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= [[OpenOntologyRepository]]: Architecture & API Workshop-X - Tue 2012_01_31 =
= [[OpenOntologyRepository]]: OOR Team Conference Call - Tue 2012_02_07 =


Topic: "'''OOR Architecture & API Specification Development Workshop-X'''"
This is a regular OOR Team meeting. ... ''please refer to proceedings from the last team meeting at [[OOR/ConferenceCall_2012_01_10]]''  
 
Session Co-chairs: '''Dr. [[ToddSchneider|Todd Schneider]] & Professor KenBaclawski'''  


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


* Date: '''Tuesday, 31-Jan-2012'''  
* Date: '''Tuesday, 7-Feb-2012'''  
* 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=1&day=31&year=2012&hour=8&min=30&sec=0&p1=224 World Clock]  
** ref: [http://www.timeanddate.com/worldclock/fixedtime.html?month=2&day=7&year=2012&hour=8&min=30&sec=0&p1=224 World Clock]  
* Expected Call Duration: ~1.5 hours  
* Expected Call Duration: 1.0~1.5 hours  


* Dial-in:  
* Dial-in:  
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** view-only password: "ontolog"  
** 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.  
** 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 point your browser directly to the '''[http://ontolog.cim3.net/file/work/OOR/oor-dev/BioPortal_Build3253_Nov2011_EA_Model--ToddSchneider_20120130/BioPortal_Build3253_EA_HTML_Report/index.html report]''' (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 point your browser directly to the '''[ slides]''' (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/oor_20120131
* '''In-session chat'''-room url: http://webconf.soaphub.org/conf/room/oor_20120207
** 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) oor_20120131@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.)
 
* 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_29
* 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_2012_02_07


* 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:  
** [[ToddSchneider|Todd Schneider]] (co-chair)  
** [[User:KennethBaclawski|Ken Baclawski]] (chair)  
** [[User:KennethBaclawski|Ken Baclawski]] (co-chair)  
** [[PeterYim|Peter P. Yim]] (scribe)  
** [[PeterYim|Peter P. Yim]]  
** [[ToddSchneider|Todd Schneider]]  
** [[MichaelGruninger|Michael Grüninger]] (has to leave early)
** [[MichaelGruninger|Michael Grüninger]]  
** [[MikeDean|Mike Dean]]  
** [[BrianDavis|Brian Davis]]  


* Expecting:  
* Expecting:  
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* Regrets:  
* Regrets:  
** [[MikeDean|Mike Dean]]
** [[LeoObrst|Leo Obrst]]
** [[TimDarr|Tim Darr]]  
** [[TimDarr|Tim Darr]]  
** [[MikeBennett|Mike Bennett]]  
** [[MikeBennett|Mike Bennett]]  
** [[LeoObrst|Leo Obrst]]


=== Session Abstract & Resources ===
== Agenda Ideas ==
 
With this workshop we'll start reviewing the [[BioPortal]] build 3253 source code (from November 2011) to see how it fits into the current OOR (draft) architecture and identify changes or additions that need to made to the source code or the architecture.
 
The review will be based on an HTML report from the Enterprise Architect (EA) UML model of the (reverse engineered) [[BioPortal]] source code build 3253 (circa November 2011).
 
The EA HTML report can be found at
http://ontolog.cim3.net/file/work/OOR/oor-dev/BioPortal_Build3253_Nov2011_EA_Model--ToddSchneider_20120130/BioPortal_Build3253_EA_HTML_Report/index.html
 
See also: '''[[OpenOntologyRepository_Architecture]]''' & '''[[OpenOntologyRepository_Architecture/Candidate03]]'''
 
In addition, there is an API of the core services that was obtained from anearlier implementation [[BioPortal]], which is not entirely compatible with the straw man architecture, but furnishes a starting point. This API will also be discussed and modified as needed.
 
* Here is the API expressed in WSDL: http://www.ccs.neu.edu/home/kenb/oor/OORService.wsdl
* Here is the API expressed in Java: http://www.ccs.neu.edu/home/kenb/oor/OORI.java
 
Finally, we need to agree on a plan for completing the development of the specification.
 
Here is the proposed organizing plan: '''[[OpenOntologyRepository_Architecture/GettingOrganized]]'''


We encourage all participants to update your candidate contributions to ensure your ideas are known and understood.
''please insert any additional items below (along with your name for follow-up purposes)''


The following are relevant prior meetings:
* postmortem of the last couple of workshops (Architecture-API-X & Metadata-V)
 
* OOR: sandbox, devbox, socop-instance status update
* Architecture & API Specification Development Workshop-X - [[OOR/ConferenceCall_2012_01_31]]'' (this session)''
* planning and coordination on upcoming OOR events
* Joint NCBO-OOR Session - "OOR Architecture & API Workshop-IX: [[BioPortal]] & OOR Synergies" - [[OOR/ConferenceCall_2011_11_29]]
* doing something at [[OntologySummit2012|Ontology Summit 2012]]  
* Architecture & API Specification Development Workshop-VIII - [[OOR/ConferenceCall_2011_10_11]]
* Member activities updates
* Architecture & API Specification Development Workshop-VII - [[OOR/ConferenceCall_2011_09_20]]
* action planning for "content drive" (getting people to upload ontologies)  
* Kicking-off the Next Phase of OOR-NCBO Collaboration - [[OOR/ConferenceCall_2011_09_13]]
* Getting us to a stage when we can run a OOR-production box
* Architecture & API Specification Development Workshop-VI - [[OOR/ConferenceCall_2011_06_17]]
* ...  
* Architecture & API Specification Development Workshop-V - [[OOR/ConferenceCall_2011_05_20]]
* Architecture & API Specification Development Workshop-IV - [[OOR/ConferenceCall_2011_04_22]]
* Architecture & API Specification Development Workshop-III - [[OOR/ConferenceCall_2011_03_25]]
* Architecture & API Specification Development Workshop-II - [[OOR/ConferenceCall_2011_03_11]]
* Architecture & API Specification Development Workshop-I - [[OOR/ConferenceCall_2011_03_04]]  
* [http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_02_04#nid2MIV 2011.02.04 discussion]
* 2010_11_19 - Friday: OOR Panel Discussion - "(Post-BioPortal fork) OOR Architecture and API - Take-II" - Co-chairs: [[User:KennethBaclawski|Ken Baclawski]] & [[MichaelGruninger|Michael Grüninger]] - Panelists: KenBaclawski+ToddSchneider, AldoGangemi+AlessandroAdamou, JouniTuominen+KimViljanen, [[EricChan|Eric Chan]] - [[OOR/ConferenceCall_2010_11_19]]
* 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]]
 
== Agenda Ideas  ==
 
* walk-thru of the (reverse engineered)(EA) UML model of the  [[BioPortal]] source
code build 3253 (circa November 2011)
* go back-and-forth with the ongoing stock "OOR Architecture & API" discussions, namely ...  
** the OOR Architecture
** the OOR API
** the Organizing Plan
** the default development platform


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


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


* [http://ontolog.cim3.net/file/work/OpenOntologyRepository/OOR-Architecture/OOR-Architecture-API-workshop/OOR_Architecture-API-workshop-X_20120131b.mp3 Audio archive of the session] ... [ 1:42:19 ; mp3 ; 11.71 ]  
* [http://ontolog.cim3.net/file/work/OpenOntologyRepository/MeetingsCalls/OOR-team-conf-call_20120207b.mp3 audio recording of the session] [ 1:08:20 ; mp3 ; 7.82 MB ]  
* [http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2012_01_31#nid33QN Chat transcript of the session] ... [ [http://ontolog.cim3.net/file/work/OpenOntologyRepository/OOR-Architecture/OOR-Architecture-API-workshop/oor-call_chat-transcript_unedited_20120131a.txt raw] ] . [ [http://ontolog.cim3.net/file/work/OpenOntologyRepository/OOR-Architecture/OOR-Architecture-API-workshop/oor-call_chat-transcript_edited_20120131b.txt edited] ]  
* [http://ontolog.cim3.net/file/work/OpenOntologyRepository/MeetingsCalls/chat-transcript_oor-team_edited_20120207b.txt chat-transcript of this session]  


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


* [[ToddSchneider|Todd Schneider]] & [[User:KennethBaclawski|Ken Baclawski]] took the chair and welcome everyone  
* [[User:KennethBaclawski|Ken Baclawski]] takes the chair and welcome everyone  
 
* [[PeterYim|Peter P. Yim]] volunteered to keep a record of the proceedings
 
* review and adopt agenda  
* review and adopt agenda  
* [[PeterYim|Peter P. Yim]] volunteered to take notes


2. Roll Call & Adoption of last meeting's minutes:  
2. Roll Call:  
 
* see [http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2012_01_31#nid33NZ above]
* introduction of new members (as required)
* review of agenda
 
3. '''Key items for review and discussion''' today:
 
* Announcements and Urgent Matters:
 
* review of the reversed engineering [[BioPortal]] build 3253 (circa Nov-2011) UML model


* discuss our plans referencing the updated [[BioPortal]] implementation
* see [http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2012_02_07#nid34BB above]  


* status review of our infrastructure and development resources and platform
* welcome and intro of new member(s) (if applicable)


''... items below are mostly from the previous workshop, and will be updated as this session progresses.''
3. Status Review and Discussion:


* Review of action item(s) from the previous meeting(s)  
* '''Review and update our "Most Critical Task(s) At Hand" list''' ...(''we will skip this stock agenda item at today's call.)''
* from 2011.06.17 - [[MichaelGruninger|Michael Grüninger]] will examine the OMV to determine which attributes are required and which are optional.  
** ref. http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository#nid17YH
* from 2011.06.17 - [[User:KennethBaclawski|Ken Baclawski]] will send KEEPER (the gatekeeping software) to [[ToddSchneider|Todd Schneider]] who will generate the UML.  


* '''"OOR Architecture & API Specification Development Workshop-VIII:"''' ([http://ontolog.cim3.net/file/work/OpenOntologyRepository/OOR-Architecture/OOR-Architecture-API-workshop/ Archives])
=== 4. Key items for review and discussion today  ===


* Gatekeeping specifies the a set of minimal requirements that any ontology within the OOR has to meet. The latter are intended to enable the users of the OOR to find quickly ontologies that fit their needs; the criteria are not supposed to ensure the quality of the ontologies.  
* postmortem of the last couple of workshops (Metadata-V & Architecture-API-X) ... ref.  
** Each OOR instance declares what ontology languages it supports.
** OOR-Metadata-V - [[OOR/ConferenceCall_2012_01_17]]
** Every OOR instance MUST support RDFS.
*** Michael: ORWG presentation and discussion, mainly OMV & CTS2 ... look toward more discussion at a next session
*** This is required because the metadata is expressed in OMV.  
*** Brian: as of this Thu (Feb-9) ORWG is suspending and wrapping into a larger project that will look into the bigger picture of standards (cf. DISR - Defense Information Standard Repository; NCRI (UK's) work; and "Cancer InfoMatrix" - http://www.ncri-onix.org.uk/portal/#S24) ... Brian and Sherri are still going to be involved
*** OMV is written in OWL, but it may be sufficient to require only RDFS. This needs to be investigated.
** OOR-Architecture-API-X - [[OOR/ConferenceCall_2012_01_31]]
** Other ontology languages MAY be supported.
*** Todd walked us through his reverse-engineered architecture of the Nov-2011 version of [[BioPortal]]
** For each metadata attribute, it will be specified whether it is required or optional.
*** 3 coordinated and branched development (tab-based) effort are starting KenBaclawski+ToddSchneider (workflow & gatekeeping), [[MikeDean|Mike Dean]] (federation) & [[MichaelGruninger|Michael Grüninger]] (metadata)
*** It MUST be specified whether the ontology is available (or to be available in the future).
**** Ken: still need some clarification from [[PaulAlexander|Paul Alexander]] on getting started on the development of a tab
*** The ontology language MUST be specified.
*** Michael will look into java code generation from OMV
*** Other attributes will be handled offline by [[MichaelGruninger|Michael Grüninger]] based on the OMV specification.
** An ontology must satisfy other requirements depending on the ontology language.
*** Syntax checking is always required.
*** Consistency checking is required with some time limit.


* Proposal for Partition of Components
* '''OOR: sandbox, devbox, socop-instance status update'''
** Presentation
** ref. http://oor-03.cim3.net is the current [[OOR_SandBox]]
*** A minimal presentation module with just search and workflow
** <oor-04.cim3.net> is up (still on CANTOR) and accessible as: http://socop.oor.net
*** Browse (already in BioPortal-based sandbox)  
** Peter: WITTGENSTEIN is not up yet, plans updated, to use this box for testing (our the next virtualization strategy based on) <nowiki>[[CentOS]]-KVM</nowiki>
*** Search (already in BioPortal-based sandbox)
** customization: Mike & Ken has customized both oor-03 & oor-04 - ref. http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR_SandBox_Customization#nid30R7
*** Mapping (already in BioPortal-based sandbox)  
** logo color still doesn't look quite right - see: http://oor-03.cim3.net (current) vs. http://oor-03.cim3.net (socop) vs. http://oor-01.cim3.net (old v2.6) vs. http://bioportal.bioontology.org/ (current BioPortal)  
*** Recommender (already in BioPortal-based sandbox)  
** re: "Feedback" to support@oor.net - which now forwards to: peter.yim@cim3.com, yimpp1@yahoo.com, mdean@bbn.com, kenb@ccs.neu.edu, tejas@tejasparikh.com, oor-users@ontolog.cim3.net
*** Annotator (already in BioPortal-based sandbox)
*** PPY: glad I have not yet allowed the posting to <oor-users@ontolog.cim3.net> and its archives ... because to date, all messages received (just a few, less than 10) were all spam messages
*** Resource Index (already in BioPortal-based sandbox)  
**** see also: comment from Tejas - he has re-enabled reCaptcha on socop.oor.net (oor-04.cim3.net) - http://ontolog.cim3.net/forum/oor-users/2012-02/msg00000.html
*** Workflow Administration
*** need better means to deal with it ... (discuss)
*** OOR Instance Administration
*** also, since we are running multiple instances, we need some means to differentiate, e.g. support questions from the sandbox, socop, or dev instance. ... [action: ...]
*** Other windows
** Workflow
*** Already developed, but needs to be documented
** Registrar
*** A minimal registrar
** Find
*** Initially adapt a SPARQL endpoint. Which one?
** Inference
*** Initially a part of the SPARQL endpoint
*** Other inference engines
** Persistence
*** Initially adapt 4Store
** Administration
*** TBD
** Federation
*** TBD


* '''Chat transcript of this session:'''  
* '''planning and coordination on upcoming OOR events'''  
** re-scheduling metadata (VI?) session: with [[MikeBennett|Mike Bennett]] on financial metadata - some time in Mar-2012 (either Mar-13) - [MichaelGruninger]
** re-scheduling Joint IAOA-OOR-Ontolog "Ontologies and Standards" mini-series session-3: on "ISO/IEC 24707 Common Logic and IKL" [MichaelGruninger & JohnBateman] ... will discuss off-line and revert (as [[OntoIOp]] is also meeting every other week now)
** OOR Architecture & API Workshop-XII  now scheduled for (either Mar-20) - Ken & Todd
** next Content workshop ...?
** ... lining up more?
** no meeting on Feb-14 & Feb-28
** we meet on Feb-21 about coding
** Mar-6 team meeting


--- Chat transcript begin: ---
* '''doing something at OntologySummit2012'''
** Todd will champion OOR by injecting it into any track where it makes sense ... also by way of NCOIC involvement
** Mike will support (technically, especially by way of the socop-oor instance) Nancy and Gary in the collaborative SOCoP-INTEROP / Summit workshop that Nancy is spearheading
** Ken will work on one presentation (on behalf of OOR), which Todd and Peter will try to slot into one of the sessions - possibility: "OOR and webservices"
** ... think of something we can engage [[DuaneNickull|Duane Nickull]] on


[[PeterYim|Peter P. Yim]]: Welcome to the
* '''Member activities updates''' - ref. [http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2012_02_07#nid34DB below] ... ''(item skipped; discussion deferred)''


= [[OpenOntologyRepository]]: Architecture & API Workshop-X - Tue 2012_01_31 =
* '''action planning for "content drive"''' ... ''(item skipped; discussion deferred)'' (getting people to upload ontologies)


Topic: "OOR Architecture & API Specification Development Workshop-X"
* '''Getting us to a stage when we can run a OOR-production box''' ... ''(item skipped; discussion deferred)''


Session Co-chairs: Dr. [[ToddSchneider|Todd Schneider]] & Professor [[User:KennethBaclawski|Ken Baclawski]]
... ''Notes below are from previous meeting(s), and will be updated as this meeting progresses.''


Conference Call Details:
* planning and coordination on upcoming OOR events
* Getting us to a stage when we can run a OOR-production box ...(''we will skip this stock agenda item at today's call.)''


* Date: Tuesday, 31-Jan-2012
* action planning for facilitating code contribution (organizing ourselves so various sub-teams can actually get to work on coding) ...(''we will skip this stock agenda item at today's call.)''


* Start Time: 8:30am PST / 11:30am EST / 5:30pm CET / 16:30 UTC
* action planning for "soliciting" content (getting people to upload ontologies) ...(''we will skip this stock agenda item at today's call.)''


* Expected Call Duration: ~1.5 hours
* Getting us to a stage when members can contribute code ... how, ETA?
** ''(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)'' ...  


Session page: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2012_01_31
* code development on an Eclipse IDE for all?  


Can't find Skype Dial pad? ... it's under the "Call" dropdown menu as "Show Dial pad"  
* Code repository - considering "git" or github?


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


== Proceedings: ==
'''Member activities updates:'''


.  
* Review: members and OOR-related activities (2012.02.07)
** OOR-sandbox status
** code repository status
** NCBO
** NEU
** Raytheon-BBN
** 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


[[PeterYim|Peter P. Yim]]: The EA HTML report Todd has just produced can be found at http://ontolog.cim3.net/file/work/OOR/oor-dev/BioPortal_Build3253_Nov2011_EA_Model--ToddSchneider_20120130/BioPortal_Build3253_EA_HTML_Report/index.html
'''Action planning for "soliciting" content''' (getting people to upload ontologies)


Todd: ref. http://ontolog.cim3.net/file/work/OOR/oor-dev/
5. '''Funding progress:'''


[[ToddSchneider|Todd Schneider]]: http://ontolog.cim3.net/file/work/OOR/oor-dev/BioPortal_Build3253_Nov2011_EA_Model--ToddSchneider_20120130/
6. '''Any Other Business:'''


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


Todd / Ken: ref. MikeDean's question: "are javadoc's available?" ... answer: seemingly "no!"
8. Schedule Next Meeting & Adjourn:  


[[PeterYim|Peter P. Yim]]: [consensus] our approach toward code contribution (/extension from the [[BioPortal]] codebase):
* Next Meetings:  
** no OOR meetings on Feb-14 & Feb-28
** we meet on Feb-21 about coding, and check progress on getting implementing our first tabs
** 2012_03_06 - next Regular OOR Team meeting - first Tuesday of the month - [[OOR/ConferenceCall_2012_03_06]]  
** next Metadata workshop (VI) on Tue 2012.03.13
** next Architecture API workshop (XI) on Tue 2012.03.20


(a) KenBaclawski-ToddSchneider to focus on "gatekeeping";
* Call adjourned at: 9:39 am PST  
 
(b) [[MikeDean|Mike Dean]] on "federation", and
 
(c) [[MichaelGruninger|Michael Gr&uuml;ninger]] on "metadata" then "mapping"
 
[[ToddSchneider|Todd Schneider]]: Action Plan: Michael and his team will focus on metadata (and then mapping); Mike Dean will focus on federation capabilities; Ken and Todd will focus on workflow
 
[[MikeDean|Mike Dean]]: like idea of an OOR service layer that includes OOR-specific services (e.g.  Find) and
 
can be easily adapted to new [[BioPortal]] releases
 
[[PeterYim|Peter P. Yim]]: as far as ncbo-RayFergerson is concerned, he'd appreciate all code extensions to be implemented on "tabs"
 
[[MikeDean|Mike Dean]]: it's easy to add new tabs to the UI
 
[[MikeDean|Mike Dean]]: http://palexander.posterous.com/extending-bioportals-rails-ui
 
[[ToddSchneider|Todd Schneider]]: The three 'action items' will have there own tabs: adjuncts to the current [[BioPortal]] UI
 
[[ToddSchneider|Todd Schneider]]: Need to find out if [[BioPortal]] data model supports 'location' (i.e., repository location/id) information
 
[[ToddSchneider|Todd Schneider]]: How will access control across federates be handled?
 
[[ToddSchneider|Todd Schneider]]: There may be additional fields from OMV that OOR will need.
 
[[ToddSchneider|Todd Schneider]]: Can the OMV interface be generated dynamically from the OMV ontology? This may break some existing [[BioPortal]] code.
 
[[ToddSchneider|Todd Schneider]]: Each of items of the 'action plan' will be added as a new tab (on the current UI).
 
[[ToddSchneider|Todd Schneider]]: The federation tab will be labeled 'Federation' (this may only be visible to administrators);
 
The workflow tab will initially expose the uploading capability of the gatekeeper functionality.
 
Other gatekeeper capabilities/functionalities will be exposed on other tabs.
 
[[ToddSchneider|Todd Schneider]]: Another action item is to agree on tab labels for the 'upload' and 'metadata' tabs.
 
[[PeterYim|Peter P. Yim]]: [action] targeting this - Mike, Ken & Michael will all try to have a prototype tab
 
(even just a "hello world" tab) done by our next workshop
 
[[User:KennethBaclawski|Ken Baclawski]]: Subject: [oor-dev] Problem with extending the UI
 
I am trying to extend the [[BioPortal]] Rails UI on oor-03 using
 
http://palexander.posterous.com/extending-bioportals-rails-ui
 
It seems one must use
 
<nowiki>cd [[OOR/ConferenceCall_2012_01_31/srv/ncbo/rails/BioPortal/current</nowiki>]]
 
rather than
 
<nowiki>cd [[OOR/ConferenceCall_2012_01_31/var/rails/BioPortal/current</nowiki>]]
 
There is a script/generate, but when I try running it, I get
 
/usr/bin/env: ruby: No such file or directory
 
Does anyone have some idea of how this can be fixed?
 
-- Ken
 
[[PeterYim|Peter P. Yim]]: Ken has fired the above question to Paul Alexander - http://ontolog.cim3.net/forum/oor-dev/2012-01/msg00016.html
 
[[PeterYim|Peter P. Yim]]: [[MikeDean|Mike Dean]] gave a brief report on the SOCoP-OOR at the INTEROP NSF PI meeting
 
[[ToddSchneider|Todd Schneider]]: Can we pose a question to [[BioPortal]] to see if they would be open to moving
 
the 'Submit New Ontology' functionality to a new tab, called 'Submit'?
 
[[ToddSchneider|Todd Schneider]]: Have to go.
 
[[User:KennethBaclawski|Ken Baclawski]]: I will continue to find out how to fix the captcha feature. Until it is fixed, captcha is off.
 
[[PeterYim|Peter P. Yim]]: who is anonymous?
 
[[PeterYim|Peter P. Yim]]: let's talk about the next workshops at next Tuesday's regular OOR team meeting
 
[[PeterYim|Peter P. Yim]]: [[MikeDean|Mike Dean]]: I'll probably be missing next week's meeting, because i'll be traveling
 
[[PeterYim|Peter P. Yim]]: good meeting ... got a lot done ... bye!
 
[[PeterYim|Peter P. Yim]]: -- session ended: 10:14am PST --
 
--- Chat transcript end: ---
 
'''Consensus, Conclusions & Follow-up Actions:'''
 
4. '''Any Other Business:'''
 
5. '''Action items:'''
 
6. Schedule Next Meeting & Adjourn:
 
* Next Meeting:
** Regular OOR team meeting next week - Tue 2012.02.07 same time - [[OOR/ConferenceCall_2012_02_07]]
*** [[MikeDean|Mike Dean]]: I'll probably have to miss that meeting, as I will be traveling.
** we'll plan other events at that meeting
 
* Call adjourned at: 10:14 am PST  


--
--


notes taken by: [[PeterYim|Peter P. Yim]] / 2012.01.31-11:01am PST
notes taken by: [[PeterYim|Peter P. Yim]] / 2012.02.07-11:45am 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 348: Line 213:
* '''[[OpenOntologyRepository|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.  
* '''[[OpenOntologyRepository|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"  
* '''"Ontology Repository" Definition''' - "An ontology repository is a facility where ontologies and related information artifacts can be stored, retrieved and managed"  
* '''Team mailling list:'''  
* '''Team mailing list:'''  
** OOR-Team discussion: [ [http://ontolog.cim3.net/forum/oor-forum/ oor-forum] ]''' message archives - http://ontolog.cim3.net/forum/oor-forum/  
** OOR-Team discussion: [ [http://ontolog.cim3.net/forum/oor-forum/ oor-forum] ]''' message archives - http://ontolog.cim3.net/forum/oor-forum/  
** OOR-Users discussion and support: [ [http://ontolog.cim3.net/forum/oor-users/ oor-users] ]''' message archives - http://ontolog.cim3.net/forum/oor-users/  
** OOR-Users discussion and support: [ [http://ontolog.cim3.net/forum/oor-users/ oor-users] ]''' message archives - http://ontolog.cim3.net/forum/oor-users/  
** Developers mailling list: '''[ [http://ontolog.cim3.net/forum/oor-dev/ oor-dev] ]''' message archives - http://ontolog.cim3.net/forum/oor-dev/  
** Developers mailing list: '''[ [http://ontolog.cim3.net/forum/oor-dev/ oor-dev] ]''' message archives - http://ontolog.cim3.net/forum/oor-dev/  
* proceedings of our '''[[OpenOntologyRepository|previous meetings, panel discussions and workshops]]'''  
* proceedings of our '''[[OpenOntologyRepository|previous meetings, panel discussions and workshops]]'''  


Line 384: Line 249:
** 2011_09_20 - Tuesday: OOR - "Architecture & API Specification Development Workshop-VII" - Co-chairs: [[User:KennethBaclawski|Ken Baclawski]] & [[ToddSchneider|Todd Schneider]] - [[OOR/ConferenceCall_2011_09_20]]  
** 2011_09_20 - Tuesday: OOR - "Architecture & API Specification Development Workshop-VII" - Co-chairs: [[User:KennethBaclawski|Ken Baclawski]] & [[ToddSchneider|Todd Schneider]] - [[OOR/ConferenceCall_2011_09_20]]  
** 2011_10_11 - Tuesday: OOR - "Architecture & API Specification Development Workshop-VIII" - Co-chairs: [[User:KennethBaclawski|Ken Baclawski]] & [[ToddSchneider|Todd Schneider]] - [[OOR/ConferenceCall_2011_10_11]]  
** 2011_10_11 - Tuesday: OOR - "Architecture & API Specification Development Workshop-VIII" - Co-chairs: [[User:KennethBaclawski|Ken Baclawski]] & [[ToddSchneider|Todd Schneider]] - [[OOR/ConferenceCall_2011_10_11]]  
** 2011_11_29 - Tuesday: Joint NCBO-OOR Session - "OOR Architecture & API Workshop-IX: [[BioPortal]] & OOR Synergies" - Co-chairs: [[User:KennethBaclawski|Ken Baclawski]] & [[ToddSchneider|Todd Schneider]] - Discussant: [[RayFergerson|Ray Fergerson]] - [[OOR/ConferenceCall_2011_11_29]]
** 2012_01_31 - Tuesday: OOR Architecture & API Workshop-X - Co-chairs: [[User:KennethBaclawski|Ken Baclawski]] & [[ToddSchneider|Todd Schneider]] - [[OOR/ConferenceCall_2012_01_31]]


*   
*   
Line 431: Line 298:
* '''OOR Project site at [[SemWebCentral]]''' - http://oor.semwebcentral.org  
* '''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:  
* '''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 (online ''now!'') - ( http://sandbox.oor.net/ - ''later'')
** '''[[OOR_DevBox]]''' - http://oor-01.cim3.net - http://dev.oor.net/  
** '''[[OOR_DevBox]]''' - http://oor-01.cim3.net - ( http://dev.oor.net/ - ''v2.6 - now obsolete'')
** '''SOCoP[http://socop.oor.net/ _OOR]''' - http://oor-04.cim3.net - http://socop.oor.net/  
** '''[[OOR_DevBox]]''' - ( http://oor-05.cim3.net - ( http://dev.oor.net/ - ''coming!''))
** '''SOCoP[http://socop.oor.net/ _OOR]''' - http://oor-04.cim3.net - http://socop.oor.net/ - (online ''now!'')
** '''[[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 07:35, 9 January 2016

OpenOntologyRepository: OOR Team Conference Call - Tue 2012_02_07

This is a regular OOR Team meeting. ... please refer to proceedings from the last team meeting at OOR/ConferenceCall_2012_01_10

Conference Call Details

  • Date: Tuesday, 7-Feb-2012
  • Start Time: 8:30am PST / 11:30am EST / 5:30pm CET / 16:30 UTC
  • Expected Call Duration: 1.0~1.5 hours
  • Dial-in:
    • Phone (US): +1 (206) 402-0100 (long distance cost may 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 point your browser directly to the [ slides] (where applicable) and running them locally. The speaker(s) will prompt you to advance the slides during the talk.
  • 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)

  • postmortem of the last couple of workshops (Architecture-API-X & Metadata-V)
  • OOR: sandbox, devbox, socop-instance status update
  • planning and coordination on upcoming OOR events
  • doing something at Ontology Summit 2012
  • Member activities updates
  • action planning for "content drive" (getting people to upload ontologies)
  • Getting us to a stage when we can run a OOR-production box
  • ...

Agenda & Proceedings

Archives:

1. Meeting called to order:

2. Roll Call:

  • welcome and intro of new member(s) (if applicable)

3. Status Review and Discussion:

4. Key items for review and discussion today

  • postmortem of the last couple of workshops (Metadata-V & Architecture-API-X) ... ref.
    • OOR-Metadata-V - OOR/ConferenceCall_2012_01_17
      • Michael: ORWG presentation and discussion, mainly OMV & CTS2 ... look toward more discussion at a next session
      • Brian: as of this Thu (Feb-9) ORWG is suspending and wrapping into a larger project that will look into the bigger picture of standards (cf. DISR - Defense Information Standard Repository; NCRI (UK's) work; and "Cancer InfoMatrix" - http://www.ncri-onix.org.uk/portal/#S24) ... Brian and Sherri are still going to be involved
    • OOR-Architecture-API-X - OOR/ConferenceCall_2012_01_31
      • Todd walked us through his reverse-engineered architecture of the Nov-2011 version of BioPortal
      • 3 coordinated and branched development (tab-based) effort are starting KenBaclawski+ToddSchneider (workflow & gatekeeping), Mike Dean (federation) & Michael Grüninger (metadata)
        • Ken: still need some clarification from Paul Alexander on getting started on the development of a tab
      • Michael will look into java code generation from OMV
  • planning and coordination on upcoming OOR events
    • re-scheduling metadata (VI?) session: with Mike Bennett on financial metadata - some time in Mar-2012 (either Mar-13) - [MichaelGruninger]
    • re-scheduling Joint IAOA-OOR-Ontolog "Ontologies and Standards" mini-series session-3: on "ISO/IEC 24707 Common Logic and IKL" [MichaelGruninger & JohnBateman] ... will discuss off-line and revert (as OntoIOp is also meeting every other week now)
    • OOR Architecture & API Workshop-XII now scheduled for (either Mar-20) - Ken & Todd
    • next Content workshop ...?
    • ... lining up more?
    • no meeting on Feb-14 & Feb-28
    • we meet on Feb-21 about coding
    • Mar-6 team meeting
  • doing something at OntologySummit2012
    • Todd will champion OOR by injecting it into any track where it makes sense ... also by way of NCOIC involvement
    • Mike will support (technically, especially by way of the socop-oor instance) Nancy and Gary in the collaborative SOCoP-INTEROP / Summit workshop that Nancy is spearheading
    • Ken will work on one presentation (on behalf of OOR), which Todd and Peter will try to slot into one of the sessions - possibility: "OOR and webservices"
    • ... think of something we can engage Duane Nickull on
  • Member activities updates - ref. below ... (item skipped; discussion deferred)
  • action planning for "content drive" ... (item skipped; discussion deferred) (getting people to upload ontologies)
  • Getting us to a stage when we can run a OOR-production box ... (item skipped; discussion deferred)

... Notes below are from previous meeting(s), and will be updated as this meeting progresses.

  • planning and coordination on upcoming OOR events
  • Getting us to a stage when we can run a OOR-production box ...(we will skip this stock agenda item at today's call.)
  • action planning for facilitating code contribution (organizing ourselves so various sub-teams can actually get to work on coding) ...(we will skip this stock agenda item at today's call.)
  • action planning for "soliciting" content (getting people to upload ontologies) ...(we will skip this stock agenda item at today's call.)
  • Getting us to a stage when members can contribute code ... how, ETA?
    • (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 development on an Eclipse IDE for all?
  • Code repository - considering "git" or github?
  • Getting us to a stage when we can run a OOR-production box ... what's still needed, ETA?
    • ...

Member activities updates:

  • Review: members and OOR-related activities (2012.02.07)
    • OOR-sandbox status
    • code repository status
    • NCBO
    • NEU
    • Raytheon-BBN
    • 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)

5. Funding progress:

6. Any Other Business:

7. Action items:

8. Schedule Next Meeting & Adjourn:

  • Next Meetings:
    • no OOR meetings on Feb-14 & Feb-28
    • we meet on Feb-21 about coding, and check progress on getting implementing our first tabs
    • 2012_03_06 - next Regular OOR Team meeting - first Tuesday of the month - OOR/ConferenceCall_2012_03_06
    • next Metadata workshop (VI) on Tue 2012.03.13
    • next Architecture API workshop (XI) on Tue 2012.03.20
  • Call adjourned at: 9:39 am PST

--

notes taken by: Peter P. Yim / 2012.02.07-11:45am PST

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

Resources

  • the OOR-IPR mini-series:
    • 2010_09_09 - Thursday: Joint OOR-Ontolog-NCBO-CC-IAOA-OASIS Panel Discussion - "IPR issues in Ontology and the OOR" session-1: an exposition on relevant IPR regimes - Keynote speaker: George Strawn - Chair: Peter P. Yim - Panelists: JamieClark, John Wilbanks, Bruce Perens - ConferenceCall_2010_09_09
    • 2010_09_16 - Thursday: Joint OOR-Ontolog-NCBO-CC-IAOA-OASIS Panel Discussion - "IPR issues in Ontology and the OOR" session-2: what are the IPR issues relating to open ontology repositories (and ontologies in general)? - Chair: Mark Musen - Panelists: Cameron Ross, Alan Rector, John F. Sowa, Bruce Perens, John Wilbanks, Peter P. Yim - ConferenceCall_2010_09_16
    • 2010_09_30 - Thursday: Joint OOR-Ontolog-NCBO-CC-IAOA-OASIS Panel Discussion - "IPR issues in Ontology and the OOR" session-3: discussion and consensus on licensing arrangements for the OOR Initiative, and positions we might take on related IPR issues - chair: Leo Obrst - Panelists: Peter P. Yim, Mike Dean, Bruce Perens, JamieClark - ConferenceCall_2010_09_30
  • the Joint IAOA-OOR-Ontolog "Ontologies and Standards" mini-series:
    • 2011_10_20 - Thursday: Joint IAOA-OOR-Ontolog "Ontologies and Standards" mini-series session-1: Introducing the ISO NP 17347 "Ontology Integration and Interoperability (OntoIOp)" Standardization Effort - Co-chairs: John Bateman & Michael Grüninger - ConferenceCall_2011_10_20
    • 2011_11_03 - Thursday: Joint IAOA-OOR-Ontolog "Ontologies and Standards" mini-series session-2: Invited Speaker: Elisa Kendall on "Ontology-Related Metadata Standards" - Co-chairs: Michael Grüninger & John Bateman - ConferenceCall_2011_11_03
    • 2011_12_15 - Thursday: Joint IAOA-OOR-Ontolog "Ontologies and Standards" mini-series session-3: "ISO/IEC 24707 Common Logic and IKL" - Co-chairs: Michael Grüninger & John Bateman - ConferenceCall_2011_12_15



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