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= [[OpenOntologyRepository]]: Architecture & API Workshop-VIII - Tue 2011_10_11 =
= [[OpenOntologyRepository]]: Metadata Workshop-IV - Tue 2011_10_18 =


Topic: "'''OOR Architecture & API Specification Development Workshop-VIII'''"
Topic: '''OOR Metadata Workshop-IV'''  


Session Co-chairs: [[User:KennethBaclawski|Ken Baclawski]] & [[ToddSchneider|Todd Schneider]]  
Session Chair: '''MichaelGruninger'''
 
== [http://ontolog.cim3.net/file/work/OpenOntologyRepository/OOR-metadata-workshop/ Archives]  ==
 
* Please refer to the proceedings of:  
** ''(This session)'' '''OOR Metadata Workshop-IV''' [http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_10_18#nid2XX1 below]
** '''OOR Metadata Workshop-III''' at [[OOR/ConferenceCall_2011_05_27]]
** '''OOR Metadata Workshop-II''' at [[OOR/ConferenceCall_2011_05_13]]
** '''OOR Metadata Workshop-I''' at [[OOR/ConferenceCall_2011_03_18]]  
* '''[http://ontolog.cim3.net/file/work/OpenOntologyRepository/OOR-metadata-workshop/oor-metadata-04_20111018b.mp3 Audio recording of this session]''' [ 1:17:07 ; mp3 ; 8.83 MB ]  
* '''[http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_10_18#nid2Y3B chat-transcript from this session]'''


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


* Date: '''Tuesday, 11-Oct-2011'''  
* Date: '''Tuesday, 18-Oct-2011'''  
* Start Time: 8:30am PDT / 11:30am EDT / 5:30pm CEST / 4:30pm BST / 15:30 UTC  
* 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=10&day=11&year=2011&hour=8&min=30&sec=0&p1=224 World Clock]  
** ref: [http://www.timeanddate.com/worldclock/fixedtime.html?month=10&day=18&year=2011&hour=8&min=30&sec=0&p1=224 World Clock]  
* Expected Call Duration: 1.0~1.5 hours  
* Expected Call Duration: 1.0~1.5 hours  
* Dial-in Number:  
* Dial-in Number:  
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** callers '''from other countries''' please dial into either one of the US or European numbers  
** 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/  
* '''In-session chat'''-room url: http://webconf.soaphub.org/conf/room/oor_20111018
 
* '''Shared-screen support''' (VNC session), if applicable, will be started 5 minutes before the call at: http://vnc2.cim3.net:5800/  
** view-only password: "ontolog"  
** 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.)  
* '''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_10_11
* 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_10_18


* Please note that this session may be recorded, and if so, the audio archive is expected to be made available as open content, along with the proceedings of the call to our community membership and the public at-large under [[WikiHomePage#Intellectual_Property_Rights_.28IPR.29_Policy|our prevailing open IPR policy]].  
* Please note that this session may be recorded, and if so, the audio archive is expected to be made available as open content, along with the proceedings of the call to our community membership and the public at-large under [[WikiHomePage#Intellectual_Property_Rights_.28IPR.29_Policy|our prevailing open IPR policy]].  
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* Attended:  
* Attended:  
** [[User:KennethBaclawski|Ken Baclawski]] (co-chair)
** [[MichaelGruninger|Michael Grüninger]] (chair)  
** [[ToddSchneider|Todd Schneider]] (co-chair)  
** [[PeterYim|Peter P. Yim]]  
** [[PeterYim|Peter P. Yim]]  
** [[TerryLongstreth|Terry Longstreth]]
** [[User:KennethBaclawski|Ken Baclawski]]
** [[NikkiaAnderson|Nikkia Anderson]] (for GailHodge)
** [[TimWilson|Tim Wilson]]
** [[TimDarr|Tim Darr]]
** [[ToddSchneider|Todd Schneider]]
** [[AliHashemi|Ali Hashemi]]
** [[XingfangLi|Xingfang Li]]


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


== Agenda Ideas  ==
== Agenda Ideas  ==
Line 68: Line 74:
''please insert any additional items below (along with your name for follow-up purposes)''  
''please insert any additional items below (along with your name for follow-up purposes)''  


* 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]]
* [[MichaelGruninger|Michael Grüninger]]: continuing from previous sessions ...
** Our goal is to evaluate the adequacy of OMV for OOR metadata.
** Our current objective is to determine the different relationships among ontologies within OOR.
** We will discuss use cases, especially two potential areas that can supply candidate ontologies -- time ontologies and geospatial ontologies.
* Peter: continue to explore what resources are needed to define a minimal set of metadata requirements for implementation into OOR-gatekeeping (so we can move from OOR-sandbox to OOR-production, and be able to stand up both servers); then we can start soliciting volunteers to upload their ontologies.  


* The specifications to be discussed at the these workshops are the following (not necessarily discussed in this order):
== References  ==
** the OOR Architecture
** the OOR API
** the Organizing Plan
** the default development platform


== Abstract  ==
* Proceedings of '''[http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_03_18 OOR Metadata Workshop-I]''' and MichaelGruninger's opening [http://ontolog.cim3.net/file/work/OpenOntologyRepository/OOR-metadata-workshop/metafuture--MichaelGruninger_20110318.pdf slides] from that session
* Proceedings of '''[http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_05_13 OOR Metadata Workshop-II]'''
* Proceedings of '''[http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_05_27 OOR Metadata Workshop-III]'''
* Metadata for Ontologies - [[OntologySummit2008_Communique|from the [[OntologySummit2008_Communique]]]]
* Metadata requirement - [[OpenOntologyRepository_IPR|as stipulated in the OOR IPR Policy]]
* Ontology Metadata Vocabulary - [[OMV]]
** Brief Description of OMV (with diagram) - http://omv2.sourceforge.net/description.html
** "OMV - Ontology Metadata Vocabulary for the SemanticWeb" - [http://ontolog.cim3.net/file/resource/OOR/OMV/OMV-Reportv2.4.1.pdf OMV v2.4.1 (final)] (Mar-2009)
* The Joint [[OpenOntologyRepository]]-OntologySummit2008 Panel Discussion Session - ConferenceCall_2008_04_10
** Presentation by [[PeterHaase|Peter Haase]] "[[ConferenceCall_2008_04_10|The OMV Ontology Metadata Vocabulary]]" at that session
* [[OpenOntologyRepository_Architecture]]
* [[OpenOntologyRepository_UseCases]] - http://www.ccs.neu.edu/home/kenb/ontologies/


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.
== Agenda & Proceedings ==


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.  
1. Meeting called to order:


The various architectures and APIs for ontology repositories presented for consideration are available at '''[[OpenOntologyRepository_Architecture]]'''
* [[MichaelGruninger|Michael Grüninger]] takes the chair and welcome everyone
* Review and adopt agenda
* [[PeterYim|Peter P. Yim]] volunteered to keep a record of the proceedings


Here is the straw man architecture: '''[[OpenOntologyRepository_Architecture/Candidate03]]'''
2. Roll Call:  


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.  
* see [http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_10_18#nid2XWP above]


Here is the API expressed in WSDL: http://www.ccs.neu.edu/home/kenb/oor/OORService.wsdl
* new participant introduction (as required)


Here is the API expressed in Java: http://www.ccs.neu.edu/home/kenb/oor/OORI.java
* Announcements (as required)
** 2011_10_20 - Thursday: Joint IAOA-OOR-Ontolog "Ontologies and Standards" mini-series session-1: Introducing the ISO/WD 17347 "Ontology Integration and Interoperability ([[OntoIOp]])" Standardization Effort - Co-chairs: [[JohnBateman|John Bateman]] & [[MichaelGruninger|Michael Grüninger]] - ConferenceCall_2011_10_20
** 2011_11_03 - Thursday: Joint IAOA-OOR-Ontolog "Ontologies and Standards" mini-series session-2: Invited Speaker: [[ElisaKendall|Elisa Kendall]] on ISO 19763 "Metamodel Framework for Interoperability (MFI)" - Co-chairs: [[MichaelGruninger|Michael Grüninger]] & [[JohnBateman|John Bateman]] - ConferenceCall_2011_11_03
* 
** we will be transitioning to another conference bridge provider (within the next couple of weeks). Need help from people to help test the new platform.  


Finally, we need to agree on a plan for completing the development of the specification.
3. Key items for review and discussion today:


Here is the proposed organizing plan: '''[[OpenOntologyRepository_Architecture/GettingOrganized]]'''
3.1 '''Opening:''' -  by [[MichaelGruninger|Michael Grüninger]]  


We encourage all participants to update your candidate contributions to ensure your ideas are known and understood.  
Today's (2011.10.18) agenda:


The following are relevant prior meetings:  
* Claim 1: For specifying properties of ontologies, OMV is sufficient for OOR use cases.


* Architecture & API Specification Development Workshop-VIII - [[OOR/ConferenceCall_2011_10_11]] ''(this session)''
* Claim 2: OMV is not sufficient for specifying the relationships between ontologies within an
* Architecture & API Specification Development Workshop-VII - [[OOR/ConferenceCall_2011_09_20]]
ontology repository.  
* 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 Grüninger]] - Panelists: KenBaclawski+ToddSchneider, AldoGangemi+AlessandroAdamou, JouniTuominen+KimViljanen, [[EricChan|Eric Chan]] - [[OOR/ConferenceCall_2010_11_19]]
* 2010_10_15 - Friday: OOR Project Team Member Conference Call - discussion on the (post-BioPortal fork) OOR Architecture and API - [[OOR/ConferenceCall_2010_10_15]]


== Agenda & Proceedings  ==
* Existing relations between ontologies within [http://ontolog.cim3.net/file/resource/OOR/OMV/OMV-Reportv2.4.1.pdf OMV (v2.4.1)]: (ref. pp. 13, 29 30)
** <nowiki>useImports</nowiki>
** <nowiki>hasPriorVersion</nowiki>
** <nowiki>isIncompatibleWith</nowiki>
** <nowiki>isBackwardsCompatible</nowiki>


[http://ontolog.cim3.net/file/work/OpenOntologyRepository/OOR-Architecture/OOR-Architecture-API-workshop/ Archives]:
* The last three relationships focus on different versions of an ontology rather than the
 
relationship between different ontologies.  
1. Meeting called to order:
 
* [[User:KennethBaclawski|Ken Baclawski]] & [[ToddSchneider|Todd Schneider]] took the chair and welcome everyone
 
* [[PeterYim|Peter P. Yim]] volunteered to keep a record of the proceedings


* review and adopt agenda
* Is useImports defined if the ontologies are axiomatized in different languages?


2. Roll Call & Adoption of last meeting's minutes:
* Heterogeneous ontologies -- ontologies that import other ontologies which are axiomatized
in different languages.  


* see [http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_10_11#nid2XI4 above]
* What is the distinction between metalogical relations between ontologies that are required for an ontology repository and relations that are needed to support the software functionality of the repository?  


* ref. proceedings of "Architecture & API Specification Development Workshop-VII" - [[OOR/ConferenceCall_2011_09_20]]
* What notion of modularity do we use within OOR? What constitutes an ontology within OOR?


* review of agenda
3.2 '''Discussion:'''


3. '''Key items for review and discussion''' today:
* see [http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_10_18#nid2Y20 archives above]


* Announcements and Urgent Matters:
* continued discussion and exploration of the above (today's main agenda items) ...


''... items below are mostly from the previous workshop, and will be updated as this session progresses.''
* continue to explore what resources are needed to define a minimal set of metadata requirements for implementation into OOR-gatekeeping (so we can move from OOR-sandbox to OOR-production, and be able to stand up both servers); and solicit volunteers


* 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]]
3.3 ===IM Chat Transcript captured during the session===
** defer the discussion to our next meeting when we will try to invite [[RayFergerson|Ray Fergerson]] to join us
* 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.


* '''"OOR Architecture & API Specification Development Workshop-VIII:"''' ([http://ontolog.cim3.net/file/work/OpenOntologyRepository/OOR-Architecture/OOR-Architecture-API-workshop/ Archives])
see raw transcript [http://ontolog.cim3.net/file/work/OpenOntologyRepository/OOR-metadata-workshop/oor-metadata-04_chat-transcript_unedited_20111018a.txt here].


* 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.  
(for better clarity, the version below is a [http://ontolog.cim3.net/file/work/OpenOntologyRepository/OOR-metadata-workshop/oor-metadata-04_chat-transcript_edited_20111018b.txt re-organized and lightly edited chat-transcript].)
** 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.  


* Proposal for Partition of Components
Participants are welcome to make light edits to their own contributions as they see fit.  
** 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


* [http://ontolog.cim3.net/file/work/OpenOntologyRepository/OOR-Architecture/OOR-Architecture-API-workshop/oor-call_chat-transcript_edited_20111011b.txt chat transcript of this session]:
-- begin in-session chat-transcript --  


--- Chat transcript begin: ---
[[PeterYim|Peter P. Yim]]: Welcome to the


Welcome to the [[OpenOntologyRepository]]: Architecture & API Workshop-VIII - Tue 2011_10_11
''' open ontology repository (oor) session - tue 2011_10_18 '''


Session co-Chairs: [[User:KennethBaclawski|Ken Baclawski]] & [[ToddSchneider|Todd Schneider]]
Topic: OOR Metadata Workshop-IV


see session page at: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_10_11
Session Chair: [[MichaelGruninger|Michael Gr&uuml;ninger]]


== Proceedings: ==
Session page: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_10_18


[[ToddSchneider|Todd Schneider]]: Here's where we are at, in terms of consensus arrived at from the
''' proceedings: '''


previous "OOR Architecture and API" workshops:
anonymous morphed into [[TimWilson|Tim Wilson]]


0) The interface for searching ontology metadata will consist of a single method
[[TimWilson|Tim Wilson]]: Hi, this is Tim Wilson.  I am having work done in my basement, it is very noisy.


0.a) The method will have a single parameter consisting of a SPARQL query.   
[[MichaelGruninger|Michael Gr&uuml;ninger]]: I am having trouble connecting by phone


0.b) The return value of the method will be a SPARQL result set.
Tim Darr: Joining ...  


0.c) Metadata will be represented using a named RDF graph.       
[[PeterYim|Peter P. Yim]]: are you trying to connect via skype?


0.d) Metadata will be based on an extension of OMV.   
[[PeterYim|Peter P. Yim]]: Michael got in!


o The OMV extension may include a notion of domain specification or
[[ToddSchneider|Todd Schneider]]: Michael, What's a 'module'?


topics, represented as text. 
anonymous morphed into [[NikkiaAnderson|Nikkia Anderson]]


0.e) Metadata will be federated, so it is a single named RDF graph, no matter
anonymous morphed into [[AliHashemi|Ali Hashemi]]


how many OOR instances there are. pics, represented as text.  
[[ToddSchneider|Todd Schneider]] / [[MichaelGruninger|Michael Gr&uuml;ninger]]: Manchester's TONES repository - http://owl.cs.manchester.ac.uk/repository/browser


0.f) Metadata will be federated, so it is a single named RDF graph, no matter
[[MichaelGruninger|Michael Gr&uuml;ninger]]: how ontologies relate to one another elevates OOR from being


how many OOR instances there are.  
"just a library of ontologies" (e.g. if you look at TONES from Manchester, that


1) Each OOR instance must declare the representation language module it supports.
is a large list of ontologies with no interaction between them)  


2) Every OOR shall support RDFS
[[AliHashemi|Ali Hashemi]]: Scenario:


3) Quality and Gatekeeping. We distinguish between gatekeeping and quality control.
Given:


Definition: Gatekeeping specifies the a set of minimal requirements that any
Ontology O1 in OWL (in OOR)


ontology within the OOR has to meet. The latter are intended to
Ontology O2 in CL (not in OOR)


enable the users of the OOR to find quickly ontologies that fit
Ontology O3 in CL (in OOR) <-- (previously: "ORR" - typo corrected)


their needs; the criteria do not ensure the quality of the ontologies.
Declare in OMV:


3.a) Gatekeeping will vet the metadata associated with an ontology to ensure
O3 hasImport O1


entrance criteria are met.
O3 hasImport O2


3.b) For each metadata attribute, it will be specified whether it is required
O1 hasLanguage OWL


or optional.
O2 hasLanguage CL


3.b.i)  It MUST be specified whether the ontology is available (or to be
O3 hasLanguage CL


available in the future). 
--- ---


3.b.ii)  The ontology language MUST be specified. 
[[AliHashemi|Ali Hashemi]]: ORR is a typo meant OOR


3.b.iii) Other attributes will be handled offline by Michael Gruninger
[[TimWilson|Tim Wilson]]: At my work, ORR is Operational Readiness Review.  


based on the OMV specification.
[[PeterYim|Peter P. Yim]]: There is actually an "ORR" - the MMI project's Ontology Registry and Repository


3.c) An ontology must satisfy other requirements depending on the ontology
(which is also [[BioPortal]] based) - see: http://mmisw.org/orr/#b


language.
If ontologies are located externally to OOR


3.d) Syntax checking is always required and the responsibility of the language
How to handle this in a workflow tool?


module
Speak to a need to differentiate between Ontologies that are registered


3.e) Consistency checking is required with some time limit.
(and axioms are available on OOR)  


3.f) Gatekeeping criteria will include an attribute to indicate whether the
[[MichaelGruninger|Michael Gr&uuml;ninger]]: Using the notion of importing ontologies, there will exist


ontology exists or the metadata represents an advertisement.
a set of ontologies that are imported by other ontologies but which do not themselves


3.g) The location of the actual ontology is the responsibility of Administration.  
import any others. Such ontologies would be "building block" modules, and we would


3.h) Metadata needs to include an attribute for the 'availability' of the ontology
require them to be registered in the repository.


3.i) 'Location' of the ontology must be provided.
[[AliHashemi|Ali Hashemi]]: hasImport --> useImports*


3.j) The representation language of the ontology is a required attribute.
[[TimWilson|Tim Wilson]]: (Very interesting discussion, but I need to go.)  


3.k) Michael will provide a preliminary list of required metadata attributes.
[[TerryLongstreth|Terry Longstreth]]: The notion of imports entrains a responsibility on the part of the OOR services to validate the imported items


3.l) Submission process will be asynchronous
[[TerryLongstreth|Terry Longstreth]]: Once validated, the imported ontology module is presumed to be an invariant


[[PeterYim|Peter P. Yim]]: moving us forward ...
[[ToddSchneider|Todd Schneider]]: OOR will automatically parse import statements and check for


[[PeterYim|Peter P. Yim]]: now that we have the partitioning (architecturally), we need to adopt a
the presence of the ontologies to be imported in OORs.


development platform (say, something like "eclipse"), and start having
[[ToddSchneider|Todd Schneider]]: Terry, invariant? With respect to what?


team members claim ownership to developing specific modules
[[TerryLongstreth|Terry Longstreth]]: With respect to the importing object


[[User:KennethBaclawski|Ken Baclawski]]: Look at http://www.eclipse.org/stp/
[[AliHashemi|Ali Hashemi]]: If you're building services in the OOR to exploit elements of an ontology,


[[ToddSchneider|Todd Schneider]]: http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository_Architecture/Candidate03
if it is not in (or transparent to) the system you can't really deploy the services


[[PeterYim|Peter P. Yim]]: also (important), please refer to the [[BioPortal]] "tab" implementation details
[[TerryLongstreth|Terry Longstreth]]: If the imported, validated module can change, than everything that


- see: http://palexander.posterous.com/extending-bioportals-rails-ui
imports it can be invalidated


[[ToddSchneider|Todd Schneider]]: The 'administration' module is responsible for advertising which
[[AliHashemi|Ali Hashemi]]: (I've got to run. Bye.)


representation languages an instance supports.  
[[TerryLongstreth|Terry Longstreth]]: ...at some arbitrary time in the future


[[PeterYim|Peter P. Yim]]: All: we might want to partition some of the work to sizes that fit,
[[ToddSchneider|Todd Schneider]]: (Sorry, but have to go.)


say, work by a student in 3-months (which might mean work that takes
[[MichaelGruninger|Michael Gr&uuml;ninger]]: How does [[BioPortal]] capture the notion of different ontology versions and the possibility of new  versions being used which are not part of BioPortal?


an experienced developer a couple of weekends or a month to do)
[[TerryLongstreth|Terry Longstreth]]: How does Bioportal reflect changes in semantics of medical ideas?


[[ToddSchneider|Todd Schneider]]: The next Architecture meeting will focus on development platform and work partitioning
[[User:KennethBaclawski|Ken Baclawski]]: There are two different notions of import.  One can import an ontology with


[[ToddSchneider|Todd Schneider]]: The next meeting will be on Tue 1 November 2011, same time  
no specification of which version is being imported. One could also have a strict import


[[ToddSchneider|Todd Schneider]]: Homework: learn more about the Eclipse and its capabilities;
that requires the imported ontology to be a specific version.  One can enforce


Read Paul Alexander's page on tabs
a strict import by specifying a checksum.


- http://palexander.posterous.com/extending-bioportals-rails-ui
[[MichaelGruninger|Michael Gr&uuml;ninger]]: Find examples within [[BioPortal]] of one ontology importing another ontology,


[[PeterYim|Peter P. Yim]]: we'll make that (choice of platform and work partitioning) as the main focus of
either internal or external to [[BioPortal]]  


our next team meeting (Tue 2011.11.01)
[[PeterYim|Peter P. Yim]]: [[MichaelGruninger|Michael Gr&uuml;ninger]]: at the next workshop, we can put some focus on "versioning"


[[ToddSchneider|Todd Schneider]]: We need to motivate contributors to provide 'comic' book level descriptions
[[MichaelGruninger|Michael Gr&uuml;ninger]]: Action Item (for everyone): find papers on ontology versioning


of their work
[[PeterYim|Peter P. Yim]]: -- session ended: 10:05 am PDT --


[[PeterYim|Peter P. Yim]]: -- session ended 9:38am --  
-- end of in-session chat-transcript --  


--- Chat transcript end: ---
4. Any Other Business:  


'''Consensus, Conclusions & Follow-up Actions:'''
* [[PeterYim|Peter P. Yim]]: we will be transitioning to another conference bridge provider (within the next couple of weeks). Need help from to help test the new platform(s). Watch out for requests, and come help if you can.


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


5. '''Action items:'''
* [[MichaelGruninger|Michael Gr&uuml;ninger]]: Action Item (for everyone): find papers on ontology versioning


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


* Next Meeting:  
* Next Meeting:  
** "OOR Metadata Workshop" - Tue 2011.10.18 same time (that's next Tuesday)
** this coming Thu 2011.10.20 - the Joint IAOA-OOR-Ontolog "Ontologies and Standards" mini-series: session-1 - see: ConferenceCall_2011_10_20
** after that, there will be an joint "Ontology and Standards" session on Thu 2011.10.20 (watch for announcements)
** we will then be having a regular OOR-team meeting -  
** no meeting during the week of Oct-24 (as [http://iswc2011.semanticweb.org/ ISWC-2011] will be in session)  
*** Date: Tue 2011.11.01 - Start time: 8:30am PDT / 11:30am EDT / 4:30pm CET / 15:30 UTC (ref. [http://www.timeanddate.com/worldclock/fixedtime.html?month=11&day=1&year=2011&hour=8&min=30&sec=0&p1=224 worldclock])  
** then we'll be having the next OOR team meeting, same time on Tue 2011.11.01
*** see developing session page is at [[OOR/ConferenceCall_2011_11_01]]  
*** where we will cover the [ items discussed today] .. and, do make sure you have time to look over what's listed as [ homework] too, before the meeting, if possible!


* Call adjourned at: 9:38 am PDT  
* Call adjourned at: 10:05 am PDT  


--
--


notes taken by: [[PeterYim|Peter P. Yim]] / 2011.10.11-10:10am PDT
notes taken by: [[PeterYim|Peter P. Yim]] / 2011.10.18-10:16am 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 395: Line 365:
** 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_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]]  
** 2011_09_20 - Tuesday: OOR - "Architecture & API Specification Development Workshop-VII" - Chair: [[User:KennethBaclawski|Ken Baclawski]] - [[OOR/ConferenceCall_2011_09_20]]  
** 2011_10_11 - Tuesday: OOR - "Architecture & API Specification Development Workshop-VIII" - Chair: [[User:KennethBaclawski|Ken Baclawski]] & [[ToddSchneider|Todd Schneider]] - [[OOR/ConferenceCall_2011_10_11]]
** 2011_10_18 - Tuesday: OOR Metadata Workshop-IV - Chair: [[MichaelGruninger|Michael Gr&uuml;ninger]] - [[OOR/ConferenceCall_2011_10_18]]
* the '''OOR-IPR mini-series''':  
* the '''OOR-IPR mini-series''':  
** 2010_09_09 - Thursday: Joint OOR-Ontolog-NCBO-CC-IAOA-OASIS Panel Discussion - "IPR issues in Ontology and the OOR" session-1: an exposition on relevant IPR regimes - Keynote speaker: [[GeorgeStrawn|George Strawn]] - Chair: [[PeterYim|Peter P. Yim]] - Panelists: [[JamieClark]], [[JohnWilbanks|John Wilbanks]], [[BrucePerens|Bruce Perens]] - ConferenceCall_2010_09_09  
** 2010_09_09 - Thursday: Joint OOR-Ontolog-NCBO-CC-IAOA-OASIS Panel Discussion - "IPR issues in Ontology and the OOR" session-1: an exposition on relevant IPR regimes - Keynote speaker: [[GeorgeStrawn|George Strawn]] - Chair: [[PeterYim|Peter P. Yim]] - Panelists: [[JamieClark]], [[JohnWilbanks|John Wilbanks]], [[BrucePerens|Bruce Perens]] - ConferenceCall_2010_09_09  

Latest revision as of 07:33, 9 January 2016

OpenOntologyRepository: Metadata Workshop-IV - Tue 2011_10_18

Topic: OOR Metadata Workshop-IV

Session Chair: MichaelGruninger

Archives

Conference Call Details

  • Date: Tuesday, 18-Oct-2011
  • Start Time: 8:30am PDT / 11:30am EDT / 5:30pm CEST / 4:30pm BST / 15:30 UTC
  • 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 applicable, will be started 5 minutes before the call at: http://vnc2.cim3.net:5800/
    • view-only password: "ontolog"
  • 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)

  • Michael Grüninger: continuing from previous sessions ...
    • Our goal is to evaluate the adequacy of OMV for OOR metadata.
    • Our current objective is to determine the different relationships among ontologies within OOR.
    • We will discuss use cases, especially two potential areas that can supply candidate ontologies -- time ontologies and geospatial ontologies.
  • Peter: continue to explore what resources are needed to define a minimal set of metadata requirements for implementation into OOR-gatekeeping (so we can move from OOR-sandbox to OOR-production, and be able to stand up both servers); then we can start soliciting volunteers to upload their ontologies.

References

Agenda & Proceedings

1. Meeting called to order:

2. Roll Call:

  • new participant introduction (as required)
  • Announcements (as required)
    • 2011_10_20 - Thursday: Joint IAOA-OOR-Ontolog "Ontologies and Standards" mini-series session-1: Introducing the ISO/WD 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 ISO 19763 "Metamodel Framework for Interoperability (MFI)" - Co-chairs: Michael Grüninger & John Bateman - ConferenceCall_2011_11_03
    • we will be transitioning to another conference bridge provider (within the next couple of weeks). Need help from people to help test the new platform.

3. Key items for review and discussion today:

3.1 Opening: - by Michael Grüninger

Today's (2011.10.18) agenda:

  • Claim 1: For specifying properties of ontologies, OMV is sufficient for OOR use cases.
  • Claim 2: OMV is not sufficient for specifying the relationships between ontologies within an

ontology repository.

  • Existing relations between ontologies within OMV (v2.4.1): (ref. pp. 13, 29 30)
    • useImports
    • hasPriorVersion
    • isIncompatibleWith
    • isBackwardsCompatible
  • The last three relationships focus on different versions of an ontology rather than the

relationship between different ontologies.

  • Is useImports defined if the ontologies are axiomatized in different languages?
  • Heterogeneous ontologies -- ontologies that import other ontologies which are axiomatized

in different languages.

  • What is the distinction between metalogical relations between ontologies that are required for an ontology repository and relations that are needed to support the software functionality of the repository?
  • What notion of modularity do we use within OOR? What constitutes an ontology within OOR?

3.2 Discussion:

  • continued discussion and exploration of the above (today's main agenda items) ...
  • continue to explore what resources are needed to define a minimal set of metadata requirements for implementation into OOR-gatekeeping (so we can move from OOR-sandbox to OOR-production, and be able to stand up both servers); and solicit volunteers

3.3 ===IM Chat Transcript captured during the session===

see raw transcript here.

(for better clarity, the version below is a re-organized and lightly edited chat-transcript.)

Participants are welcome to make light edits to their own contributions as they see fit.

-- begin in-session chat-transcript --

Peter P. Yim: Welcome to the

open ontology repository (oor) session - tue 2011_10_18

Topic: OOR Metadata Workshop-IV

Session Chair: Michael Grüninger

Session page: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_10_18

proceedings:

anonymous morphed into Tim Wilson

Tim Wilson: Hi, this is Tim Wilson. I am having work done in my basement, it is very noisy.

Michael Grüninger: I am having trouble connecting by phone

Tim Darr: Joining ...

Peter P. Yim: are you trying to connect via skype?

Peter P. Yim: Michael got in!

Todd Schneider: Michael, What's a 'module'?

anonymous morphed into Nikkia Anderson

anonymous morphed into Ali Hashemi

Todd Schneider / Michael Grüninger: Manchester's TONES repository - http://owl.cs.manchester.ac.uk/repository/browser

Michael Grüninger: how ontologies relate to one another elevates OOR from being

"just a library of ontologies" (e.g. if you look at TONES from Manchester, that

is a large list of ontologies with no interaction between them)

Ali Hashemi: Scenario:

Given:

Ontology O1 in OWL (in OOR)

Ontology O2 in CL (not in OOR)

Ontology O3 in CL (in OOR) <-- (previously: "ORR" - typo corrected)

Declare in OMV:

O3 hasImport O1

O3 hasImport O2

O1 hasLanguage OWL

O2 hasLanguage CL

O3 hasLanguage CL

--- ---

Ali Hashemi: ORR is a typo meant OOR

Tim Wilson: At my work, ORR is Operational Readiness Review.

Peter P. Yim: There is actually an "ORR" - the MMI project's Ontology Registry and Repository

(which is also BioPortal based) - see: http://mmisw.org/orr/#b

If ontologies are located externally to OOR

How to handle this in a workflow tool?

Speak to a need to differentiate between Ontologies that are registered

(and axioms are available on OOR)

Michael Grüninger: Using the notion of importing ontologies, there will exist

a set of ontologies that are imported by other ontologies but which do not themselves

import any others. Such ontologies would be "building block" modules, and we would

require them to be registered in the repository.

Ali Hashemi: hasImport --> useImports*

Tim Wilson: (Very interesting discussion, but I need to go.)

Terry Longstreth: The notion of imports entrains a responsibility on the part of the OOR services to validate the imported items

Terry Longstreth: Once validated, the imported ontology module is presumed to be an invariant

Todd Schneider: OOR will automatically parse import statements and check for

the presence of the ontologies to be imported in OORs.

Todd Schneider: Terry, invariant? With respect to what?

Terry Longstreth: With respect to the importing object

Ali Hashemi: If you're building services in the OOR to exploit elements of an ontology,

if it is not in (or transparent to) the system you can't really deploy the services

Terry Longstreth: If the imported, validated module can change, than everything that

imports it can be invalidated

Ali Hashemi: (I've got to run. Bye.)

Terry Longstreth: ...at some arbitrary time in the future

Todd Schneider: (Sorry, but have to go.)

Michael Grüninger: How does BioPortal capture the notion of different ontology versions and the possibility of new versions being used which are not part of BioPortal?

Terry Longstreth: How does Bioportal reflect changes in semantics of medical ideas?

Ken Baclawski: There are two different notions of import. One can import an ontology with

no specification of which version is being imported. One could also have a strict import

that requires the imported ontology to be a specific version. One can enforce

a strict import by specifying a checksum.

Michael Grüninger: Find examples within BioPortal of one ontology importing another ontology,

either internal or external to BioPortal

Peter P. Yim: Michael Grüninger: at the next workshop, we can put some focus on "versioning"

Michael Grüninger: Action Item (for everyone): find papers on ontology versioning

Peter P. Yim: -- session ended: 10:05 am PDT --

-- end of in-session chat-transcript --

4. Any Other Business:

  • Peter P. Yim: we will be transitioning to another conference bridge provider (within the next couple of weeks). Need help from to help test the new platform(s). Watch out for requests, and come help if you can.

5. Action items:

6. Schedule Next Meeting & Adjourn:

  • Next Meeting:
    • this coming Thu 2011.10.20 - the Joint IAOA-OOR-Ontolog "Ontologies and Standards" mini-series: session-1 - see: ConferenceCall_2011_10_20
    • we will then be having a regular OOR-team meeting -
  • Call adjourned at: 10:05 am PDT

--

notes taken by: Peter P. Yim / 2011.10.18-10:16am PDT

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

Resources



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