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= Joint [[NCBO]]-[[OOR]] Panel Discussion: "Kicking-off the Next Phase of Collaboration" - Tue 13-Sep-2011 =
= [[OpenOntologyRepository]]: Architecture & API Workshop-VII - Tue 2011_09_20 =


'''This is an important milestone for the [[OpenOntologyRepository]] initiative, and will mark a new phase of collaboration between the [[NCBO]]-BioPortal team and the [[OOR]] team. Join us to find out more on where things stand, what changes are in store, some of the vision going forward, and provide us your input.'''  
Topic: "'''OOR Architecture & API Specification Development Workshop-VII'''"


''Note that we have a hard stop at 10:00am PDT for this session. To make sure we can get the best out of the 90 minutes available for this session, we will start and end promptly on time. Please dial into the conference line a few minutes before the scheduled start time.''
Session Chair: [[User:KennethBaclawski|Ken Baclawski]] & [[ToddSchneider|Todd Schneider]]


* Co-chairs: '''Dr. RayFergerson''' ([[NCBO]]; Stanford) and '''Mr. PeterYim''' ([[OOR]]; [[Ontolog]]; CIM3)  
=== [[MeetingsCalls|Conference Call]] Details  ===
 
* Date: '''Tuesay, 20-Sep-2011'''
* Start Time: 8:30am PDT / 11:30am EDT / 5:30pm CEST / 4:30pm BST / 15:30 UTC
** ref: [http://www.timeanddate.com/worldclock/fixedtime.html?month=9&day=20&year=2011&hour=8&min=30&sec=0&p1=224 World Clock]
* Expected Call Duration: 1.0~1.5 hours
* Dial-in Number:
** from a '''US telephone (US): +1-218-844-8060''' (domestic long distance cost will apply)
** When calling in from a phone, use '''Conference ID: "4389979#"'''
** '''from Europe, call:'''  
*** Austria 0820-4000-1577
*** Belgium 070-35-9992
*** France 0826-100-280
*** Germany 01805-00-7642
*** Ireland 0818-270-037
*** Italy 848-390-179
*** Spain 0902-886-056
*** Switzerland 0848-560-327
*** UK 0844-581-9148
** callers '''from other countries''' please dial into either one of the US or European numbers
 
* '''Shared-screen support''' (VNC session), if needed, 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, and where appropriate, please download the '''[ slides]''' and running them locally. The speaker(s) will prompt you to advance the slides during the talk.
 
* '''Discussions and Q & A:'''
** (Unless the conference host has already muted everyone) '''Please mute your phone, by pressing "*2"''' on your phone keypad, when a presentation is in progress. '''To un-mute, press "*3"'''
** You can '''type in your questions or comments through the browser''' based [[ConferenceCall_2005_09_01|chat session]] by:
*** pointing a separate browser tab (or window) to http://webconf.soaphub.org/conf/room and enter: Room="'''ontolog_20110920'''" and My Name="Your Own Name" (e.g. "JaneDoe")
** or point your browser to: http://webconf.soaphub.org/conf/room/ontolog_20110920
*** instructions: once you got access to the page, click on the "settings" button, and identify yourself (by modifying the Name field). 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.
** (when everyone is muted) '''If you want to speak''' or have questions or remarks to make, '''please "raise your hand (virtually)" by click on the "hand button" (lower right) on the chat session page. You may speak when acknowledged by the speaker or the session moderator (again, press "*3" on your phone to unmute). ''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 "*2" on your phone to mute yourself after you are done speaking.)
** 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_20110920@soaphub.org ... Handy for mobile devices!
 
* 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.)
 
* 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_09_20
 
* 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]].  
 
== Attendees  ==
 
* Attended:
** [[User:KennethBaclawski|Ken Baclawski]] (co-chair)
** [[ToddSchneider|Todd Schneider]] (co-chair)
** [[PeterYim|Peter P. Yim]]
** [[TerryLongstreth|Terry Longstreth]]
** [[MikeDean|Mike Dean]]
 
* Expecting:
** [[RaviSharma|Ravi Sharma]] (joined us as we were wrapping up)
* 
** ... ''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.'' ...
 
* Regrets:
** [[YuriyMilov|Yuriy Milov]]
** [[LeoObrst|Leo Obrst]]
** ...
 
== Agenda Ideas  ==
 
''please insert any additional items below (along with your name for follow-up purposes)''
 
* [[PeterYim|Peter P. Yim]] (2011.09.19): need a quick discussion on options regarding the [[OOR_SandBox]] install; so we can support the upcoming SOCoP presentation scheduled for late this month
 
* Discussion on possible adjustments in the OOR architecture and work plans in view of what transpired from last week's Joint [[NCBO]]-[[OOR]] Team Meeting - ref. [[OOR/ConferenceCall_2011_09_13]]  
 
* The specifications to be discussed at the these workshops are the following (not necessarily discussed in this order):
** the OOR Architecture
** the OOR API
** the Organizing Plan
** the default development platform
 
== Abstract  ==
 
As a result of the two [[OOR]] Architecture and API panel sessions back in Oct & Nov-2010, we have been exposed to a large number of architecture and API candidates for ontology repositories. We have had requirements for the [[OOR]], at least in broad outline form, since the Ontology Summit 2008.  We have been running an [http://oor-01.cim3.net/ontologies OOR sandbox] based on BioPortal. Most recently, we have forked from the [[BioPortal]] code base with the intention of proceeding separately with the development of a reference implementation.
 
At this 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.


* Panelists:
The various architectures and APIs for ontology repositories presented for consideration are available at '''[[OpenOntologyRepository_Architecture]]'''  
** '''Professor MarkMusen''' ([[NCBO]]; Stanford)
** '''Dr. NatashaNoy''' ([[NCBO]]; Stanford)
** '''Dr. TrishWhetzel''' ([[NCBO]]; Stanford)
** '''Dr. LeoObrst''' ([[OOR]]; MITRE)
** '''Professor KenBaclawski''' ([[OOR]]; Northeastern U)
** '''Dr. ToddSchneider''' ([[OOR]]; Raytheon)


* [http://ontolog.cim3.net/file/work/OpenOntologyRepository/2011-09-13_NCBO-OOR-Collaboration-2/ Archive]:
Here is the straw man architecture: '''[[OpenOntologyRepository_Architecture/Candidate03]]'''  
** '''[http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_09_13#nid2WXS Agenda & Proceedings]'''
** '''[http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_09_13#nid2WY0 Abstract]'''
** '''Prepared presentation material''' can be accessed by clicking on each of the [http://ontolog.cim3.net/file/work/OpenOntologyRepository/2011-09-13_NCBO-OOR-Collaboration-2/ title links] below:
*** '''[ 0-Opening:Musen''' (no slides) '''] . [ [http://ontolog.cim3.net/file/work/OpenOntologyRepository/2011-09-13_NCBO-OOR-Collaboration-2/BioPortal-Status-n-Plans--RayFergerson-NCBO_20110913.pdf 1-BioPortal:Fergerson] ] . [ [http://ontolog.cim3.net/file/work/OpenOntologyRepository/2011-09-13_NCBO-OOR-Collaboration-2/The-OOR-Initiative_an-update--KenBaclawski-MikeDean-LeoObrst-ToddSchneider-PeterYim_20110913.pdf 2-OOR:Yim-Obrst-Schneider-Baclawski)] ]'''
** '''[http://ontolog.cim3.net/file/work/OpenOntologyRepository/2011-09-13_NCBO-OOR-Collaboration-2/NCBO-OOR-Collaboration-2_20110913b.mp3 audio recording of the session]''' [ 1:23:44 ; mp3 ; 9.6MB ]
** '''[http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_09_13#nid2WY7 Transcript of the online chat session]''' during the panel discussion
** Other '''[http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_09_13#nid2WX8 Resources]'''  


== Agenda & Proceedings  ==
In addition, there is an API of the core services that was obtained from [[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.


'''Session Topic: "Kicking-off the Next Phase of [[NCBO]]-[[OOR]] Collaboration"'''
The following are relevant prior meetings:  


* '''Session Format & Agenda:''' this is a virtual session conducted over an augmented conference call:
* Kicking-off the Next Phase of OOR-NCBO Collaboration - [[OOR/ConferenceCall_2011_09_13]]
** 1. Opening Remarks - Mark Musen (5 min.)
* Architecture & API Specification Development Workshop-VI - [[OOR/ConferenceCall_2011_06_17]]
** 2. [[NCBO]] Briefing - [[RayFergerson|Ray Fergerson]] (20 min.) ... [ [http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_09_13#nid2WWQ slides] ]  
* Architecture & API Specification Development Workshop-V - [[OOR/ConferenceCall_2011_05_20]]
** 3. [[OOR]] Briefings - LeoObrst-PeterYim, KenBaclawski-ToddSchneider (2 presentations, 10 min. each)
* Architecture & API Specification Development Workshop-IV - [[OOR/ConferenceCall_2011_04_22]]
** 3. Q & A and open discussion - All (30 min.) ... please refer to [http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_09_13#nid2WWZ process above]  
* Architecture & API Specification Development Workshop-III - [[OOR/ConferenceCall_2011_03_25]]
** 4. Conclusion / Follow-up - co-chairs
* 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]]


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


* '''Topic: "Kicking-off the Next Phase of [[NCBO]]-[[OOR]] Collaboration"'''
[http://ontolog.cim3.net/file/work/OpenOntologyRepository/OOR-Architecture/OOR-Architecture-API-workshop/ Archives]:
** by [[PeterYim|Peter P. Yim]] & [[RayFergerson|Ray Fergerson]]  


::'''This is an important milestone for the [[OpenOntologyRepository]] initiative, and will mark a new phase of collaboration between the [[NCBO]]-BioPortal team and the [[OOR]] team.'''  
* '''[http://ontolog.cim3.net/file/work/OpenOntologyRepository/OOR-Architecture/OOR-Architecture-API-workshop/OOR_Architecture-API-workshop-VII_20110920b.mp3 audio recording of the session]''' ( 1:10:31 ; mp3 ; 8.87 MB ) 
* '''[http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_09_20#nid2WSB chat-transcript of this session]'''  


:: '''Professor Mark Musen, Principal Investigator of [[NCBO]], and a staunch supporter of the [[OOR]] initiative will kick-off this session for us. His opening will be followed by briefings from both the NCBO-BioPortal team and the OOR team. The briefings will include reports on the current status, important changes and plans that are underway, and how the teams see things both at a high-level (vision, strategy, ...) and low-level (tactics, implementations, coding, operations, ...) going forward.'''
1. Meeting called to order:  


::'''The breifings will be followed by an extended discussion among the panelists and all participants at this session, where we hope to be able to collect input from the community on their expectations, as well as insights on how we can get the best synergy from this next phase of the [[NCBO]]-[[OOR]] collaboration.'''
* [[User:KennethBaclawski|Ken Baclawski]] & [[ToddSchneider|Todd Schneider]] took the chair and welcome everyone


::'''Come join us at this session to find out more on where things stand, what changes are in store, some of the vision going forward, and provide us your input.'''
* [[PeterYim|Peter P. Yim]] volunteered to keep a record of the proceedings


=== Transcript of the online chat during the session  ===
* review and adopt agenda


see raw transcript [http://ontolog.cim3.net/file/work/OpenOntologyRepository/2011-09-13_NCBO-OOR-Collaboration-2/chat-transcript_unedited_20110913a.txt here].  
2. Roll Call & Adoption of last meeting's minutes:


(for better clarity, the version below is a [http://ontolog.cim3.net/file/work/OpenOntologyRepository/2011-09-13_NCBO-OOR-Collaboration-2/chat-transcript_edited_20110913b.txt re-organized and lightly edited chat-transcript].)
* see [http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_09_20#nid2WQF above]  


Participants are welcome to make light edits to their own contributions as they see fit.  
* ref. proceedings of "Architecture & API Specification Development Workshop-VI" - [[OOR/ConferenceCall_2011_06_17]]


-- begin of chat session --
* review of agenda


[08:19] [[PeterYim|Peter P. Yim]]: Welcome to the
3. '''Key items for review and discussion''' today:  


= Joint NCBO-OOR Panel Discussion - Tue 13-Sep-2011 =
* Announcements and Urgent Matters:


Topic: : "Kicking-off the Next Phase of NCBO-OOR Collaboration"  
* Quick discussion on options regarding the [[OOR_SandBox]] install; so we can support the upcoming SOCoP presentation scheduled for late this month
** Peter gave synopsis of the state of affairs, and the need for SOCoP folks to make a SOCoP-OOR presentation/demo in about a week
** Mike: was able to install a v0.2 "NCBO Appliance" VMware image on his notebook (a fairly old Mac); doing the same for v0.3 was mixed, but was able to make most things work (with some exceptions)
*** Ken (will follow Mike's install process and) arrange to have a "NCBO Appliance v0.3" VM run on an NEU hosted machines
**** Ken will drop in the new logo, and customize the IPR License
**** once running, Ken & Tejas will provide Mike with access to the vm
**** Mike / Ken / Tejas / Peter will start a wiki page to capture - [[OOR_SandBox_Customization]] - ... will use the [oor-dev] list too, for email exchange
**** Peter will add the dns record map that instance to socop.oor.net (Ken to provide IP) - it would be either 129.10.112.163 or 129.10.112.167 - Ken will confirm later after checking up on available resources
*** ALL: the aim is to get all the above up and running within 24 to 48 hours, so the SOCoP folks can start doing their "content" work and prepare their presentation


Co-chairs: Dr. [[RayFergerson|Ray Fergerson]] (NCBO; Stanford) and Mr. [[PeterYim|Peter P. Yim]] (OOR; Ontolog; CIM3)
* Discussion on possible adjustments in the OOR architecture and work plans in view of what transpired from last week's Joint [[NCBO]]-[[OOR]] Team Meeting - ref. [[OOR/ConferenceCall_2011_09_13]]  
** defer the discussion to our next meeting when we will try to invite [[RayFergerson|Ray Fergerson]] to join us


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


Professor Mark Musen (NCBO; Stanford)  
* Review of action item(s) from the previous meeting(s)
* from 2011.06.17 - [[MichaelGruninger|Michael Gr&uuml;ninger]] will examine the OMV to determine which attributes are required and which are optional.
* from 2011.06.17 - [[User:KennethBaclawski|Ken Baclawski]] will send KEEPER (the gatekeeping software) to [[ToddSchneider|Todd Schneider]] who will generate the UML.


Dr. Natasha Noy (NCBO; Stanford)  
* '''"OOR Architecture & API Specification Development Workshop-VII:"''' ([http://ontolog.cim3.net/file/work/OpenOntologyRepository/OOR-Architecture/OOR-Architecture-API-workshop/ Archives])  


Dr. [[TrishWhetzel|Trish Whetzel]] (NCBO; Stanford)
* 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.


Dr. [[LeoObrst|Leo Obrst]] (OOR; MITRE)
* [http://ontolog.cim3.net/file/work/OpenOntologyRepository/OOR-Architecture/OOR-Architecture-API-workshop/chat-transcript_edited_20110920b.txt chat transcript of this session]:


Professor [[User:KennethBaclawski|Ken Baclawski]] (OOR; Northeastern U)
--- Chat transcript begin: ---


Dr. [[ToddSchneider|Todd Schneider]] (OOR; Raytheon)
[[PeterYim|Peter P. Yim]]: Welcome to the


Please refer to details on session page
= [[OpenOntologyRepository]]: Architecture & API Workshop-VII - Tue 2011_09_20 =


at: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_09_13
Topic: "OOR Architecture & API Specification Development Workshop-VII"


Participants will be muted before session starts
Session Co-chairs: [[User:KennethBaclawski|Ken Baclawski]] & [[ToddSchneider|Todd Schneider]]


To unmute phone: press *3 ... to put phone on mute again: *2
Session page: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_09_20


.  
.


= Proceedings =
== Proceedings ==


.  
.  


[08:22] [[MikeDean|Mike Dean]]: I'll need to drop off around 12:10, but will lurk until then
[[ToddSchneider|Todd Schneider]]: Ken, I was able to login.


[08:24] [[PeterYim|Peter P. Yim]]: Hi Mike ... thanks for being here
[[User:KennethBaclawski|Ken Baclawski]]: Tejas set up a VMWare on a machine in my office at NEU. I can give access to anyone


[08:26] [[ToddSchneider|Todd Schneider]]: Peter, I may need to leave after the first hour. I'll try and stay as long as possible.
who needs it. The main machine is lisf.ccs.neu.edu, and the domains we can use are


[08:27] anonymous morphed into [[TimWilson|Tim Wilson]]
ontology.ccs.neu.edu and kiwi.ccs.neu.edu.


[08:28] [[TimWilson|Tim Wilson]]: Will there be sound on "hopper"? Does the VNC have sound?  
[[PeterYim|Peter P. Yim]]: please use this page to capture customization details - http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR_SandBox_Customization


[08:59] [[PeterYim|Peter P. Yim]]: @Tim - the HOPPER server (i.e. vnc2) is only for screen sharing ... no voice support
[[User:KennethBaclawski|Ken Baclawski]]: The static IP address of ontology.ccs.neu.edu is 129.10.112.163.  The one for kiwi.ccs.neu.edu is 129.10.112.167.  


[08:28] anonymous morphed into Niranjan Manjunath
[[ToddSchneider|Todd Schneider]]: where are we with the discussion ... ref. http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_04_22#nid2ST2


[08:30] anonymous morphed into [[RayFergerson|Ray Fergerson]]
= The interface for searching ontology metadata will consist of a single method:   (2SSS)


[08:30] Kathy Ellis2 morphed into [[KathyEllis|Kathy Ellis]]
* The method will be called find.    (2SST)


[08:32] anonymous morphed into [[ElizabethFlorescu|Elizabeth Florescu]]
* The method will have a single parameter consisting of a SPARQL query.    (2SSU)


[08:36] [[ToddSchneider|Todd Schneider]]: Peter, I'm having phone issues.  
* The return value of the method will be a SPARQL result set.   (2SSV)


[08:37] [[User:KennethBaclawski|Ken Baclawski]]: Todd, let me know if you need me to take over for you in our talk.  
* Metadata will be represented using a named RDF graph.   (2SSW)


[08:38] [[ToddSchneider|Todd Schneider]]: Ken, I now have a voice connection.  
* The metadata RDF graph will use the following name: http://metadata.oor.net    (2SSX)


[08:36] anonymous morphed into [[ChuckRehberg|Chuck Rehberg]]
* Metadata will be based on an extension of OMV.    (2SSY)


[08:38] anonymous morphed into Dave Hau (NCI) [DavidHau]
o The OMV extension may include a notion of domain specification or topics, represented as text.    (2SSZ)


[08:40] [[ToddSchneider|Todd Schneider]]: Ray, can you speak louder?
* Metadata will be federated, so it is a single named RDF graph, no matter how many OOR instances there are.


[08:40] anonymous morphed into [[FrankOlken|Frank Olken]]  
[[ToddSchneider|Todd Schneider]]: also ref. http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_06_17#nid2V8P


[08:44] anonymous morphed into [[MyCoyne]]
o Quality and Gatekeeping. We distinguish between gatekeeping and quality control.


[08:53] [[FrankOlken|Frank Olken]]: I still did not catch which RDF triple store is being used.
Gatekeeping criteria are a set of minimal requirements that any ontology within


[08:53] [[PeterYim|Peter P. Yim]]: @Frank - let's ask Ray during the discussion later
the OOR has to meet. The latter are intended to enable the users of the OOR to


[08:54] anonymous morphed into YefimZhuk
find quickly ontologies that fit their needs; the criteria are not supposed to


[08:40] pradeep: not able to dial from south korea
ensure the quality of the ontologies.    (2VB8)


[08:40] pradeep: any help? sorry
o Gatekeeping impacts metadata    (2VB9)


[08:52] [[PeterYim|Peter P. Yim]]: @pradeep - besides the US conference nbr, can you try some of the other (EU) phone numbers?
o Gatekeeping will need to vet the metadata to ensure entrance criteria are met.   (2VBA)


[09:04] pradeep: @PeterYim tried all the numbers not able to connect. Will wait for the audio files.  
o Syntax checking is the responsibility of the language module.   (2VBB)


Any possibility of using skype ? I am highly interested in the talk please help me.
o Each OOR instance must declare the representation languages    (2VBD)


[09:05] [[PeterYim|Peter P. Yim]]: @pradeep - too bad ... the audio archive will be ready in a couple of days
o Each OOR instance must declare the representation language module it spports.   (2VBE)


[09:02] YefimZhuk: Ray, thanks for a very informative talk! which RDF Triplestore do you use in the BioPortal?  
o Will OOR Metadata be represented in OWL?   (2VBF)


[09:06] [[ChuckRehberg|Chuck Rehberg]]: I need to leave - he can have my phone line
o Every OOR shall support RDF    (2VBG)


[09:06] [[PeterYim|Peter P. Yim]]: @Chuck - thanks ... it's not the limitation of lines that is the problem, unfortunately
o Correction: Every OOR shall support RDFS    (2VBI)


[09:10] pradeep: @PeterYim thank you.  
o OMV is written in OWL    (2VBK) - From Chapter 5 of the OMV Report 2.4.1: As aforementioned, OMV is formalized as an OWL ontology.   (2VBO)


[09:13] [[JohnBateman|John Bateman]]: @Todd: multiple representation languages: +10 :-)  
o Gatekeeping criteria will include an attribute to indicate whether the ontology exists or the metadata represents an advertisement.    (2VBR)


[09:13] [[PeterYim|Peter P. Yim]]: @JohnBateman - that's where you guys come in!
o The location of the actual ontology is the responsibility of Administration.   (2VBT)


[09:14] [[ToddSchneider|Todd Schneider]]: John, support for multiple representation languages requires the independence of the functionality.
o Metadata needs to include an attribute for the 'availability' of the ontology    (2VBW)


[09:21] [[LeoObrst|Leo Obrst]]: Ray, Mark, can you elaborate a bit on what you envision for licensing ontologies?
o 'Location' of the ontology must be provided.    (2VBX)


[09:40] [[FrankOlken|Frank Olken]]: What backend are you planning to use? The audio is distorted? What triple store?
o Representation language of the ontology is a required attribute.    (2VBY)


[09:42] [[FrankOlken|Frank Olken]]: [RayFergerson mentioned 4store as a strong candidate] Looking at 4store triple store.  
o Michael will provide a preliminary list of required metadata attributes.   (2VBZ)


Will it support SPQRQL 1.1?
o Submission process will be asynchronous    (2VC0)


[09:58] [[FrankOlken|Frank Olken]]: http://4store.org/ is the web site for 4store triple store.
o Minimal language dependency submission is syntax validation    (2VC1)


[09:44] [[ToddSchneider|Todd Schneider]]: Have to go. Cheers.
o Consistency checking, to some extent, will be required for submission    (2VC2)


[09:59] [[LeoObrst|Leo Obrst]]: Thanks, all! Goodbye.
o Need an attribute to represent that it is consistent, which then will require


[09:59] [[PeterYim|Peter P. Yim]]: great sessions ... thanks, everyone!
another field to identify the reasoner used to do the consistency checking    (2VC3)


[09:59] [[PeterYim|Peter P. Yim]]: -- session ended: 10:00 am PDT --
o Ken has already developed the gatekeeper module which should provide enough to specify it for OOR    (2VC4)


-- end of chat session --
o Ken's gatekeeper module already has a mechanism to configure the registration workflow for a community    (2VC5)


* Further Question & Remarks - please post them to the [ [http://ontolog.cim3.net/forum/oor-forum/ oor-forum] ] listserv
[[ToddSchneider|Todd Schneider]]: Gatekeeper - notification(), subscription(), register()?
** if you are already subscribed, post to <oor-forum [at] ontolog.cim3.net>
** (if you are not yet subscribed) you may subscribe yourself to the [ oor-forum ] listserv listserv, by sending a blank email to <oor-forum-join [at] ontolog.cim3.net> from your subscribing email address, and then follow the instructions you receive back from the mailing list system.


=== Resources  ===
[[ToddSchneider|Todd Schneider]]: subscription is for particular ontology and particular user


* '''[[NCBO]] - National Center for Biomedical Ontology''' - http://www.bioontology.org/
[[ToddSchneider|Todd Schneider]]: subscription - sends notices about events related to ontology
* The '''BioPortal''' - http://bioportal.bioontology.org/
* '''[[OpenOntologyRepository]]''' - Homepage for the OOR initiative
* A recent presentation on OOR - [http://ontolog.cim3.net/file/work/OOR/OOR_presentations_publications/OOR-SemTech_Jun2010.pdf OOR Presentation at SemTech2010]
* The OOR_SandBox (powered by the NCBO BioPortal) instance, now online at: http://sandbox.oor.net
* OOR Project site and code repository at [[SemWebCentral]] - http://oor.semwebcentral.org
* [[OpenOntologyRepository_IPR]] Policy
* 2010_09_17 - Friday: OOR Panel Discussion - "Getting OOR Development Going - Take-IV" Workshop - Co-chairs: Dr. [[ToddSchneider|Todd Schneider]] & Professor [[MichaelGruninger|Michael Gr&uuml;ninger]] - Panelists: Dr. [[ToddSchneider|Todd Schneider]] (Raytheon), Mr. [[MikeDean|Mike Dean]] (Raytheon-BBN), Dr. Natasha Noy (NCBO, Stanford University), Dr. [[ImmanuelNormann|Immanuel Normann]] (Bremen University, BORG), Professor [[User:KennethBaclawski|Ken Baclawski]] (Northeastern University), Professor [[MichaelGruninger|Michael Gr&uuml;ninger]] (University of Toronto) - [[OOR/ConferenceCall_2010_09_17]]
* 2009_10_15 - Thursday: "OOR-BioPortal Comparative Analysis" panel discussion - Chair: [[ToddSchneider|Todd Schneider]] - Panelists: Natasha Noy, MichaelDorf, [[User:KennethBaclawski|Ken Baclawski]], [[ElisaKendall|Elisa Kendall]] & [[MikeDean|Mike Dean]] - ConferenceCall_2009_10_15
* 2009_07_30 - Thursday: Joint Ontolog-OOR Panel Discussion: "BioPortal and related Ontology Repository Implementations and Development" (Take-3) - Chair: Natasha Noy - Panelists: [[CarlosRueda|Carlos Rueda]], [[PaulAlexander|Paul Alexander]], [[JohnGraybeal|John Graybeal]], [[MikeDean|Mike Dean]], StephenGranite, AlexGarcia, [[User:KennethBaclawski|Ken Baclawski]] - ConferenceCall_2009_07_30
* 2009_02_19 - Thursday: Joint Ontolog-OOR Panel Discussion: "Getting OOR Development Off the Ground (Take-2): the work begins" - Chair: [[ToddSchneider|Todd Schneider]]; Panelists: Mark Musen, Natasha Noy, [[MikeDean|Mike Dean]], [[PaulBuitelaar|Paul Buitelaar]] / [[AndreasHarth|Andreas Harth]], [[MathieuDaquin|Mathieu Daquin]], [[User:KennethBaclawski|Ken Baclawski]], [[MichaelGruninger|Michael Gr&uuml;ninger]] - ConferenceCall_2009_02_19
* 2008_08_22 - Friday: OOR Panel Discussion: "Getting OOR Development Off the Ground: Identifying Synergies & Gaps" (Take-1) - Chair: [[LeoObrst|Leo Obrst]]; Panelists: [[MikeDean|Mike Dean]], Mark Musen, [[LiDing|Li Ding]], [[Bargmeyer|Bruce Bargmeyer]] & [[BillAndersen|Bill Andersen]] - ConferenceCall_2008_08_22
* 2008_04_29 - Our team made a presentation with our history, status, OOR rationale and requirements, and a proposed roadmap at the [[OntologySummit2008|Ontology Summit 2008]] - see: http://ontolog.cim3.net/cgi-bin/wiki.pl?OntologySummit2008/FaceToFaceAgenda#nid1BLS
* 2007_12_06 - Thursday: Invited Speaker - Professor Mark Musen: "If we build it, will they come? Social-engineering of new technology to disseminate biomedical ontologies" - ConferenceCall_2007_12_06
* '''OntologySummit2008 - "Toward An Open Ontology Repository"'''
** '''[[OntologySummit2008_Communique]]'''
* our most recent regular OOR-team meeting - [[OOR/ConferenceCall_2011_09_06]]
* [ [http://ontolog.cim3.net/forum/oor-forum/ oor-forum] ] message archive - http://ontolog.cim3.net/forum/oor-forum/
** (if you are not yet subscribed) you may subscribe yourself to the [ [http://ontolog.cim3.net/mailman/listinfo/oor-forum/ oor-forum] ] listserv, by sending a blank email to <oor-forum-join [at] ontolog.cim3.net> from your subscribing email address, and then follow the instructions you receive back from the mailing list system.
** check out our other mailing lists and [[OpenOntologyRepository|join us]]


== Audio Recording of this Session  ==
[[TerryLongstreth|Terry Longstreth]]: Create ontology == prepare system for new ontology?


* To download the [http://ontolog.cim3.net/file/work/OpenOntologyRepository/2011-09-13_NCBO-OOR-Collaboration-2/NCBO-OOR-Collaboration-2_20110913b.mp3 audio recording of the session], click '''[http://ontolog.cim3.net/file/work/OpenOntologyRepository/2011-09-13_NCBO-OOR-Collaboration-2/NCBO-OOR-Collaboration-2_20110913b.mp3 here]'''
[[ToddSchneider|Todd Schneider]]: registrar - creates the entry in the OOR; to do so the required metadata needs to be created
** the playback of the audio files require the proper setup, and an MP3 compatible player on your computer.
* Conference Date and Time: 13-Sep-2011 8:30am ~ 10:00pm Pacific Daylight Time
* Duration of Recording: 1 Hour 24 Minutes
* Recording File Size:         9.6 MB (in mp3 format)


* suggestion: its best that you listen to the session while having the [http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_09_13#nid2WWQ presentation] opened in front of you. You'll be prompted to advance slides by the speaker.
[[PeterYim|Peter P. Yim]]: -- session ended: 9:41am PDT --
* Take a look, also, at the rich body of knowledge that this community has built together, over the years, by going through the [[WikiHomePage|archives of noteworthy past Ontolog events.]] (References on how to subscribe to our podcast can also be found there.)


----
--- Chat transcript end: ---  


''For the record ...''  
'''Consensus, Conclusions & Follow-up Actions:'''  


== How To Join (while the session is in progress)  ==
4. '''Any Other Business:'''


* '''1.''' Dial in with a phone: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_09_13#nid2WCB
5. '''Action items:'''  
* '''2.''' Open chat in a new browser window: http://webconf.soaphub.org/conf/room/ontolog_20110913
* '''3.''' Download presentations for each speaker here: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_09_13#nid2WWQ
** or, '''3.1''' optionally, [http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_09_13#nid2WWV access our shared-screen vnc server], if you are not behind a corporate firewall


=== [[MeetingsCalls|Conference Call]] Details ===
* (ref. [http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_09_20#nid2X19 above]) Peter to contact [[RayFergerson|Ray Fergerson]] and invite him to join us on the Oct-4 call to do a "Architectural review and discussion"
** no prepared presentations, but we need an agenda and enumerate things to discuss - Ken and Todd will prepare
*** Peter will set up the [[OOR/ConferenceCall_2011_10_04]] meeting page quickly, so Ken, Todd, Ray and anyone else can add things to it.  ... ( done! --ppy/2011.09.20-15:50 PDT )  


* Date: '''Tuesday, 13-Sep-2011'''
6. Schedule Next Meeting & Adjourn:  
* Start Time: 8:30am PDT / 11:30am EDT / 5:30pm CEST / 4:30pm BST / 15:30 UTC
** ref: [http://www.timeanddate.com/worldclock/fixedtime.html?month=9&day=13&year=2011&hour=8&min=30&sec=0&p1=224 World Clock]
* Expected Call Duration: 1.5 hours
* Dial-in Number:
** from a '''US telephone (US): +1-218-844-8060''' (domestic long distance cost will apply)
** When calling in from a phone, use '''Conference ID: "4389979#"'''
** '''from Europe, call:'''
*** Austria 0820-4000-1577
*** Belgium 070-35-9992
*** France 0826-100-280
*** Germany 01805-00-7642
*** Ireland 0818-270-037
*** Italy 848-390-179
*** Spain 0902-886-056
*** Switzerland 0848-560-327
*** UK 0844-581-9148
** callers '''from other countries''' please dial into either one of the US or European numbers
 
* '''Shared-screen support''' (VNC session) 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 '''[http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_09_13#nid2WWQ slides above]''' and running them locally. The speaker(s) will prompt you to advance the slides during the talk.


* '''Discussions and Q & A:'''
* Next Meeting:  
** (Unless the conference host has already muted everyone) '''Please mute your phone, by pressing "*2"''' on your phone keypad, when a presentation is in progress. '''To un-mute, press "*3"'''  
** since the SOCoP folks will be getting ready to travel, and Peter cannot join on Sep-27, we will skip next week's
** You can '''type in your questions or comments through the browser''' based [[ConferenceCall_2005_09_01|chat session]] by:
** next meeting will therefore be, at the same time on 2011_10_04 Tuesday: regular OOR-team call
*** pointing a separate browser tab (or window) to http://webconf.soaphub.org/conf/room and enter: Room="'''ontolog_20110913'''" and My Name="Your Own Name" (e.g. "JaneDoe")
** or point your browser to: http://webconf.soaphub.org/conf/room/ontolog_20110913
*** instructions: once you got access to the page, click on the "settings" button, and identify yourself (by modifying the Name field). 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.
** (when everyone is muted) '''If you want to speak''' or have questions or remarks to make, '''please "raise your hand (virtually)" by click on the "hand button" (lower right) on the chat session page. You may speak when acknowledged by the speaker or the session moderator (again, press "*3" on your phone to unmute). ''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 "*2" on your phone to mute yourself after you are done speaking.)
** 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_20110913@soaphub.org ... Handy for mobile devices!


* Please review our Virtual Session Tips and Ground Rules - see: [[VirtualSpeakerSessionTips]]
* Call adjourned at: 9:41 am PDT


* '''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_09_13
notes taken by: [[PeterYim|Peter P. Yim]] / 2011.09.20-9:41am PDT


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


== Attendees  ==
----


* Attended (and a few registered participants who may have joined after the roll call):
== Resources ==
** [[RayFergerson|Ray Fergerson]] (co-chair)
** [[PeterYim|Peter P. Yim]] (co-chair)
** Mark Musen
** Natasha Noy
** [[TrishWhetzel|Trish Whetzel]]
** [[MikeDean|Mike Dean]]
** [[LeoObrst|Leo Obrst]]
** [[KathleenEllis|Kathleen Ellis]]
** [[User:KennethBaclawski|Ken Baclawski]]
** [[ToddSchneider|Todd Schneider]]
** [[YuriyMilov|Yuriy Milov]]
** [[TimWilson|Tim Wilson]]
** Niranjan Manjunath (NEU)
** [[TimDarr|Tim Darr]]
** YefimZhuk
** Gilberto Fragoso (NIH/NCI)
** [[ChuckRehberg|Chuck Rehberg]]
** [[ElizabethFlorescu|Elizabeth Florescu]]
** [[JohnBateman|John Bateman]]
** [[NancyWiegand|Nancy Wiegand]]
** [[DavidHau|David Hau]]
** [[FrankOlken|Frank Olken]]
** [[MyCoyne]]
** [[TerryLongstreth|Terry Longstreth]]
** [[DeborahMacPherson]]
** [[PaulCourtney|Paul Courtney]]
**  
** ... ''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.''


* Regrets:  
* homepage - '''[[OpenOntologyRepository]]''' - http://OpenOntologyRepository.org
** [[MikeBennett|Mike Bennett]]  
* '''[[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.
** [[MichaelGruninger|Michael Gr&uuml;ninger]]  
* '''"Ontology Repository" Definition''' - "An ontology repository is a facility where ontologies and related information artifacts can be stored, retrieved and managed"
** ...  
* '''Team mailling list:'''
** OOR-Team discussion: [ [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/
** Developers mailling 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]]'''
* the '''Joint [[OOR]]-OntologySummit2008 Panel Discussions''':
** 2008_02_28 - Thursday: Joint OOR-OntologySummit2008 Panel Discussion: "Ontology Registry and Repository Technology & Infrastructure Landscape" - Co-chairs: [[LeoObrst|Leo Obrst]] & [[FrankOlken|Frank Olken]]; Panelists: [[Bargmeyer|Bruce Bargmeyer]], [[MikeDean|Mike Dean]], Mark Musen, [[FarrukhNajmi|Farrukh Najmi]] & [[PeterYim|Peter P. Yim]] - ConferenceCall_2008_02_28
** 2008_03_27 - Thursday: Joint OOR-OntologySummit2008 Panel Discussion: "An Open Ontology Repository: Rationale, Expectations & Requirements - Session-1" - Chair: [[LeoObrst|Leo Obrst]] & [[FabianNeuhaus|Fabian Neuhaus]]; Panelists: [[WilliamBug|William Bug]], [[EvanWallace|Evan Wallace]], [[JohnLMcCarthy]], [[User:KennethBaclawski|Ken Baclawski]], [[PeterBenson|Peter Benson]] & [[RexBrooks|Rex Brooks]] - ConferenceCall_2008_03_27
** 2008_04_03 - Thursday: Joint OOR-OntologySummit2008 Panel Discussion: "An Open Ontology Repository: Rationale, Expectations & Requirements - Session-2" - Chair: [[LeoObrst|Leo Obrst]] & [[FabianNeuhaus|Fabian Neuhaus]]; Panelists: [[DougLenat|Doug Lenat]], [[DekeSmith|Deke Smith]], [[MarciaZeng|Marcia Zeng]], [[DeniseBedford|Denise Bedford]], [[PatHayes|Pat Hayes]], [[MalaMehrotra|Mala Mehrotra]] & [[RobRaskin|Rob Raskin]] - ConferenceCall_2008_04_03
** 2008_04_10 - Thursday: Joint OOR-OntologySummit2008 Panel Discussion: "Developing an Ontology of Ontologies for OOR" - Co-chairs: [[BarrySmith|Barry Smith]] & [[MichaelGruninger|Michael Gr&uuml;ninger]]; Panelists: [[MichaelGruninger|Michael Gr&uuml;ninger]], [[PeterHaase|Peter Haase]], Natasha Noy & [[ElisaKendall|Elisa Kendall]] - ConferenceCall_2008_04_10
* the '''OOR Development panel sessions''':
** 2008_08_22 - Friday: OOR Panel Discussion: "Getting OOR Development Off the Ground: Identifying Synergies & Gaps" (Take-1) - Chair: [[LeoObrst|Leo Obrst]]; Panelists: [[MikeDean|Mike Dean]], Mark Musen, [[LiDing|Li Ding]], [[Bargmeyer|Bruce Bargmeyer]] & [[BillAndersen|Bill Andersen]] - ConferenceCall_2008_08_22
** 2009_02_19 - Thursday: Joint Ontolog-OOR Panel Discussion: "Getting OOR Development Off the Ground (Take-2): the work begins" - Chair: [[ToddSchneider|Todd Schneider]]; Panelists: Mark Musen, Natasha Noy, [[MikeDean|Mike Dean]], [[PaulBuitelaar|Paul Buitelaar]] / [[AndreasHarth|Andreas Harth]], [[MathieuDaquin|Mathieu Daquin]], [[User:KennethBaclawski|Ken Baclawski]], [[MichaelGruninger|Michael Gr&uuml;ninger]] - ConferenceCall_2009_02_19
** 2009_07_16 - Thursday: Joint Ontolog-OOR Panel Discussion: "Integrated tools for ontology development and management: A field guide to the Stanford technology" - Chair: Mark Musen - Panelists: [[TaniaTudorache|Tania Tudorache]], [[TimRedmond|Tim Redmond]], Natasha Noy - ConferenceCall_2009_07_16
** 2009_07_30 - Thursday: Joint Ontolog-OOR Panel Discussion: "BioPortal and related Ontology Repository Implementations and Development" (Take-3) - Chair: Natasha Noy - Panelists: [[CarlosRueda|Carlos Rueda]], [[PaulAlexander|Paul Alexander]], [[JohnGraybeal|John Graybeal]], [[MikeDean|Mike Dean]], StephenGranite, AlexGarcia, [[User:KennethBaclawski|Ken Baclawski]] - ConferenceCall_2009_07_30
** 2010_02_19 - Friday: OOR Panel Discussion: "Coordinating our Open Ontology Repository Software Development" - Chair: [[MikeDean|Mike Dean]] - Panelists: [[JimChatigny|Jim Chatigny]], [[MichaelGruninger|Michael Gr&uuml;ninger]], [[User:KennethBaclawski|Ken Baclawski]], Natasha Noy - [[OOR/ConferenceCall_2010_02_19]]
** 2010_04_01 - Thursday: Joint OOR-Ontolog Panel Session: "OOR Use Cases - Take-3" - Chair: [[User:KennethBaclawski|Ken Baclawski]] & [[ToddSchneider|Todd Schneider]] - Panelists: [[ToddSchneider|Todd Schneider]], [[MatthewHettinger|Matthew Hettinger]], [[User:KennethBaclawski|Ken Baclawski]] and [[MaximoGurmendez|M&aacute;ximo Gurm&eacute;ndez]] - ConferenceCall_2010_04_01
** 2010_09_10 - Friday: Joint SIO-OOR-Ontolog Panel Discussion: "Common Logic (CL) Support for OOR" - Chair: [[JohnSowa|John F. Sowa]] - Panelists: JohnBateman-TillMossakowski, [[MichaelGruninger|Michael Gr&uuml;ninger]], [[CameronRoss|Cameron Ross]], [[AdamPease|Adam Pease]], [[PatHayes|Pat Hayes]] - ConferenceCall_2010_09_10
** 2010_09_17 - Friday: OOR Panel Discussion - "Getting OOR Development Going - Take-IV" Workshop - Co-chairs: [[ToddSchneider|Todd Schneider]] & [[MichaelGruninger|Michael Gr&uuml;ninger]] - Panelists: [[ToddSchneider|Todd Schneider]], [[MikeDean|Mike Dean]], Natasha Noy, [[ImmanuelNormann|Immanuel Normann]], [[User:KennethBaclawski|Ken Baclawski]], [[MichaelGruninger|Michael Gr&uuml;ninger]] - [[OOR/ConferenceCall_2010_09_17]]
** 2010_10_15 - Friday: OOR Project Team Member Conference Call - discussion on the (post-BioPortal fork) OOR Architecture and API - [[OOR/ConferenceCall_2010_10_15]]
** 2010_11_19 - Friday: OOR Panel Discussion - "(Post-BioPortal fork) OOR Architecture and API - Take-II" - Co-chairs: [[User:KennethBaclawski|Ken Baclawski]] & [[MichaelGruninger|Michael Gr&uuml;ninger]] - Panelists: KenBaclawski+ToddSchneider, AldoGangemi+AlessandroAdamou, JouniTuominen+KimViljanen, [[EricChan|Eric Chan]] - [[OOR/ConferenceCall_2010_11_19]]
** 2011_03_04 - Friday: OOR "Architecture & API Specification Development Workshop-I" - Co-chairs: [[User:KennethBaclawski|Ken Baclawski]] & [[ToddSchneider|Todd Schneider]] - [[OOR/ConferenceCall_2011_03_04]]
** 2011_03_11 - Friday: OOR - "Architecture & API Specification Development Workshop-II" - Co-chairs: [[User:KennethBaclawski|Ken Baclawski]] & [[ToddSchneider|Todd Schneider]] - [[OOR/ConferenceCall_2011_03_11]]
** 2011_03_18 - Friday: OOR Metadata Workshop-I - Chair: [[MichaelGruninger|Michael Gr&uuml;ninger]] - [[OOR/ConferenceCall_2011_03_18]]
** 2011_03_25 - Friday: OOR - "Architecture & API Specification Development Workshop-III" - Co-chairs: [[User:KennethBaclawski|Ken Baclawski]] & [[ToddSchneider|Todd Schneider]] - [[OOR/ConferenceCall_2011_03_25]]
** 2011_04_22 - Friday: OOR - "Architecture & API Specification Development Workshop-IV" - Co-chairs: [[User:KennethBaclawski|Ken Baclawski]] & [[ToddSchneider|Todd Schneider]] - [[OOR/ConferenceCall_2011_04_22]]  
** 2011_05_13 - Friday: OOR Metadata Workshop-II - Chair: [[MichaelGruninger|Michael Gr&uuml;ninger]] - [[OOR/ConferenceCall_2011_05_13]]
** 2011_05_20 - Friday: OOR - "Architecture & API Specification Development Workshop-V" - Co-chairs: [[User:KennethBaclawski|Ken Baclawski]] & [[ToddSchneider|Todd Schneider]] - [[OOR/ConferenceCall_2011_05_20]]
** 2011_05_27 - Friday: OOR Metadata Workshop-III - Chair: [[MichaelGruninger|Michael Gr&uuml;ninger]] - [[OOR/ConferenceCall_2011_05_27]]
** 2011_06_17 - Friday: OOR - "Architecture & API Specification Development Workshop-VI" - Co-chairs: [[User:KennethBaclawski|Ken Baclawski]] & [[ToddSchneider|Todd Schneider]] - [[OOR/ConferenceCall_2011_06_17]]
** 2011_09_13 - Tuesday: Joint NCBO-OOR Team Meeting - "Kicking-off the Next Phase of Collaboration" - Co-chairs: [[RayFergerson|Ray Fergerson]] & [[PeterYim|Peter P. Yim]] - [[OOR/ConferenceCall_2011_09_13]]
** 2011_09_20 - Tuesday: OOR - "Architecture & API Specification Development Workshop-VII" - Chair: [[User:KennethBaclawski|Ken Baclawski]] - [[OOR/ConferenceCall_2011_09_20]]
* the '''OOR-IPR mini-series''':
** 2010_09_09 - Thursday: Joint OOR-Ontolog-NCBO-CC-IAOA-OASIS Panel Discussion - "IPR issues in Ontology and the OOR" session-1: an exposition on relevant IPR regimes - Keynote speaker: [[GeorgeStrawn|George Strawn]] - Chair: [[PeterYim|Peter P. Yim]] - Panelists: [[JamieClark]], [[JohnWilbanks|John Wilbanks]], [[BrucePerens|Bruce Perens]] - ConferenceCall_2010_09_09
** 2010_09_16 - Thursday: Joint OOR-Ontolog-NCBO-CC-IAOA-OASIS Panel Discussion - "IPR issues in Ontology and the OOR" session-2: what are the IPR issues relating to open ontology repositories (and ontologies in general)? - Chair: Mark Musen - Panelists: [[CameronRoss|Cameron Ross]], [[AlanRector|Alan Rector]], [[JohnSowa|John F. Sowa]], [[BrucePerens|Bruce Perens]], [[JohnWilbanks|John Wilbanks]], [[PeterYim|Peter P. Yim]] - ConferenceCall_2010_09_16
** 2010_09_30 - Thursday: Joint OOR-Ontolog-NCBO-CC-IAOA-OASIS Panel Discussion - "IPR issues in Ontology and the OOR" session-3: discussion and consensus on licensing arrangements for the OOR Initiative, and positions we might take on related IPR issues - chair: [[LeoObrst|Leo Obrst]] - Panelists: [[PeterYim|Peter P. Yim]], [[MikeDean|Mike Dean]], [[BrucePerens|Bruce Perens]], [[JamieClark]] - ConferenceCall_2010_09_30
* '''OntologySummit2008''' homepage
** '''[[OntologySummit2008_Communique]]'''
** '''[[OntologySummit2008/FaceToFaceAgenda]] & Proceedings'''
** The '''[http://ontolog.cim3.net/file/work/OntologySummit2008/2008-04-2829_F2F-workshop/OntologySummit2008_OOR-Presentation--MikeDean-LeoObrst-PeterYim_20080429.ppt OOR Project] Presentation''' (delivered at the [[OntologySummit2008|Ontology Summit 2008]] face-to-face workshop)
* '''[ [http://ontolog.cim3.net/forum/ontology-summit/ ontology-summit] ]''' discussion archives - http://ontolog.cim3.net/forum/ontology-summit/2008-01/ (~5 months exchanges starting from Jan-2008)
* Our key content pages:
** '''[[OpenOntologyRepository_Scope]]'''
** '''[[OpenOntologyRepository_Organization]]'''
** '''[[OpenOntologyRepository_Process]]'''
** '''[[OpenOntologyRepository_Policy]]'''
** '''[[OpenOntologyRepository_IPR]]'''
** '''[[OpenOntologyRepository_Requirement]]'''
** '''[[OpenOntologyRepository_UseCases]]'''
** '''[[OpenOntologyRepository_Architecture]]'''
** '''[[OpenOntologyRepository_Approach]]'''
** '''[[OpenOntologyRepository_Roadmap]]'''
** '''[[OpenOntologyRepository_Plan]]'''
** '''[[OpenOntologyRepository_Funding]]'''
** '''[[OpenOntologyRepository_ResearchIssues]]'''
** '''[[OpenOntologyRepository_ResearchActivity]]'''
** '''[[OpenOntologyRepository_Development]]'''
** '''[[OpenOntologyRepository_Metadata]]'''
* '''[[OOR/ActiveMemberContribution]]'''
* '''OOR Project site at [[SemWebCentral]]''' - http://oor.semwebcentral.org
* '''Public sandbox instance of OOR (OOR-sandbox) - http://sandbox.oor.net/ontologies''' (previously http://oor-02.cim3.net/ontologies)
** '''[[OOR_SandBox]]'''
* '''Development instance of OOR (OOR-dev) - http://oor-01.cim3.net/''' - to browse: http://oor-01.cim3.net/ontologies - http://dev.oor.net/
** '''[[OOR_DevBox]]'''
** [[NCBO]] - [http://bioportal.bioontology.org/ BioPortal]
*** BioPortal's [bioontology-support] mailing list - see: https://mailman.stanford.edu/mailman/listinfo/bioontology-support
** NCBO-OOR development documentation - http://www.bioontology.org/wiki/index.php/NCBO-OOR_Development


[[Category:Event_Meeting]]    [[Category:OOR]]
[[Category:Event_Meeting]]    [[Category:OOR]]

Latest revision as of 07:33, 9 January 2016

OpenOntologyRepository: Architecture & API Workshop-VII - Tue 2011_09_20

Topic: "OOR Architecture & API Specification Development Workshop-VII"

Session Chair: Ken Baclawski & Todd Schneider

Conference Call Details

  • Date: Tuesay, 20-Sep-2011
  • Start Time: 8:30am PDT / 11:30am EDT / 5:30pm CEST / 4:30pm BST / 15:30 UTC
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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) ontolog_20110920@soaphub.org ... Handy for mobile devices!
  • 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)

  • Peter P. Yim (2011.09.19): need a quick discussion on options regarding the OOR_SandBox install; so we can support the upcoming SOCoP presentation scheduled for late this month
  • Discussion on possible adjustments in the OOR architecture and work plans in view of what transpired from last week's Joint NCBO-OOR Team Meeting - ref. OOR/ConferenceCall_2011_09_13
  • The specifications to be discussed at the these workshops are the following (not necessarily discussed in this order):
    • the OOR Architecture
    • the OOR API
    • the Organizing Plan
    • the default development platform

Abstract

As a result of the two OOR Architecture and API panel sessions back in Oct & Nov-2010, we have been exposed to a large number of architecture and API candidates for ontology repositories. We have had requirements for the OOR, at least in broad outline form, since the Ontology Summit 2008. We have been running an OOR sandbox based on BioPortal. Most recently, we have forked from the BioPortal code base with the intention of proceeding separately with the development of a reference implementation.

At this 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 straw man architecture: OpenOntologyRepository_Architecture/Candidate03

In addition, there is an API of the core services that was obtained from 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.

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:

  • review of agenda

3. Key items for review and discussion today:

  • Announcements and Urgent Matters:
  • Quick discussion on options regarding the OOR_SandBox install; so we can support the upcoming SOCoP presentation scheduled for late this month
    • Peter gave synopsis of the state of affairs, and the need for SOCoP folks to make a SOCoP-OOR presentation/demo in about a week
    • Mike: was able to install a v0.2 "NCBO Appliance" VMware image on his notebook (a fairly old Mac); doing the same for v0.3 was mixed, but was able to make most things work (with some exceptions)
      • Ken (will follow Mike's install process and) arrange to have a "NCBO Appliance v0.3" VM run on an NEU hosted machines
        • Ken will drop in the new logo, and customize the IPR License
        • once running, Ken & Tejas will provide Mike with access to the vm
        • Mike / Ken / Tejas / Peter will start a wiki page to capture - OOR_SandBox_Customization - ... will use the [oor-dev] list too, for email exchange
        • Peter will add the dns record map that instance to socop.oor.net (Ken to provide IP) - it would be either 129.10.112.163 or 129.10.112.167 - Ken will confirm later after checking up on available resources
      • ALL: the aim is to get all the above up and running within 24 to 48 hours, so the SOCoP folks can start doing their "content" work and prepare their presentation
  • Discussion on possible adjustments in the OOR architecture and work plans in view of what transpired from last week's Joint NCBO-OOR Team Meeting - ref. OOR/ConferenceCall_2011_09_13
    • defer the discussion to our next meeting when we will try to invite Ray Fergerson to join us

... 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)
  • from 2011.06.17 - Michael Grüninger will examine the OMV to determine which attributes are required and which are optional.
  • from 2011.06.17 - Ken Baclawski will send KEEPER (the gatekeeping software) to Todd Schneider who will generate the UML.
  • "OOR Architecture & API Specification Development Workshop-VII:" (Archives)
  • 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.

--- Chat transcript begin: ---

Peter P. Yim: Welcome to the

OpenOntologyRepository: Architecture & API Workshop-VII - Tue 2011_09_20

Topic: "OOR Architecture & API Specification Development Workshop-VII"

Session Co-chairs: Ken Baclawski & Todd Schneider

Session page: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_09_20

.

Proceedings

.

Todd Schneider: Ken, I was able to login.

Ken Baclawski: Tejas set up a VMWare on a machine in my office at NEU. I can give access to anyone

who needs it. The main machine is lisf.ccs.neu.edu, and the domains we can use are

ontology.ccs.neu.edu and kiwi.ccs.neu.edu.

Peter P. Yim: please use this page to capture customization details - http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR_SandBox_Customization

Ken Baclawski: The static IP address of ontology.ccs.neu.edu is 129.10.112.163. The one for kiwi.ccs.neu.edu is 129.10.112.167.

Todd Schneider: where are we with the discussion ... ref. http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_04_22#nid2ST2

= The interface for searching ontology metadata will consist of a single method: (2SSS)

  • The method will be called find. (2SST)
  • The method will have a single parameter consisting of a SPARQL query. (2SSU)
  • The return value of the method will be a SPARQL result set. (2SSV)
  • Metadata will be represented using a named RDF graph. (2SSW)
  • Metadata will be based on an extension of OMV. (2SSY)

o The OMV extension may include a notion of domain specification or topics, represented as text. (2SSZ)

  • Metadata will be federated, so it is a single named RDF graph, no matter how many OOR instances there are.

Todd Schneider: also ref. http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_06_17#nid2V8P

o Quality and Gatekeeping. We distinguish between gatekeeping and quality control.

Gatekeeping criteria are 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. (2VB8)

o Gatekeeping impacts metadata (2VB9)

o Gatekeeping will need to vet the metadata to ensure entrance criteria are met. (2VBA)

o Syntax checking is the responsibility of the language module. (2VBB)

o Each OOR instance must declare the representation languages (2VBD)

o Each OOR instance must declare the representation language module it spports. (2VBE)

o Will OOR Metadata be represented in OWL? (2VBF)

o Every OOR shall support RDF (2VBG)

o Correction: Every OOR shall support RDFS (2VBI)

o OMV is written in OWL (2VBK) - From Chapter 5 of the OMV Report 2.4.1: As aforementioned, OMV is formalized as an OWL ontology. (2VBO)

o Gatekeeping criteria will include an attribute to indicate whether the ontology exists or the metadata represents an advertisement. (2VBR)

o The location of the actual ontology is the responsibility of Administration. (2VBT)

o Metadata needs to include an attribute for the 'availability' of the ontology (2VBW)

o 'Location' of the ontology must be provided. (2VBX)

o Representation language of the ontology is a required attribute. (2VBY)

o Michael will provide a preliminary list of required metadata attributes. (2VBZ)

o Submission process will be asynchronous (2VC0)

o Minimal language dependency submission is syntax validation (2VC1)

o Consistency checking, to some extent, will be required for submission (2VC2)

o Need an attribute to represent that it is consistent, which then will require

another field to identify the reasoner used to do the consistency checking (2VC3)

o Ken has already developed the gatekeeper module which should provide enough to specify it for OOR (2VC4)

o Ken's gatekeeper module already has a mechanism to configure the registration workflow for a community (2VC5)

Todd Schneider: Gatekeeper - notification(), subscription(), register()?

Todd Schneider: subscription is for particular ontology and particular user

Todd Schneider: subscription - sends notices about events related to ontology

Terry Longstreth: Create ontology == prepare system for new ontology?

Todd Schneider: registrar - creates the entry in the OOR; to do so the required metadata needs to be created

Peter P. Yim: -- session ended: 9:41am PDT --

--- Chat transcript end: ---

Consensus, Conclusions & Follow-up Actions:

4. Any Other Business:

5. Action items:

  • (ref. above) Peter to contact Ray Fergerson and invite him to join us on the Oct-4 call to do a "Architectural review and discussion"
    • no prepared presentations, but we need an agenda and enumerate things to discuss - Ken and Todd will prepare
      • Peter will set up the OOR/ConferenceCall_2011_10_04 meeting page quickly, so Ken, Todd, Ray and anyone else can add things to it. ... ( done! --ppy/2011.09.20-15:50 PDT )

6. Schedule Next Meeting & Adjourn:

  • Next Meeting:
    • since the SOCoP folks will be getting ready to travel, and Peter cannot join on Sep-27, we will skip next week's
    • next meeting will therefore be, at the same time on 2011_10_04 Tuesday: regular OOR-team call
  • Call adjourned at: 9:41 am PDT

--

notes taken by: Peter P. Yim / 2011.09.20-9:41am PDT

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

Resources



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