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= [[OpenOntologyRepository]]: OOR Team Conference Call - Tue 2011_11_01 =
= [[OpenOntologyRepository]]: OOR Development Workshop-V - Tue 2011_11_08 =


This is a regular OOR Team meeting. ... ''please refer to proceedings from the last team meeting at [[OOR/ConferenceCall_2011_10_04]]''
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 ...


'''* * * Please pay special attention to the time of this event, as the US is still on Daylight Saving Time (summer time), while Europe is back to Standard Time (winter time) * * *'''  
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! * * *'''  
'''* * * Please also note that we are calling into a new conference bridge starting from this session, note the new dial-in information! * * *'''  
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=== [[MeetingsCalls|Conference Call]] Details  ===
=== [[MeetingsCalls|Conference Call]] Details  ===


* Date: '''Tuesday, 1-Nov-2011'''  
* Date: '''Tuesday, 8-Nov-2011'''  
* Start Time: 8:30am PDT / 11:30am EDT / 4:30pm CET / 15:30 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=1&year=2011&hour=8&min=30&sec=0&p1=224 World Clock]  
** ref: [http://www.timeanddate.com/worldclock/fixedtime.html?month=11&day=8&year=2011&hour=8&min=30&sec=0&p1=224 World Clock]  
* Expected Call Duration: 1.0~1.5 hours  
* Expected Call Duration: ~1.5 hours  


* Dial-in:  
* Dial-in:  
** '''Phone (US): +1 (206) 402-0100''' (long distance cost will apply)  
** '''Phone (US): +1 (206) 402-0100''' ''(long distance cost will apply)'' ... [ backup nbr: (415) 671-4335 ]
** '''Skype: joinconference'''  
** '''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_20111101
* '''In-session chat'''-room url: http://webconf.soaphub.org/conf/room/oor_20111108
 
* '''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_20111108
** 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_20111108@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 [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.)
 
* Please review our Virtual Session Tips and Ground Rules - see: [[VirtualSpeakerSessionTips]]


* '''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_01
* 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


* 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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* Attended:  
* Attended:  
** [[User:KennethBaclawski|Ken Baclawski]] (chair)  
** [[MikeDean|Mike Dean]] (chair)  
** [[PeterYim|Peter P. Yim]]  
** [[PeterYim|Peter P. Yim]] (scribe)
** [[User:KennethBaclawski|Ken Baclawski]]  
** [[MichaelGruninger|Michael Grüninger]]  
** [[MichaelGruninger|Michael Grüninger]]  
** [[EricChan|Eric Chan]] (discussant)
** [[ToddSchneider|Todd Schneider]]  
** [[ToddSchneider|Todd Schneider]]  
** [[MikeBennett|Mike Bennett]]


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


== 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)''  


* OOR-sandbox and OOR-devbox status update
* identifying issues that are holding back the OOR-oss-dev work
* Member activities updates
* Is a common IDE good for us? Is Eclipse an optimal answer?
* planning and coordination on upcoming OOR events
* Task distribution and getting organized
** OOR Architecture-API sessions, OOR Metadata sessions, Standards sessions, next regular team meeting, ... more
* Action planning (with consensus milestones)  
* action planning for facilitating code contribution (organizing ourselves so various teams can actually get to work on coding)
* Getting us to a stage when we can run a OOR-production box
* action planning for "soliciting" content (getting people to upload ontologies)  
* ...
* [[PeterYim|Peter P. Yim]]: after we are done with the regular OOR team agenda, we need help from everyone who can stay to test an alternate conference bridge as well


* ...  
* ... ''(please add to the above)''


== Agenda & Proceedings  ==
== Agenda & Proceedings  ==


'''[http://ontolog.cim3.net/file/work/OpenOntologyRepository/MeetingsCalls/ Archives]:'''  
'''[http://ontolog.cim3.net/file/work/OpenOntologyRepository/OOR-dev/ Archives]:'''  


* [http://ontolog.cim3.net/file/work/OpenOntologyRepository/MeetingsCalls/OOR-team-conf-call_20111101b.mp3 audio recording of the session]  
* '''[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/MeetingsCalls/chat-transcript_oor-team_20111101b.txt chat-transcript of this session] ''(lightly edited)''  
* '''[http://ontolog.cim3.net/file/work/OpenOntologyRepository/OOR-dev/oor_chat-transcript_20111108a.txt chat-transcript of this session]'''  


1. Meeting called to order:  
1. Meeting called to order:  


* [[User:KennethBaclawski|Ken Baclawski]] takes the chair and welcome everyone  
* [[MikeDean|Mike Dean]] takes the chair and welcome everyone  
* review and adopt agenda  
* review and adopt agenda  
* [[PeterYim|Peter P. Yim]] volunteered to take notes  
* [[PeterYim|Peter P. Yim]] volunteered to take notes  
* the first conference bridge we were planning to test (FZM) did not work out (we hit full capacity after a few connections), therefore, moved directly to testing the alternate conference bridge (ITS2).


2. Roll Call:  
2. Roll Call:  


* see [http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_11_01#nid2Y0M above]  
* see [http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_11_08#nid2YTI above]  


* welcome and intro of new member(s) (as needed)  
* welcome and intro of new member(s) (as needed)  
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3. Status Review and Discussion:  
3. Status Review and Discussion:  


* '''Review and update our "Most Critical Task(s) At Hand" list''' ...(''we will skip this stock agenda item at today's call.)''  
* '''Review and update our "Most Critical Task(s) At Hand" list'''  
** 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  ===


* OOR-sandbox and OOR-devbox status update - see [http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_11_01#nid2YDX below]  
Topic: "'''Getting OOR Development Going (V), on Eclipse?'''"
 
* identifying issues that are holding back the OOR-oss-dev work
 
* Is a common IDE good for us? Is Eclipse an optimal answer?
** 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
and there is really nothing special to talk about. The only thing that
Paul mentioned is to enable the [http://www.eclipse.org/webtools/ "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 [[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:
** [[EricChan|Eric Chan]]: most of my comments will be in the form of questions
** [[EricChan|Eric Chan]]: assuming there will an svn to host the source code
*** [[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]
 
--- Chat transcript begin ---  
 
[08:31] [[PeterYim|Peter P. Yim]]: Welcome to the
 
[[OpenOntologyRepository]]: OOR Development Workshop-V - Tue 2011_11_08
 
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.


* planning and coordination on upcoming OOR events - see [http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_11_01#nid2YE5 below]
[09:17] Eric S. Chan: bioportal provides background processing for validation (theorem proving),  
** OOR Architecture-API sessions, OOR Metadata sessions, Standards sessions, next regular team meeting, ... more


* Member activities updates - see [http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_11_01#nid2YG7 below] ... ''(discussion postponed)''
OOR may define these processes as SOA services


* action planning for facilitating code contribution (organizing ourselves so various teams can actually get to work on coding) ... ''(discussion postponed)''
[09:28] Eric S. Chan: E:\jaxb-ri-20110115\bin\xjc.bat schema-obh-xjc.xsd schema-obr.xsd -extension


* Getting us to a stage when we can run a OOR-production box ... ''(discussion postponed)''
[09:37] [[MikeDean|Mike Dean]]: It would help bootstrap development to create an OOR Developer Tools page with


* action planning for "soliciting" content (getting people to upload ontologies) ... ''(discussion postponed)''
links to JAXRS specifications, tools to generate client bindings, and (soon) results of


* we need help from everyone who can stay to test an alternate conference bridge "ITS2" as a candidate for future calls
generating those bindings.


* OOR-sandbox and OOR-devbox status update
[09:45] [[PeterYim|Peter P. Yim]]: see: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_11_08#nid2YYK
** new OOR logo now on the OOR-Sandbox - see: http://sandbox.oor.net
** NCBO [[BioPortal]] v3.3 released on 2011.10.19 - ref. http://ontolog.cim3.net/forum/oor-forum/2011-10/msg00027.html
** Xen vm image of the latest NCBO Appliance almost ready (as of our 2011.10.31 communication with the NCBO team)
** <support@oor.net> mail forwarder created:
*** people can just mail this address or enter into "Send Feedback" form on the OOR Sandbox
*** which currently gets forwarded to: [[TejasParikh|Tejas Parikh]], [[User:KennethBaclawski|Ken Baclawski]], [[MikeDean|Mike Dean]], [[PeterYim|Peter P. Yim]] and <oor-users@ontolog.cim3.net>  ''(--PeterYim/2011.10.14)''
*** remember to tweak this too, after the new vm image is in place - ref. http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR_SandBox_Customization#nid2X3C


* planning and coordination on upcoming OOR events - workshop plans
the placeholder page is up at: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR_DeveloperTools
** Michael: ISO 19763 - Thu Nov-3 (12:30 EDT)
*** Peter will get a reminder out (after this meeting) based on prelim material received from [[ElisaKendall|Elisa Kendall]] (at least as a placeholder)
** Session on "Getting OOR Development going on Eclipse" - aim for Tue 2011.11.08 (if not then Tue 2011.11.22)
*** candidate panel: [[MikeDean|Mike Dean]], [[CameronRoss|Cameron Ross]], [[EricChan|Eric Chan]], [[PaulAlexander|Paul Alexander]]
** Ken / Todd - OOR-Architecture-API IX - "NCBO-OOR architectural considerations and synergies" + "creating [[BioPortal]] Tabs" - Tue 2011.11.29 (RayFergerson is ok with this date; he is not available on 2011.11.22)
** Michael: OOR-Metadata V - ??? ... [[MikeBennett|Mike Bennett]] will send something he will contribute to Michael;
** [[OntologiesAndStandards]] III - on "Common Logic" - tentative Thu 2011.12.15 ... - candidate panel: [[FabianNeuhaus|Fabian Neuhaus]], [[LeoObrst|Leo Obrst]], ... - Chair: [[MichaelGruninger|Michael Gr&uuml;ninger]] & [[JohnBateman|John Bateman]]
*** ... then,  [[OntologiesAndStandards]] IV a session on IDIOM
** [[FactGuru|Fact Guru]] incorporation & integration?
** more on SIO ...?  
** other sessions of interest ???
** next regular OOR team meeting Tue 2011.12.06 (11:30 EDT)


... ''Notes below are from previous meeting(s), and will be updated as this meeting progresses.''
[09:55] Eric S. Chan: http://java.net/projects/open-icom/pages/Home


* assessing a strengthened OOR-NCBO collaborative relationship
[09:59] [[ToddSchneider|Todd Schneider]]: Have to go. Cheers.  
* OOR-sandbox and OOR-devbox status update
** http://oor-01.cim3.net/ - now: http://sandbox.oor.net/ --> to become our OOR-devbox (OOR development server)
** http://oor-02.cim3.net/ - to be designated: http://sandbox.oor.net/


* Discussion: the [http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_07_15#nid2VYW newly adopted dual-track OOR approach]  
[10:11] [[PeterYim|Peter P. Yim]]: very productive meeting ... Thanks, everyone!
** action planning
*** we run (for now) 2 instances - a sandbox instance[1] on the OOR-01 vm, and an experimental instance[2] on the OOR-02 vm
**** [1] this will be a straight forward, and updated [[BioPortal]] code install, with customization only for: the logo, the IP / License statement, categories.  
**** [2] this will be the instance we use to continue the current work of further development in Architecture, API, metadata, CL support, etc.  
**** consensus: both instances would use the same database (so ontologies uploaded are accessible by both instances, and are obviously "in sync" ... saving us the need to "import" as we ad discussed at the last meeting)
*** Peter: the next things to push is to have "gatekeeping" in place so we can stand up a "production" OOR


* updating "categories"
[10:11] [[PeterYim|Peter P. Yim]]: -- session ended: 10:10am PST --  
** Peter: the ICOM people suggests adding the categories of "standards" and "collaboration" (the latter probably belongs under "Cultural"
** Mike: something like Dublin Core should go under "metadata" - we are adding this category, "process" too
** discussed - see updated "category" list at: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_08_05#nid2W6B
** one can select multiple categories by doing a "ctrl-click" (or "cmd" for Mac users)
** Ken: the software stores "categories" in an OMV ontology, and support a hierarchy of nested categories
*** Mike: there is a GUI interface for adding categories
** All: we probably want to leave it simple (one level) and support "addition of categories" on demand
** Todd: For some categories, e.g., science, subcategories will be needed. Since the provided listing is linear, subcategories could be listed as pairs or triples: Science, Science - Biology, Science-Physics, Science-Physics-Gravitation, etc.
** Leo: we might consider adopting some standard categorization, like what the Library of Congress has put out (maybe not the entire hierarchy, but only the very upper level(s)
* Category list (based on MikeDean's list): (updated 2011.08.05)
** Upper Ontologies
** Standards (for example, Measurement)
** Science (for example, Biomedical)
** Financial
** Government
** Cultural (for example, Social Networking, People)
** Geospatial
** Commercial
** Literature
** Technology
** Provenance
** Defense
** Metadata (for example, OMV, Dublin Core)
** Process (for example, PSL)
** Other


* Status and action review: OOR-dev box - http://oor-03.cim3.net
--- Chat transcript end ---


* Status and action review: SOCoP presentation box - http://socop.oor.net (at BBN?)  
* Task distribution and Getting organized ... ''(discussion deferred to the next session)''


* Getting us to a stage when members can contribute code ... how, ETA?
* Action planning with consensus milestones ... ''(discussion deferred to the next session)''  
** ''(discussion 2011.05.06):''
*** an adopted Architecture & API is definitely crucial, but that's not all
** All team members are encouraged to mull over how we can get to that state effectively
*** in particular ... how do we make this a "successful" community-driven, open source project!?
** (discussion 2011.06.03)'' ...


* Code repository - considering "git" or github?
5. '''Getting Organized:'''


* getting the OOR code repository at semwebcentral started (for real!) - http://oor.semwebcentral.org/
* [[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  
** [[OOR_SandBox]] - http://sandbox.oor.net/ontologies (previously http://oor-01.cim3.net/ontologies)
** OOR code-repository and re-assessing the 'branch instead of fork' (what does that mean?) [MikeDean, [[User:KennethBaclawski|Ken Baclawski]], et al.]  
** categories - ref. MikeDean's msg - http://ontolog.cim3.net/forum/oor-dev/2011-02/msg00012.html
** 2011.02.18: *'''Important Note'''* - we will start afresh on the OOR sandbox content (i.e. uploaded ontologies) after the update install - everyone who has uploaded ontologies so far should note
*** those who are "using" the OOR sandbox content now, should note down the ontologies they need, and may need to contact the authors to upload them again if they don't show up. (presumably, those content relating to biomedicine, previously federated from [[BioPortal]], will not be there any more, at least not automatically.) Also, links to ontologies or elements within ontologies established previously will no longer be valid after the content gets re-populated - Ken will make a post about this on [oor-forum]
** workplan:
*** update codebase to appropriate oor install code
**** The consensus is that we should use a uniform language in each component to make it easier for people to contribute code and add extensions.
**** customize banner/logo
**** customize IPR statement
**** re-establish categories - ref. [http://ontolog.cim3.net/forum/oor-dev/2011-02/msg00012.html MikeDean's input]


* Getting us to a stage when we can run a OOR-production box ... what's still needed, ETA?
6. '''Action items:'''
** ...


'''Member activities updates:'''
* [[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)


* Review: members and OOR-related activities (2011.11.01)
* [[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
** OOR-sandbox status
** code repository status
** NCBO
** NEU
** Raytheon-BBN
*** [[MikeDean|Mike Dean]]: I am attending [http://ontolog.cim3.net/cgi-bin/wiki.pl?SocopWorkshops/Spatial_Semantics_And_Ontologies_2011 SSO 2011], sponsored by SOCoP and am making a brief presentation of OOR as a lightning talk.
** Bremen
** UToronto
** Ryerson
** Mathet
** [[SOCoP_INTEROP]]  
** [[DataONE]]
** [[NeOn]] (KMi and STL)
** ONKI
** KBSI
** MMI
** Use Cases
** Architecture
** API
** Gatekeeping
** production OOR instance
** SIO
** Funding
** ICOM / DERI


''' Action planning for "soliciting" '''content''' (getting people to upload ontologies)
* 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]


5. '''Funding progress:'''  
7. '''Any Other Business:'''  


6. '''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


7. '''Action items:'''
* [[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 Meeting:  
** next session - Joint IAOA-OOR-Ontolog "Ontologies and Standards" mini-series: session-2 - Invited Speaker: [[ElisaKendall|Elisa Kendall]] on ISO 19763 - this Thursday ConferenceCall_2011_11_03
** 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
** next OOR-team meeting - Tue 2011.12.06 same time - [[ OOR/ConferenceCall_2011_12_06 ]]  
** 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]]
*** in the mean time, address the action items identified today!
** 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: 9:37 am PDT
* Call adjourned at: 10:10 am PST


--
--


notes taken by: [[PeterYim|Peter P. Yim]] / 2011.11.01-9:38am PDT
notes taken by: [[PeterYim|Peter P. Yim]] / 2011.11.08-10:10am 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.  
Line 319: Line 332:
* '''Public instances of OOR - http://sandbox.oor.net/ontologies''' (previously http://oor-01.cim3.net/ontologies) ... we are in process to standing up:  
* '''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_SandBox]]''' - http://oor-03.cim3.net - http://sandbox.oor.net/  
** '''[[OOR_DevBox]]''' - http://oor-01.cim3.net - http://devbox.oor.net/  
** '''[[OOR_DevBox]]''' - http://oor-01.cim3.net - http://dev.oor.net/  
** [[NCBO]] - [http://bioportal.bioontology.org/ BioPortal]  
** [[NCBO]] - [http://bioportal.bioontology.org/ BioPortal]  
*** BioPortal's [bioontology-support] mailing list - see: https://mailman.stanford.edu/mailman/listinfo/bioontology-support  
*** BioPortal's [bioontology-support] mailing list - see: https://mailman.stanford.edu/mailman/listinfo/bioontology-support  

Latest revision as of 07:33, 9 January 2016

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
  • 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_20111108
    • 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_20111108@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
  • 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:

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 (http://sakaiproject.org/) 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: 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] 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: 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] 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.

Resources



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