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Joint NCBO-OOR Workshop: "BioPortal and OOR Synergies" - Tue 29-Nov-2011     (1)

Topic: "OOR Architecture & API Workshop-IX: BioPortal & OOR Synergies"     (1A)

Session Co-chairs: Professor KenBaclawski and Dr. ToddSchneider     (1B)

Discussant: Dr. Ray Fergerson [ slides ]     (1C)

Abstract     (1D)

Topic: "OOR Architecture & API Workshop-IX: BioPortal & OOR Synergies"     (1D1)

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.     (1D2)
The session will revolve around the following two subjects:     (1D3)
1. BioPortal - OOR Differences: Current & Future     (1D4)
2. How to extend BioPortal to meet OOR Goals     (1D5)

Agenda Proceedings     (1E)

1. Meeting called to order:     (1E5)

2. Roll Call:     (1E9)

3. Key items for review and discussion today:     (1E12)

Topic: "OOR Architecture & API Workshop-IX: BioPortal & OOR Synergies"     (1E13)

3.1 "BioPortal - OOR Differences: Current & Future" - (RayFergerson et al.)     (1E14)

3.2 "How to extend BioPortal to meet OOR Goals" - (All)     (1E15)

3.3 Discussion Notes     (1E17)

3.4 Transcript of the online chat during the session     (1E18)

see raw transcript here.     (1E19)

(for better clarity, the version below is a re-organized and lightly edited chat-transcript.)     (1E20)

Participants are welcome to make light edits to their own contributions as they see fit.     (1E21)

-- begin of chat session --     (1E22)

Joint NCBO-OOR Workshop: "BioPortal and OOR Synergies" - Tue 29-Nov-2011     (2)

Topic: "OOR Architecture & API Workshop-IX: BioPortal & OOR Synergies"     (2A)

Session Co-chairs: Professor Ken Baclawski and Dr. Todd Schneider     (2B)

Discussant: Dr. Ray Fergerson     (2C)

Phone keypad controls: To un-mute, press "*7" ... To mute, press "*6"     (2E)

Proceedings:     (2F)

anonymous morphed into Gilberto Fragoso     (2F1)

Mike Riben: mike riben listening in on skype     (2F2)

Mike Riben: not sure I have a mic     (2F3)

anonymous morphed into Carlos Rueda     (2F5)

anonymous morphed Deanna Marino     (2F6)

anonymous morphed into Paul Courtney     (2F7)

anonymous morphed into Trish Whetzel     (2F8)

Todd Schneider: For those not familiar with OOR requirements or goals, please ask.     (2F9)

Todd Schneider: OOR high level requirements: Storing, Management, Governance of Ontologies & Related     (2F10)

Items; Discovery / Searching Ontologies; Scalable (Parallelism, Federation); Multi-Language Support;     (2F11)

Arbitrary Knowledge Domain; Platform Independent     (2F12)

anonymous morphed into Line Pouchard     (2F13)

Line Pouchard: Q about searches: it seems that Boolean searches are not supported for term searches.     (2F14)

Are there plans to support this?     (2F15)

Line Pouchard: What does it take to make it a big requirement?     (2F16)

Trish Whetzel: Hi Line - would you like to submit this as a feature request?     (2F17)

Line Pouchard: Sourceforge bug tracking, sounds good, thanks.     (2F18)

Line Pouchard: Trish, yes I would like to.     (2F19)

Trish Whetzel: Ok, I'll submit this as a feature request and as Ray mentioned we'll get this into the     (2F20)

development cycle. If you come across any other feature requests or bug reports, feel free to send     (2F21)

these to our user support mailing list: support@bioontology.org     (2F22)

Todd Schneider: Eric, I see your 'hand' is up. Do you have a question for Ray?     (2F23)

Eric S. Chan: Do you consider using an ontology for reification of notes, discussions, reviews,     (2F24)

etc., that can be attached to the Biomedical Ontology? Peter Yim and I had suggested OASIS ICOM     (2F25)

reification of collaborative contents in OOR.     (2F27)

Todd Schneider: Eric, can we ask your question when Ray is done with his presentation?     (2F28)

Eric S. Chan: yes, I can ask the question during the Q/A     (2F29)

Todd Schneider: Ray, don't encourage the use of UML.     (2F30)

Peter P. Yim: @ALL: for everyone's information Michael Gruninger who champions our OOR-Metadata     (2F31)

workshop, is planning one on Dec-13 ... there is plan to invite Harold Solbrig (Mayo) over to talk     (2F32)

about their recent ontology metadata "crosswalk" study, which, among others, included OMV, CTS2. ...     (2F33)

Please mark your calendars ... we'll look forward to having you at the session on Tue 2011.12.13     (2F34)

Mike Bennett: On notes and annotations, are the bioportal notes ontology items aligned with or     (2F36)

reusing concepts in SKOS that relate to notes?     (2F37)

Todd Schneider: Mike's query raises an interesting capability, the ability to sufficiently     (2F38)

distinguish the domains covered by a particular ontology repository (to support distributed     (2F39)

queries).     (2F40)

Todd Schneider: Carlos, did you want to ask Ray?     (2F41)

Carlos Rueda: My question is just about a topic already in the agenda: "how to extend BioPortal"     (2F42)

Trish Whetzel: While not limited to ontology repositories, but geared more towards the content of     (2F43)

triple stores, there is an effort to catalog the contents of triple stores via the dbcatalog group,     (2F44)

Peter P. Yim: great session ... thank you, Ray, Todd, Ken and All!     (2F46)

Peter P. Yim: -- session ended: 10:02am PST --     (2F47)

-- end of chat session --     (2F48)

  • Further Question & Remarks - please post them to the [ oor-forum ] listserv     (2F49)
    • if you are already subscribed, post to <oor-forum [at] ontolog.cim3.net>     (2F49A)
    • (if you are not yet subscribed) you may subscribe yourself to the [ oor-forum ] listserv 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.     (2F49B)

4. Action items:     (2F50)

5. Any Other Business:     (2F51)

6. Schedule Next Meeting & Adjourn:     (2F52)

notes taken by: Peter P. Yim / 2011.11.29-___am PST     (2F56)

All participants, please review and edit to enhance accuracy and granularity of the documented proceedings.     (2F57)


Resources     (2G)


For the record ...     (2G22)

How To Join (while the session is in progress)     (2H)

  • Shared-screen support (VNC session), if applicable, will be started 5 minutes before the call at: http://vnc2.cim3.net:5800/     (2H4E)
    • view-only password: "ontolog"     (2H4E1)
    • 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.     (2H4E2)
    • people behind corporate firewalls may have difficulty accessing this. If that is the case, please download the slides (where applicable) and running them locally. The speaker(s) will prompt you to advance the slides during the talk.     (2H4E3)
    • instructions: once you got access to the page, click on the "settings" button, and identify yourself (by modifying the Name field from "anonymous" to your real name, like "JaneDoe").     (2H4F1)
    • 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.     (2H4F2)
    • 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) oor_20111129@soaphub.org ... Handy for mobile devices!     (2H4F3)
  • Discussions and Q & A:     (2H4G)
    • Nominally, when a presentation is in progress, the moderator will mute everyone, except for the speaker.     (2H4G1)
    • To un-mute, press "*7" ... To mute, press "*6" (please mute your phone, especially if you are in a noisy surrounding, or if you are introducing noise, echoes, etc. into the conference line.)     (2H4G2)
    • we will usually save all questions and discussions till after all presentations are through. You are encouraged to jot down questions onto the chat-area in the mean time (that way, they get documented; and you might even get some answers in the interim, through the chat.)     (2H4G3)
    • During the Q&A / discussion segment (when everyone is muted), If you want to speak or have questions or remarks to make, please raise your hand (virtually) by clicking on the "hand button" (lower right) on the chat session page. You may speak when acknowledged by the session moderator (again, press "*7" on your phone to un-mute). 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 "*6" on your phone to mute yourself after you are done speaking.)     (2H4G4)
  • 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.)     (2H4I)
  • 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.     (2H4K)

Attendees     (2I)

  • Expecting:     (2I2)
    • ... 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. ...     (2I3A)


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