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= [[OpenOntologyRepository]]: OOR Team Conference Call - Tue 2012_05_01 =
= [[OpenOntologyRepository]]: Architecture & API Workshop-XII - Tue 2012_05_08 =


This is a regular OOR Team meeting. ... ''please refer also to proceedings from the last team meeting at [[OOR/ConferenceCall_2012_04_03]]''  
Topic: "'''OOR Architecture & API Workshop-XII: To tab or not to tab'''"
 
Session Co-chairs: '''Professor [[User:KennethBaclawski|Ken Baclawski]] & Dr. ToddSchneider'''  


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


* Date: '''Tuesday, 1-May-2012'''  
* Date: '''Tuesday, 8-May-2012'''  
* Start Time: 8:30am PDT / 11:30am EDT / 5:30pm CEST / 15:30 UTC  
* Start Time: 8:30am PDT / 11:30am EDT / 5:30pm CEST / 15:30 UTC  
** ref: [http://www.timeanddate.com/worldclock/fixedtime.html?month=5&day=1&year=2012&hour=8&min=30&sec=0&p1=224 World Clock]  
** ref: [http://www.timeanddate.com/worldclock/fixedtime.html?month=5&day=8&year=2012&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 may apply)''  
** '''Phone (US): +1 (206) 402-0100''' ''(long distance cost may apply)''  
*** ... [ backup nbr: (415) 671-4335 ]  
*** ... [ backup nbr: (415) 671-4335 ]  
** '''Skype: joinconference''' ... (generally free-of-charge, when connecting from your computer)  
** '''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#'''  


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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 '''[ slides]''' (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 '''[ presentation(s)]''' (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_20120508
** 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_20120508@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.)


* '''In-session chat'''-room url: http://webconf.soaphub.org/conf/room/oor_20120501
* 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_2012_05_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_2012_05_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:  
** [[MikeDean|Mike Dean]] (chair)  
** [[User:KennethBaclawski|Ken Baclawski]] (co-chair)  
** [[User:KennethBaclawski|Ken Baclawski]]  
** [[ToddSchneider|Todd Schneider]] (co-chair)
** [[PeterYim|Peter P. Yim]] (scribe)
** [[PeterYim|Peter P. Yim]]  
** [[MichaelGruninger|Michael Grüninger]]  
** [[MichaelGruninger|Michael Grüninger]] (need to leave after the first 30 min.)
** [[ToddSchneider|Todd Schneider]]  
** [[MikeDean|Mike Dean]]  
** [[FrankOlken|Frank Olken]]  
** [[MaximoGurmendez|Máximo Gurméndez]]  
** ...


* Expecting:  
* 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.'' ...  
** ... ''if you are coming to the meeting, please add your name (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.'' ...  


* Regrets:  
* Regrets:  
** [[LeoObrst|Leo Obrst]]  
** [[RayFergerson|Ray Fergerson]] (written input provided ... see [http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2012_05_08#nid3AQR below])
** ...  
** ...  


=== Agenda Ideas  ===
== Agenda Ideas  ==


''please insert any additional items below (along with your name for follow-up purposes)''
* Discussion
** Tabbing: to tab or not to tab
*** understanding where the [[BioPortal]] folks come from, in terms of their "tab" architecture for adding/removing functionalities
*** related issues faced by OOR code contributors
*** the OOR team's take and disposition
* stock items  
** the OOR Architecture
** the OOR API
** the Organizing Plan
** moving from OOR sandbox to OOR production


* postmortem of the last couple of OOR events:
=== Session Abstract & Resources  ===
** Demos of various OOR instances at the [[OntologySummit2012_Symposium]] on Apr-13
** Metadata-VII: Ontology Mapping - [[OOR/ConferenceCall_2012_04_24]]
* upcoming activities / virtual-session planning
** [new - ppy/2012.05.02] collaborating with NYC & Data.gov communities in "Big Open Data"
* OOR: sandbox, devbox, test-instance, socop, colore, ornl-daac, mmi-orr, new ncbo-appliance, ... status update and coordination
* 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  ==
The main subject for today's session is tabbing. We will be looking into the rationale of the [[BioPortal]] team's architectural decision to use "tabs" as the mechanism to add/remove functionality, and how code extensions "plugin" to their exisiting codebase. We will review issues that have been encountered, and attempt to make a disposition on how we shall approach this.
 
[[BioPortal]] "tab" implementation details (provided by PaulAlexander) are at: http://palexander.posterous.com/extending-bioportals-rails-ui


'''[http://ontolog.cim3.net/file/work/OpenOntologyRepository/MeetingsCalls/ Archives]:'''
At this "OOR Architecture & API" series of meetings, we are going through the process of producing the actual OOR specification. It will be run as a workshop where the straw man proposal will be discussed and modified as needed.  


* [http://ontolog.cim3.net/file/work/OpenOntologyRepository/MeetingsCalls/OOR-team-conf-call_20120501b.mp3 audio recording of the session] [ 1:15:42 ; mp3 ; 8.67 MB ]
The various architectures and APIs for ontology repositories presented for consideration are available at [[OpenOntologyRepository_Architecture]]  
* [http://ontolog.cim3.net/file/work/OpenOntologyRepository/MeetingsCalls/chat-transcript_oor-team_20120501b.txt chat-transcript of this session]  


1. Meeting called to order:  
Here is the status of the strawman architecture: [[OpenOntologyRepository_Architecture/Candidate03]]


* [[MikeDean|Mike Dean]] takes the chair and welcomes everyone
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.  
* [[PeterYim|Peter P. Yim]] volunteered to take notes
* review and adopt agenda


2. Roll Call:  
* 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


* see [http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2012_05_01#nid3AEB above]
Finally, we need to agree on a plan for completing the development of the specification.  


* welcome and intro of new member(s) (if applicable)
Here is the proposed organizing plan: '''[[OpenOntologyRepository_Architecture/GettingOrganized]]'''


3. Status Review and Discussion:
We encourage all participants to update your candidate contributions to ensure your ideas are known and understood.  


* '''Review and update our "Most Critical Task(s) At Hand" list''' ... ''(discussion deferred; maybe: revisit towards end of this call?)''
The following are relevant prior meetings:  
** ref. http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository#nid17YH


=== 4. Key items for review and discussion today  ===
* Architecture & API Specification Development Workshop-XII: To tab or not to tab - [[OOR/ConferenceCall_2012_05_08]] '' (this session)''
* Architecture & API Specification Development Workshop-XI - [[OOR/ConferenceCall_2012_03_20]]
* Architecture & API Specification Development Workshop-X - [[OOR/ConferenceCall_2012_01_31]]
* Joint NCBO-OOR Session - "OOR Architecture & API Workshop-IX: [[BioPortal]] & OOR Synergies" - [[OOR/ConferenceCall_2011_11_29]]
* Architecture & API Specification Development Workshop-VIII - [[OOR/ConferenceCall_2011_10_11]]
* Architecture & API Specification Development Workshop-VII - [[OOR/ConferenceCall_2011_09_20]]
* Kicking-off the Next Phase of OOR-NCBO Collaboration - [[OOR/ConferenceCall_2011_09_13]]
* 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 Gr&uuml;ninger]] - 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]]


* '''postmortem of the last couple of OOR events:'''
== Agenda & Proceedings  ==
** Demos of various OOR instances at the [[OntologySummit2012_Symposium]] on Apr-13
*** Michael: 6 demos presented; 3 were OOR-related (SOCoP-OOR, Ontohub-OOR & COLORE-OOR)
*** Peter: thanks to all on the oor.net federation making it possible for us to have a rather coherent presentation to the audience ... great, especially this is an extended effort from one of the earlier OntologySummit's (2008 to be exact)
** Metadata-VII: Ontology Mapping - [[OOR/ConferenceCall_2012_04_24]]
*** Michael: presentation from the [[OntoIOp]] (DOL) team, [[JeromeEuzenat|Jerome Euzenat]] & [[NCBO]] folks
*** Todd: very interesting session
*** Michael: follow-up meeting needed to go into representation language(s) for mapping
*** [[PeterYim|Peter P. Yim]]: would love to engage [[JeromeEuzenat|Jerome Euzenat]] (and incorporate his "mapping engine" into OOR as a value added service, especially on the database-schema-to-ontology mapping functionality.) Any others who are working on the state-of-the-art in converting database schemas to ontologies? ... who else is doing work in database schema to ontology conversion?
**** [[FrankOlken|Frank Olken]]: Dan Miranker (Univ. of Texas Austin) and his grad student JuanSequeda have been working on translating SQL schemas to ontologies (on a small scale).
**** [[MikeDean|Mike Dean]]: we have something - the <nowiki>AutoMapper</nowiki> component of Asio tool suite - see http://asio.bbn.com ... but this is not opensource sw
**** [[MikeDean|Mike Dean]]: D2RQ and D2R from Chris Bizer's group
**** [[FrankOlken|Frank Olken]]: Juan Sequeda, Marcelo Arenas, Daniel P. Miranker: On directly mapping relational databases to RDF and OWL. WWW 2012: 649-658
**** [[PeterYim|Peter P. Yim]]: maybe [[ElisaKendall|Elisa Kendall]] too
**** [[PeterYim|Peter P. Yim]]: the interest above stems from my earlier (Mar-2010) proposal I made to the NCO_NITRD on systematically developing ontologies from the data.gov (ref. http://data.gov) datasets (more than 390,000 of them now), possibly developing those "ontologies" from database schemas and from "vocabularies" the the RPI folks have been doing for some of those) and then hosting these ontologies on OOR for public reference and consumption. This approach (mapping database schemas to some ontology/ies) was one of the kep approaches we took when [[LeoObrst|Leo Obrst]], I and others were working for <nowiki>VerticalNet</nowiki> circa year 2000 too.)
*** [[PeterYim|Peter P. Yim]]: consider doing a virtual session on this ... Michael: possibly an Ontolog topic more than an straight OOR topic (which deals with things that are already ontologies)


* '''previous action item status review'''
[http://ontolog.cim3.net/file/work/OpenOntologyRepository/OOR-Architecture/OOR-Architecture-API-workshop/ Archives]:  
** [action-2012.03.13] Michael will try to get [[MikeBennett|Mike Bennett]] to upload his ontology to OOR  
*** Michael: I'll work on a "Content coordination among OOR instances" session
** [action-2012.03.13] Ken will continue to work on implementing "gatekeeping" (and get back with an ETA) so we can move from "sandbox" to "production"
*** Ken: I can start looking into this more, now that summer has started


* '''upcoming activities / virtual-session planning'''
* prepared '''[http://ontolog.cim3.net/file/work/OpenOntologyRepository/OOR-Architecture/OOR-Architecture-API-workshop/OOR-Tabbing--KenBaclawski-ToddSchneider_20120508.pdf slides]''' from the co-chairs
** Architecture-API-XII - Tue 2012.05.08 ... Ken & Todd will work on this offline and send Peter an abstract shortly ... possibly addressing some of the architectural & API aspects of the "BioPortal tab" issues
* [http://ontolog.cim3.net/file/work/OpenOntologyRepository/OOR-Architecture/OOR-Architecture-API-workshop/OOR_Architecture-API-workshop-XII_20120508b.mp3 Audio archive of the session] ... [ 1:30:06 ; mp3 ; 10.31 MB ]  
** Metadata-VIII - will try to fix a date on 4/24 during the "Metadata in Ontology Mapping" session ... [[MichaelGruninger|Michael Gr&uuml;ninger]] will try to come up with a date via email
* [http://ontolog.cim3.net/file/work/OpenOntologyRepository/OOR-Architecture/OOR-Architecture-API-workshop/oor_chat-transcript_20120508b.txt Chat transcript of the session]  
** OOR-Dev-VIII - Tue 2012.05.22 - Chair: [[MikeDean|Mike Dean]]
*** NEU, BBN, Toronto, Bremen, ... SOCoP, ORNL, MMI,
*** code contributors to compare notes on "adding tabs" ... and trying to engage the other potential code contributors
** OOR-Content-II - Tue 2012.05.29 - Co-chair: [[MichaelGruninger|Michael Gr&uuml;ninger]] & [[MikeDean|Mike Dean]]  
*** "Content coordination among OOR instances" - Michael will pursue
*** look back at the [[PatCassidy|Pat Cassidy]] + [[DeniseBedford|Denise Bedford]] "OOR-Content-I" session - [[OOR/ConferenceCall_2010_03_12]]
* 
** [new - ppy/2012.05.02] collaborating with NYC & Data.gov communities in "Big Open Data"
*** Ken: ICOM as a collaboration standard
** engaging [[JeromeEuzenat|Jerome Euzenat]] ... (?)
*** Michael: I will try to engage Jerome, probably with more concrete things, like the next virtual seesion


* '''OOR:''' sandbox, devbox, test-instance, socop, colore, ornl-daac, mmi-orr, new ncbo-appliance, ... '''status update and coordination'''
1. Meeting called to order:  
** thanks to everyone's support from the OOR, SOCoP, COLORE, ORNL-DAAC, MMI, NCBO teams; the following were finalized, and wereup and running at the [[OntologySummit2012_Symposium]] (and showed during the Apr-13 demo session.)
** new '''OOR homepage''' - http://oor.net - opens to the index page for accessing any of the OOR instances; takes one to the OOR project homepage after 15 seconds (if user did not select an OOR instance in the mean time)
** new '''OOR project homepage''' - http://www.oor.net - opens to the OOR project homepage on this wiki (same effect as http://OpenOntologyRepository.org )
** servers/instances:
** OOR-01 - (old instance, being retired) re-direct to project homepage
** OOR-02 - ci server
** OOR-03 - sandbox - http://sandbox.oor.net
** OOR-04 - socop - http://socop.oor.net
** OOR-05 - devbox - http://dev.oor.net
** OOR-06 - test-00 - http://test-00.oor.net
** ''(coming!)'' ... OOR-07 - new instance - ncbo-applicance-0.5 ... still having trouble with standing appliance up from the KVM image (Shinya might ask NCBO for a Xen image; or, alternatively, should we skip this upgrade?)
** SOCoP-OOR - http://socop.oor.net/ontologies
** COLORE: colore.oor.net -> http://code.google.com/p/colore/source/browse/#svn%2Ftrunk%2Fontologies
** ONTOHUB: ontohub.oor.net -> http://ontohub.informatik.uni-bremen.de/
** ORNL-DAAC: ornl-daac.oor.net -> http://mercury-ncbo.ornl.gov/ontologies
** MMI-ORR: mmisw.oor.net -> http://mmisw.org/orr/
** [[BioPortal]] - http://bioportal.bioontology.org/


* '''Member activities updates''' ... ''(below)''
* [[User:KennethBaclawski|Ken Baclawski]] & [[ToddSchneider|Todd Schneider]] took the chair and welcome everyone


* '''action planning for "content drive"''' (getting people to upload ontologies) ... ''(below)''
* [[PeterYim|Peter P. Yim]] volunteered to keep a record of the proceedings


* '''Getting us to a stage when we can run a OOR-production box''' ... ''(below)''
* review and adopt agenda


... ''Notes below are from previous meeting(s), and will be updated as this meeting progresses.''
2. Roll Call & Adoption of last meeting's minutes:


'''Member activities updates:'''' ... ''(discussion deferred)''
* see [http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2012_05_08#nid3AOF above]
* introduction of new members (as required)  
* review of agenda


* Review: members and OOR-related activities
3. '''Key items for review and discussion''' today:  
** OOR-sandbox status
** code repository status
** NCBO
** NEU
** Raytheon-BBN
** UToronto
** Bremen
** Ryerson
** Mathet
** [[SOCoP_INTEROP]]
** [[DataONE]]
** [[NeOn]] (KMi and STL)
** ONKI
** KBSI
** MMI
** Use Cases
** Architecture
** API
** Gatekeeping
** production OOR instance
** SIO
** ICOM / DERI
** [[OntoIOp]]
** [[OntologySummit2012|Ontology Summit 2012]]
** content drive
** Funding


* '''action planning for "content drive"''' (getting people to upload ontologies)
* '''Tabbing: to tab or not to tab''' ... [http://ontolog.cim3.net/file/work/OpenOntologyRepository/OOR-Architecture/OOR-Architecture-API-workshop/OOR-Tabbing--KenBaclawski-ToddSchneider_20120508.pdf slides]
** session planned for 2012.05.29 - OOR-Content-II - co-chair: [[MichaelGruninger|Michael Gr&uuml;ninger]] & [[MikeDean|Mike Dean]]  
** understanding where the [[BioPortal]] folks come from ...
*** [[RayFergerson|Ray Fergerson]]: Unfortunately I cannot make this meeting. I can provide the background here though for the reasoning about using tabs as a code modification mechanism. ... This idea is inspired by the widely used tab extension mechanism in
Protege. The designer of that system suggested it to me. :-) ... The idea is that this mechanism allows the maximum amount of flexibility to end users while providing the minimum amount of coupling to existing software. You can do whatever you want on a tab and it will not affect the rest of the system. You can even replace existing tabs with new ones that do
similar things in different ways. It goes a long ways toward making your additions to the system independent of changes to the system that we make. Thus the "forking and merge problem" is almost entirely eliminated.
** related issues faced by OOR code contributors
** the OOR team's take and disposition


* '''Getting us to a stage when we can run a OOR-production box''' ... ''(discussion deferred)''
''... items below are mostly from the previous workshop, and will be updated as this session progresses.''  
** ''(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?
* Review of action item(s) from the previous meeting(s)


* Code repository - considering "git" or github?
* 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.
** Each OOR instance declares what ontology languages it supports.
** Every OOR instance MUST support RDFS.
*** This is required because the metadata is expressed in OMV.
*** OMV is written in OWL, but it may be sufficient to require only RDFS. This needs to be investigated.
** Other ontology languages MAY be supported.
** For each metadata attribute, it will be specified whether it is required or optional.
*** It MUST be specified whether the ontology is available (or to be available in the future).
*** The ontology language MUST be specified.
*** Other attributes will be handled offline by [[MichaelGruninger|Michael Gr&uuml;ninger]] 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.


5. '''Funding progress:''' ... ''(discussion deferred)''
* Proposal for Partition of Components
** Presentation
*** A minimal presentation module with just search and workflow
*** Browse (already in BioPortal-based sandbox)
*** Search (already in BioPortal-based sandbox)
*** Mapping (already in BioPortal-based sandbox)
*** Recommender (already in BioPortal-based sandbox)
*** Annotator (already in BioPortal-based sandbox)
*** Resource Index (already in BioPortal-based sandbox)  
*** Workflow Administration
*** OOR Instance Administration
*** 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


6. '''Any Other Business:'''  
4. '''Consensus, Conclusions & Follow-up Actions:'''  


7. '''Action items:'''  
5. '''Any Other Business:'''  


8. Schedule Next Meeting & Adjourn:  
6. Next Meeting & Adjourn:  


* Next Meetings:  
* Upcoming Meetings:  
** 2012_05_08 - Architecture-API-XII - Co-chair: [[User:KennethBaclawski|Ken Baclawski]] & [[ToddSchneider|Todd Schneider]]
** 2012_05_15 - no OOR meeting  
** 2012_05_15 - no OOR meeting  
** 2012_05_10 & 2012_05_17 - (being staged) "Big Open Data" with NYC, Data.gov, SMW/PSMW & OOR - please mark your calendars and come!  
** 2012_05_10 & 2012_05_17 - (being staged) "Big Open Data" with NYC, Data.gov, SMW/PSMW & OOR - please mark your calendars and come!  
** 2012_05_22 - OOR-Dev-VIII - Tue 2012.05.22 - Chair: [[MikeDean|Mike Dean]]  
** 2012_05_22 - OOR-Dev-VIII - Tue 2012.05.22 - Chair: [[MikeDean|Mike Dean]]  
** 2012_05_29 - OOR-Content-II - Tue 2012.05.29 - Co-chair: [[MichaelGruninger|Michael Gr&uuml;ninger]] & [[MikeDean|Mike Dean]]  
** 2012_05_29 - OOR-Content-II - Tue 2012.05.29 - Co-chair: [[MichaelGruninger|Michael Gr&uuml;ninger]] & [[MikeDean|Mike Dean]]  
** 2012_06_05 - no OOR meeting, [[SemTech]] will be in session  
** 2012_06_05 - no OOR meeting, [[SemTech|SemTech]] will be in session  
** 2012_06_12 - next Regular OOR Team meeting - first Tuesday of the month - [[OOR/ConferenceCall_2012_06_12]]  
** 2012_06_12 - next Regular OOR Team meeting - first Tuesday of the month - [[OOR/ConferenceCall_2012_06_12]]  


* Call adjourned at: 9:53 am PDT  
* Call adjourned at: 10:07 am PDT  


--
--


notes taken by: [[PeterYim|Peter P. Yim]] / 2012.05.01-9:58am PDT
notes taken by: [[PeterYim|Peter P. Yim]] / 2012.05.08-10:07am PDT


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 272: Line 267:
** 2012_01_31 - Tuesday: OOR - "Architecture & API Workshop-X" - Co-chairs: [[ToddSchneider|Todd Schneider]] & [[User:KennethBaclawski|Ken Baclawski]] - [[OOR/ConferenceCall_2012_01_31]]  
** 2012_01_31 - Tuesday: OOR - "Architecture & API Workshop-X" - Co-chairs: [[ToddSchneider|Todd Schneider]] & [[User:KennethBaclawski|Ken Baclawski]] - [[OOR/ConferenceCall_2012_01_31]]  
** 2012_03_20 - Tuesday: OOR - "Architecture & API Workshop-XI" - Co-chairs: [[ToddSchneider|Todd Schneider]] & [[User:KennethBaclawski|Ken Baclawski]] - [[OOR/ConferenceCall_2012_03_20]]  
** 2012_03_20 - Tuesday: OOR - "Architecture & API Workshop-XI" - Co-chairs: [[ToddSchneider|Todd Schneider]] & [[User:KennethBaclawski|Ken Baclawski]] - [[OOR/ConferenceCall_2012_03_20]]  
** 2012_05_08 - Tuesday: OOR - "Architecture & API Workshop-XII" - Co-chairs: [[ToddSchneider|Todd Schneider]] & [[User:KennethBaclawski|Ken Baclawski]] - [[OOR/ConferenceCall_2012_05_08]]


*   
*   

Latest revision as of 07:36, 9 January 2016

OpenOntologyRepository: Architecture & API Workshop-XII - Tue 2012_05_08

Topic: "OOR Architecture & API Workshop-XII: To tab or not to tab"

Session Co-chairs: Professor Ken Baclawski & Dr. ToddSchneider

Conference Call Details

  • Date: Tuesday, 8-May-2012
  • Start Time: 8:30am PDT / 11:30am EDT / 5:30pm CEST / 15:30 UTC
  • Expected Call Duration: ~1.5 hours
  • Dial-in:
    • Phone (US): +1 (206) 402-0100 (long distance cost may apply)
      • ... [ backup nbr: (415) 671-4335 ]
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    • 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_20120508@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.)
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    • 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 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 (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

  • Discussion
    • Tabbing: to tab or not to tab
      • understanding where the BioPortal folks come from, in terms of their "tab" architecture for adding/removing functionalities
      • related issues faced by OOR code contributors
      • the OOR team's take and disposition
  • stock items
    • the OOR Architecture
    • the OOR API
    • the Organizing Plan
    • moving from OOR sandbox to OOR production

Session Abstract & Resources

The main subject for today's session is tabbing. We will be looking into the rationale of the BioPortal team's architectural decision to use "tabs" as the mechanism to add/remove functionality, and how code extensions "plugin" to their exisiting codebase. We will review issues that have been encountered, and attempt to make a disposition on how we shall approach this.

BioPortal "tab" implementation details (provided by PaulAlexander) are at: http://palexander.posterous.com/extending-bioportals-rails-ui

At this "OOR Architecture & API" series of meetings, we are going through the process of producing the actual OOR specification. It will be run as a workshop where the straw man proposal will be discussed and modified as needed.

The various architectures and APIs for ontology repositories presented for consideration are available at OpenOntologyRepository_Architecture

Here is the status of the strawman 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.

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.

The following are relevant prior meetings:

Agenda & Proceedings

Archives:

1. Meeting called to order:

  • Peter P. Yim volunteered to keep a record of the proceedings
  • review and adopt agenda

2. Roll Call & Adoption of last meeting's minutes:

  • see above
  • introduction of new members (as required)
  • review of agenda

3. Key items for review and discussion today:

  • Tabbing: to tab or not to tab ... slides
    • understanding where the BioPortal folks come from ...
      • Ray Fergerson: Unfortunately I cannot make this meeting. I can provide the background here though for the reasoning about using tabs as a code modification mechanism. ... This idea is inspired by the widely used tab extension mechanism in

Protege. The designer of that system suggested it to me. :-) ... The idea is that this mechanism allows the maximum amount of flexibility to end users while providing the minimum amount of coupling to existing software. You can do whatever you want on a tab and it will not affect the rest of the system. You can even replace existing tabs with new ones that do similar things in different ways. It goes a long ways toward making your additions to the system independent of changes to the system that we make. Thus the "forking and merge problem" is almost entirely eliminated.

    • related issues faced by OOR code contributors
    • the OOR team's take and disposition

... items below are mostly from the previous workshop, and will be updated as this session progresses.

  • Review of action item(s) from the previous meeting(s)
  • 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.
    • Each OOR instance declares what ontology languages it supports.
    • Every OOR instance MUST support RDFS.
      • This is required because the metadata is expressed in OMV.
      • OMV is written in OWL, but it may be sufficient to require only RDFS. This needs to be investigated.
    • Other ontology languages MAY be supported.
    • For each metadata attribute, it will be specified whether it is required or optional.
      • It MUST be specified whether the ontology is available (or to be available in the future).
      • The ontology language MUST be specified.
      • Other attributes will be handled offline by 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
    • Presentation
      • A minimal presentation module with just search and workflow
      • Browse (already in BioPortal-based sandbox)
      • Search (already in BioPortal-based sandbox)
      • Mapping (already in BioPortal-based sandbox)
      • Recommender (already in BioPortal-based sandbox)
      • Annotator (already in BioPortal-based sandbox)
      • Resource Index (already in BioPortal-based sandbox)
      • Workflow Administration
      • OOR Instance Administration
      • 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

4. Consensus, Conclusions & Follow-up Actions:

5. Any Other Business:

6. Next Meeting & Adjourn:

  • Upcoming Meetings:
    • 2012_05_15 - no OOR meeting
    • 2012_05_10 & 2012_05_17 - (being staged) "Big Open Data" with NYC, Data.gov, SMW/PSMW & OOR - please mark your calendars and come!
    • 2012_05_22 - OOR-Dev-VIII - Tue 2012.05.22 - Chair: Mike Dean
    • 2012_05_29 - OOR-Content-II - Tue 2012.05.29 - Co-chair: Michael Grüninger & Mike Dean
    • 2012_06_05 - no OOR meeting, SemTech will be in session
    • 2012_06_12 - next Regular OOR Team meeting - first Tuesday of the month - OOR/ConferenceCall_2012_06_12
  • Call adjourned at: 10:07 am PDT

--

notes taken by: Peter P. Yim / 2012.05.08-10:07am PDT

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



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