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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

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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

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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


Date

Tuesday, December 8 - Thursday, December 10, 2015

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

 

  

Tuesday, December 8

  
TimeLocationTopics

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  • Do we need to coordinate LexEVS and tools updates?
  • Are there updates other than Java 8 to plan now?

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  • 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
  • End user approach to LexEVS
    • Tutorial on how to query the LexEVS API
    • Review of existing LexEVS documentation

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ParticipantsResources
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
 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

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  •  Discuss a REST Framework that includes CTS2 and other calls (extensions)
  •  CTS2 REST vs additional (extensions) REST calls like bulk download  
    • 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
 2:00 PM - 4:00 PM

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

  
TimeLocationTopicsParticipantsResources
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 - 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)
  • 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

  
TimeLocationTopicsParticipantsResources
9:00 AM - 9:30 AM

6E030

Recap and Planning  
9:30 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
  

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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  • Issues with OWL2, MeDRA and HL7.
  • Tutorial/education on creating and using loaders.

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Horizontal Coding Scheme searches 

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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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