OOR/ConferenceCall 2011 11 08

= 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
 * ref: World Clock
 * Expected Call Duration: ~1.5 hours


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 * RSVP  to [mailto:peter.yim@cim3.com peter.yim@cim3.com] appreciated, ... or simply just by adding yourself to the "Expected Attendee" list below (if you are a member of the community.)


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 * This session, like all other Ontolog events, is open to the public. Information relating to this session is shared on this wiki page: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_11_08


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Attendees

 * Attended:
 * MikeDean (chair)
 * PeterYim (scribe)
 * KenBaclawski
 * MichaelGruninger
 * EricChan (discussant)
 * ToddSchneider


 * 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  so that we can reserve enough resources to support everyone's participation. ...
 * ... 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. ...


 * Regrets:
 * LeoObrst
 * RayFergerson (offline input)
 * PaulAlexander (offline input)
 * CameronRoss (offline input)
 * TimDarr

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
Archives:


 * audio recording of the session
 * chat-transcript of this session

1. Meeting called to order:


 * MikeDean takes the chair and welcome everyone
 * review and adopt agenda
 * PeterYim volunteered to take notes

2. Roll Call:


 * see above


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

3. Status Review and Discussion:


 * Review and update our "Most Critical Task(s) At Hand" list
 * ref. http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository#nid17YH

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."
 * Is a common IDE good for us? Is Eclipse an optimal answer?
 * input from RayFergerson & PaulAlexander (NCBO): - RayFergerson: "Talked to PaulAlexander about Eclipse usage. We use the vanilla J2EE installation
 * input from CameronRoss: - "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:
 * EricChan: most of my comments will be in the form of questions
 * EricChan: assuming there will an svn to host the source code
 * MikeDean: yes, BioPortal is on an svn repository ... although there are talks about considering moving this to git.
 * EricChan: is this an open source project under OOR, or under other more high profile projects (e.g. Apache, Eclipse, ...)?
 * EricChan: OOR does have a svn repository going at semwebcentral; we'll probably run on our own (OOR initiative, rather than under other opensource projects)
 * EricChan: are codes going to be contributed back to BioPortal
 * MikeDean: the BioPortal folks are receptive; but we will see when things are more mature
 * EricChan: triple store may not be most optimal for OOR, a mysql may be more appropriate
 * MikeDean: 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
 * EricChan: 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
 * KenBaclawski: we have developed use cases, and your user types are already included as actors in our use cases
 * EricChan: 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
 * ToddSchneider: we will have different modules (based on different structures) for content that is in different constructs/languages ... that would be our "language modules"
 * EricChan: 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
 * MichaelGruninger: the OntoIOp people are trying to provide something that would help tackle "heterogeneous" ontologies - allowing interactions between ontologies of different languages
 * EricChan: the Sakai Project (http://sakaiproject.org/) learning management system (which started using jackrabbit) used a mysql backend quite successfully (in terms of scalability)
 * EricChan: what are we using for indexing? (their tweak was to offload the indexing from JCR ...)
 * MikeDean: lucene is being used now
 * EricChan: how about scalability issues if costly functions need to be performed at the server side (e.g. validation, inferencing)?
 * KenBaclawski: currently, for things like validation, BioPortal does that in the background, and come back when it is done
 * EricChan: 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] PeterYim: Welcome to the

OpenOntologyRepository: OOR Development Workshop-V - Tue 2011_11_08

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

Session Chair: MikeDean

Session page: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_11_08

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

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

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

[08:43] ToddSchneider: 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] MikeDean: 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] MikeDean: 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] MikeDean: 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] PeterYim: see: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_11_08#nid2YYK the placeholder page is up at: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR_DeveloperTools

[09:55] Eric S. Chan: http://java.net/projects/open-icom/pages/Home

[09:59] ToddSchneider: Have to go. Cheers.

[10:11] PeterYim: very productive meeting ... Thanks, everyone!

[10:11] PeterYim: -- 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:


 * MikeDean: 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:


 * KenBaclawski: it would be helpful to find out from PaulAlexander which specific "[[WebTools]" package](s) he is using ... question for the Nov-29 session (if not sooner)


 * MikeDean 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:

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."
 * 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 RayFergerson & PaulAlexander (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
 * Preparation for the Nov-29 session: all developers are requested to have reviewed the BioPortal "tab" development criteria, and hopefully, has done a "hello world" tab, prior to this session.
 * ref. details at: at: http://palexander.posterous.com/extending-bioportals-rails-ui


 * MikeDean: 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: MikeDean - 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: PeterYim / 2011.11.08-10:10am PST All participants, please review and edit to enhance accuracy and granularity of the documented proceedings.

Resources

 * homepage - OpenOntologyRepository - http://OpenOntologyRepository.org
 * OOR Charter - To promote the global use and sharing of ontologies by: 1. establishing a hosted registry-repository; 2. enabling and facilitating open, federated, collaborative ontology repositories; 3. establishing best practices for expressing interoperable ontology and taxonomy work in registry-repositories.
 * "Ontology Repository" Definition - "An ontology repository is a facility where ontologies and related information artifacts can be stored, retrieved and managed"
 * Team mailling list:
 * OOR-Team discussion: [ oor-forum ]''' message archives - http://ontolog.cim3.net/forum/oor-forum/
 * OOR-Users discussion and support: [ oor-users ]''' message archives - http://ontolog.cim3.net/forum/oor-users/
 * Developers mailling list: [ oor-dev ] message archives - http://ontolog.cim3.net/forum/oor-dev/
 * proceedings of our previous meetings, panel discussions and workshops
 * the Joint OOR-OntologySummit2008 Panel Discussions:
 * 2008_02_28 - Thursday: Joint OOR-OntologySummit2008 Panel Discussion: "Ontology Registry and Repository Technology & Infrastructure Landscape" - Co-chairs: LeoObrst & FrankOlken; Panelists: BruceBargmeyer, MikeDean, MarkMusen, FarrukhNajmi & PeterYim - ConferenceCall_2008_02_28
 * 2008_03_27 - Thursday: Joint OOR-OntologySummit2008 Panel Discussion: "An Open Ontology Repository: Rationale, Expectations & Requirements - Session-1" - Chair: LeoObrst & FabianNeuhaus; Panelists: WilliamBug, EvanWallace, JohnLMcCarthy, KenBaclawski, PeterBenson & RexBrooks - ConferenceCall_2008_03_27
 * 2008_04_03 - Thursday: Joint OOR-OntologySummit2008 Panel Discussion: "An Open Ontology Repository: Rationale, Expectations & Requirements - Session-2" - Chair: LeoObrst & FabianNeuhaus; Panelists: DougLenat, DekeSmith, MarciaZeng, DeniseBedford, PatHayes, MalaMehrotra & RobRaskin - ConferenceCall_2008_04_03
 * 2008_04_10 - Thursday: Joint OOR-OntologySummit2008 Panel Discussion: "Developing an Ontology of Ontologies for OOR" - Co-chairs: BarrySmith & MichaelGruninger; Panelists: MichaelGruninger, PeterHaase, NatashaNoy & ElisaKendall - ConferenceCall_2008_04_10
 * the OOR Development panel sessions:
 * 2008_08_22 - Friday: OOR Panel Discussion: "Getting OOR Development Off the Ground: Identifying Synergies & Gaps" (Take-1) - Chair: LeoObrst; Panelists: MikeDean, MarkMusen, LiDing, BruceBargmeyer & BillAndersen - ConferenceCall_2008_08_22
 * 2009_02_19 - Thursday: Joint Ontolog-OOR Panel Discussion: "Getting OOR Development Off the Ground (Take-2): the work begins" - Chair: ToddSchneider; Panelists: MarkMusen, NatashaNoy, MikeDean, PaulBuitelaar / AndreasHarth, MathieuDaquin, KenBaclawski, MichaelGruninger - ConferenceCall_2009_02_19
 * 2009_07_16 - Thursday: Joint Ontolog-OOR Panel Discussion: "Integrated tools for ontology development and management: A field guide to the Stanford technology" - Chair: MarkMusen - Panelists: TaniaTudorache, TimRedmond, NatashaNoy - ConferenceCall_2009_07_16
 * 2009_07_30 - Thursday: Joint Ontolog-OOR Panel Discussion: "BioPortal and related Ontology Repository Implementations and Development" (Take-3) - Chair: NatashaNoy - Panelists: CarlosRueda, PaulAlexander, JohnGraybeal, MikeDean, StephenGranite, AlexGarcia, KenBaclawski - ConferenceCall_2009_07_30
 * 2010_02_19 - Friday: OOR Panel Discussion: "Coordinating our Open Ontology Repository Software Development" - Chair: MikeDean - Panelists: JimChatigny, MichaelGruninger, KenBaclawski, NatashaNoy - OOR/ConferenceCall_2010_02_19
 * 2010_04_01 - Thursday: Joint OOR-Ontolog Panel Session: "OOR Use Cases - Take-3" - Chair: KenBaclawski & ToddSchneider - Panelists: ToddSchneider, MatthewHettinger, KenBaclawski and MaximoGurmendez - ConferenceCall_2010_04_01
 * 2010_09_10 - Friday: Joint SIO-OOR-Ontolog Panel Discussion: "Common Logic (CL) Support for OOR" - Chair: JohnSowa - Panelists: JohnBateman-TillMossakowski, MichaelGruninger, CameronRoss, AdamPease, PatHayes - ConferenceCall_2010_09_10
 * 2010_09_17 - Friday: OOR Panel Discussion - "Getting OOR Development Going - Take-IV" Workshop - Co-chairs: ToddSchneider & MichaelGruninger - Panelists: ToddSchneider, MikeDean, NatashaNoy, ImmanuelNormann, KenBaclawski, MichaelGruninger - OOR/ConferenceCall_2010_09_17
 * 2010_10_15 - Friday: OOR Project Team Member Conference Call - discussion on the (post-BioPortal fork) OOR Architecture and API - OOR/ConferenceCall_2010_10_15
 * 2010_11_19 - Friday: OOR Panel Discussion - "(Post-BioPortal fork) OOR Architecture and API - Take-II" - Co-chairs: KenBaclawski & MichaelGruninger - Panelists: KenBaclawski+ToddSchneider, AldoGangemi+AlessandroAdamou, JouniTuominen+KimViljanen, EricChan - OOR/ConferenceCall_2010_11_19
 * 2011_03_04 - Friday: OOR "Architecture & API Specification Development Workshop-I" - Co-chairs: KenBaclawski & ToddSchneider - OOR/ConferenceCall_2011_03_04
 * 2011_03_11 - Friday: OOR - "Architecture & API Specification Development Workshop-II" - Co-chairs: KenBaclawski & ToddSchneider - OOR/ConferenceCall_2011_03_11
 * 2011_03_18 - Friday: OOR Metadata Workshop-I - Chair: MichaelGruninger - OOR/ConferenceCall_2011_03_18
 * 2011_03_25 - Friday: OOR - "Architecture & API Specification Development Workshop-III" - Co-chairs: KenBaclawski & ToddSchneider - OOR/ConferenceCall_2011_03_25
 * 2011_04_22 - Friday: OOR - "Architecture & API Specification Development Workshop-IV" - Co-chairs: KenBaclawski & ToddSchneider - OOR/ConferenceCall_2011_04_22
 * 2011_05_13 - Friday: OOR Metadata Workshop-II - Chair: MichaelGruninger - OOR/ConferenceCall_2011_05_13
 * 2011_05_20 - Friday: OOR - "Architecture & API Specification Development Workshop-V" - Co-chairs: KenBaclawski & ToddSchneider - OOR/ConferenceCall_2011_05_20
 * 2011_05_27 - Friday: OOR Metadata Workshop-III - Chair: MichaelGruninger - OOR/ConferenceCall_2011_05_27
 * 2011_06_17 - Friday: OOR - "Architecture & API Specification Development Workshop-VI" - Co-chairs: KenBaclawski & ToddSchneider - OOR/ConferenceCall_2011_06_17
 * 2011_09_13 - Tuesday: Joint NCBO-OOR Team Meeting - "Kicking-off the Next Phase of Collaboration" - Co-chairs: RayFergerson & PeterYim - OOR/ConferenceCall_2011_09_13
 * 2011_09_20 - Tuesday: OOR - "Architecture & API Specification Development Workshop-VII" - Co-chairs: KenBaclawski & ToddSchneider - OOR/ConferenceCall_2011_09_20
 * 2011_10_11 - Tuesday: OOR - "Architecture & API Specification Development Workshop-VII" - Co-chairs: KenBaclawski & ToddSchneider - OOR/ConferenceCall_2011_10_11
 * 2011_10_18 - Friday: OOR Metadata Workshop-IV - Chair: MichaelGruninger - OOR/ConferenceCall_2011_10_18
 * 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: GeorgeStrawn - Chair: PeterYim - Panelists: JamieClark, JohnWilbanks, BrucePerens - 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: MarkMusen - Panelists: CameronRoss, AlanRector, JohnSowa, BrucePerens, JohnWilbanks, PeterYim - 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: LeoObrst - Panelists: PeterYim, MikeDean, BrucePerens, JamieClark - ConferenceCall_2010_09_30
 * OntologySummit2008 homepage
 * OntologySummit2008_Communique
 * OntologySummit2008/FaceToFaceAgenda & Proceedings
 * The OOR Project Presentation (delivered at the OntologySummit2008 face-to-face workshop)
 * [ ontology-summit ] discussion archives - http://ontolog.cim3.net/forum/ontology-summit/2008-01/ (~5 months exchanges starting from Jan-2008)
 * Our key content pages:
 * OpenOntologyRepository_Scope
 * OpenOntologyRepository_Organization
 * OpenOntologyRepository_Process
 * OpenOntologyRepository_Policy
 * OpenOntologyRepository_IPR
 * OpenOntologyRepository_Requirement
 * OpenOntologyRepository_UseCases
 * OpenOntologyRepository_Architecture
 * OpenOntologyRepository_Approach
 * OpenOntologyRepository_Roadmap
 * OpenOntologyRepository_Plan
 * OpenOntologyRepository_Funding
 * OpenOntologyRepository_ResearchIssues
 * OpenOntologyRepository_ResearchActivity
 * OpenOntologyRepository_Development
 * OpenOntologyRepository_Metadata
 * OOR/ActiveMemberContribution
 * OOR Project site at SemWebCentral - http://oor.semwebcentral.org
 * Public instances of OOR - http://sandbox.oor.net/ontologies (previously http://oor-01.cim3.net/ontologies) ... we are in process to standing up:
 * OOR_SandBox - http://oor-03.cim3.net - http://sandbox.oor.net/
 * OOR_DevBox - http://oor-01.cim3.net - http://dev.oor.net/
 * NCBO - BioPortal
 * BioPortal's [bioontology-support] mailing list - see: https://mailman.stanford.edu/mailman/listinfo/bioontology-support
 * NCBO-OOR development documentation - http://www.bioontology.org/wiki/index.php/NCBO-OOR_Development