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OpenOntologyRepository: Metadata Workshop-IV - Tue 2011_10_18

Topic: OOR Metadata Workshop-IV

Session Chair: MichaelGruninger


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:
    • view-only password: "ontolog"
  • RSVP to 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.


  • 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. ...

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.


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:


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 -

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:


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:

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: 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.