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OpenOntologyRepository: Architecture & API Workshop-VII - Tue 2011_09_20

Topic: "OOR Architecture & API Specification Development Workshop-VII"

Session Chair: Ken Baclawski & Todd Schneider

Conference Call Details

  • Date: Tuesay, 20-Sep-2011
  • Start Time: 8:30am PDT / 11:30am EDT / 5:30pm CEST / 4:30pm BST / 15:30 UTC
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  • 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)

  • Peter P. Yim (2011.09.19): need a quick discussion on options regarding the OOR_SandBox install; so we can support the upcoming SOCoP presentation scheduled for late this month
  • Discussion on possible adjustments in the OOR architecture and work plans in view of what transpired from last week's Joint NCBO-OOR Team Meeting - ref. OOR/ConferenceCall_2011_09_13
  • The specifications to be discussed at the these workshops are the following (not necessarily discussed in this order):
    • the OOR Architecture
    • the OOR API
    • the Organizing Plan
    • the default development platform

Abstract

As a result of the two OOR Architecture and API panel sessions back in Oct & Nov-2010, we have been exposed to a large number of architecture and API candidates for ontology repositories. We have had requirements for the OOR, at least in broad outline form, since the Ontology Summit 2008. We have been running an OOR sandbox based on BioPortal. Most recently, we have forked from the BioPortal code base with the intention of proceeding separately with the development of a reference implementation.

At this series of meetings, we are going through the process of producing the actual OOR specification. It will be run as a workshop where the straw man proposal will be discussed and modified as needed.

The various architectures and APIs for ontology repositories presented for consideration are available at OpenOntologyRepository_Architecture

Here is the straw man architecture: OpenOntologyRepository_Architecture/Candidate03

In addition, there is an API of the core services that was obtained from BioPortal, which is not entirely compatible with the straw man architecture, but furnishes a starting point. This API will also be discussed and modified as needed.

Here is the API expressed in WSDL: http://www.ccs.neu.edu/home/kenb/oor/OORService.wsdl

Here is the API expressed in Java: http://www.ccs.neu.edu/home/kenb/oor/OORI.java

Finally, we need to agree on a plan for completing the development of the specification.

Here is the proposed organizing plan: OpenOntologyRepository_Architecture/GettingOrganized

We encourage all participants to update your candidate contributions to ensure your ideas are known and understood.

The following are relevant prior meetings:

Agenda & Proceedings

Archives:

1. Meeting called to order:

  • Peter P. Yim volunteered to keep a record of the proceedings
  • review and adopt agenda

2. Roll Call & Adoption of last meeting's minutes:

  • review of agenda

3. Key items for review and discussion today:

  • Announcements and Urgent Matters:
  • Quick discussion on options regarding the OOR_SandBox install; so we can support the upcoming SOCoP presentation scheduled for late this month
    • Peter gave synopsis of the state of affairs, and the need for SOCoP folks to make a SOCoP-OOR presentation/demo in about a week
    • Mike: was able to install a v0.2 "NCBO Appliance" VMware image on his notebook (a fairly old Mac); doing the same for v0.3 was mixed, but was able to make most things work (with some exceptions)
      • Ken (will follow Mike's install process and) arrange to have a "NCBO Appliance v0.3" VM run on an NEU hosted machines
        • Ken will drop in the new logo, and customize the IPR License
        • once running, Ken & Tejas will provide Mike with access to the vm
        • Mike / Ken / Tejas / Peter will start a wiki page to capture - OOR_SandBox_Customization - ... will use the [oor-dev] list too, for email exchange
        • Peter will add the dns record map that instance to socop.oor.net (Ken to provide IP) - it would be either 129.10.112.163 or 129.10.112.167 - Ken will confirm later after checking up on available resources
      • ALL: the aim is to get all the above up and running within 24 to 48 hours, so the SOCoP folks can start doing their "content" work and prepare their presentation
  • Discussion on possible adjustments in the OOR architecture and work plans in view of what transpired from last week's Joint NCBO-OOR Team Meeting - ref. OOR/ConferenceCall_2011_09_13
    • defer the discussion to our next meeting when we will try to invite Ray Fergerson to join us

... items below are mostly from the previous workshop, and will be updated as this session progresses.

  • Review of action item(s) from the previous meeting(s)
  • from 2011.06.17 - Michael Grüninger will examine the OMV to determine which attributes are required and which are optional.
  • from 2011.06.17 - Ken Baclawski will send KEEPER (the gatekeeping software) to Todd Schneider who will generate the UML.
  • "OOR Architecture & API Specification Development Workshop-VII:" (Archives)
  • Gatekeeping specifies the a set of minimal requirements that any ontology within the OOR has to meet. The latter are intended to enable the users of the OOR to find quickly ontologies that fit their needs; the criteria are not supposed to ensure the quality of the ontologies.
    • Each OOR instance declares what ontology languages it supports.
    • Every OOR instance MUST support RDFS.
      • This is required because the metadata is expressed in OMV.
      • OMV is written in OWL, but it may be sufficient to require only RDFS. This needs to be investigated.
    • Other ontology languages MAY be supported.
    • For each metadata attribute, it will be specified whether it is required or optional.
      • It MUST be specified whether the ontology is available (or to be available in the future).
      • The ontology language MUST be specified.
      • Other attributes will be handled offline by Michael Grüninger based on the OMV specification.
    • An ontology must satisfy other requirements depending on the ontology language.
      • Syntax checking is always required.
      • Consistency checking is required with some time limit.

--- Chat transcript begin: ---

Peter P. Yim: Welcome to the

OpenOntologyRepository: Architecture & API Workshop-VII - Tue 2011_09_20

Topic: "OOR Architecture & API Specification Development Workshop-VII"

Session Co-chairs: Ken Baclawski & Todd Schneider

Session page: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_09_20

.

Proceedings

.

Todd Schneider: Ken, I was able to login.

Ken Baclawski: Tejas set up a VMWare on a machine in my office at NEU. I can give access to anyone

who needs it. The main machine is lisf.ccs.neu.edu, and the domains we can use are

ontology.ccs.neu.edu and kiwi.ccs.neu.edu.

Peter P. Yim: please use this page to capture customization details - http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR_SandBox_Customization

Ken Baclawski: The static IP address of ontology.ccs.neu.edu is 129.10.112.163. The one for kiwi.ccs.neu.edu is 129.10.112.167.

Todd Schneider: where are we with the discussion ... ref. http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_04_22#nid2ST2

= The interface for searching ontology metadata will consist of a single method: (2SSS)

  • The method will be called find. (2SST)
  • The method will have a single parameter consisting of a SPARQL query. (2SSU)
  • The return value of the method will be a SPARQL result set. (2SSV)
  • Metadata will be represented using a named RDF graph. (2SSW)
  • Metadata will be based on an extension of OMV. (2SSY)

o The OMV extension may include a notion of domain specification or topics, represented as text. (2SSZ)

  • Metadata will be federated, so it is a single named RDF graph, no matter how many OOR instances there are.

Todd Schneider: also ref. http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_06_17#nid2V8P

o Quality and Gatekeeping. We distinguish between gatekeeping and quality control.

Gatekeeping criteria are a set of minimal requirements that any ontology within

the OOR has to meet. The latter are intended to enable the users of the OOR to

find quickly ontologies that fit their needs; the criteria are not supposed to

ensure the quality of the ontologies. (2VB8)

o Gatekeeping impacts metadata (2VB9)

o Gatekeeping will need to vet the metadata to ensure entrance criteria are met. (2VBA)

o Syntax checking is the responsibility of the language module. (2VBB)

o Each OOR instance must declare the representation languages (2VBD)

o Each OOR instance must declare the representation language module it spports. (2VBE)

o Will OOR Metadata be represented in OWL? (2VBF)

o Every OOR shall support RDF (2VBG)

o Correction: Every OOR shall support RDFS (2VBI)

o OMV is written in OWL (2VBK) - From Chapter 5 of the OMV Report 2.4.1: As aforementioned, OMV is formalized as an OWL ontology. (2VBO)

o Gatekeeping criteria will include an attribute to indicate whether the ontology exists or the metadata represents an advertisement. (2VBR)

o The location of the actual ontology is the responsibility of Administration. (2VBT)

o Metadata needs to include an attribute for the 'availability' of the ontology (2VBW)

o 'Location' of the ontology must be provided. (2VBX)

o Representation language of the ontology is a required attribute. (2VBY)

o Michael will provide a preliminary list of required metadata attributes. (2VBZ)

o Submission process will be asynchronous (2VC0)

o Minimal language dependency submission is syntax validation (2VC1)

o Consistency checking, to some extent, will be required for submission (2VC2)

o Need an attribute to represent that it is consistent, which then will require

another field to identify the reasoner used to do the consistency checking (2VC3)

o Ken has already developed the gatekeeper module which should provide enough to specify it for OOR (2VC4)

o Ken's gatekeeper module already has a mechanism to configure the registration workflow for a community (2VC5)

Todd Schneider: Gatekeeper - notification(), subscription(), register()?

Todd Schneider: subscription is for particular ontology and particular user

Todd Schneider: subscription - sends notices about events related to ontology

Terry Longstreth: Create ontology == prepare system for new ontology?

Todd Schneider: registrar - creates the entry in the OOR; to do so the required metadata needs to be created

Peter P. Yim: -- session ended: 9:41am PDT --

--- Chat transcript end: ---

Consensus, Conclusions & Follow-up Actions:

4. Any Other Business:

5. Action items:

  • (ref. above) Peter to contact Ray Fergerson and invite him to join us on the Oct-4 call to do a "Architectural review and discussion"
    • no prepared presentations, but we need an agenda and enumerate things to discuss - Ken and Todd will prepare
      • Peter will set up the OOR/ConferenceCall_2011_10_04 meeting page quickly, so Ken, Todd, Ray and anyone else can add things to it. ... ( done! --ppy/2011.09.20-15:50 PDT )

6. Schedule Next Meeting & Adjourn:

  • Next Meeting:
    • since the SOCoP folks will be getting ready to travel, and Peter cannot join on Sep-27, we will skip next week's
    • next meeting will therefore be, at the same time on 2011_10_04 Tuesday: regular OOR-team call
  • Call adjourned at: 9:41 am PDT

--

notes taken by: Peter P. Yim / 2011.09.20-9:41am PDT

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

Resources



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