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Document 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

Contents of this Page

The purpose of this document is to document the technical face to face meeting details between the NCI and Mayo for the National Cancer Institute Center for Biomedical Informatics and Information Technology (NCI CBIIT) LexEVS Release 6.3 and LexEVS Release 6.4.

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

Conference Details
1-866-660-5416 # 2398515  
Join WebEx meeting   
Meeting number: 732 008 454  
Meeting password: 4NCI-new  

Attendees

NameRoleAttend? (Y/N)

Wright, Larry

NIH/NCI  

 

Fragoso, Gilberto

NIH/NCI    

 

De Coronado, Sherri    

NIH/NCI   

 

Safran, Tracy

NIH/NCI   

 

Ong, Kim L

IS

 

Lucas, Jason R

IS

 

Bauer, Scott  

Mayo

Y

Stancl, Craig

Mayo

Y

Endle,  Cory

Mayo

Y 

Wynne, Robert    

NIH/NCI

 

Tran, Tin    

NIH/NCI [C]

 

Carlsen, Brian

(NIH/NCI) [C]

 

Wong, Joanne 

  

Kuntipuram, Kumar

  


Agenda

 

  

Tuesday, December 8

  
TimeLocationTopicsParticipantsNotes
9:00 AM - 9:30 AM

1W030

Overview and Planning  
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: 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
  • Determine next steps/roadmap
  
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
  
 2:00 PM - 4:00 PM

4W030

Information Session: End User Usage of LexEVS Query API

  • Overview to demonstrate how to query using LexEVS API
  • Review of existing LexEVS API documentation
  • Open discussion - specific usecases
  
4:00 PM - 5:00 PM4W030Overflow/Additional Topics  
  

Wednesday, December 9

  
TimeLocationTopicsParticipantsNotes
9:00 AM - 9:30 AM

2E914

Recap and Planning  
9:30AM - Noon

2E914

Discussion: Coding Scheme Search and Indexing

  • Determine requirements/usecases for horizontal coding scheme searches
  • Overview of indexing of qualifiers
  • Overview of search results in 6.4
  
  

Discussion: LEXEVS Loader Improvements

  • Discuss known issues for OWL2, MeDRA and HL7 Loaders
  • Determine next steps/roadmap
  
Noon - 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: Loader Implementation

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

Tracy
Rob
 

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

Thursday, December 10

  
TimeLocationTopicsParticipantsNotes
9:00 AM - 9:30 AM

6E030

Recap and Planning  
9:30 AM - Noon

6E030

Discussion: Triple Store/Graph Database

  
  

Discussion: Cloud Considerations

  • NCI to provide requirements/use cases for supporting a cloud environment
  
  

Discussion: Build and Deployment Process

  • DevOps and continuous integration
  • Changes for build, deployment and distribution
    • Changes to support 6.4
    • Triple Store/Graph DB
    • Cloud Infrastructure
  • Mayo's continuous integration server
  • Determine next steps/roadmap
  
Noon - 1:00 PM LunchAll 
1:00 PM - 3:00 PM

1W030

Discussion: Value Set Editor (Authoring)

  • NCI to provide requirements/use cases
  
 

 

Discussion: The Future of lbGUI

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

1W030

Debrief

  • Prioritize
  • Determine next steps/roadmap
  

 

 

 

 

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.

 

 

  

 

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