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= [[OpenOntologyRepository]]: OOR Development Workshop-V - Tue 2011_11_08 =
= [[OpenOntologyRepository]]: OOR Development Workshop-VI - Tue 2011_11_22 =


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


Topic: "'''Getting OOR Development Going, on Eclipse?'''"  
Topic: "'''Getting OOR Development Going - Take VI'''"  


Session Chair: '''MikeDean'''  
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! * * *'''


=== [[MeetingsCalls|Conference Call]] Details  ===
=== [[MeetingsCalls|Conference Call]] Details  ===


* Date: '''Tuesday, 8-Nov-2011'''  
* Date: '''Tuesday, 22-Nov-2011'''  
* Start Time: 8:30am PST / 11:30am EST / 5:30pm CET / 16:30 UTC  
* Start Time: 8:30am PST / 11:30am EST / 5:30pm CET / 16:30 UTC  
** ref: [http://www.timeanddate.com/worldclock/fixedtime.html?month=11&day=8&year=2011&hour=8&min=30&sec=0&p1=224 World Clock]  
** ref: [http://www.timeanddate.com/worldclock/fixedtime.html?month=11&day=22&year=2011&hour=8&min=30&sec=0&p1=224 World Clock]  
* Expected Call Duration: ~1.5 hours  
* Expected Call Duration: ~1.5 hours  


* Dial-in:  
* Dial-in:  
** '''Phone (US): +1 (206) 402-0100''' ''(long distance cost will apply)'' ... [ backup nbr: (415) 671-4335 ]  
** '''Phone (US): +1 (206) 402-0100''' ''long distance cost will apply)''  
*** ... [ backup nbr: (415) 671-4335 ]  
** '''Skype: joinconference''' ... ''(free-of-charge if you connect through skype from your computer/device with an Internet connection)''  
** '''Skype: joinconference''' ... ''(free-of-charge if you connect through skype from your computer/device with an Internet connection)''  
** when prompted enter '''PIN: 141184#'''  
** when prompted enter '''PIN: 141184#'''  


* '''In-session chat'''-room url: http://webconf.soaphub.org/conf/room/oor_20111108
* '''In-session chat'''-room url: http://webconf.soaphub.org/conf/room/oor_20111122


* '''Shared-screen support''' (VNC session), if applicable, will be started 5 minutes before the call at: http://vnc2.cim3.net:5800/  
* '''Shared-screen support''' (VNC session), if applicable, will be started 5 minutes before the call at: http://vnc2.cim3.net:5800/  
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** people behind corporate firewalls may have difficulty accessing this. If that is the case, please download the '''[ slides above]''' (where applicable) and running them locally. The speaker(s) will prompt you to advance the slides during the talk.  
** people behind corporate firewalls may have difficulty accessing this. If that is the case, please download the '''[ slides above]''' (where applicable) and running them locally. The speaker(s) will prompt you to advance the slides during the talk.  


* '''In-session chat'''-room url: http://webconf.soaphub.org/conf/room/ontolog_20111108
* '''In-session chat'''-room url: http://webconf.soaphub.org/conf/room/ontolog_20111122
** 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").  
** 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").  
** 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.  
** 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.  
** thanks to the soaphub.org 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) ontolog_20111108@soaphub.org ... Handy for mobile devices!  
** thanks to the soaphub.org 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) ontolog_20111122@soaphub.org ... Handy for mobile devices!  


* '''Discussions and Q & A:'''  
* '''Discussions and Q & A:'''  
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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 team.)  
* '''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 team.)  


* 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
* 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_22


* 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 [[WikiHomePage#Intellectual_Property_Rights_.28IPR.29_Policy|our prevailing open IPR policy]].  
* 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 [[WikiHomePage#Intellectual_Property_Rights_.28IPR.29_Policy|our prevailing open IPR policy]].  
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** [[PeterYim|Peter P. Yim]] (scribe)  
** [[PeterYim|Peter P. Yim]] (scribe)  
** [[User:KennethBaclawski|Ken Baclawski]]  
** [[User:KennethBaclawski|Ken Baclawski]]  
** [[ToddSchneider|Todd Schneider]]
** [[MichaelGruninger|Michael Grüninger]]  
** [[MichaelGruninger|Michael Grüninger]]  
** [[EricChan|Eric Chan]] (discussant)
** [[BrianDavis|Brian Davis]]  
** [[ToddSchneider|Todd Schneider]]  


* Expecting:  
* Expecting:  
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* Regrets:  
* Regrets:  
** [[LeoObrst|Leo Obrst]]  
** [[LeoObrst|Leo Obrst]]  
** [[RayFergerson|Ray Fergerson]] (offline input)
** [[PaulAlexander|Paul Alexander]] (offline input)
** [[CameronRoss|Cameron Ross]] (offline input)
** [[TimDarr|Tim Darr]]


== Agenda Ideas  ==
== Agenda Ideas  ==
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''please insert any additional items below (along with your name for follow-up purposes)''  
''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  
* Identifying issues that are holding back the OOR-oss-dev work  
* Is a common IDE good for us? Is Eclipse an optimal answer?
* Review what it takes to develop upon BioPortal's existing development framework
* Refine how we should move development forward from here
* Task distribution and getting organized  
* Task distribution and getting organized  
* Action planning (with consensus milestones)  
* Action planning (with consensus milestones)  
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'''[http://ontolog.cim3.net/file/work/OpenOntologyRepository/OOR-dev/ Archives]:'''  
'''[http://ontolog.cim3.net/file/work/OpenOntologyRepository/OOR-dev/ Archives]:'''  


* '''[http://ontolog.cim3.net/file/work/OpenOntologyRepository/OOR-dev/OOR-dev-V_20111108b.mp3 audio recording of the session]'''  
* '''[http://ontolog.cim3.net/file/work/OpenOntologyRepository/OOR-dev/OOR-dev-VI_20111122b.mp3 audio recording of the session]''' [ 1:15:41 ; mp3 ; 8.66 MB ]
* '''[http://ontolog.cim3.net/file/work/OpenOntologyRepository/OOR-dev/oor_chat-transcript_20111108a.txt chat-transcript of this session]'''  
* '''[http://ontolog.cim3.net/file/work/OpenOntologyRepository/OOR-dev/oor_chat-transcript_20111122b.txt chat-transcript of this session]'''  


1. Meeting called to order:  
1. Meeting called to order:  
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2. Roll Call:  
2. Roll Call:  


* see [http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_11_08#nid2YTI above]  
* see [http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_11_22#nid2Z91 above]  


* welcome and intro of new member(s) (as needed)  
* welcome and intro of new member(s) (as needed)  
** [[BrianDavis|Brian Davis]] from caBIG's [https://wiki.nci.nih.gov/display/VCDE/Ontology+Representation+WG ORWG] joined us and made an intro of [[ORWG]] and himself


3. Status Review and Discussion:  
3. Status Review and Discussion:  


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


=== 4. Key items for review and discussion today  ===
=== 4. Key items for review and discussion today  ===


Topic: "'''Getting OOR Development Going (V), on Eclipse?'''"  
Topic: "'''Getting OOR Development Going - Take VI'''"  


* identifying issues that are holding back the OOR-oss-dev work  
* identifying issues that are holding back the OOR-dev work  
** [[MikeDean|Mike Dean]]: issues:  limited (or no) time and funding
** [[ToddSchneider|Todd Schneider]]: What to code or fix.
** [[MikeDean|Mike Dean]]: issues:  architectural uncertainty (being resolved)
** [[MichaelGruninger|Michael Grüninger]]: the current implementation restricts ontologies to be specified in OWL
** [[PeterYim|Peter P. Yim]]: being a totally volunteered project does present a challenge
** [[MikeDean|Mike Dean]]: issues:  platform distribution/installation changes (being resolved)


* Is a common IDE good for us? Is Eclipse an optimal answer?
* Issues we could discuss at the Nov-29 joint NCBO-OOR session
** input from [[RayFergerson|Ray Fergerson]] & [[PaulAlexander|Paul Alexander]] (NCBO): - [[RayFergerson|Ray Fergerson]]: "Talked to [[PaulAlexander|Paul Alexander]] about Eclipse usage. We use the vanilla J2EE installation
** [[MikeDean|Mike Dean]]: status of export/import/upgrade process for NCBO appliance
and there is really nothing special to talk about. The only thing that
** [[MikeDean|Mike Dean]]: availability of Java, Ruby, or other client stubs for invoking [[BioPortal]] REST services
Paul mentioned is to enable the [http://www.eclipse.org/webtools/ "WebTools" package]. This comes standard
** [[ToddSchneider|Todd Schneider]]: BioPortal's Roadmap or priorities
with the J2EE version of Eclipse. It can be enabled in the UI in the
** [[PeterYim|Peter P. Yim]]: clearly identify functionalities that either the NCBO or the OOR development team will be pursuing
"Servers" view. This tool allows you to start and stop tomcat easily and
*** [[MikeDean|Mike Dean]]: federation (BBN is happy to contribute their earlier code)
to set breakpoints in your code. Probably any Eclipse user already knows
** [[MikeDean|Mike Dean]]: which specific [http://www.eclipse.org/webtools/ "WebTools" package](s) is [[PaulAlexander|Paul Alexander]] using
about it."
** [[PeterYim|Peter P. Yim]]: I would still hope aligning architecture and API and creating synergies would still be the main focus for that session
** input from [[CameronRoss|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:
* Refine how we should move development forward from here
** [[EricChan|Eric Chan]]: most of my comments will be in the form of questions
** MikeDean/2011.11.08: suggest starting a wiki page for [[OOR_DeveloperTools]] to share some of the experience and provide some consensus on tools to use  
** [[EricChan|Eric Chan]]: assuming there will an svn to host the source code
** KenBaclawski/2011.11.08: it would be helpful to find out from [[PaulAlexander|Paul Alexander]] which specific [http://www.eclipse.org/webtools/ "WebTools" package](s) he is using ... question for the Nov-29 session (if not sooner)  
*** [[MikeDean|Mike Dean]]: yes, [[BioPortal]] is on an svn repository ... although there are talks about considering moving this to git.
** [[EricChan|Eric Chan]]: is this an open source project under OOR, or under other more high profile projects (e.g. Apache, Eclipse, ...)?
*** [[EricChan|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)
** [[EricChan|Eric Chan]]: are codes going to be contributed back to [[BioPortal]]
*** [[MikeDean|Mike Dean]]: the [[BioPortal]] folks are receptive; but we will see when things are more mature
** [[EricChan|Eric Chan]]: triple store may not be most optimal for OOR, a mysql may be more appropriate
*** [[MikeDean|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
** [[EricChan|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
*** [[User:KennethBaclawski|Ken Baclawski]]: we have developed use cases, and your user types are already included as actors in our use cases
** [[EricChan|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
*** [[ToddSchneider|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"
**** [[EricChan|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
*** [[MichaelGruninger|Michael Grüninger]]: the [[OntoIOp]] people are trying to provide something that would help tackle "heterogeneous" ontologies - allowing interactions between ontologies of different languages
** [[EricChan|Eric Chan]]: the Sakai Project (http://sakaiproject.org/) learning management system (which started using jackrabbit) used a mysql backend quite successfully (in terms of scalability)
** [[EricChan|Eric Chan]]: what are we using for indexing? (their tweak was to offload the indexing from JCR ...)
*** [[MikeDean|Mike Dean]]: lucene is being used now
** [[EricChan|Eric Chan]]: how about scalability issues if costly functions need to be performed at the server side (e.g. validation, inferencing)?
*** [[User:KennethBaclawski|Ken Baclawski]]: currently, for things like validation, [[BioPortal]] does that in the background, and come back when it is done
** [[EricChan|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]
* Task distribution and getting organized - ''(deferred)''
** ...


--- Chat transcript begin ---
* Action planning (with consensus milestones)
 
** [2011.11.08] [[MikeDean|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
[08:31] [[PeterYim|Peter P. Yim]]: Welcome to the  
** [2011.11.08] 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]  
 
** [2011.11.08] '''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.  
[[OpenOntologyRepository]]: OOR Development Workshop-V - Tue 2011_11_08
*** ref. details at: at: http://palexander.posterous.com/extending-bioportals-rails-ui
 
Topic: "Getting OOR Development Going, on Eclipse?"
 
Session Chair: [[MikeDean|Mike Dean]]
 
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|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] [[MikeDean|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] [[MikeDean|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] [[MikeDean|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] [[PeterYim|Peter P. Yim]]: 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|Todd Schneider]]: Have to go. Cheers.
 
[10:11] [[PeterYim|Peter P. Yim]]: very productive meeting ... Thanks, everyone!
 
[10:11] [[PeterYim|Peter P. Yim]]: -- session ended: 10:10am PST --
 
--- Chat transcript end ---  


* Task distribution and Getting organized ... ''(discussion deferred to the next session)''
* ref. also: discussion as captured in the [http://ontolog.cim3.net/file/work/OpenOntologyRepository/OOR-dev/oor_chat-transcript_20111122b.txt in-session chat]
 
* Action planning with consensus milestones ... ''(discussion deferred to the next session)''


5. '''Getting Organized:'''  
5. '''Getting Organized:'''  


* [[MikeDean|Mike Dean]]: suggest starting a wiki page for [[OOR_DeveloperTools]] to share some of the experience and provide some consensus on tools to use
* ''(discussion deferred)''


6. '''Action items:'''  
6. '''Action items:'''  


* [[User:KennethBaclawski|Ken Baclawski]]: it would be helpful to find out from [[PaulAlexander|Paul Alexander]] which specific [http://www.eclipse.org/webtools/ "WebTools" package](s) he is using ... question for the Nov-29 session (if not sooner)
* [2011.11.22]: Peter to start a Nov-29 preparation email thread with Ken, Todd, Ray et al. to tie down the agenda for the 11/29 session  


* [[MikeDean|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
* [2011.11.22]: Brian will post wiki link to HaroldSolbrig's metadata cross-walk work ... and Michael will invite Harold to present that work on Dec-13 for us
 
* 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:'''  
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 [[RayFergerson|Ray Fergerson]] & [[PaulAlexander|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."
** '''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|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:  
8. Schedule Next Meeting & Adjourn:  


* Next Meeting:  
* Next Meetings:  
** we agreed that there will be no OOR meeting next week (Nov-15) because [http://stids.c4i.gmu.edu/ STIDS] will be in session that week
** 2011_11_29: Joint OOR-NCBO "Architecture-API" session - co-chair: [[User:KennethBaclawski|Ken Baclawski]] & [[ToddSchneider|Todd Schneider]] - [[OOR/ConferenceCall_2011_11_29]]  
** what shall we focus on for the Tue 2011.11.22 OOR meeting - "Getting OOR Development Going - VI" - Chair: [[MikeDean|Mike Dean]] - [[OOR/ConferenceCall_2011_11_22]]  
** 2011_12_06: regular OOR team meeting - [[OOR/ConferenceCall_2011_12_06]]
*** in the mean time, address the action items identified today!
** 2011_12_13: OOR-metadata workshop take-V - chair: [[MichaelGruninger|Michael Grüninger]] - [[OOR/ConferenceCall_2011_12_13]]  
** after that, it will be the Joint OOR-NCBO "Architecture-API" session described [http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_11_08#nid2YUO above] -  - [[OOR/ConferenceCall_2011_11_29]]  


* Call adjourned at: 10:10 am PST  
* Call adjourned at: 9:51 am PST  


--
--


notes taken by: [[PeterYim|Peter P. Yim]] / 2011.11.08-10:10am PST
notes taken by: [[PeterYim|Peter P. Yim]] / 2011.11.08-10:03am PST


All participants, please review and edit to enhance accuracy and granularity of the documented proceedings.  
All participants, please review and edit to enhance accuracy and granularity of the documented proceedings.  
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** 2011_10_11 - Tuesday: OOR - "Architecture & API Specification Development Workshop-VII" - Co-chairs: [[User:KennethBaclawski|Ken Baclawski]] & [[ToddSchneider|Todd Schneider]] - [[OOR/ConferenceCall_2011_10_11]]  
** 2011_10_11 - Tuesday: OOR - "Architecture & API Specification Development Workshop-VII" - Co-chairs: [[User:KennethBaclawski|Ken Baclawski]] & [[ToddSchneider|Todd Schneider]] - [[OOR/ConferenceCall_2011_10_11]]  
** 2011_10_18 - Friday: OOR Metadata Workshop-IV - Chair: [[MichaelGruninger|Michael Grüninger]] - [[OOR/ConferenceCall_2011_10_18]]  
** 2011_10_18 - Friday: OOR Metadata Workshop-IV - Chair: [[MichaelGruninger|Michael Grüninger]] - [[OOR/ConferenceCall_2011_10_18]]  
** 2011_11_08 - Tuesday: "Getting OOR Development Going - Take-V" Workshop - Chair: [[MikeDean|Mike Dean]] - "Getting OOR Development going, on Eclipse?" - [[OOR/ConferenceCall_2011_11_08]]
** 2011_11_22 - Tuesday: "Getting OOR Development Going - Take-VI" Workshop - Chair: [[MikeDean|Mike Dean]] - [[OOR/ConferenceCall_2011_11_22]]
* the '''OOR-IPR mini-series''':  
* 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|George Strawn]] - Chair: [[PeterYim|Peter P. Yim]] - Panelists: [[JamieClark]], [[JohnWilbanks|John Wilbanks]], [[BrucePerens|Bruce Perens]] - ConferenceCall_2010_09_09  
** 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|George Strawn]] - Chair: [[PeterYim|Peter P. Yim]] - Panelists: [[JamieClark]], [[JohnWilbanks|John Wilbanks]], [[BrucePerens|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: [[CameronRoss|Cameron Ross]], [[AlanRector|Alan Rector]], [[JohnSowa|John F. Sowa]], [[BrucePerens|Bruce Perens]], [[JohnWilbanks|John Wilbanks]], [[PeterYim|Peter P. Yim]] - ConferenceCall_2010_09_16  
** 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: [[CameronRoss|Cameron Ross]], [[AlanRector|Alan Rector]], [[JohnSowa|John F. Sowa]], [[BrucePerens|Bruce Perens]], [[JohnWilbanks|John Wilbanks]], [[PeterYim|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: [[LeoObrst|Leo Obrst]] - Panelists: [[PeterYim|Peter P. Yim]], [[MikeDean|Mike Dean]], [[BrucePerens|Bruce Perens]], [[JamieClark]] - ConferenceCall_2010_09_30  
** 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|Leo Obrst]] - Panelists: [[PeterYim|Peter P. Yim]], [[MikeDean|Mike Dean]], [[BrucePerens|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: [[JohnBateman|John Bateman]] & [[MichaelGruninger|Michael Grüninger]] - [[ConferenceCall_2011_10_20]]
** 2011_11_03 - Thursday: Joint IAOA-OOR-Ontolog "Ontologies and Standards" mini-series session-2: Invited Speaker: [[ElisaKendall|Elisa Kendall]] on "Ontology-Related Metadata Standards" - Co-chairs: [[MichaelGruninger|Michael Grüninger]] & [[JohnBateman|John Bateman]] - [[ConferenceCall_2011_11_03]]
* '''OntologySummit2008''' homepage  
* '''OntologySummit2008''' homepage  
** '''[[OntologySummit2008_Communique]]'''  
** '''[[OntologySummit2008_Communique]]'''  

Latest revision as of 07:33, 9 January 2016

OpenOntologyRepository: OOR Development Workshop-VI - Tue 2011_11_22

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

Topic: "Getting OOR Development Going - Take VI"

Session Chair: MikeDean

Conference Call Details

  • Date: Tuesday, 22-Nov-2011
  • Start Time: 8:30am PST / 11:30am EST / 5:30pm CET / 16:30 UTC
  • Expected Call Duration: ~1.5 hours
  • Dial-in:
    • Phone (US): +1 (206) 402-0100 long distance cost will apply)
      • ... [ backup nbr: (415) 671-4335 ]
    • Skype: joinconference ... (free-of-charge if you connect through skype from your computer/device with an Internet connection)
    • when prompted enter PIN: 141184#
  • Shared-screen support (VNC session), if applicable, will be started 5 minutes before the call at: http://vnc2.cim3.net:5800/
    • view-only password: "ontolog"
    • 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.
    • people behind corporate firewalls may have difficulty accessing this. If that is the case, please download the [ slides above] (where applicable) and running them locally. The speaker(s) will prompt you to advance the slides during the talk.
  • In-session chat-room url: http://webconf.soaphub.org/conf/room/ontolog_20111122
    • 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").
    • 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.
    • thanks to the soaphub.org 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) ontolog_20111122@soaphub.org ... Handy for mobile devices!
  • Discussions and Q & A:
    • Nominally, when a presentation is in progress, the moderator will mute everyone, except for the speaker.
    • 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.)
    • 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.)
    • 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.)
  • 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 community.)
  • 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. ...

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
  • Review what it takes to develop upon BioPortal's existing development framework
  • Refine how we should move development forward from here
  • Task distribution and getting organized
  • Action planning (with consensus milestones)
  • ... (please add to the above)

Agenda & Proceedings

Archives:

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 - Take VI"

  • identifying issues that are holding back the OOR-dev work
    • Mike Dean: issues: limited (or no) time and funding
    • Todd Schneider: What to code or fix.
    • Mike Dean: issues: architectural uncertainty (being resolved)
    • Michael Grüninger: the current implementation restricts ontologies to be specified in OWL
    • Peter P. Yim: being a totally volunteered project does present a challenge
    • Mike Dean: issues: platform distribution/installation changes (being resolved)
  • Issues we could discuss at the Nov-29 joint NCBO-OOR session
    • Mike Dean: status of export/import/upgrade process for NCBO appliance
    • Mike Dean: availability of Java, Ruby, or other client stubs for invoking BioPortal REST services
    • Todd Schneider: BioPortal's Roadmap or priorities
    • Peter P. Yim: clearly identify functionalities that either the NCBO or the OOR development team will be pursuing
      • Mike Dean: federation (BBN is happy to contribute their earlier code)
    • Mike Dean: which specific "WebTools" package(s) is Paul Alexander using
    • Peter P. Yim: I would still hope aligning architecture and API and creating synergies would still be the main focus for that session
  • Refine how we should move development forward from here
    • MikeDean/2011.11.08: suggest starting a wiki page for OOR_DeveloperTools to share some of the experience and provide some consensus on tools to use
    • KenBaclawski/2011.11.08: it would be helpful to find out from Paul Alexander which specific "WebTools" package(s) he is using ... question for the Nov-29 session (if not sooner)
  • Task distribution and getting organized - (deferred)
    • ...
  • Action planning (with consensus milestones)
    • [2011.11.08] 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
    • [2011.11.08] 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]
    • [2011.11.08] 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.

5. Getting Organized:

  • (discussion deferred)

6. Action items:

  • [2011.11.22]: Peter to start a Nov-29 preparation email thread with Ken, Todd, Ray et al. to tie down the agenda for the 11/29 session
  • [2011.11.22]: Brian will post wiki link to HaroldSolbrig's metadata cross-walk work ... and Michael will invite Harold to present that work on Dec-13 for us

7. Any Other Business:

8. Schedule Next Meeting & Adjourn:

  • Call adjourned at: 9:51 am PST

--

notes taken by: Peter P. Yim / 2011.11.08-10:03am 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:



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