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Date/Time: Thursday, December 15, 2011; 10-11 AM ET

Attendees

Brian Davis, Sherri de Coronado, Sharron Lewis, Stuart Turner, Larry Wright

Agenda

  • Upcoming Meeting? Cancel 29th?
  • OOR Update – Brian Davis (5 min)
  • Discuss the issue and solution(s) between terminology versions – Sherri de Coronado and Troy Bleek(10 min)
  • Review of list of instances of BioPortal and discussion of issues and next- Trish Whetzel (15 min)
  • Discuss “RoadShow” Use Case feedback (ICR WS and CTMS WS)- Brian Davis and Sharron Lewis (10 min)
  • Action Item Review (5 min)

Assigned To

Description

Due Date

Trish Whetzel

Find out about the federation then we can maybe find out the actual people using it instead of just downloading.

12/15/2011

Sherri de Coronado

Why there might be problems with federation issues

12/15/2011

Sharron Lewis

Ask the WS Faciltators for a list of possible Use Cases from their community

12/22/2011

Sherri and Troy

Come up with a list issues

12/15/2011

Notes

OOR Update

  • Last thurs (12/8) discussed Ontolog Summit theme About 25 people on the call (including Barry Smith and Mike Riben)
    • March/April, 2011 at NIST, Gaithersburg MD
    • Culminates in a 2-day Ontology Summit Workshop & Symposium (supporting both face-to-face & virtual participation)
    • There were two seperate tracks they were thinking about discussing - Solutions for systems Engineering or Enineering Big Data
    • Ontology: Solutions for Systems Engineering
    • alt1: Tackling Real System Engineering Problems with Ontology
    • alt2: Tackling Real Systems Engineering Problems
    • alt3: Ontology: Engineering Systems of the Future
    • Ontology: Engineering Big Data
    • alt1: Ontology: Throwing a lifeline to Big Data
    • alt2: Making Sense of Big Data
    • Maybe a combination of both Ontology in “Complex Systems”
    • Discussion around whether to be broad (Ontologies as part of enterprise system) or immediate solution oritented (How it can solve some problem with topical “Big Data”)
  • Tuesday Dec 13:
    • 1. Thanks to all the people who contributed to make this happen - folks from NCBO/Stanford, CIM3, NEU, Raytheon-BBN, ... etc. - the upgraded instance of the OOR Sandbox is now online at:http://oor-03.cim3.net/
    • 2. The team will continue to do various customization and testing, through the rest of this month, and is expected to start with a "content drive" once we return from the Holidays ... to get everyone to upload ontologies (back) in to the OOR sandbox again.

Any people who wants to help with the testing are welcome to do so too (if you are willing to to patient, and to provide feedback on any irregularities that you have discovered in the mean time.) ... So, get ready to upload your ontologies to the upgraded OOR!

  • Q Is that the newest version of the BIOPortal?
  • A I am not sure but we can ask - OWL can't do common logic - that was a point they made

Discuss the issue and solution(s) between terminology versions

  • Beyond the scope of this group to figure out the federation and let the OOR figure it out - Sherri thinks it requires the same set of software - our scope should be to figure out the metadata.
  • We realized that we really need the input from Harold.
  • NCi has a significant number of terminiologies - so the moment the metadata we have is incompatible in format not the same.
  • If we want to standardization its not yet in the OMB plus format and another issue will reside in the BKC table- It's possible that we could pull all the NCBO and Lexevs and put it in a set of tables if that makes any since to do- not 100% if that is the best thing to do - NcBO have over lapping terms
  • The interest is registry versus repository - a true repository would be checking in and checking out
  • Repository vs registry is a big challenge - wherever the ontologies will reside unless they build somewhere new.
  • BKC primary function is a registry
  • Getting a registry a usable - one that is being shared and updated is a big win - reliable registry will have it to point to where it may reside-
  • I think that is as far we can go -
  • We dont have it today
  • Q Are their standsards that surround a registry and repository?
  • A I don't think so- a Registry is one that subscribes. A repoistory would have much more detail.
  • Q Does the OMV prestandards make a distinction in their write ups? just looking for an authoritative source- can we point somewhere?
  • A I don't think there is one but maybe we can look for one.
  • A Registry is dynamic so it should provide current information. The distinction is what we are federating and be clear on the immediate goals.
  • Q Do you have anys senseof where OOR is or have a stable instance
  • A No they are still tryng to figure out what fits in the vision and what doesn't.Thats why they were excited aobut to Ray Ferguson.
  • A They are focused on the formats on Ontologies- allow people to not upload anything until its in OWl and mapping. No action plans or timelines.
  • Don't know if any terminologies that is common logic - that is probably very small - In the future this is going to be important
  • There is probably some industrial use - using common logic - Dont think that anyone is using large ontologies in it..
  • The registry can actually use everything

Discuss “RoadShow” Use Case feedback (ICR WS and CTMS WS)

  • During the past week about the topic of the roadshow and how to present it to people and finding out what they need and trying
    to find solutions for them - Stuart think that there is a way to identify something in the middle.
  • If your going to WG meetings try to find more interest in Ontologies and have it describe the best they can.
  • In the past John Speakman gave useful comments - in the past they would ask how would you used vocabularies and that some people were like "what"?
  • We need to imbeded in almost of activities - to be able to answer the questions whey they come up but it is labor intensive and can't attend all meetings.
  • Elaine and ICR:
    • Distinguish between “Scientific End user and Bioinformaticists” (maybe Human Semantics vs. Machine Semantics)
    • ICR has prob of getting to “scientific end users” too
    • Probably not right audience at ICR WS meetings: investigate new ones?
    • Some of the questions seem right on (validation)
  • Ken Wiley CTMS and Kimberly Baldwin, CDL
    • Distinguish between clinical end user and medical Informaticist.
    • CTMS WS has a problem separating clinical end users and medical Informaticists., too.
    • Only some questions seem relevant (they don’t consider 1000’s, they know where to start)
    • Story of “club” do as others, narrow filed
    • But “differences, pros and cons of that narrow field seems very important”
    • Other, more granular concerns could come from CDLs
    • They will think of possible people to interact with directly.
  • The registry could serve as a middle layer - and could present the information in a central way to serve as a mapping.
  • Unless you know you going to know when you are going deploy and the timeline - there is a lot of uncertainty
  • Before building middleware, I'm sure we have to straighten out things with LexEVS before we can build new software
  • I don't think we have the resources at the time
  • AI - We start thinking and planning and writing for registry terminilogy and repository terminology -Then we can see if can satisfy some individuals needs with the registry
  • We need to go talk to the liaison of these Workspaces to get use cases and then post them for crowd peer review to see what comments and responses they have
  • Q Should we have a meeting next week?
  • AI - Sharron will send out an email on Tuesday to verify the people attending the meeting.

Action Items

Assigned To

Description

Due Date

Trish Whetzel

Find out about the federation then we can maybe find out the actual people using it instead of just downloading.

1/05/2012

Sherri de Coronado

Why there might be problems with federation- talk to Harold

1/5/2012

Sharron Lewis

Ask the WS Faciltators for a list of possible Use Cases from their community (Imaging and TBPT)

12/23/2011

ORWG

Start thinking and planning and writing for registry terminology and repository terminology -Then we can see if can satisfy some individuals needs with the registry

Ongoing

Sharron Lewis

Will send out an email on Tuesday to verify the people attending the meeting

12/22/2011

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