Ontolog Forum
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
- Fergerson slides
- audio recording of the session [ 1:24:22 ; MP3 ; 9.66MB ]
- chat-transcript of this session
1. Meeting called to order:
- Ken Baclawski & Todd Schneider took the chair and welcome everyone
- review and adopt agenda
- Peter P. Yim 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
- Peter P. Yim: 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 Paul Alexander 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 --
Peter P. Yim: 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 Ken Baclawski and Dr. Todd Schneider
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
Mike Riben: mike riben listening in on skype
Mike Riben: not sure I have a mic
Peter P. Yim: Hi Michael
anonymous morphed into Carlos Rueda
anonymous morphed Deanna Marino
anonymous morphed into Paul Courtney
anonymous morphed into Trish Whetzel
Todd Schneider: For those not familiar with OOR requirements or goals, please ask.
Todd Schneider: 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 Line Pouchard
Line Pouchard: Q about searches: it seems that Boolean searches are not supported for term searches.
Are there plans to support this?
Line Pouchard: What does it take to make it a big requirement?
Trish Whetzel: Hi Line - would you like to submit this as a feature request?
Line Pouchard: Sourceforge bug tracking, sounds good, thanks.
Line Pouchard: Trish, yes I would like to.
Trish Whetzel: 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
Todd Schneider: 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.
Todd Schneider: 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
Todd Schneider: Ray, don't encourage the use of UML.
Peter P. Yim: @ALL: for everyone's information Michael Gruninger who champions our OOR-Metadata
workshop, is planning one on Dec-13 ... there is plan to invite Harold Solbrig (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
Mike Bennett: On notes and annotations, are the bioportal notes ontology items aligned with or
reusing concepts in SKOS that relate to notes?
Todd Schneider: Mike's query raises an interesting capability, the ability to sufficiently
distinguish the domains covered by a particular ontology repository (to support distributed
queries).
Todd Schneider: Carlos, did you want to ask Ray?
Carlos Rueda: My question is just about a topic already in the agenda: "how to extend BioPortal"
Trish Whetzel: 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
Peter P. Yim: great session ... thank you, Ray, Todd, Ken and All!
Peter P. Yim: -- session ended: 10:02am PST --
-- end of chat session --
- Further Question & Remarks - please post them to the [ oor-forum ] listserv
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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: Michael Grüninger - OOR/ConferenceCall_2011_12_13
- Call adjourned at: 10:02 am PST
--
notes taken by: Peter P. Yim / 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. Ray Fergerson & Mr. Peter P. Yim - Panelists: Professor Mark Musen (NCBO; Stanford), Dr. Natasha Noy (NCBO; Stanford), Dr. Trish Whetzel (NCBO; Stanford), Dr. Leo Obrst (OOR; MITRE), Professor Ken Baclawski (OOR; Northeastern U) & Dr. Todd Schneider (OOR; Raytheon) - OOR/ConferenceCall_2011_09_13
- 2010_09_17 - Friday: OOR Panel Discussion - "Getting OOR Development Going - Take-IV" Workshop - Co-chairs: Dr. Todd Schneider & Professor Michael Grüninger - Panelists: Dr. Todd Schneider (Raytheon), Mr. Mike Dean (Raytheon-BBN), Dr. Natasha Noy (NCBO, Stanford University), Dr. Immanuel Normann (Bremen University, BORG), Professor Ken Baclawski (Northeastern University), Professor Michael Grüninger (University of Toronto) - OOR/ConferenceCall_2010_09_17
- 2009_10_15 - Thursday: "OOR-BioPortal Comparative Analysis" panel discussion - Chair: Todd Schneider - Panelists: Natasha Noy, MichaelDorf, Ken Baclawski, Elisa Kendall & Mike Dean - ConferenceCall_2009_10_15
- 2009_07_30 - Thursday: Joint Ontolog-OOR Panel Discussion: "BioPortal and related Ontology Repository Implementations and Development" (Take-3) - Chair: Natasha Noy - Panelists: Carlos Rueda, Paul Alexander, John Graybeal, Mike Dean, StephenGranite, AlexGarcia, Ken Baclawski - 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: Todd Schneider; Panelists: Mark Musen, Natasha Noy, Mike Dean, Paul Buitelaar / Andreas Harth, Mathieu Daquin, Ken Baclawski, Michael Grüninger - ConferenceCall_2009_02_19
- 2008_08_22 - Friday: OOR Panel Discussion: "Getting OOR Development Off the Ground: Identifying Synergies & Gaps" (Take-1) - Chair: Leo Obrst; Panelists: Mike Dean, Mark Musen, Li Ding, Bruce Bargmeyer & Bill Andersen - 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 Ontology Summit 2008 - see: http://ontolog.cim3.net/cgi-bin/wiki.pl?OntologySummit2008/FaceToFaceAgenda#nid1BLS
- 2007_12_06 - Thursday: Invited Speaker - Professor Mark Musen: "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"
- 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 <oor-forum-join [at] ontolog.cim3.net> 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
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Conference Call Details
- Date: Tuesday, 29-Nov-2011
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Attendees
- Attended:
- Ken Baclawski (co-chair)
- Todd Schneider (co-chair)
- Ray Fergerson (discussant)
- Peter P. Yim (scribe)
- Gilberto Fragoso (NIH/NCI)
- Michael Riben
- Mike Dean
- Carlos Rueda
- YefimZhuk
- MyCoyne
- Brian Davis
- Deanna Marino
- Paul Courtney
- Trish Whetzel
- Line Pouchard
- Eric Chan
- Mike Bennett
- 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. ...
- Regrets: