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= [[OpenOntologyRepository]]: Metadata Workshop-VII - Tue 2012_04_24 =
= [[OpenOntologyRepository]]: OOR Team Conference Call - Tue 2012_05_01 =


Topic: '''OOR Metadata Workshop-VII: Metadata in Ontology Mapping'''
This is a regular OOR Team meeting. ... ''please refer also to proceedings from the last team meeting at [[OOR/ConferenceCall_2012_04_03]]''  
 
Session Chair: '''Professor MichaelGruninger''' (University of Toronto)
 
Panelists:
 
* '''Dr. [[OliverKutz|Oliver Kutz]] / Dr. [[ChristophLange|Christoph Lange]] / Dr. TillMossakowski''' (University of Bremen, Germany) - "Ontology Links in the Distributed Ontology Language (DOL)" [ [http://ontolog.cim3.net/file/work/OpenOntologyRepository/OOR-metadata-workshop/OOR_links-in-DOL--OliverKutz-ChristophLange-TillMossakowski_20120424b.pdf slides] ]
* '''Dr. JeromeEuzenat''' (INRIA & LIG, France) - "Ontology alignment metadata" ... [ [http://ontolog.cim3.net/file/work/OpenOntologyRepository/OOR-metadata-workshop/OOR_ontology-alignment-metadata--JeromeEuzenat_20120424.pdf slides] ]
* '''Dr. NatashaNoy''' (Stanford University, USA) - "Mapping repository in BioPortal" ... [ [http://ontolog.cim3.net/file/work/OpenOntologyRepository/OOR-metadata-workshop/OOR_Mapping-Metadata--NatashaNoy_20120424.pdf slides] ]
 
[http://ontolog.cim3.net/file/work/OpenOntologyRepository/OOR-metadata-workshop/ Archives]:
 
* '''[http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2012_04_24#nid3A1I Abstract]'''  
* '''[http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2012_04_24#nid3A24 Agenda & Proceedings]'''
* '''Prepared presentation material (slides)''' can be accessed by clicking on each of the [http://ontolog.cim3.net/file/work/OpenOntologyRepository/OOR-metadata-workshop/ title links] below:
** '''[ 0-Chair (no slides) ] . [ [http://ontolog.cim3.net/file/work/OpenOntologyRepository/OOR-metadata-workshop/OOR_links-in-DOL--OliverKutz-ChristophLange-TillMossakowski_20120424b.pdf 1-Kutz-Lange-Mossakowski] ] . [ [http://ontolog.cim3.net/file/work/OpenOntologyRepository/OOR-metadata-workshop/OOR_ontology-alignment-metadata--JeromeEuzenat_20120424.pdf 2-Euzenat] ] . [ [http://ontolog.cim3.net/file/work/OpenOntologyRepository/OOR-metadata-workshop/OOR_Mapping-Metadata--NatashaNoy_20120424.pdf 3-Noy] ]'''
* '''[http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2012_04_24#nid3A1N References]'''
* [ audio recording of the session] ... ''(coming!)''
* '''[http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2012_04_24#nid3A2B Transcript of the online chat session]''' during the panel discussion ... ''(raw transcript is now online; cleaned-up version coming!)''
* '''[http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2012_04_24#nid3A2O Additional Resources]'''  


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


* Date: '''Tuesday, 24-April-2012'''  
* Date: '''Tuesday, 1-May-2012'''  
* Start Time: 8:30am PDT / 11:30am EDT / 5:30pm CEST / 15:30 UTC  
* Start Time: 8:30am PDT / 11:30am EDT / 5:30pm CEST / 15:30 UTC  
** ref: [http://www.timeanddate.com/worldclock/fixedtime.html?month=4&day=24&year=2012&hour=8&min=30&sec=0&p1=224 World Clock]  
** ref: [http://www.timeanddate.com/worldclock/fixedtime.html?month=5&day=1&year=2012&hour=8&min=30&sec=0&p1=224 World Clock]  
* Expected Call Duration: 1.5~2.0 hours  
* Expected Call Duration: 1.0~1.5 hours  


* Dial-in:  
* Dial-in:  
** '''Phone (US): +1 (206) 402-0100''' (long distance cost will apply)  
** '''Phone (US): +1 (206) 402-0100''' ''(long distance cost may apply)''
*** ... ''backup nbr (US): +1 (415) 671-4335''
*** ... [ backup nbr: (415) 671-4335 ]
** '''Skype: joinconference''' ... generally free-of-charge, when connecting from your computer)  
** '''Skype: joinconference''' ... (generally free-of-charge, when connecting from your computer)  
** when prompted enter '''PIN: 141184#'''  
** when prompted enter '''PIN: 141184#'''  


* '''Shared-screen support'''  
* '''Shared-screen support''' (VNC session), if applicable, will be started 5 minutes before the call at: http://vnc2.cim3.net:5800/  
** VNC session: 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.  
*** if you plan to be logging into this shared-screen option (which the speaker may be navigating), and you are not familiar with the process, please try to call in 5 minutes before the start of the session so that we can work out the connection logistics. Help on this will generally not be available once the presentation starts.  
** people behind corporate firewalls may have difficulty accessing this. If that is the case, please point your browser directly to the '''[ slides]''' (where applicable) and running them locally. The speaker(s) will prompt you to advance the slides during the talk.  
** people behind corporate firewalls may have difficulty accessing this. If that is the case, please download the '''[http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2012_04_24#nid3A06 slides above]''' (where applicable) and running them locally. The speaker(s) will prompt you to advance the slides during the talk.  


* '''In-session chat'''-room url: http://webconf.soaphub.org/conf/room/oor_20120424
* '''In-session chat'''-room url: http://webconf.soaphub.org/conf/room/oor_20120501
** instructions: once you got access to the page, click on the "settings" button, and identify yourself (by modifying the Name field from "anonymous" to your real name, like "JaneDoe").
** You can indicate that you want to ask a question verbally by clicking on the "hand" button, and wait for the moderator to call on you; or, type and send your question into the chat window at the bottom of the screen.
** thanks to the soaphub.org folks, one can now use a jabber/xmpp client (e.g. gtalk) to join this chatroom. Just add the room as a buddy - (in our case here) oor_20120424@soaphub.org ... Handy for mobile devices!


* '''Discussions and Q & A:'''
* '''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.)  
** Nominally, when a presentation is in progress, the moderator will mute everyone, except for the speaker.
** '''To un-mute, press "*7"''' ... '''To mute, press "*6"''' (please mute your phone, especially if you are in a noisy surrounding, or if you are introducing noise, echoes, etc. into the conference line.)
** we will usually save all questions and discussions till after all presentations are through. You are encouraged to jot down questions onto the chat-area in the mean time (that way, they get documented; and you might even get some answers in the interim, through the chat.)
** During the Q&A / discussion segment (when everyone is muted), '''If you want to speak''' or have questions or remarks to make, '''please raise your hand''' (virtually) '''by clicking on the "hand button"''' (lower right) on the chat session page. You may speak when acknowledged by the session moderator (again, press "*7" on your phone to un-mute). ''Test your voice and introduce yourself first before proceeding with your remarks, please.'' (Please remember to click on the "hand button" again (to lower your hand) and press "*6" on your phone to mute yourself after you are done speaking.)  
 
* Please review our Virtual Session Tips and Ground Rules - see: [[VirtualSpeakerSessionTips]]


* This session, like all other Ontolog events, is open to the public. Information relating to this session is shared on this wiki page: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2012_04_24
* This session, like all other Ontolog events, is open to the public. Information relating to this session is shared on this wiki page: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2012_05_01


* 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]].  
* '''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.)


== Attendees  ==
== Attendees  ==


* Attended:  
* Attended:  
** [[MichaelGruninger|Michael Grüninger]] (chair)  
** [[MikeDean|Mike Dean]] (chair)  
** [[JeromeEuzenat|Jerome Euzenat]]
** [[PeterYim|Peter P. Yim]]
** [[User:KennethBaclawski|Ken Baclawski]]  
** [[User:KennethBaclawski|Ken Baclawski]]  
** [[TillMossakowski|Till Mossakowski]]  
** [[PeterYim|Peter P. Yim]] (scribe)
** [[OliverKutz|Oliver Kutz]]
** [[MichaelGruninger|Michael Grüninger]]  
** [[ChristophLange|Christoph Lange]]
** Natasha Noy
** [[MikeDean|Mike Dean]]
** [[ChristopherSpottiswoode|Christopher Spottiswoode]]
** [[DaliaVaranka|Dalia Varanka]]
** [[TerryLongstreth|Terry Longstreth]]  
** [[ToddSchneider|Todd Schneider]]  
** [[ToddSchneider|Todd Schneider]]  
** [[TaraAthan|Tara Athan]]
** [[JeffreyWallk|Jeffrey Wallk]]
** [[VictorAgroskin|Victor Agroskin]]
** [[AliHashemi|Ali Hashemi]]
** [[FrankOlken|Frank Olken]]  
** [[FrankOlken|Frank Olken]]  
** [[MikeBennett|Mike Bennett]]
** PavithraKenjige...
** [[SeanMcBride]]


* Expecting:  
* Expecting:  
** [[DanielMekonnen|Daniel Mekonnen]]
*   
*   
** ... ''if you are coming to the meeting, please add your name above (plus your affiliation, if you aren't already a member of the community) above, or e-mail <peter.yim@cim3.com> so that we can reserve enough resources to support everyone's participation.'' ...  
** ... ''if you are coming to the meeting, please add your name 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:  
* Regrets:  
** [[LeoObrst|Leo Obrst]]
** ...  
** ...  


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


Topic: '''OOR Metadata Workshop-VII: Metadata in Ontology Mapping'''
* postmortem of the last couple of OOR events:  
** Demos of various OOR instances at the [[OntologySummit2012_Symposium]] on Apr-13
** Metadata-VII: Ontology Mapping - [[OOR/ConferenceCall_2012_04_24]]
* upcoming activities / virtual-session planning
** [new - ppy/2012.05.02] collaborating with NYC & Data.gov communities in "Big Open Data"
* OOR: sandbox, devbox, test-instance, socop, colore, ornl-daac, mmi-orr, new ncbo-appliance, ... status update and coordination
* Member activities updates
* action planning for "content drive" (getting people to upload ontologies)
* Getting us to a stage when we can run a OOR-production box
* ...


by: [[MichaelGruninger|Michael Gr&uuml;ninger]]
== Agenda & Proceedings  ==


The OOR Metadata Workshop series is devoted to exploring existing and proposed approaches to the specification of metadata for ontologies, particularly in the context of ontology repositories.  
'''[http://ontolog.cim3.net/file/work/OpenOntologyRepository/MeetingsCalls/ Archives]:'''


The workshop today will focus on ontology metadata for ontology mappings.  
* [http://ontolog.cim3.net/file/work/OpenOntologyRepository/MeetingsCalls/OOR-team-conf-call_20120501b.mp3 audio recording of the session] [ 1:15:42 ; mp3 ; 8.67 MB ] 
* [http://ontolog.cim3.net/file/work/OpenOntologyRepository/MeetingsCalls/chat-transcript_oor-team_20120501b.txt chat-transcript of this session]


== References  ==
1. Meeting called to order:


* 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
* [[MikeDean|Mike Dean]] takes the chair and welcomes everyone
* Proceedings of '''[http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_05_13 OOR Metadata Workshop-II]'''
* [[PeterYim|Peter P. Yim]] volunteered to take notes
* Proceedings of '''[http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_05_27 OOR Metadata Workshop-III]'''
* review and adopt agenda
* Proceedings of '''[http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_10_18 OOR Metadata Workshop-IV]'''
* Proceedings of '''[http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2012_01_17 OOR Metadata Workshop-V]'''
* Proceedings of '''[http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2012_03_06 OOR Metadata Workshop-VI]'''
* Proceedings of '''[http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2012_04_24 OOR Metadata Workshop-VII]''' ''(this session)''
* 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/


== Agenda & Proceedings  ==
2. Roll Call:
 
* see [http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2012_05_01#nid3AEB above]
 
* welcome and intro of new member(s) (if applicable)
 
3. Status Review and Discussion:
 
* '''Review and update our "Most Critical Task(s) At Hand" list''' ... ''(discussion deferred; maybe: revisit towards end of this call?)''
** ref. http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository#nid17YH


Full proceedings will be made available in our [http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2012_04_24#nid3A03 archives] after the session.  
=== 4. Key items for review and discussion today  ===


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


2. Introduction of the panel - chair: [[MichaelGruninger|Michael Gr&uuml;ninger]] (~5 min.)  
* '''previous action item status review'''
** [action-2012.03.13] Michael will try to get [[MikeBennett|Mike Bennett]] to upload his ontology to OOR
*** Michael: I'll work on a "Content coordination among OOR instances" session
** [action-2012.03.13] Ken will continue to work on implementing "gatekeeping" (and get back with an ETA) so we can move from "sandbox" to "production"
*** Ken: I can start looking into this more, now that summer has started


3. Presentation by the the panelists (~20 min. each) ... [ [http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2012_04_24#nid3A06 slides] ]  
* '''upcoming activities / virtual-session planning'''
** Architecture-API-XII - Tue 2012.05.08 ... Ken & Todd will work on this offline and send Peter an abstract shortly ... possibly addressing some of the architectural & API aspects of the "BioPortal tab" issues
** Metadata-VIII - will try to fix a date on 4/24 during the "Metadata in Ontology Mapping" session ... [[MichaelGruninger|Michael Gr&uuml;ninger]] will try to come up with a date via email
** OOR-Dev-VIII - Tue 2012.05.22 - Chair: [[MikeDean|Mike Dean]]
*** NEU, BBN, Toronto, Bremen, ... SOCoP, ORNL, MMI,
*** code contributors to compare notes on "adding tabs" ... and trying to engage the other potential code contributors
** OOR-Content-II - Tue 2012.05.29 - Co-chair: [[MichaelGruninger|Michael Gr&uuml;ninger]] & [[MikeDean|Mike Dean]]
*** "Content coordination among OOR instances" - Michael will pursue
*** look back at the [[PatCassidy|Pat Cassidy]] + [[DeniseBedford|Denise Bedford]] "OOR-Content-I" session - [[OOR/ConferenceCall_2010_03_12]]
** [new - ppy/2012.05.02] collaborating with NYC & Data.gov communities in "Big Open Data"
*** Ken: ICOM as a collaboration standard
** engaging [[JeromeEuzenat|Jerome Euzenat]] ... (?)
*** Michael: I will try to engage Jerome, probably with more concrete things, like the next virtual seesion


* [[OliverKutz|Oliver Kutz]] / [[ChristophLange|Christoph Lange]] / [[TillMossakowski|Till Mossakowski]] - "Ontology Links in the Distributed Ontology Language (DOL)"
* '''OOR:''' sandbox, devbox, test-instance, socop, colore, ornl-daac, mmi-orr, new ncbo-appliance, ... '''status update and coordination'''
** ''Abstract:'' The Distributed Ontology Language DOL, which is currently being standardised as ISO WD 17347 within the [[OntoIOp]] (Ontology Integration and Interoperability) activity of ISO/TC 37/SC 3, aims at providing a unified framework for
** thanks to everyone's support from the OOR, SOCoP, COLORE, ORNL-DAAC, MMI, NCBO teams; the following were finalized, and wereup and running at the [[OntologySummit2012_Symposium]] (and showed during the Apr-13 demo session.)
**
** new '''OOR homepage''' - http://oor.net - opens to the index page for accessing any of the OOR instances; takes one to the OOR project homepage after 15 seconds (if user did not select an OOR instance in the mean time)  
**** ontologies formalised in heterogeneous logics,  
** new '''OOR project homepage''' - http://www.oor.net - opens to the OOR project homepage on this wiki (same effect as http://OpenOntologyRepository.org )
**** modular ontologies,
** servers/instances:
**** links between ontologies, and
** OOR-01 - (old instance, being retired) re-direct to project homepage
**** annotation of ontologies.  
** OOR-02 - ci server
*** A DOL ontology consists of modules formalised in basic ontology languages, such as OWL or Common Logic, which are serialised in the existing syntaxes of these languages. On top of this, DOL provides a meta-level which allows for expressing heterogeneous ontologies and links between ontologies. This talk focuses on the latter. Links include
** OOR-03 - sandbox - http://sandbox.oor.net
**** logical links: (heterogeneous) imports and theory interpretations, as well as
** OOR-04 - socop - http://socop.oor.net
**** alignments, which largely follow the syntax specified by [http://alignapi.gforge.inria.fr/ the Alignment API].
** OOR-05 - devbox - http://dev.oor.net
DOL also supports the combination of ontologies via links (technically, these combinations are colimits). Tool support for DOL is provided by the Heterogeneous Tool Set (Hets).  
** OOR-06 - test-00 - http://test-00.oor.net
* [[JeromeEuzenat|Jerome Euzenat]] - "Ontology alignment metadata"
** ''(coming!)'' ... OOR-07 - new instance - ncbo-applicance-0.5 ... still having trouble with standing appliance up from the KVM image (Shinya might ask NCBO for a Xen image; or, alternatively, should we skip this upgrade?)
** ''Abstract:'' It is very important to be able to publish and address ontology alignments,
** SOCoP-OOR - http://socop.oor.net/ontologies
i.e., sets of correspondences between entities of two ontologies. Competing
** COLORE: colore.oor.net -> http://code.google.com/p/colore/source/browse/#svn%2Ftrunk%2Fontologies
alignments may exists between the same pair of ontologies for many reasons such
** ONTOHUB: ontohub.oor.net -> http://ontohub.informatik.uni-bremen.de/
as completeness, correctness, or expressiveness. It is worth being able of
** ORNL-DAAC: ornl-daac.oor.net -> http://mercury-ncbo.ornl.gov/ontologies
identify such alignments. Metadata on alignments, and correspondences, are
** MMI-ORR: mmisw.oor.net -> http://mmisw.org/orr/
helpful to retrieve and to qualify them. Such metadata may be used for
** [[BioPortal]] - http://bioportal.bioontology.org/  
alignment characterisation, provenance, or quality. Metadata for alignments is
not a stabilised area so it is preferable to offer an extensible annotation
framework. I will report on how this is dealt with in the Alignment API and the
Alignment server.  
** Additional material:  
*** J. Euzenat, P. Shvaiko, Ontology matching, Springer, 2007 - http://book.ontologymatching.org
*** Alignment API and server: http://alignapi.gforge.inria.fr
*** Alignment annotations: http://alignapi.gforge.inria.fr/labels.html


* Natasha Noy - "Mapping repository in BioPortal"
* '''Member activities updates''' ... ''(below)''
** ''Abstract:'' [[BioPortal]], the open ontology repository developed by the National Center for Biomedical Ontology, contains more than 300 ontologies. These ontologies inevitably overlap in content. Thus, in addition to serving as an ontology repository, [[BioPortal]] also provides a repository of mappings between the terms in the ontologies. This repository contains the mappings that the [[BioPortal]] team generates automatically, the mappings created by the users interactively through the [[BioPortal]] user interface, and the mappings that our users have created elsewhere and contributed to BioPortal. The metadata for mappings describes the provenance of the mappings, enables users to comment on and discuss the mappings, and allows users to add extra information such as transformation scripts.  


4. Q & A and Open discussion (~20 min.) ... (ref. [http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2012_04_24#nid3A0R process above])  
* '''action planning for "content drive"''' (getting people to upload ontologies) ... ''(below)''


6. Wrap-up: Announcements and Follow-up actions (where applicable) - chair: [[MichaelGruninger|Michael Gr&uuml;ninger]] (~5 min.)  
* '''Getting us to a stage when we can run a OOR-production box''' ... ''(below)''


== Transcript of the online chat during the session  ==
... ''Notes below are from previous meeting(s), and will be updated as this meeting progresses.''


see raw transcript [http://ontolog.cim3.net/file/work/OpenOntologyRepository/OOR-metadata-workshop/oor-metadata-07_chat-transcript_edited_20120424a.txt here].  
'''Member activities updates:'''' ... ''(discussion deferred)''


(for better clarity, the version below is a [ re-organized and lightly edited chat-transcript].)
* Review: members and OOR-related activities
** OOR-sandbox status
** code repository status
** NCBO
** NEU
** Raytheon-BBN
** UToronto
** Bremen
** Ryerson
** Mathet
** [[SOCoP_INTEROP]]
** [[DataONE]]
** [[NeOn]] (KMi and STL)  
** ONKI
** KBSI
** MMI
** Use Cases
** Architecture
** API
** Gatekeeping
** production OOR instance
** SIO
** ICOM / DERI
** [[OntoIOp]]
** [[OntologySummit2012|Ontology Summit 2012]]
** content drive
** Funding


Participants are welcome to make light edits to their own contributions as they see fit.  
* '''action planning for "content drive"''' (getting people to upload ontologies)
** session planned for 2012.05.29 - OOR-Content-II - co-chair: [[MichaelGruninger|Michael Gr&uuml;ninger]] & [[MikeDean|Mike Dean]]


-- begin in-session chat-transcript --
* '''Getting us to a stage when we can run a OOR-production box''' ... ''(discussion deferred)''
** ''(discussion 2011.05.06):''
*** an adopted Architecture & API is definitely crucial, but that's not all
** All team members are encouraged to mull over how we can get to that state effectively
*** in particular ... how do we make this a "successful" community-driven, open source project!?
** (discussion 2011.06.03)'' ...


-- end of in-session chat-transcript --
* code development on an Eclipse IDE for all?


6.1 Any Other Business:
* Code repository - considering "git" or github?


6.2 Action items:  
5. '''Funding progress:''' ... ''(discussion deferred)''


6.3 Schedule Next Meeting & Adjourn:  
6. '''Any Other Business:'''


* Next Meeting:  
7. '''Action items:'''
** regular monthly OOR team meeting next week - Tue 2012.05.01
** then the "OOR Architecture & API Workshop-XII" on Tue 2012.05.08


* Call adjourned at: 10:27 am PDT  
8. Schedule Next Meeting & Adjourn:
 
* Next Meetings:
** 2012_05_08 - Architecture-API-XII - Co-chair: [[User:KennethBaclawski|Ken Baclawski]] & [[ToddSchneider|Todd Schneider]]
** 2012_05_15 - no OOR meeting
** 2012_05_10 & 2012_05_17 - (being staged) "Big Open Data" with NYC, Data.gov, SMW/PSMW & OOR - please mark your calendars and come!
** 2012_05_22 - OOR-Dev-VIII - Tue 2012.05.22 - Chair: [[MikeDean|Mike Dean]]
** 2012_05_29 - OOR-Content-II - Tue 2012.05.29 - Co-chair: [[MichaelGruninger|Michael Gr&uuml;ninger]] & [[MikeDean|Mike Dean]]
** 2012_06_05 - no OOR meeting, [[SemTech]] will be in session
** 2012_06_12 - next Regular OOR Team meeting - first Tuesday of the month - [[OOR/ConferenceCall_2012_06_12]]
 
* Call adjourned at: 9:53 am PDT  


--
--


notes taken by: [[PeterYim|Peter P. Yim]] / 2012.04.24-12:11pm PDT
notes taken by: [[PeterYim|Peter P. Yim]] / 2012.05.01-9:58am 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 309: Line 335:
*** BioPortal's [bioontology-support] mailing list - see: https://mailman.stanford.edu/mailman/listinfo/bioontology-support  
*** BioPortal's [bioontology-support] mailing list - see: https://mailman.stanford.edu/mailman/listinfo/bioontology-support  
** NCBO-OOR development documentation - http://www.bioontology.org/wiki/index.php/NCBO-OOR_Development  
** NCBO-OOR development documentation - http://www.bioontology.org/wiki/index.php/NCBO-OOR_Development  
----
== How To Join (while the session is in progress)  ==
* '''1.''' Dial in with a phone and connect through skype: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2012_04_24#nid3A0H
* '''2.''' Open chat in a new browser window: http://webconf.soaphub.org/conf/room/oor_20120424
* '''3.''' Download the speaker's presentation (slides) here: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2012_04_24#nid3A06
** or, '''3.1''' [http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2012_04_24#nid3A0N access our shared-screen vnc server], if you are not behind a corporate firewall


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

Latest revision as of 07:36, 9 January 2016

OpenOntologyRepository: OOR Team Conference Call - Tue 2012_05_01

This is a regular OOR Team meeting. ... please refer also to proceedings from the last team meeting at OOR/ConferenceCall_2012_04_03

Conference Call Details

  • Date: Tuesday, 1-May-2012
  • Start Time: 8:30am PDT / 11:30am EDT / 5:30pm CEST / 15:30 UTC
  • Expected Call Duration: 1.0~1.5 hours
  • Dial-in:
    • Phone (US): +1 (206) 402-0100 (long distance cost may apply)
      • ... [ backup nbr: (415) 671-4335 ]
    • Skype: joinconference ... (generally free-of-charge, when connecting from your computer)
    • when prompted enter PIN: 141184#
  • Shared-screen support (VNC session), if applicable, will be started 5 minutes before the call at: http://vnc2.cim3.net:5800/
    • view-only password: "ontolog"
    • if you plan to be logging into this shared-screen option (which the speaker may be navigating), and you are not familiar with the process, please try to call in 5 minutes before the start of the session so that we can work out the connection logistics. Help on this will generally not be available once the presentation starts.
    • people behind corporate firewalls may have difficulty accessing this. If that is the case, please point your browser directly to the [ slides] (where applicable) and running them locally. The speaker(s) will prompt you to advance the slides during the talk.
  • RSVP to peter.yim@cim3.com appreciated, ... or simply just by adding yourself to the "Expected Attendee" list below (if you are a member of the team.)
  • Please note that this session may be recorded, and if so, the audio archive is expected to be made available as open content, along with the proceedings of the call to our community membership and the public at-large under our prevailing open IPR policy.

Attendees

  • Expecting:
    • ... if you are coming to the meeting, please add your name above (plus your affiliation, if you aren't already a member of the community) above, or e-mail <peter.yim@cim3.com> so that we can reserve enough resources to support everyone's participation. ...

Agenda Ideas

please insert any additional items below (along with your name for follow-up purposes)

  • postmortem of the last couple of OOR events:
  • upcoming activities / virtual-session planning
    • [new - ppy/2012.05.02] collaborating with NYC & Data.gov communities in "Big Open Data"
  • OOR: sandbox, devbox, test-instance, socop, colore, ornl-daac, mmi-orr, new ncbo-appliance, ... status update and coordination
  • Member activities updates
  • action planning for "content drive" (getting people to upload ontologies)
  • Getting us to a stage when we can run a OOR-production box
  • ...

Agenda & Proceedings

Archives:

1. Meeting called to order:

  • Mike Dean takes the chair and welcomes everyone
  • Peter P. Yim volunteered to take notes
  • review and adopt agenda

2. Roll Call:

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

3. Status Review and Discussion:

4. Key items for review and discussion today

  • postmortem of the last couple of OOR events:
    • Demos of various OOR instances at the OntologySummit2012_Symposium on Apr-13
      • Michael: 6 demos presented; 3 were OOR-related (SOCoP-OOR, Ontohub-OOR & COLORE-OOR)
      • Peter: thanks to all on the oor.net federation making it possible for us to have a rather coherent presentation to the audience ... great, especially this is an extended effort from one of the earlier OntologySummit's (2008 to be exact)
    • Metadata-VII: Ontology Mapping - OOR/ConferenceCall_2012_04_24
      • Michael: presentation from the OntoIOp (DOL) team, Jerome Euzenat & NCBO folks
      • Todd: very interesting session
      • Michael: follow-up meeting needed to go into representation language(s) for mapping
      • Peter P. Yim: would love to engage Jerome Euzenat (and incorporate his "mapping engine" into OOR as a value added service, especially on the database-schema-to-ontology mapping functionality.) Any others who are working on the state-of-the-art in converting database schemas to ontologies? ... who else is doing work in database schema to ontology conversion?
        • Frank Olken: Dan Miranker (Univ. of Texas Austin) and his grad student JuanSequeda have been working on translating SQL schemas to ontologies (on a small scale).
        • Mike Dean: we have something - the AutoMapper component of Asio tool suite - see http://asio.bbn.com ... but this is not opensource sw
        • Mike Dean: D2RQ and D2R from Chris Bizer's group
        • Frank Olken: Juan Sequeda, Marcelo Arenas, Daniel P. Miranker: On directly mapping relational databases to RDF and OWL. WWW 2012: 649-658
        • Peter P. Yim: maybe Elisa Kendall too
        • Peter P. Yim: the interest above stems from my earlier (Mar-2010) proposal I made to the NCO_NITRD on systematically developing ontologies from the data.gov (ref. http://data.gov) datasets (more than 390,000 of them now), possibly developing those "ontologies" from database schemas and from "vocabularies" the the RPI folks have been doing for some of those) and then hosting these ontologies on OOR for public reference and consumption. This approach (mapping database schemas to some ontology/ies) was one of the kep approaches we took when Leo Obrst, I and others were working for VerticalNet circa year 2000 too.)
      • Peter P. Yim: consider doing a virtual session on this ... Michael: possibly an Ontolog topic more than an straight OOR topic (which deals with things that are already ontologies)
  • previous action item status review
    • [action-2012.03.13] Michael will try to get Mike Bennett to upload his ontology to OOR
      • Michael: I'll work on a "Content coordination among OOR instances" session
    • [action-2012.03.13] Ken will continue to work on implementing "gatekeeping" (and get back with an ETA) so we can move from "sandbox" to "production"
      • Ken: I can start looking into this more, now that summer has started
  • upcoming activities / virtual-session planning
    • Architecture-API-XII - Tue 2012.05.08 ... Ken & Todd will work on this offline and send Peter an abstract shortly ... possibly addressing some of the architectural & API aspects of the "BioPortal tab" issues
    • Metadata-VIII - will try to fix a date on 4/24 during the "Metadata in Ontology Mapping" session ... Michael Grüninger will try to come up with a date via email
    • OOR-Dev-VIII - Tue 2012.05.22 - Chair: Mike Dean
      • NEU, BBN, Toronto, Bremen, ... SOCoP, ORNL, MMI,
      • code contributors to compare notes on "adding tabs" ... and trying to engage the other potential code contributors
    • OOR-Content-II - Tue 2012.05.29 - Co-chair: Michael Grüninger & Mike Dean
    • [new - ppy/2012.05.02] collaborating with NYC & Data.gov communities in "Big Open Data"
      • Ken: ICOM as a collaboration standard
    • engaging Jerome Euzenat ... (?)
      • Michael: I will try to engage Jerome, probably with more concrete things, like the next virtual seesion
  • Member activities updates ... (below)
  • action planning for "content drive" (getting people to upload ontologies) ... (below)
  • Getting us to a stage when we can run a OOR-production box ... (below)

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

Member activities updates:' ... (discussion deferred)

  • Review: members and OOR-related activities
    • OOR-sandbox status
    • code repository status
    • NCBO
    • NEU
    • Raytheon-BBN
    • UToronto
    • Bremen
    • Ryerson
    • Mathet
    • SOCoP_INTEROP
    • DataONE
    • NeOn (KMi and STL)
    • ONKI
    • KBSI
    • MMI
    • Use Cases
    • Architecture
    • API
    • Gatekeeping
    • production OOR instance
    • SIO
    • ICOM / DERI
    • OntoIOp
    • Ontology Summit 2012
    • content drive
    • Funding
  • action planning for "content drive" (getting people to upload ontologies)
  • Getting us to a stage when we can run a OOR-production box ... (discussion deferred)
    • (discussion 2011.05.06):
      • an adopted Architecture & API is definitely crucial, but that's not all
    • All team members are encouraged to mull over how we can get to that state effectively
      • in particular ... how do we make this a "successful" community-driven, open source project!?
    • (discussion 2011.06.03) ...
  • code development on an Eclipse IDE for all?
  • Code repository - considering "git" or github?

5. Funding progress: ... (discussion deferred)

6. Any Other Business:

7. Action items:

8. Schedule Next Meeting & Adjourn:

  • Next Meetings:
    • 2012_05_08 - Architecture-API-XII - Co-chair: Ken Baclawski & Todd Schneider
    • 2012_05_15 - no OOR meeting
    • 2012_05_10 & 2012_05_17 - (being staged) "Big Open Data" with NYC, Data.gov, SMW/PSMW & OOR - please mark your calendars and come!
    • 2012_05_22 - OOR-Dev-VIII - Tue 2012.05.22 - Chair: Mike Dean
    • 2012_05_29 - OOR-Content-II - Tue 2012.05.29 - Co-chair: Michael Grüninger & Mike Dean
    • 2012_06_05 - no OOR meeting, SemTech will be in session
    • 2012_06_12 - next Regular OOR Team meeting - first Tuesday of the month - OOR/ConferenceCall_2012_06_12
  • Call adjourned at: 9:53 am PDT

--

notes taken by: Peter P. Yim / 2012.05.01-9:58am PDT

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


Resources

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