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Panel
titleDocument Information

Author:  Craig Stancl, Scott Bauer, Cory Endle
Email:  Stancl.craig@mayo.edu, bauer.scott@mayo.edu, endle.cory@mayo.edu
Team:  LexEVS
Contract:   S13-500 MOD4
Client:  NCI CBIIT
National Institutes of Heath
US Department of Health and Human Services

...

December Face-to-Face (December 8 - 10, 2015)

Meeting Details

NCI Shady Grove Campus
9609 Medical Center Drive
Rockville, MD 20850
http://www.cancer.gov/about-nci/visit

Rooms:

Day 1  (8-1): 08-Dec-2015 08:00 AM - 01:00 PM  1W030
Day 1  (1-5): 08-Dec-2015 01:00 PM - 05:00 PM  4W030

Day 2       : 09-Dec-2015 08:00 AM - 05:00 PM  2E914

Day 3 (8-12): 10-Dec-2015 08:00 AM - 12:00 PM  6E030
Day 3 (12-5): 10-Dec-2015 12:00 PM - 05:00 PM  1W030

Conference Details
 1-866-660-5416 # 2398515  
 

WebEx by Day:

Topic: Mayo-NCI EVS F2F Day 1 (Monday)
Date and Time:
Tuesday, December 8, 2015 8:00 am, Eastern Standard Time (New York, GMT-05:00)
Event number: 315 782 024
Event password: 4NCI-new
Panelist password: The Event has no Panelist Password
Host key: 317579 (Use this to reclaim host privileges.)
Event address for attendees: https://cbiit.webex.com/cbiit/onstage/g.php?d=315782024&t=a
Event address for panelists: https://cbiit.webex.com/cbiit/onstage/g.php?d=315782024&t=p

Topic: Mayo-NCI EVS F2F Day 2 (Tuesday)
Date and Time:
Wednesday, December 9, 2015 8:00 am, Eastern Standard Time (New York, GMT-05:00)
Event number: 318 104 865
Event password: 4NCI-new
Panelist password: The Event has no Panelist Password
Host key: 149718 (Use this to reclaim host privileges.)
Event address for attendees: https://cbiit.webex.com/cbiit/onstage/g.php?d=318104865&t=a
Event address for panelists: https://cbiit.webex.com/cbiit/onstage/g.php?d=318104865&t=p

Topic: Mayo-NCI EVS F2F Day 3 (Wednesday)
Date and Time:
Thursday, December 10, 2015 8:00 am, Eastern Standard Time (New York, GMT-05:00)
Event number: 313 684 532
Event password: 4NCI-new
Panelist password: The Event has no Panelist Password
Host key: 914157 (Use this to reclaim host privileges.)
Event address for attendees: https://cbiit.webex.com/cbiit/onstage/g.php?d=313684532&t=a
Event address for panelists: https://cbiit.webex.com/cbiit/onstage/g.php?d=313684532&t=p


Attendees

NameRoleAttend? (Y/N)

Wright, Larry

NIH/NCI  

 Y

Fragoso, Gilberto

NIH/NCI    

 Y

De Coronado, Sherri    

NIH/NCI   

 Y

Safran, Tracy

NIH/NCI   

 		Y

Ong, Kim L

IS

 Y

Lucas, Jason R

IS

 Y

Bauer, Scott  

Mayo

Y

Stancl, Craig

Mayo

Y

Endle,  Cory

Mayo

Y 

Wynne, Robert    

NIH/NCI

 Y

Tran, Tin    

NIH/NCI [C]

 Y

Carlsen, Brian

(NIH/NCI) [C]

 

Wong, Joanne 

  

Kuntipuram, Kumar

  

Meeting Notes

2015.12 Technical Face-To-Face Meeting Notes

2015.12 Technical Face-To-Face Prioritization List

Agenda

 

 

Discussion: Triple Store/Graph Database

  • NCI to provide requirements/use cases 
  • Discuss plans based on Triple Store Capability Research and Analysis wiki pages
  • Demo of ArangoDB (https://www.arangodb.com/)
    •   
      

    Tuesday, December 8

    		  
    TimeLocationTopicsParticipantsNotesResources
    9:00 AM - 9:30 AM

    1W030

    		Overview and Planning  

    Discussion: Deployment Process

  • DevOps and continuous integration
  • Changes for build, deployment and distribution
    • Mayo's continuous integration server    		  
    9:30 AM - Noon

    1W030

    		 

    Discussion: Tech Stack Updates

    • Migration to Java 8
    • Migration to centOS 7
    • Migration to Spring 4
    		    
    • Determine next steps/roadmap
    		  
      

    Discussion: The Future of lbGUI

    • Discuss future requirements
    • Review issues - JIRA and others
    • Develop a roadmap to address technical debt
    		  
      

    Discussion: Value Set Editor (Authoring)

    • NCI to provide requirements/use cases
    		  
      

    Discussion: LEXEVS Loader Improvements

    • Discuss known issues for OWL2, MeDRA and HL7 Loaders
    • Determine next steps/roadmap
    		  
      

    Discussion: Horizontal Coding Scheme Searches

    • NCI to provide requirements/use cases
    		  
      

    Discussion: Cloud Support

    • NCI to provide requirements/use cases for supporting a cloud environment
    		  2015.12 - NCI F2F - Tech Stack.pptx
      

    Discussion: LEXEVS API/Browser Performance and Usability Improvements

    • NCI to provide requirements/use cases
    • Areas for discussion:
      • value set
      • mapping 
      • multi-namespace
      • relationship querying
      • inferred data
    • Discuss the removal of caCORE and refactor Remote API
    • Determine next steps/roadmap
    		 2015.12 - NCI F2F - LEXEVS API:Browser Performance and Usability Improvements.pptx
    Noon - 1:00 PM LunchAll  
    1:00 PM - 2:00 PM

    4W030

    Discussion: Enhancing the LEXEVS CTS2 REST Interface

    • NCI to provide requirements/use cases
    • Areas for discussion:
      • Expanding to include Associations
      • Specialized REST calls (e.g., bulk download) to CTS2 service framework
      • Provide the capability to use data from one endpoint to query another
      • Provide a framework that includes both CTS2 and Extensions
      • Bulk downloads/special user requirements
    • Determine next steps/roadmap
    		  2015.12 - NCI F2F - CTS2 API Notes.pptx
     212:00 PM - 14:00 PM LunchAll 
         

    4W030

    Information Session: Using LexEVS Query API and CTS2 API

    • Overview to demonstrate how to query using LexEVS APIs
    • Review of existing LexEVS API documentation
    • Open discussion - specific use cases
    		 2015.12 - NCI F2F - Using LexEVS Query API and CTS2 API .pptx
    4:00 PM - 5:00 PM4W030Overflow/Additional Topics     
      

    Wednesday, December 9

    		  
    TimeLocationTopicsParticipantsNotes
         
    Resources
    8:00 AM - 9:00 AM2E914Discussion: Review Lucene

    Kim Ong
    Scott Bauer 

    		 
    9:00 AM - 9:30 AM

    2E914

    		Recap and Planning  
    9:30AM - Noon

    2E914

    Discussion: Coding Scheme Search and Indexing

    • Determine requirements/use cases for horizontal coding scheme searches
    • Overview of indexing of qualifiers
    • Overview of search results in 6.4
    		 2015.12 - NCI F2F - Coding Scheme Search and Indexing.pptx
      

    Discussion: LEXEVS Loader Improvements

    • Discuss known issues for OWL2, MedDRA and HL7 Loaders
    • Other loader improvements
    • Determine next steps/roadmap
    		 2015.12 - NCI F2F - LexEVS Loader Improvements.pptx
    Noon 12:00 PM - 1:00 PM LunchAll 
    1:00 PM - 1:30 PM2E914

    EVS Tools (LexEVS & EVS Focus) Meeting

    • Open topics
    		  
    1:30 PM - 4:00 PM 

    2E914

    Tutorial/Discussion: Loader Implementation and Requirements

    • Overview of LexEVS Loader development process
    • Implement a simple LexEVS loader (hands-on)
    • Review existing loaders and identify where changes could be made
    		  
      

    Tutorial: End User Usage of LexEVS Query API

    •  Overview to demonstrate how to query using LexEVS API
    •  Review of existing LexEVS API documentation
    		  
    • Discussion of entry points into various loaders for purposes of updating
    • Discuss automating data loads and customization 

    Tracy
    Rob
    Kim 

     

    2015.12 - NCI F2F - Loader Tutorial.pptx

    2015.12 - NCI F2F - Tutorial Env Set Up.pptx

    4:00 PM - 5:00 PM2E914Overflow/Additional Topics   
       

    Thursday, December 10

    		  
    TimeLocationTopicsParticipantsNotesResources
    9:00 AM - 9:30 AM

    6E030

    		Recap and Planning     
    129:00 PM - 1:00 PM LunchAll    30 AM - Noon

    6E030

    Discussion: Triple Store/Graph Database

    		 2015.12 - NCI F2F - Triple Store:Graph Database.pptx
        

     

    Discussion: Cloud Considerations

    • NCI to provide requirements/use cases for supporting a cloud environment
    		 2015.12 - NCI F2F - Cloud Considerations.pptx
     
      

    Topics

     

    • Tech stack updates, esp. Java 8
      • Do we need to coordinate LexEVS and tools updates?
      • Are there updates other than Java 8 to plan now?
      • Need to invite Jacob to tech stack related meetings.
      • Discuss update potentially updating Spring to version 4.
    • Development process
      • Changes to build and distribution process
      • DevOps and CI: How Mayo implemented their CI server and what NCI's plan is for their own server.
      • Loaders
        • how to create one from scratch
        • Create a simple example of a loader
        • Point out places in code where simple updates can be made for different loaders. 
      • End user approach to LexEVS
        • Tutorial on how to query the LexEVS API
        • Review of existing LexEVS documentation
    • CTS2 REST services 
      • Expand to include associations?
      • Relationship of specialized REST calls (e.g., bulk download) to CTS2 service framework.
      • Discussion about one client should be able to connect to multiple instances of a service.  Can one endpoint provide data to query against another?  How can CTS2 be used in a manner that provides uri's that are not a part of the local resources.
      • Future uses/extensions of resolver
        •  Discuss a REST Framework that includes CTS2 and other calls (extensions)
        •  CTS2 REST vs additional (extensions) REST calls like bulk download  
    • Loaders
      • Issues with OWL2, MeDRA and HL7.
      • Tutorial/education on creating and using loaders.
    • GUI updates
    • RDF Triple Store or graph database LexEVS backing
    • End-user Value Set editor
    • Model updates to support additional Value Set functionality

    • Horizontal Coding Scheme searches 

    • Browser/LexEVS performance

    • Optional Tasks (from SOW, for reference):

     

      • LEXEVS API Performance and Usability Improvements

     

    LEXEVS API performance and usability will be a major focus area for this effort.   EVS and other users have hit a number of bugs and missing features that significantly affect the usability of the APIs, with special effort needed to improve value set, mapping, multi-namespace support as well as querying of relationship and inferred data.

     

    Active LEXEVS support in all indicated areas is important to the quality and efficiency of ongoing EVS operations and services, and to the growing community of LEXEVS adopters for whom it provides a shared conceptual and technical terminology model supporting community standards and interoperability.

     

      • LEXEVS Loader Improvements

     

    The subcontractor shall address LEXEVS Loader Improvements.  The LEXEVS Loaders are a set of Java programs and configuration files that transform and load terminology data from the various file formats and source terminology data structures into the unified LEXEVS server data model.  They are crucial to data access and quality, and a top priority for the current effort.  Key areas of effort are improving and extending loaders to better handle current and new sources and formats, and improved documentation and error handling.

     

      • Enhancing the LEXEVS CTS2 REST Interface

     

    The subcontractor shall address improvements to the CTS2 REST API and related resources.  The previously existing REST API was created as a prototype to prove that such an interface will have value.  It succeeded in that task.  Unfortunately, that older API is tied very closely to the underlying structure of the data rather than being tied to the usage of the data.  This effort will extend the new CTS2 API, tools and documentation to fill gaps in coverage of the CTS2 REST specification and focus on the user of the API, providing them with a clean, complete API that is easier to use than the current heavyweight solution.

     

      • Cloud Support

     

    The subcontractor will address the deployment, customization and maintenance of cloud-based LEXEVS services in order to address the challenges associated with the growth of biomedical research data, and the computational limitations currently experienced by biomedical researchers.

     

     

     

    Discussion: Build and Deployment Process

    • DevOps and continuous integration
    • Changes for build, deployment and distribution
      • Changes to support 6.4
      • Considerations for Triple Store/Graph DB
      • Considerations for Cloud Infrastructure
    • Mayo's continuous integration server
    • Demo of Docker
    • Determine next steps/roadmap
    		 2015.12 - NCI F2F - Build and Deployment Process.pptx
    Noon - 1:00 PM LunchAll 
    1:00 PM - 3:00 PM

    1W030

    Discussion: Value Set Editor (Authoring)

    • NCI to provide requirements/use cases
    		 2015.12 - NCI F2F - Value Set Editor.pptx
     

     

    Discussion: The Future of lbGUI

    • Discuss future requirements
    • Review issues - JIRA and others
    • Develop a roadmap to address technical debt
    • Determine next steps/roadmap
    		 2015.12 - NCI F2F - lbGUI.pptx
    3:00 PM - 5:00 PM

    1W030

    Debrief

    • Prioritize
    • Determine next steps/roadmap
    		  

     

     

     

     

     

     

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