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OpenOntologyRepository: OOR Development Workshop-V - Tue 2011_11_08

This is our "Getting OOR Development Going - Take V" workshop which we will devote to the topic of how best to getting real OOR-related open source software development work going ...

Topic: "Getting OOR Development Going, on Eclipse?"

Session Chair: MikeDean

* * * Please pay special attention to the time of this event, as both the US and Europe are back to Standard Time (winter time) already! * * *

* * * Please also note that we are calling into a new conference bridge starting from this session, note the new dial-in information! * * *

Conference Call Details

  • Date: Tuesday, 8-Nov-2011
  • 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 appreciated, ... or simply just by adding yourself to the "Expected Attendee" list below (if you are a member of the team.)
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  • Expecting:
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Agenda Ideas

please insert any additional items below (along with your name for follow-up purposes)

  • identifying issues that are holding back the OOR-oss-dev work
  • Is a common IDE good for us? Is Eclipse an optimal answer?
  • Task distribution and getting organized
  • Action planning (with consensus milestones)
  • ... (please add to the above)

Agenda & Proceedings


1. Meeting called to order:

  • Mike Dean takes the chair and welcome everyone
  • review and adopt agenda
  • Peter P. Yim volunteered to take notes

2. Roll Call:

  • welcome and intro of new member(s) (as needed)

3. Status Review and Discussion:

4. Key items for review and discussion today

Topic: "Getting OOR Development Going (V), on Eclipse?"

  • identifying issues that are holding back the OOR-oss-dev work

and there is really nothing special to talk about. The only thing that Paul mentioned is to enable the "WebTools" package. This comes standard with the J2EE version of Eclipse. It can be enabled in the UI in the "Servers" view. This tool allows you to start and stop tomcat easily and to set breakpoints in your code. Probably any Eclipse user already knows about it."

    • input from Cameron Ross: - "For what it's worth, I do believe that Eclipse is the right choice for a tooling platform to support BioPortal development."
    • Discussion - 2011.11.08
  • EricChan's views and some responses:
    • Eric Chan: most of my comments will be in the form of questions
    • Eric Chan: assuming there will an svn to host the source code
      • Mike Dean: yes, BioPortal is on an svn repository ... although there are talks about considering moving this to git.
    • Eric Chan: is this an open source project under OOR, or under other more high profile projects (e.g. Apache, Eclipse, ...)?
      • Eric Chan: OOR does have a svn repository going at semwebcentral; we'll probably run on our own (OOR initiative, rather than under other opensource projects)
    • Eric Chan: are codes going to be contributed back to BioPortal
    • Eric Chan: triple store may not be most optimal for OOR, a mysql may be more appropriate
      • Mike Dean: I am torn on this; I believe this move by BioPortal is good. I know CL may be an issue, but maybe we can do some trick on indexing
    • Eric Chan: as I see it, you are addressing 3 sets of users: (i) developers of the OOR system, (ii) those using OOR to host, manage and/or even edit their ontologies, and (iii) end users who will be applying the ontologies hosted on OOR
      • Ken Baclawski: we have developed use cases, and your user types are already included as actors in our use cases
    • Eric Chan: how are we managing metadata? maybe the metadata can be in the triple store? I have not seen triple stores being used for big chunks of data
      • Todd Schneider: we will have different modules (based on different structures) for content that is in different constructs/languages ... that would be our "language modules"
        • Eric Chan: it would be best if there is a "guideline on how to develop a language module" and the API for language module developers to plug into
      • Todd / Mike: most are already covered by the way BioPortal has implemented it; the outliers are Common Logic (CLIF) languages and Rules languages
      • Michael Grüninger: the OntoIOp people are trying to provide something that would help tackle "heterogeneous" ontologies - allowing interactions between ontologies of different languages
    • Eric Chan: the Sakai Project ( learning management system (which started using jackrabbit) used a mysql backend quite successfully (in terms of scalability)
    • Eric Chan: what are we using for indexing? (their tweak was to offload the indexing from JCR ...)
    • Eric Chan: how about scalability issues if costly functions need to be performed at the server side (e.g. validation, inferencing)?
      • Ken Baclawski: currently, for things like validation, BioPortal does that in the background, and come back when it is done
    • Eric Chan: the OOR team will need a small team of "gatekeepers" to qualify and admit code contributions, in this open source software setting
  • Discussion as captured in the [ in-session chat]

--- Chat transcript begin ---

[08:31] Peter P. Yim: Welcome to the

OpenOntologyRepository: OOR Development Workshop-V - Tue 2011_11_08

Topic: "Getting OOR Development Going, on Eclipse?"

Session Chair: Mike Dean

Session page:

When everyone is muted: To un-mute, press "*7" ... To mute, press "*6"


[08:40] Eric S. Chan: dual track, bioportal release and OOR branch

[08:41] Eric S. Chan: subversion repository for OOR

[08:43] Todd Schneider: Mike, how decouple the indexing from the language representation?

[08:58] Eric S. Chan: the infrastructure will manage content and metadata

[08:59] Eric S. Chan: content may be persisted in some CMS with version control support

[08:59] Eric S. Chan: metadata may be triple store and Lucene indices

[09:03] Eric S. Chan: persistent layer is pluggable (a language module may provide a persistence mechanism)

[09:11] Mike Dean: OOR should allow for ontologies containing components in different languages

(e.g. OWL and RIF or OWL and Common Logic, like OWL Time). This also relates to views and modules.

[09:16] Mike Dean: It might be interesting to provide at least a SPARQL endpoint for Jackrabbit.

This could make a good student project.

[09:17] Eric S. Chan: bioportal provides background processing for validation (theorem proving),

OOR may define these processes as SOA services

[09:28] Eric S. Chan: E:\jaxb-ri-20110115\bin\xjc.bat schema-obh-xjc.xsd schema-obr.xsd -extension

[09:37] Mike Dean: It would help bootstrap development to create an OOR Developer Tools page with

links to JAXRS specifications, tools to generate client bindings, and (soon) results of

generating those bindings.

[09:45] Peter P. Yim: see:

the placeholder page is up at:

[09:55] Eric S. Chan:

[09:59] Todd Schneider: Have to go. Cheers.

[10:11] Peter P. Yim: very productive meeting ... Thanks, everyone!

[10:11] Peter P. Yim: -- session ended: 10:10am PST --

--- Chat transcript end ---

  • Task distribution and Getting organized ... (discussion deferred to the next session)
  • Action planning with consensus milestones ... (discussion deferred to the next session)

5. Getting Organized:

  • Mike Dean: suggest starting a wiki page for OOR_DeveloperTools to share some of the experience and provide some consensus on tools to use

6. Action items:

  • Mike Dean will look through the current BioPortal project to see what they are using; which will eventually get us to a reference developer platform for OOR developers
  • Develop a "guideline on how to develop a language module" and the API for language module developers to plug into [suggested by Eric - Ken & Todd to work on]

7. Any Other Business:

  • The Joint NCBO-OOR session: OOR-Architecture-API IX - "NCBO-OOR architectural considerations and synergies" + "creating BioPortal Tabs" is now scheduled for Tue 2011.11.29; same time
    • input from Ray Fergerson & Paul Alexander (NCBO): "We also agree that it would be best, rather than scheduling a meeting now, that developers just install the "hello world" tab and get it up and

going. This is likely to lead to both narrow and broad questions. The narrow ones Paul can handle in email and the broad ones may require either a phone call or additional example code. We would rather this be a pull system, where developers request information just in time, rather than a push one where we try to push information out in the hopes that it will be useful."

  • Mike Dean: an emerging developer team may come up to do work for SOCoP, with student from UWM, James Madison U & U of Maryland College Park

8. Schedule Next Meeting & Adjourn:

  • Next Meeting:
    • we agreed that there will be no OOR meeting next week (Nov-15) because STIDS will be in session that week
    • what shall we focus on for the Tue 2011.11.22 OOR meeting - "Getting OOR Development Going - VI" - Chair: Mike Dean - OOR/ConferenceCall_2011_11_22
      • in the mean time, address the action items identified today!
    • after that, it will be the Joint OOR-NCBO "Architecture-API" session described above - - OOR/ConferenceCall_2011_11_29
  • Call adjourned at: 10:10 am PST


notes taken by: Peter P. Yim / 2011.11.08-10:10am PST

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