration: ~1.5 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:
    • ... 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 <peter.yim@cim3.com> so that we can reserve enough resources to support everyone's participation. ...

Session Abstract & Resources

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.

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).

The EA HTML report can be found at http://ontolog.cim3.net/file/work/OOR/oor-dev/BioPortal_Build3253_Nov2011_EA_Model--ToddSchneider_20120130/BioPortal_Build3253_EA_HTML_Report/index.html

See also: OpenOntologyRepository_Architecture & OpenOntologyRepository_Architecture/Candidate03

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.

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

Here is the proposed organizing plan: OpenOntologyRepository_Architecture/GettingOrganized

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

The following are relevant prior meetings:

Agenda Ideas

  • walk-thru of the (reverse engineered)(EA) UML model of the BioPortal source

code build 3253 (circa November 2011)

  • go back-and-forth with the ongoing stock "OOR Architecture & API" discussions, namely ...
    • the OOR Architecture
    • the OOR API
    • the Organizing Plan
    • the default development platform

Agenda & Proceedings

Archives:

1. Meeting called to order:

  • Peter P. Yim volunteered to keep a record of the proceedings
  • review and adopt agenda

2. Roll Call & Adoption of last meeting's minutes:

  • see above
  • introduction of new members (as required)
  • review of agenda

3. Key items for review and discussion today:

  • Announcements and Urgent Matters:
  • review of the reversed engineering BioPortal build 3253 (circa Nov-2011) UML model
  • discuss our plans referencing the updated BioPortal implementation
  • status review of our infrastructure and development resources and platform

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

  • Review of action item(s) from the previous meeting(s)
  • from 2011.06.17 - Michael Grüninger will examine the OMV to determine which attributes are required and which are optional.
  • from 2011.06.17 - Ken Baclawski will send KEEPER (the gatekeeping software) to Todd Schneider who will generate the UML.
  • "OOR Architecture & API Specification Development Workshop-VIII:" (Archives)
  • 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.
    • Each OOR instance declares what ontology languages it supports.
    • Every OOR instance MUST support RDFS.
      • This is required because the metadata is expressed in OMV.
      • OMV is written in OWL, but it may be sufficient to require only RDFS. This needs to be investigated.
    • Other ontology languages MAY be supported.
    • For each metadata attribute, it will be specified whether it is required or optional.
      • It MUST be specified whether the ontology is available (or to be available in the future).
      • The ontology language MUST be specified.
      • Other attributes will be handled offline by Michael Grüninger based on the OMV specification.
    • An ontology must satisfy other requirements depending on the ontology language.
      • Syntax checking is always required.
      • Consistency checking is required with some time limit.
  • Proposal for Partition of Components
    • Presentation
      • A minimal presentation module with just search and workflow
      • Browse (already in BioPortal-based sandbox)
      • Search (already in BioPortal-based sandbox)
      • Mapping (already in BioPortal-based sandbox)
      • Recommender (already in BioPortal-based sandbox)
      • Annotator (already in BioPortal-based sandbox)
      • Resource Index (already in BioPortal-based sandbox)
      • Workflow Administration
      • OOR Instance Administration
      • Other windows
    • Workflow
      • Already developed, but needs to be documented
    • Registrar
      • A minimal registrar
    • Find
      • Initially adapt a SPARQL endpoint. Which one?
    • Inference
      • Initially a part of the SPARQL endpoint
      • Other inference engines
    • Persistence
      • Initially adapt 4Store
    • Administration
      • TBD
    • Federation
      • TBD
  • Chat transcript of this session:

--- Chat transcript begin: ---

Peter P. Yim: Welcome to the

OpenOntologyRepository: Architecture & API Workshop-X - Tue 2012_01_31

Topic: "OOR Architecture & API Specification Development Workshop-X"

Session Co-chairs: Dr. Todd Schneider & Professor Ken Baclawski

Conference Call Details:

  • Date: Tuesday, 31-Jan-2012
  • Start Time: 8:30am PST / 11:30am EST / 5:30pm CET / 16:30 UTC
  • Expected Call Duration: ~1.5 hours

Session page: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2012_01_31

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

.

Proceedings:

.

Peter P. Yim: The EA HTML report Todd has just produced can be found at http://ontolog.cim3.net/file/work/OOR/oor-dev/BioPortal_Build3253_Nov2011_EA_Model--ToddSchneider_20120130/BioPortal_Build3253_EA_HTML_Report/index.html

Todd: ref. http://ontolog.cim3.net/file/work/OOR/oor-dev/

Todd Schneider: http://ontolog.cim3.net/file/work/OOR/oor-dev/BioPortal_Build3253_Nov2011_EA_Model--ToddSchneider_20120130/

Todd: the xml file is at: http://ontolog.cim3.net/file/work/OOR/oor-dev/BioPortal_Build3253_Nov2011_EA_Model--ToddSchneider_20120130/BioPortal_Build3253_Nov2011_EA_Model.xml

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

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

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

(b) Mike Dean on "federation", and

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

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

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

can be easily adapted to new BioPortal releases

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

Mike Dean: it's easy to add new tabs to the UI

Mike Dean: http://palexander.posterous.com/extending-bioportals-rails-ui

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

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

Todd Schneider: How will access control across federates be handled?

Todd Schneider: There may be additional fields from OMV that OOR will need.

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

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

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

The workflow tab will initially expose the uploading capability of the gatekeeper functionality.

Other gatekeeper capabilities/functionalities will be exposed on other tabs.

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

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

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

Ken Baclawski: Subject: [oor-dev] Problem with extending the UI

I am trying to extend the BioPortal Rails UI on oor-03 using

http://palexander.posterous.com/extending-bioportals-rails-ui

It seems one must use

cd [[OOR/ConferenceCall_2012_01_31/srv/ncbo/rails/BioPortal/current]]

rather than

cd [[OOR/ConferenceCall_2012_01_31/var/rails/BioPortal/current]]

There is a script/generate, but when I try running it, I get

/usr/bin/env: ruby: No such file or directory

Does anyone have some idea of how this can be fixed?

-- Ken

Peter P. Yim: Ken has fired the above question to Paul Alexander - http://ontolog.cim3.net/forum/oor-dev/2012-01/msg00016.html

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

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

the 'Submit New Ontology' functionality to a new tab, called 'Submit'?

Todd Schneider: Have to go.

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

Peter P. Yim: who is anonymous?

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

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

Peter P. Yim: good meeting ... got a lot done ... bye!

Peter P. Yim: -- session ended: 10:14am PST --

--- Chat transcript end: ---

Consensus, Conclusions & Follow-up Actions:

4. Any Other Business:

5. Action items:

6. Schedule Next Meeting & Adjourn:

  • Next Meeting:
    • Regular OOR team meeting next week - Tue 2012.02.07 same time - OOR/ConferenceCall_2012_02_07
      • Mike Dean: I'll probably have to miss that meeting, as I will be traveling.
    • we'll plan other events at that meeting
  • Call adjourned at: 10:14 am PST

--

notes taken by: Peter P. Yim / 2012.01.31-11:01am PST

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

Resources

  • 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
  • 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
    • 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



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