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OpenOntologyRepository: Architecture & API Workshop-VII - Tue 2011_09_20     (1)

Topic: "OOR Architecture & API Specification Development Workshop-VII"     (1A)

  • Shared-screen support (VNC session), if needed, will be started 5 minutes before the call at: http://vnc2.cim3.net:5800/     (1C5)
    • view-only password: "ontolog"     (1C5A)
    • if you plan to be logging into this shared-screen option (which the speaker may be navigating), and you are not familiar with the process, please try to call in 5 minutes before the start of the session so that we can work out the connection logistics. Help on this will generally not be available once the presentation starts.     (1C5B)
    • people behind corporate firewalls may have difficulty accessing this. If that is the case, and where appropriate, please download the [ slides] and running them locally. The speaker(s) will prompt you to advance the slides during the talk.     (1C5C)
  • Discussions and Q & A:     (1C6)
    • (Unless the conference host has already muted everyone) Please mute your phone, by pressing "*2" on your phone keypad, when a presentation is in progress. To un-mute, press "*3"     (1C6A)
    • You can type in your questions or comments through the browser based chat session by:     (1C6B)
      • instructions: once you got access to the page, click on the "settings" button, and identify yourself (by modifying the Name field). You can indicate that you want to ask a question verbally by clicking on the "hand" button, and wait for the moderator to call on you; or, type and send your question into the chat window at the bottom of the screen.     (1C6C1)
    • (when everyone is muted) If you want to speak or have questions or remarks to make, please "raise your hand (virtually)" by click on the "hand button" (lower right) on the chat session page. You may speak when acknowledged by the speaker or the session moderator (again, press "*3" on your phone to unmute). Test your voice and introduce yourself first before proceeding with your remarks, please. (Please remember to click on the "hand button" again (to lower your hand) and press "*2" on your phone to mute yourself after you are done speaking.)     (1C6D)
    • thanks to the soaphub.org folks, one can now use a jabber/xmpp client (e.g. gtalk) to join this chatroom. Just add the room as a buddy - (in our case here) ontolog_20110920@soaphub.org ... Handy for mobile devices!     (1C6E)
  • 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.)     (1C8)
  • 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.     (1C10)

Attendees     (1E)

  • Expecting:     (1E2)
    • ... 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. ...     (1E3A)

Agenda Ideas     (1F)

please insert any additional items below (along with your name for follow-up purposes)     (1F1)

  • 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     (1F2)

Abstract     (1G)

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.     (1G1)

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.     (1G2)

The various architectures and APIs for ontology repositories presented for consideration are available at OpenOntologyRepository_Architecture     (1G3)

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.     (1G5)

Finally, we need to agree on a plan for completing the development of the specification.     (1G8)

We encourage all participants to update your candidate contributions to ensure your ideas are known and understood.     (1G10)

The following are relevant prior meetings:     (1G11)

Agenda & Proceedings     (1H)

1. Meeting called to order:     (1H4)

2. Roll Call & Adoption of last meeting's minutes:     (1H8)

3. Key items for review and discussion today:     (1H12)

  • Quick discussion on options regarding the OOR_SandBox install; so we can support the upcoming SOCoP presentation scheduled for late this month     (1H14)
    • 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     (1H14A)
    • 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)     (1H14B)
      • Ken (will follow Mike's install process and) arrange to have a "NCBO Appliance v0.3" VM run on an NEU hosted machines     (1H14B1)
        • Ken will drop in the new logo, and customize the IPR License     (1H14B1A)
        • once running, Ken & Tejas will provide Mike with access to the vm     (1H14B1B)
        • Mike / Ken / Tejas / Peter will start a wiki page to capture - OOR_SandBox_Customization - ... will use the [oor-dev] list too, for email exchange     (1H14B1C)
        • 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     (1H14B1D)
      • 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     (1H14B2)

... items below are mostly from the previous workshop, and will be updated as this session progresses.     (1H16)

  • 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.     (1H21)

--- Chat transcript begin: ---     (1H23)

OpenOntologyRepository: Architecture & API Workshop-VII - Tue 2011_09_20     (2)

Topic: "OOR Architecture & API Specification Development Workshop-VII"     (2A)

Proceedings     (2E)

Todd Schneider: Ken, I was able to login.     (2E2)

Ken Baclawski: Tejas set up a VMWare on a machine in my office at NEU. I can give access to anyone     (2E3)

who needs it. The main machine is lisf.ccs.neu.edu, and the domains we can use are     (2E4)

ontology.ccs.neu.edu and kiwi.ccs.neu.edu.     (2E5)

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.     (2E7)

= The interface for searching ontology metadata will consist of a single method: (2SSS)     (2E9)

  • The method will have a single parameter consisting of a SPARQL query. (2SSU)     (2E11)
  • The return value of the method will be a SPARQL result set. (2SSV)     (2E12)
  • Metadata will be represented using a named RDF graph. (2SSW)     (2E13)

o The OMV extension may include a notion of domain specification or topics, represented as text. (2SSZ)     (2E16)

  • Metadata will be federated, so it is a single named RDF graph, no matter how many OOR instances there are.     (2E17)

o Quality and Gatekeeping. We distinguish between gatekeeping and quality control.     (2E19)

Gatekeeping criteria are a set of minimal requirements that any ontology within     (2E20)

the OOR has to meet. The latter are intended to enable the users of the OOR to     (2E21)

find quickly ontologies that fit their needs; the criteria are not supposed to     (2E22)

ensure the quality of the ontologies. (2VB8)     (2E23)

o Gatekeeping impacts metadata (2VB9)     (2E24)

o Gatekeeping will need to vet the metadata to ensure entrance criteria are met. (2VBA)     (2E25)

o Syntax checking is the responsibility of the language module. (2VBB)     (2E26)

o Each OOR instance must declare the representation languages (2VBD)     (2E27)

o Each OOR instance must declare the representation language module it spports. (2VBE)     (2E28)

o Will OOR Metadata be represented in OWL? (2VBF)     (2E29)

o Every OOR shall support RDF (2VBG)     (2E30)

o Correction: Every OOR shall support RDFS (2VBI)     (2E31)

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)     (2E32)

o Gatekeeping criteria will include an attribute to indicate whether the ontology exists or the metadata represents an advertisement. (2VBR)     (2E33)

o The location of the actual ontology is the responsibility of Administration. (2VBT)     (2E34)

o Metadata needs to include an attribute for the 'availability' of the ontology (2VBW)     (2E35)

o 'Location' of the ontology must be provided. (2VBX)     (2E36)

o Representation language of the ontology is a required attribute. (2VBY)     (2E37)

o Michael will provide a preliminary list of required metadata attributes. (2VBZ)     (2E38)

o Submission process will be asynchronous (2VC0)     (2E39)

o Minimal language dependency submission is syntax validation (2VC1)     (2E40)

o Consistency checking, to some extent, will be required for submission (2VC2)     (2E41)

o Need an attribute to represent that it is consistent, which then will require     (2E42)

another field to identify the reasoner used to do the consistency checking (2VC3)     (2E43)

o Ken has already developed the gatekeeper module which should provide enough to specify it for OOR (2VC4)     (2E44)

o Ken's gatekeeper module already has a mechanism to configure the registration workflow for a community (2VC5)     (2E45)

Todd Schneider: Gatekeeper - notification(), subscription(), register()?     (2E46)

Todd Schneider: subscription is for particular ontology and particular user     (2E47)

Todd Schneider: subscription - sends notices about events related to ontology     (2E48)

Terry Longstreth: Create ontology == prepare system for new ontology?     (2E49)

Todd Schneider: registrar - creates the entry in the OOR; to do so the required metadata needs to be created     (2E50)

Peter P. Yim: -- session ended: 9:41am PDT --     (2E51)

--- Chat transcript end: ---     (2E52)

Consensus, Conclusions & Follow-up Actions:     (2E53)

4. Any Other Business:     (2E54)

5. Action items:     (2E55)

  • (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"     (2E56)
    • no prepared presentations, but we need an agenda and enumerate things to discuss - Ken and Todd will prepare     (2E56A)

6. Schedule Next Meeting & Adjourn:     (2E57)

  • Next Meeting:     (2E58)
    • since the SOCoP folks will be getting ready to travel, and Peter cannot join on Sep-27, we will skip next week's     (2E58A)
    • next meeting will therefore be, at the same time on 2011_10_04 Tuesday: regular OOR-team call     (2E58B)

notes taken by: Peter P. Yim / 2011.09.20-9:41am PDT     (2E61)

All participants, please review and edit to enhance accuracy and granularity of the documented proceedings.     (2E62)


Resources     (2F)


This page has been migrated from the OntologWiki - Click here for original page     (2F16)