OntologWiki: OOR/ConferenceCall 2009 09 04

OpenOntologyRepository: OOR Team Conference Call - Fri 2009-09-04 (20QS)

OpenOntologyRepository team conference call, Fri 2009-09-04, 1.0~1.5 Hr. call starting 12:00pm EDT / 9:00am PDT / 6:00pm CET / 5:00pm GMT / 17:00 UTC (20QT)

Conference Call Details: (20QU)

Date: Friday, September 4, 2009 (20QV)
Start Time: 12:00pm EDT / 9:00am PDT / 6:00pm CEST / 5:00pm BST / 16:00 UTC (20QW)
- ref: World Clock (20QX)
Expected Call Duration: 1.0~1.5 hours (20QY)
Dial-in Number: (20QZ)
- from a US telephone (US): +1-218-844-8060 (domestic long distance cost will apply) (20R0)
- When calling in from a phone, use Conference ID: "4389979#" (20R1)
- from Europe, call: (20R2)
  - Austria 0820-4000-1577 (20R3)
  - Belgium 070-35-9992 (20R4)
  - France 0826-100-280 (20R5)
  - Germany 01805-00-7642 (20R6)
  - Ireland 0818-270-037 (20R7)
  - Italy 848-390-179 (20R8)
  - Spain 0902-886-056 (20R9)
  - Switzerland 0848-560-327 / 0848-414-110 (20RA)
  - UK 0870-738-0765 (20RB)
- callers from other countries please dial into either one of the US or European numbers (20RC)

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.) (20RD)

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_2009_09_04 (20RE)

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. (20RF)

Attendees (20RG)

Attended: (20RH)
- LeoObrst (chair) (20RK)
- KenBaclawski (20RX)
- MikeDean (20RJ)
- PaulAlexander (MMI) (20Z4)
- RaviSharma (20Z5)
- SteveRay (20Z6)
- ToddSchneider (20Z7)
- BartGajderowicz (20S0)

Expecting: (20RI)

Regrets: (20RM)
- PeterYim (20RN)

Agenda Ideas: (20RO)

progress review on planned OOR-related events (20RQ)
reports on member activities that are OOR-related (20TA)

Agenda & Proceedings (20TB)

1. Meeting called to order: (20TC)

LeoObrst takes the chair and welcomed everyone (20TD)
KenBaclawski volunteers to take minutes of the meeting (20TE)

review and adopt agenda (20TF)

2. Roll Call: (20TG)

see above (20TH)

3. Status Review and Discussion: (20TI)

Urgent issues: (20TJ)
- none (20TK)

Logistics and Communications (20TL)
- populate - OOR/ActiveMemberContribution (20TM)

Key item for discussion at this call: (20TN)

items below are from the previous meeting(s); they will be updated as this meeting progresses ... (20TO)

postmortem and follow-up action review after the three(3) recent joint Ontolog-OOR panel sessions (20TP)
- 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 T (20TQ)
- 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 T (20TR)
- 2009_08_06 - Thursday: Joint Ontolog-OOR Panel Discussion: "Ontology Repository Research Issues" - Chair: KenBaclawski - Panelists: MichaelGruninger, ElisaKendall, BartGajderowicz, MathieuDaquin & ToddSchneider - ConferenceCall_2009_08_06 T (20TS)
  - The chat session was captured on the session page. (20TT)
  - BartGajderowicz will be setting up a wiki page the topics raised by the meeting. (20TU)
    - UPDATE: The new OOR/ResearchActivity page has been setup. Was this page setup by BartGajderowicz? (20TV)

ToddSchneider and NCBO folks might walk us through the UML-EA diagrams of the NCBO BioPortal system 2.1d (v1016 of Jul-2009) which Todd posted on 2009.07.29 and is now available at: http://ontolog.cim3.net/file/work/OOR/oor-dev/BioPortal_ver1016_UML-EA_Model--NCBO_ToddSchneider_20090729a/BioPortal_v1016_Jul2009_HTML/ (20TW)
- The diagrams suggest that the design is not entirely appropriate for the goals and requirements of OOR. This suggests that we should open a dialog with the BioPortal community concerning this. ToddSchneider will take the lead on a session to be held tentatively on October 1. Tentative panelists may include KenBaclawski, NatashaNoy, ToddSchneider, MishaDorf. (20TX)
- MichaelGruninger asked the question: How does the notion of module and imports in Common Logic map to the architecture of BioPortal? (20TY)
- We should contact ElisaKendall about these topics. (20TZ)

Progress review on planned OOR-related events: (20U0)

ISWC 2009 - Poster - see Todd's first draft: http://ontolog.cim3.net/file/work/OOR/OOR_ISWC-2009/OOR_ISWC-2009_poster/wip/ (20U1)
- An outline: ... (20U2)
- KenBaclawski has an OOR slide deck, so does FrankOlken, KatherineGoodier, and a MikeDean-PeterYim lightning talk they made at ISWC2008 (20U3)
  - Let's try to get them all under the "Publications & References" section of the OOR homepage - http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository#nid1LSM (20U4)
  - authorship, ... communicating author, discussed (20U5)
  - Mike: the poster can also show a screenshot of our OOR instance, and describe what we are doing at the demo (20U6)
KenBaclawski has written a paper dealing with requirements and research challenges at http://ontolog.cim3.net/file/work/OOR/OOR-Requirements-Research/Requirements-and-Challenges--KenBaclawski_20090814.pdf He is seeking help for further developing this paper. It has been submitted to NatashaNoy's workshop, but it should be possible to revise it later. KenBaclawski has not yet seen the reviews. (20U7)

OOR-related project and activities status updates: (20U8)

Overview on UML diagrams of BioPortal systems (20U9)
- see: http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository_Architecture#nid1XRD (20UA)
- Todd: UML diagrams generated by "Enterprise Architect" ... will be posting the full set ... (20UB)
- Misha: the diagrams are complete; slightly difficult to read now -- some parts not 'relevant' to BioPortal could be removed to make it more readable; with the new update, a lot of changes coming in anyway as an ontology is being used (20UC)
  - Misha will help provide a list of the 'relevant' subset of classes (20UD)
- Benjamin: MDA? (20UE)
  - ... Todd: probably stick with UML now, and eventually move to CL? (20UF)
- Peter / Todd: will add revision level onto the diagrams in the future ... the ones from before, we'll add a date for identification purposes (20UG)
- Peter: MishaDorf suggested a full UML diagram and a highlight diagram ... guess Todd is working on them (haven't heard from him yet) (20UH)
- Todd/2009.07.10 - full set of UML diagrams (on BioPortal 2.0) uploaded to the server (as of 2009.06.14) (20UI)
  - see: http://ontolog.cim3.net/file/work/OOR/oor-dev/BioPortal_3Mar2009_UML-Model_ToddSchneider_20090614/index.html (20UJ)
- ALL: vote of thanks to Todd (20UK)
- Todd: (ref. Misha's suggestion of doing a "highlighted" version with some of the packages removed) think it is better use of time to do another set of diagrams oo the recently updated version of BioPortal (v2.1d) instead (20UL)
  - Peter: suggest that Todd might ping Misha via the [oor-dev] list to get his advice on when best to grab the new codes for reverse engineering (20UM)
  - Misha already responded - see: http://ontolog.cim3.net/forum/oor-dev/2009-07/msg00001.html (20UN)
  - Todd: just downloaded the new BioPortal v2.1d released codes (1016) - will have the UML diagrams by the next call (20UO)
  - Todd: will try to upload the UML diagrams for that before the 7/30 panel session (20UP)

Potential for collaboration with the geospatial ontology folks''' - NancyWiegand / GaryBergCross (20UQ)
- Nancy: intro; SOCoP - submitting a grant proposal to NSF again; possibility of using OOR for their work (20UR)
- Gary: intro - SOCoP secretary; use of ontology repository for interoperability, social aspect of sharing; (20US)
- Mike: welcome the collaboration; probably some additional features needed to support geospatial ontologies (20UT)
  - Nancy: how much development is expected? (20UU)
- K: how much data will be involved .. using data.gov? (20UV)
  - Gary: possibly using some USGS data (K: which is already linked to data.gov) (20UW)
- Nancy: supporting data store ... or just ontologies (20UX)
- Todd: OOR not supposed to provide data store ... but can consider a extension project to work on (20UY)
- Nancy: is the infrastructure stable ... and expected to be around for many years? (20UZ)
  - Mike: the intent is "Yes!" (20V0)
- Gary: Nancy is the PI; proposal due in July; (20V1)
- K: National Geospatial Symposium ... (20V2)
- Ken: already has a grant ... can share some of the language used ... Nancy will contact Ken (20V3)
  - Ken: will work with Nancy on this offline (20V4)
- Ken/2009.07.10 update - I am working with Nancy to supply her some of the language for her proposal (20V5)
- Peter: Ontolog has provided Nancy and Gary a "Letter of Collaboration" to NSF - see: the Letter (20V6)
- Mike/2009.07.10 - will do "Support Letter" to NSF (for this proposal) on behalf of OOR too (--done! MikeDean/2009.07.20) - see: the Letter (20V7)
- Ken: coming from the experience as a review panelist, these letters can help (as well as hurt) a proposal (20V8)

OOR sandbox instance - status review - http://oor-01.cim3.net (20V9)
- Benjamin: major update - BioPortal v2.1d - to be released on 12-Jun-2009 (20VA)
  - Natasha/2009.06.12 - slightly delayed, release date could now be a couple of week out (20VB)
- Peter: hardware for OOR sandbox-2 (and later the production instance of OOR) will be ready fairly soon (next few days). (20VC)
  - an updated version of the CODS server will also be installed on that hardware cluster (20VD)
- Peter/2009.07.10 - hardware is now ready ... once the Stanford / NCBO are back from their International Conference (this week) in Amsterdam (20VE)
  - Peter is now traveling ... will address this after his return (2nd week of September) (20VF)

OOR Outreach (20VG)

ISWC 2009 (20VH)
- candidates: A poster on OOR; also presentation as a "Lightning Talk"; BOF meeting (20VI)
- Todd, K & Ken will champion and coordinate this group of efforts (20VJ)
  - Ken/2009.7.10: work the poster is in progress (20VK)
  - Mike: would be great if we could also do a demo ... Ken: we'll submit that (a demo) as part of the proposal. (20VL)
  - Ken / Mike / Michael: we'll do something to demo Common Logic support too (20VM)

Natasha: "Workshop on Collaborative Construction, Management and Linking of Structured Knowledge" proposal for ISWC2009 - proposal went in 2009.05.01 (20VN)
- CFP is out - see: http://ontolog.cim3.net/forum/oor-forum/2009-06/msg00001.html - submission deadline 10 August 2009 (20VO)
- maybe results from the Aug-6 "Research Issues" panel can give us ammunition to make a report during that workshop (20VP)

Semantic Web meetings. These are local meetings. KenBaclawski will be developing a slide deck for possible presentation in Cambridge next week. This will be posted, and others could use/modify it for their own local meetings. See: http://semweb.meetup.com/ (20Z8)

Other potential venues. Please add them here... (20Z9)

OOR development activities (20VQ)
- Michael: running into issues with trying to add FOL/CL upload/download onto the BioPortal codebase (20VR)
  - Michael: issues with inherent binary relationship limitation with the existing OWL implementation (based on Protege) (20VS)
  - Natasha: BioPortal now supports two backends now - the Protege backend and the LexGrid (OBO/Mayo) backend (20VT)
  - PatCassidy: translate? ... having a CL backend for Protege would be useful (20VU)
- Peter: please continue this conversation on the [oor-dev] list (20VV)
- K: possibly add another use case for CL (20VW)
- Peter/2009.07.10: would love to see Mike's team (or Mike to take the lead on a broader effort) would do a native FOL backend for the OOR (20VX)
- Ken/2009.07.10: we need internal interfaces ... modularization ... [Ken, please elaborate ...] (20VY)
- Todd/2009.07.10: need to re-emphasize that we should keep a focus on storing and retrieving "stuff" (so far, the focus has been too much on "ontologies") ... need separation of concerns (20VZ)
  - one issue is adaptability (20W0)
- Michael/2009.07.10 - we'll get some questions about working on a CL backend onto the [oor-dev] list, and look forward to the Jul-16 & Jul-30 sessions to get some clarification. (20W1)

Other Progress updates and Discussions: (20W2)

no discussion (20W3)

Funding and proposals (20W4)
- Peter: suggest picking up the effort ... NSF solicitation like INTEROP (07-565) (due 2009.07.23), STCI (PD 06-7231) (due 2009.08.13) (20W5)
  - Peter: (in the spirit of the encouraged pairwise collaboration) I'll be making proposals to the INTEROP and STCI programs with MarkMusen (20W6)
  - Ken: I'll look into either INTEROP or STCI to see if we can do something (20W7)
  - My initial investigation into STCI funding was discouraging, but later discussions were much more encouraging although I will still need to discuss OOR with more NSF people next week. This will be awkward because I will be traveling next week, but I try to continue the investigation. (20W8)
- Bart: what kind of help can we get (for proposals in Canada) (20W9)
  - Ken: ping me off-line for some reference on previously submitted proposal (20WA)
  - Mike: we can provide a "Letter of Collaboration" (20WB)

Short-Term Funding Plans (20WC)
- Peter: we need to get a stake in the ground so that we can say OOR or OOR-related projects are funded (and be able to list those projects) (20WD)
- members of this team are highly encouraged to go out (by themselves, or form pairs or small teams) with proposals where the "OOR" label is prominently featured (20WE)
- Ken: trying to get some seed money from NSF (20WF)
- Carlos: we just submitted (yesterday) with OOR being a key aspect in the proposal (20WG)

short term activity and action plans (20WH)

4. New Issues: (20WJ)

5. Any Other Business: (20WK)

6. Action items: (20WL)

Short-term plan: (20WM)
- ToddSchneider panel (20ZA)
- Add other outreach venues above (20ZB)
- Course at NU will start soon (20ZC)
- KenBaclawski will try to edit this page to remove redundancy. (20ZD)
- RaviSharma will be contacting CoryCasanave, ElisaKendall and EvanWallace regarding OMG related ontology repository efforts. There could be interest in a joint OMG-OOR panel meeting in the Ontolog Forum. We need to determine what they are doing. (20ZE)

7. Schedule Next Meeting & Adjourn: (20WQ)

Next Meeting: (20WR)
- next regular team call Fri 2009.09.18 12:00pm ET / 9:00am PT / 16:00 GMT/UTC - see (closer to the time) session page at: OOR/ConferenceCall_2009_09_18 (20WS)
- Note: earlier resolution: all team members please (if possible) block out Fridays 1.5 Hr starting 12:00pm ET / 9:00am PT / 16:00 GMT/UTC (20WT)

Call adjourned at: 9:53 PDT (20WU)

 --
 notes taken by: KenBaclawski / 2009.09.04-12:53pm EDT
 All participants, please review and edit to enhance accuracy and granularity of the documented proceedings.    (20WV)

Resources (20WW)

homepage - OpenOntologyRepository - http://OpenOntologyRepository.org (20WX)
proceedings of our previous meetings (20WY)
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. (20Y0)
"Ontology Repository" Definition - "An ontology repository is a facility where ontologies and related information artifacts can be stored, retrieved and managed" (20Y1)
OpenOntologyRepository_Scope - documentation related to this OOR initiative's mission, charter, objectives, goals, terms of reference, definitions, scope, ... etc. (20Y2)
OpenOntologyRepository_Requirement - documentation related to the requirements of the "open ontology repository" we are planning to implement through this OOR initiative. (20Y3)
- OpenOntologyRepository_UseCases (20Y4)
OpenOntologyRepository_Approach - documentation related to this OOR initiative's approach, and the process we will be using. (20Y5)
OpenOntologyRepository_Architecture - documentation related to the architecture of the "open ontology repository" we are planning to implement through this OOR initiative. (20Y6)
OpenOntologyRepository_Plan (20Y7)
OOR/ActiveMemberContribution (20Y8)
Team mailling list: [ oor-forum ] discussion archives - http://ontolog.cim3.net/forum/oor-forum/ (20Y9)
Developers mailling list: [ oor-dev ] discussion archives - http://ontolog.cim3.net/forum/oor-dev/ (20YA)
the four joint OOR-OntologySummit2008 Panel Discussions: (20YB)
- 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 T (20YC)
- 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 T (20YD)
- 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 T (20YE)
- 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 T (20YF)
the OOR-dev: Synergies & Gaps panel session: (20YG)
- 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 T (20YH)
OntologySummit2008 homepage (20YI)
- OntologySummit2008_Communique (20YJ)
- OntologySummit2008/FaceToFaceAgenda (20YK)
- The OOR Project Presentation (delivered at the OntologySummit2008 face-to-face workshop) (20YL)
[ ontology-summit ] discussion archives - http://ontolog.cim3.net/forum/ontology-summit/ (20YM)
Our key content pages: (20YN)
- OpenOntologyRepository_Scope (20YO)
- OpenOntologyRepository_Organization (20YP)
- OpenOntologyRepository_Process (20YQ)
- OpenOntologyRepository_Policy (20YR)
- OpenOntologyRepository_IPR (20YS)
- OpenOntologyRepository_Requirement (20YT)
- OpenOntologyRepository_UseCases (20YU)
- OpenOntologyRepository_Architecture (20YV)
- OpenOntologyRepository_Approach (20YW)
- OpenOntologyRepository_Roadmap (20YX)
- OpenOntologyRepository_Plan (20YY)
- OpenOntologyRepository_Funding (20YZ)
- OpenOntologyRepository_ResearchIssues (20Z0)
OOR Project site at SemWebCentral - http://oor.projects.semwebcentral.org (20Z1)
our first sandbox instance of OOR - http://oor-01.cim3.net/ (20Z2)
- NCBO-OOR development documentation - http://www.bioontology.org/wiki/index.php/NCBO-OOR_Development (20Z3)

OOR/ConferenceCall 2009 09 04

OpenOntologyRepository: OOR Team Conference Call - Fri 2009-09-04 (20QS)

Conference Call Details: (20QU)

Attendees (20RG)

Agenda Ideas: (20RO)

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