Ontolog Forum
OpenOntologyRepository: Metadata Workshop-IV - Tue 2011_10_18
Topic: OOR Metadata Workshop-IV
Session Chair: MichaelGruninger
Archives
- Please refer to the proceedings of:
- (This session) OOR Metadata Workshop-IV 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
- Audio recording of this session [ 1:17:07 ; mp3 ; 8.83 MB ]
- chat-transcript from this session
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
- ref: 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
- 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"
- 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.)
- 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 our prevailing open IPR policy.
Attendees
- Attended:
- Michael Grüninger (chair)
- Peter P. Yim
- Terry Longstreth
- Ken Baclawski
- Nikkia Anderson (for GailHodge)
- Tim Wilson
- Tim Darr
- Todd Schneider
- Ali Hashemi
- Xingfang Li
- 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. ...
- Regrets:
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
- Proceedings of OOR Metadata Workshop-I and MichaelGruninger's opening slides from that session
- Proceedings of OOR Metadata Workshop-II
- Proceedings of OOR Metadata Workshop-III
- Metadata for Ontologies - [[OntologySummit2008_Communique|from the OntologySummit2008_Communique]]
- Metadata requirement - 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" - OMV v2.4.1 (final) (Mar-2009)
- The Joint OpenOntologyRepository-OntologySummit2008 Panel Discussion Session - ConferenceCall_2008_04_10
- Presentation by Peter Haase "The OMV Ontology Metadata Vocabulary" at that session
- OpenOntologyRepository_Architecture
- OpenOntologyRepository_UseCases - http://www.ccs.neu.edu/home/kenb/ontologies/
Agenda & Proceedings
1. Meeting called to order:
- Michael Grüninger takes the chair and welcome everyone
- Review and adopt agenda
- Peter P. Yim volunteered to keep a record of the proceedings
2. Roll Call:
- see above
- 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:
- see archives above
- 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:
- Michael Grüninger: Action Item (for everyone): find papers on ontology versioning
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 -
- Date: Tue 2011.11.01 - Start time: 8:30am PDT / 11:30am EDT / 4:30pm CET / 15:30 UTC (ref. worldclock)
- see developing session page is at OOR/ConferenceCall_2011_11_01
- 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
- homepage - OpenOntologyRepository - http://OpenOntologyRepository.org
- OOR Charter - To promote the global use and sharing of ontologies by: 1. establishing a hosted registry-repository; 2. enabling and facilitating open, federated, collaborative ontology repositories; 3. establishing best practices for expressing interoperable ontology and taxonomy work in registry-repositories.
- "Ontology Repository" Definition - "An ontology repository is a facility where ontologies and related information artifacts can be stored, retrieved and managed"
- Team mailling list:
- OOR-Team discussion: [ oor-forum ] message archives - http://ontolog.cim3.net/forum/oor-forum/
- OOR-Users discussion and support: [ oor-users ] message archives - http://ontolog.cim3.net/forum/oor-users/
- Developers mailling list: [ oor-dev ] message archives - http://ontolog.cim3.net/forum/oor-dev/
- proceedings of our 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: Leo Obrst & Frank Olken; Panelists: Bruce Bargmeyer, Mike Dean, Mark Musen, Farrukh Najmi & 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: Leo Obrst & Fabian Neuhaus; Panelists: William Bug, Evan Wallace, JohnLMcCarthy, Ken Baclawski, Peter Benson & 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: Leo Obrst & Fabian Neuhaus; Panelists: Doug Lenat, Deke Smith, Marcia Zeng, Denise Bedford, Pat Hayes, Mala Mehrotra & Rob Raskin - ConferenceCall_2008_04_03
- 2008_04_10 - Thursday: Joint OOR-OntologySummit2008 Panel Discussion: "Developing an Ontology of Ontologies for OOR" - Co-chairs: Barry Smith & Michael Grüninger; Panelists: Michael Grüninger, Peter Haase, Natasha Noy & 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: Leo Obrst; Panelists: Mike Dean, Mark Musen, Li Ding, Bruce Bargmeyer & 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: Todd Schneider; Panelists: Mark Musen, Natasha Noy, Mike Dean, Paul Buitelaar / Andreas Harth, Mathieu Daquin, Ken Baclawski, Michael Grüninger - 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: Tania Tudorache, 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: Carlos Rueda, Paul Alexander, John Graybeal, Mike Dean, StephenGranite, AlexGarcia, Ken Baclawski - ConferenceCall_2009_07_30
- 2010_02_19 - Friday: OOR Panel Discussion: "Coordinating our Open Ontology Repository Software Development" - Chair: Mike Dean - Panelists: Jim Chatigny, Michael Grüninger, Ken Baclawski, Natasha Noy - OOR/ConferenceCall_2010_02_19
- 2010_04_01 - Thursday: Joint OOR-Ontolog Panel Session: "OOR Use Cases - Take-3" - Chair: Ken Baclawski & Todd Schneider - Panelists: Todd Schneider, Matthew Hettinger, Ken Baclawski and Máximo Gurméndez - ConferenceCall_2010_04_01
- 2010_09_10 - Friday: Joint SIO-OOR-Ontolog Panel Discussion: "Common Logic (CL) Support for OOR" - Chair: John F. Sowa - Panelists: JohnBateman-TillMossakowski, Michael Grüninger, Cameron Ross, Adam Pease, Pat Hayes - ConferenceCall_2010_09_10
- 2010_09_17 - Friday: OOR Panel Discussion - "Getting OOR Development Going - Take-IV" Workshop - Co-chairs: Todd Schneider & Michael Grüninger - Panelists: Todd Schneider, Mike Dean, Natasha Noy, Immanuel Normann, Ken Baclawski, Michael Grüninger - 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: Ken Baclawski & Michael Grüninger - Panelists: KenBaclawski+ToddSchneider, AldoGangemi+AlessandroAdamou, JouniTuominen+KimViljanen, Eric Chan - OOR/ConferenceCall_2010_11_19
- 2011_03_04 - Friday: OOR "Architecture & API Specification Development Workshop-I" - Co-chairs: Ken Baclawski & Todd Schneider - OOR/ConferenceCall_2011_03_04
- 2011_03_11 - Friday: OOR - "Architecture & API Specification Development Workshop-II" - Co-chairs: Ken Baclawski & Todd Schneider - OOR/ConferenceCall_2011_03_11
- 2011_03_18 - Friday: OOR Metadata Workshop-I - Chair: Michael Grüninger - OOR/ConferenceCall_2011_03_18
- 2011_03_25 - Friday: OOR - "Architecture & API Specification Development Workshop-III" - Co-chairs: Ken Baclawski & Todd Schneider - OOR/ConferenceCall_2011_03_25
- 2011_04_22 - Friday: OOR - "Architecture & API Specification Development Workshop-IV" - Co-chairs: Ken Baclawski & Todd Schneider - OOR/ConferenceCall_2011_04_22
- 2011_05_13 - Friday: OOR Metadata Workshop-II - Chair: Michael Grüninger - OOR/ConferenceCall_2011_05_13
- 2011_05_20 - Friday: OOR - "Architecture & API Specification Development Workshop-V" - Co-chairs: Ken Baclawski & Todd Schneider - OOR/ConferenceCall_2011_05_20
- 2011_05_27 - Friday: OOR Metadata Workshop-III - Chair: Michael Grüninger - OOR/ConferenceCall_2011_05_27
- 2011_06_17 - Friday: OOR - "Architecture & API Specification Development Workshop-VI" - Co-chairs: Ken Baclawski & 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: Ray Fergerson & Peter P. Yim - OOR/ConferenceCall_2011_09_13
- 2011_09_20 - Tuesday: OOR - "Architecture & API Specification Development Workshop-VII" - Chair: Ken Baclawski - OOR/ConferenceCall_2011_09_20
- 2011_10_11 - Tuesday: OOR - "Architecture & API Specification Development Workshop-VIII" - Chair: Ken Baclawski & Todd Schneider - OOR/ConferenceCall_2011_10_11
- 2011_10_18 - Tuesday: OOR Metadata Workshop-IV - Chair: Michael Grüninger - OOR/ConferenceCall_2011_10_18
- 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
- OntologySummit2008 homepage
- OntologySummit2008_Communique
- OntologySummit2008/FaceToFaceAgenda & Proceedings
- The OOR Project Presentation (delivered at the Ontology Summit 2008 face-to-face workshop)
- [ 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)
- 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 - 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