OOR/ConferenceCall 2011 11 29

= Joint NCBO-OOR Workshop: "BioPortal and OOR Synergies" - Tue 29-Nov-2011 =

Topic: "OOR Architecture & API Workshop-IX: BioPortal & OOR Synergies"

Session Co-chairs: Professor KenBaclawski and Dr. ToddSchneider

Discussant: Dr. Ray Fergerson [ slides ]

Abstract
Topic: "OOR Architecture & API Workshop-IX: BioPortal & OOR Synergies"


 * This workshop will examine the current differences between BioPortal and OOR requirements and draft architecture and address the plan of action to extend BioPortal to satisfy the OOR requirements.


 * The session will revolve around the following two subjects:


 * 1. BioPortal - OOR Differences: Current & Future
 * 2. How to extend BioPortal to meet OOR Goals

Agenda Proceedings
Archives:


 * Fergerson slides
 * audio recording of the session [ 1:24:22 ; MP3 ; 9.66MB ]
 * chat-transcript of this session

1. Meeting called to order:


 * KenBaclawski & ToddSchneider took the chair and welcome everyone
 * review and adopt agenda
 * PeterYim volunteered to take notes

2. Roll Call:


 * see above


 * welcome and intro of new member(s) (as needed)

3. Key items for review and discussion today:

Topic: "OOR Architecture & API Workshop-IX: BioPortal & OOR Synergies"

3.1 "BioPortal - OOR Differences: Current & Future" - (RayFergerson et al.)

3.2 "How to extend BioPortal to meet OOR Goals" - (All)


 * (ref. suggested) Issues we could discuss at this joint NCBO-OOR session
 * BioPortal's Roadmap or priorities
 * PeterYim: aligning BioPortal & OOR architecture and API to create and maximize synergies
 * clearly identify functionalities that either the NCBO or the OOR development team will be pursuing
 * federation (BBN is happy to contribute their earlier code)
 * which specific "[[WebTools]" package](s) is PaulAlexander using
 * status of export/import/upgrade process for NCBO appliance
 * availability of Java, Ruby, or other client stubs for invoking BioPortal REST services

3.3 Discussion Notes

3.4 Transcript of the online chat 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 of chat session --

PeterYim: Welcome to the

= Joint NCBO-OOR Workshop: "BioPortal and OOR Synergies" - Tue 29-Nov-2011 =

Topic: "OOR Architecture & API Workshop-IX: BioPortal & OOR Synergies"

Session Co-chairs: Professor KenBaclawski and Dr. ToddSchneider

Discussant: Dr. Ray Fergerson

Session page: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_11_29

Phone keypad controls: To un-mute, press "*7" ... To mute, press "*6"

Proceedings:
anonymous morphed into Gilberto Fragoso

MikeRiben: mike riben listening in on skype

MikeRiben: not sure I have a mic

PeterYim: Hi Michael

anonymous morphed into CarlosRueda

anonymous morphed Deanna Marino

anonymous morphed into PaulCourtney

anonymous morphed into TrishWhetzel

ToddSchneider: For those not familiar with OOR requirements or goals, please ask.

ToddSchneider: OOR high level requirements: Storing, Management, Governance of Ontologies & Related Items; Discovery / Searching Ontologies; Scalable (Parallelism, Federation); Multi-Language Support; Arbitrary Knowledge Domain; Platform Independent

anonymous morphed into LinePouchard

LinePouchard: Q about searches: it seems that Boolean searches are not supported for term searches. Are there plans to support this?

LinePouchard: What does it take to make it a big requirement?

TrishWhetzel: Hi Line - would you like to submit this as a feature request?

LinePouchard: Sourceforge bug tracking, sounds good, thanks.

LinePouchard: Trish, yes I would like to.

TrishWhetzel: Ok, I'll submit this as a feature request and as Ray mentioned we'll get this into the development cycle. If you come across any other feature requests or bug reports, feel free to send these to our user support mailing list: support@bioontology.org

ToddSchneider: Eric, I see your 'hand' is up. Do you have a question for Ray?

Eric S. Chan: Do you consider using an ontology for reification of notes, discussions, reviews, etc., that can be attached to the Biomedical Ontology? Peter Yim and I had suggested OASIS ICOM ontology (http://www.oasis-open.org/committees/download.php/44405/icom-ics-v1.0-csprd02.zip) for reification of collaborative contents in OOR.

ToddSchneider: Eric, can we ask your question when Ray is done with his presentation?

Eric S. Chan: yes, I can ask the question during the Q/A

ToddSchneider: Ray, don't encourage the use of UML.

PeterYim: @ALL: for everyone's information Michael Gruninger who champions our OOR-Metadata workshop, is planning one on Dec-13 ... there is plan to invite HaroldSolbrig (Mayo) over to talk about their recent ontology metadata "crosswalk" study, which, among others, included OMV, CTS2. ... Please mark your calendars ... we'll look forward to having you at the session on Tue 2011.12.13 see development details at: http://ontolog.cim3.net/cgi-bin/wiki.pl?OOR/ConferenceCall_2011_12_13

MikeBennett: On notes and annotations, are the bioportal notes ontology items aligned with or reusing concepts in SKOS that relate to notes?

ToddSchneider: Mike's query raises an interesting capability, the ability to sufficiently distinguish the domains covered by a particular ontology repository (to support distributed queries).

ToddSchneider: Carlos, did you want to ask Ray?

CarlosRueda: My question is just about a topic already in the agenda: "how to extend BioPortal"

TrishWhetzel: While not limited to ontology repositories, but geared more towards the content of triple stores, there is an effort to catalog the contents of triple stores via the dbcatalog group, http://groups.google.com/group/dbcatalog

PeterYim: great session ... thank you, Ray, Todd, Ken and All!

PeterYim: -- session ended: 10:02am PST --

-- end of chat session --


 * Further Question & Remarks - please post them to the [ oor-forum ] listserv
 * if you are already subscribed, post to 
 * (if you are not yet subscribed) you may subscribe yourself to the [ oor-forum ] listserv listserv, by sending a blank email to  from your subscribing email address, and then follow the instructions you receive back from the mailing list system.

4. Action items:

5. Any Other Business:

6. Schedule Next Meeting & Adjourn:


 * Next Meetings:
 * 2011_12_06: regular OOR team meeting - OOR/ConferenceCall_2011_12_06
 * 2011_12_13: OOR-metadata workshop take-V - chair: MichaelGruninger - OOR/ConferenceCall_2011_12_13


 * Call adjourned at: 10:02 am PST

-- notes taken by: PeterYim / 2011.11.29-___am PST All participants, please review and edit to enhance accuracy and granularity of the documented proceedings.

Resources

 * NCBO - National Center for Biomedical Ontology - http://www.bioontology.org/
 * The BioPortal - http://bioportal.bioontology.org/
 * OpenOntologyRepository - Homepage for the OOR initiative
 * A recent presentation on OOR - OOR Presentation at SemTech2010
 * OpenOntologyRepository_IPR Policy
 * OpenOntologyRepository_Requirement
 * OpenOntologyRepository_UseCases
 * OpenOntologyRepository_Architecture
 * 2011_09_13 - Tuesday: Joint NCBO-OOR Panel Discussion: "Kicking-off the Next Phase of Collaboration" - Co-chairs: Dr. RayFergerson & Mr. PeterYim - Panelists: Professor MarkMusen (NCBO; Stanford), Dr. NatashaNoy (NCBO; Stanford), Dr. TrishWhetzel (NCBO; Stanford), Dr. LeoObrst (OOR; MITRE), Professor KenBaclawski (OOR; Northeastern U) & Dr. ToddSchneider (OOR; Raytheon) - OOR/ConferenceCall_2011_09_13
 * 2010_09_17 - Friday: OOR Panel Discussion - "Getting OOR Development Going - Take-IV" Workshop - Co-chairs: Dr. ToddSchneider & Professor MichaelGruninger - Panelists: Dr. ToddSchneider (Raytheon), Mr. MikeDean (Raytheon-BBN), Dr. NatashaNoy (NCBO, Stanford University), Dr. ImmanuelNormann (Bremen University, BORG), Professor KenBaclawski (Northeastern University), Professor MichaelGruninger (University of Toronto) - OOR/ConferenceCall_2010_09_17
 * 2009_10_15 - Thursday: "OOR-BioPortal Comparative Analysis" panel discussion - Chair: ToddSchneider - Panelists: NatashaNoy, MichaelDorf, KenBaclawski, ElisaKendall & MikeDean - ConferenceCall_2009_10_15
 * 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
 * 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
 * 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
 * 2008_04_29 - Our team made a presentation with our history, status, OOR rationale and requirements, and a proposed roadmap at the OntologySummit2008 - see: http://ontolog.cim3.net/cgi-bin/wiki.pl?OntologySummit2008/FaceToFaceAgenda#nid1BLS
 * 2007_12_06 - Thursday: Invited Speaker - Professor MarkMusen: "If we build it, will they come? Social-engineering of new technology to disseminate biomedical ontologies" - ConferenceCall_2007_12_06
 * OntologySummit2008 - "Toward An Open Ontology Repository"
 * OntologySummit2008_Communique
 * our most recent regular OOR-team meeting - OOR/ConferenceCall_2011_09_06
 * [ oor-forum ] message archive - http://ontolog.cim3.net/forum/oor-forum/
 * (if you are not yet subscribed) you may subscribe yourself to the [ oor-forum ] listserv, by sending a blank email to  from your subscribing email address, and then follow the instructions you receive back from the mailing list system.
 * check out our other mailing lists and join us
 * OOR Project site at SemWebCentral - http://oor.semwebcentral.org
 * Public instances of OOR - http://sandbox.oor.net/ontologies (previously http://oor-01.cim3.net/ontologies) ... we are in process to standing up:
 * OOR_SandBox - http://oor-03.cim3.net - http://sandbox.oor.net/
 * OOR_DevBox - http://oor-01.cim3.net - http://devbox.oor.net/
 * 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

For the record ...

How To Join (while the session is in progress)

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Conference Call Details:

 * Date: Tuesday, 29-Nov-2011
 * Start Time: 8:30am PST / 11:30am EST / 5:30pm CET / 16:30 UTC
 * ref: World Clock
 * Expected Call Duration: ~1.5 hours


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Attendees

 * Attended:
 * KenBaclawski (co-chair)
 * ToddSchneider (co-chair)
 * RayFergerson (discussant)
 * PeterYim (scribe)
 * Gilberto Fragoso (NIH/NCI)
 * MichaelRiben
 * MikeDean
 * CarlosRueda
 * YefimZhuk
 * MyCoyne
 * BrianDavis
 * Deanna Marino
 * PaulCourtney
 * TrishWhetzel
 * LinePouchard
 * EricChan
 * MikeBennett


 * 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. ...
 * ... 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:
 * TimDarr
 * MichaelGruninger