OOR/ConferenceCall 2011 10 18

= 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 [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_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:
 * MichaelGruninger (chair)
 * PeterYim
 * TerryLongstreth
 * KenBaclawski
 * NikkiaAnderson (for GailHodge)
 * TimWilson
 * TimDarr
 * ToddSchneider
 * AliHashemi
 * XingfangLi


 * 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  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  so that we can reserve enough resources to support everyone's participation. ...


 * Regrets:
 * MikeBennett
 * MikeDean
 * LeoObrst

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


 * MichaelGruninger: 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 - 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 PeterHaase "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:


 * MichaelGruninger takes the chair and welcome everyone
 * Review and adopt agenda
 * PeterYim 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: JohnBateman & MichaelGruninger - ConferenceCall_2011_10_20
 * 2011_11_03 - Thursday: Joint IAOA-OOR-Ontolog "Ontologies and Standards" mini-series session-2: Invited Speaker: ElisaKendall on ISO 19763 "Metamodel Framework for Interoperability (MFI)" - Co-chairs: MichaelGruninger & JohnBateman - 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.
 * 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 MichaelGruninger

Today's (2011.10.18) agenda:


 * Claim 1: For specifying properties of ontologies, OMV is sufficient for OOR use cases.

ontology repository.
 * Claim 2: OMV is not sufficient for specifying the relationships between ontologies within an


 * Existing relations between ontologies within OMV (v2.4.1): (ref. pp. 13, 29 30)
 * useImports
 * hasPriorVersion
 * isIncompatibleWith
 * isBackwardsCompatible

relationship between different ontologies.
 * The last three relationships focus on different versions of an ontology rather than the


 * Is useImports defined if the ontologies are axiomatized in different languages?

in different languages.
 * Heterogeneous ontologies -- ontologies that import other ontologies which are axiomatized


 * 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 --

PeterYim: Welcome to the

= open ontology repository (oor) session - tue 2011_10_18 =

Topic: OOR Metadata Workshop-IV

Session Chair: MichaelGruninger

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

proceedings:
anonymous morphed into TimWilson

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

MichaelGruninger: I am having trouble connecting by phone

Tim Darr: Joining ...

PeterYim: are you trying to connect via skype?

PeterYim: Michael got in!

ToddSchneider: Michael, What's a 'module'?

anonymous morphed into NikkiaAnderson

anonymous morphed into AliHashemi

ToddSchneider / MichaelGruninger: Manchester's TONES repository - http://owl.cs.manchester.ac.uk/repository/browser

MichaelGruninger: 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)

AliHashemi: 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

--- ---

AliHashemi: ORR is a typo meant OOR

TimWilson: At my work, ORR is Operational Readiness Review.

PeterYim: 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)

MichaelGruninger: 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.

AliHashemi: hasImport --> useImports*

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

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

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

ToddSchneider: OOR will automatically parse import statements and check for the presence of the ontologies to be imported in OORs.

ToddSchneider: Terry, invariant? With respect to what?

TerryLongstreth: With respect to the importing object

AliHashemi: 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

TerryLongstreth: If the imported, validated module can change, than everything that imports it can be invalidated

AliHashemi: (I've got to run. Bye.)

TerryLongstreth: ...at some arbitrary time in the future

ToddSchneider: (Sorry, but have to go.)

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

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

KenBaclawski: 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.

MichaelGruninger: Find examples within BioPortal of one ontology importing another ontology, either internal or external to BioPortal

PeterYim: MichaelGruninger: at the next workshop, we can put some focus on "versioning"

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

PeterYim: -- session ended: 10:05 am PDT --

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

4. Any Other Business:


 * PeterYim: 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:


 * MichaelGruninger: 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: PeterYim / 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: LeoObrst & FrankOlken; Panelists: BruceBargmeyer, MikeDean, MarkMusen, FarrukhNajmi & PeterYim - ConferenceCall_2008_02_28
 * 2008_03_27 - Thursday: Joint OOR-OntologySummit2008 Panel Discussion: "An Open Ontology Repository: Rationale, Expectations & Requirements - Session-1" - Chair: LeoObrst & FabianNeuhaus; Panelists: WilliamBug, EvanWallace, JohnLMcCarthy, KenBaclawski, PeterBenson & RexBrooks - ConferenceCall_2008_03_27
 * 2008_04_03 - Thursday: Joint OOR-OntologySummit2008 Panel Discussion: "An Open Ontology Repository: Rationale, Expectations & Requirements - Session-2" - Chair: LeoObrst & FabianNeuhaus; Panelists: DougLenat, DekeSmith, MarciaZeng, DeniseBedford, PatHayes, MalaMehrotra & RobRaskin - ConferenceCall_2008_04_03
 * 2008_04_10 - Thursday: Joint OOR-OntologySummit2008 Panel Discussion: "Developing an Ontology of Ontologies for OOR" - Co-chairs: BarrySmith & MichaelGruninger; Panelists: MichaelGruninger, PeterHaase, NatashaNoy & ElisaKendall - ConferenceCall_2008_04_10
 * the OOR Development panel sessions:
 * 2008_08_22 - Friday: OOR Panel Discussion: "Getting OOR Development Off the Ground: Identifying Synergies & Gaps" (Take-1) - Chair: LeoObrst; Panelists: MikeDean, MarkMusen, LiDing, BruceBargmeyer & BillAndersen - ConferenceCall_2008_08_22
 * 2009_02_19 - Thursday: Joint Ontolog-OOR Panel Discussion: "Getting OOR Development Off the Ground (Take-2): the work begins" - Chair: ToddSchneider; Panelists: MarkMusen, NatashaNoy, MikeDean, PaulBuitelaar / AndreasHarth, MathieuDaquin, KenBaclawski, MichaelGruninger - 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: MarkMusen - Panelists: TaniaTudorache, TimRedmond, NatashaNoy - ConferenceCall_2009_07_16
 * 2009_07_30 - Thursday: Joint Ontolog-OOR Panel Discussion: "BioPortal and related Ontology Repository Implementations and Development" (Take-3) - Chair: NatashaNoy - Panelists: CarlosRueda, PaulAlexander, JohnGraybeal, MikeDean, StephenGranite, AlexGarcia, KenBaclawski - ConferenceCall_2009_07_30
 * 2010_02_19 - Friday: OOR Panel Discussion: "Coordinating our Open Ontology Repository Software Development" - Chair: MikeDean - Panelists: JimChatigny, MichaelGruninger, KenBaclawski, NatashaNoy - OOR/ConferenceCall_2010_02_19
 * 2010_04_01 - Thursday: Joint OOR-Ontolog Panel Session: "OOR Use Cases - Take-3" - Chair: KenBaclawski & ToddSchneider - Panelists: ToddSchneider, MatthewHettinger, KenBaclawski and MaximoGurmendez - ConferenceCall_2010_04_01
 * 2010_09_10 - Friday: Joint SIO-OOR-Ontolog Panel Discussion: "Common Logic (CL) Support for OOR" - Chair: JohnSowa - Panelists: JohnBateman-TillMossakowski, MichaelGruninger, CameronRoss, AdamPease, PatHayes - ConferenceCall_2010_09_10
 * 2010_09_17 - Friday: OOR Panel Discussion - "Getting OOR Development Going - Take-IV" Workshop - Co-chairs: ToddSchneider & MichaelGruninger - Panelists: ToddSchneider, MikeDean, NatashaNoy, ImmanuelNormann, KenBaclawski, MichaelGruninger - 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: KenBaclawski & MichaelGruninger - Panelists: KenBaclawski+ToddSchneider, AldoGangemi+AlessandroAdamou, JouniTuominen+KimViljanen, EricChan - OOR/ConferenceCall_2010_11_19
 * 2011_03_04 - Friday: OOR "Architecture & API Specification Development Workshop-I" - Co-chairs: KenBaclawski & ToddSchneider - OOR/ConferenceCall_2011_03_04
 * 2011_03_11 - Friday: OOR - "Architecture & API Specification Development Workshop-II" - Co-chairs: KenBaclawski & ToddSchneider - OOR/ConferenceCall_2011_03_11
 * 2011_03_18 - Friday: OOR Metadata Workshop-I - Chair: MichaelGruninger - OOR/ConferenceCall_2011_03_18
 * 2011_03_25 - Friday: OOR - "Architecture & API Specification Development Workshop-III" - Co-chairs: KenBaclawski & ToddSchneider - OOR/ConferenceCall_2011_03_25
 * 2011_04_22 - Friday: OOR - "Architecture & API Specification Development Workshop-IV" - Co-chairs: KenBaclawski & ToddSchneider - OOR/ConferenceCall_2011_04_22
 * 2011_05_13 - Friday: OOR Metadata Workshop-II - Chair: MichaelGruninger - OOR/ConferenceCall_2011_05_13
 * 2011_05_20 - Friday: OOR - "Architecture & API Specification Development Workshop-V" - Co-chairs: KenBaclawski & ToddSchneider - OOR/ConferenceCall_2011_05_20
 * 2011_05_27 - Friday: OOR Metadata Workshop-III - Chair: MichaelGruninger - OOR/ConferenceCall_2011_05_27
 * 2011_06_17 - Friday: OOR - "Architecture & API Specification Development Workshop-VI" - Co-chairs: KenBaclawski & ToddSchneider - OOR/ConferenceCall_2011_06_17
 * 2011_09_13 - Tuesday: Joint NCBO-OOR Team Meeting - "Kicking-off the Next Phase of Collaboration" - Co-chairs: RayFergerson & PeterYim - OOR/ConferenceCall_2011_09_13
 * 2011_09_20 - Tuesday: OOR - "Architecture & API Specification Development Workshop-VII" - Chair: KenBaclawski - OOR/ConferenceCall_2011_09_20
 * 2011_10_11 - Tuesday: OOR - "Architecture & API Specification Development Workshop-VIII" - Chair: KenBaclawski & ToddSchneider - OOR/ConferenceCall_2011_10_11
 * 2011_10_18 - Tuesday: OOR Metadata Workshop-IV - Chair: MichaelGruninger - 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: GeorgeStrawn - Chair: PeterYim - Panelists: JamieClark, JohnWilbanks, BrucePerens - 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: MarkMusen - Panelists: CameronRoss, AlanRector, JohnSowa, BrucePerens, JohnWilbanks, PeterYim - ConferenceCall_2010_09_16
 * 2010_09_30 - Thursday: Joint OOR-Ontolog-NCBO-CC-IAOA-OASIS Panel Discussion - "IPR issues in Ontology and the OOR" session-3: discussion and consensus on licensing arrangements for the OOR Initiative, and positions we might take on related IPR issues - chair: LeoObrst - Panelists: PeterYim, MikeDean, BrucePerens, JamieClark - ConferenceCall_2010_09_30
 * OntologySummit2008 homepage
 * OntologySummit2008_Communique
 * OntologySummit2008/FaceToFaceAgenda & Proceedings
 * The OOR Project Presentation (delivered at the OntologySummit2008 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)
 * OOR_SandBox
 * Development instance of OOR (OOR-dev) - http://oor-01.cim3.net/ - to browse: http://oor-01.cim3.net/ontologies - http://dev.oor.net/
 * OOR_DevBox
 * NCBO - 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