OOR/ConferenceCall 2011 09 20

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

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

Session Chair: KenBaclawski & ToddSchneider

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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 * Expected Call Duration: 1.0~1.5 hours
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Attendees

 * Attended:
 * KenBaclawski (co-chair)
 * ToddSchneider (co-chair)
 * PeterYim
 * TerryLongstreth
 * MikeDean


 * Expecting:
 * RaviSharma (joined us as we were wrapping up)
 * ... 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:
 * YuriyMilov
 * LeoObrst

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


 * PeterYim (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:


 * Kicking-off the Next Phase of OOR-NCBO Collaboration - OOR/ConferenceCall_2011_09_13
 * Architecture & API Specification Development Workshop-VI - OOR/ConferenceCall_2011_06_17
 * Architecture & API Specification Development Workshop-V - OOR/ConferenceCall_2011_05_20
 * Architecture & API Specification Development Workshop-IV - OOR/ConferenceCall_2011_04_22
 * Architecture & API Specification Development Workshop-III - OOR/ConferenceCall_2011_03_25
 * Architecture & API Specification Development Workshop-II - OOR/ConferenceCall_2011_03_11
 * Architecture & API Specification Development Workshop-I - OOR/ConferenceCall_2011_03_04
 * 2011.02.04 discussion
 * 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
 * 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

Agenda & Proceedings
Archives:


 * audio recording of the session ( 1:10:31 ; mp3 ; 8.87 MB )
 * chat-transcript of this session

1. Meeting called to order:


 * KenBaclawski & ToddSchneider took the chair and welcome everyone


 * PeterYim volunteered to keep a record of the proceedings


 * review and adopt agenda

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


 * see above


 * ref. proceedings of "Architecture & API Specification Development Workshop-VI" - OOR/ConferenceCall_2011_06_17


 * 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 RayFergerson 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 - MichaelGruninger will examine the OMV to determine which attributes are required and which are optional.
 * from 2011.06.17 - KenBaclawski will send KEEPER (the gatekeeping software) to ToddSchneider 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 MichaelGruninger 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 of this session:

--- Chat transcript begin: ---

PeterYim: Welcome to the

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

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

Session Co-chairs: KenBaclawski & ToddSchneider

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

.

Proceedings:
.

ToddSchneider: Ken, I was able to login.

KenBaclawski: 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.

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

KenBaclawski: 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.

ToddSchneider: 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) o The OMV extension may include a notion of domain specification or topics, represented as text. (2SSZ)
 * 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)
 * The metadata RDF graph will use the following name: http://metadata.oor.net   (2SSX)
 * Metadata will be based on an extension of OMV.   (2SSY)
 * Metadata will be federated, so it is a single named RDF graph, no matter how many OOR instances there are.

ToddSchneider: 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)

ToddSchneider: Gatekeeper - notification, subscription, register?

ToddSchneider: subscription is for particular ontology and particular user

ToddSchneider: subscription - sends notices about events related to ontology

TerryLongstreth: Create ontology == prepare system for new ontology?

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

PeterYim: -- 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 RayFergerson 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: PeterYim / 2011.09.20-9:41am 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
 * 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