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  • Value Sets
    • Would like LexEVS to support production of value sets with more rich structure. (to more efficiently assemble this deliverable)
    • 100K downloads from FTP site.  Fewer users use the browser to download the value sets.  
  • Mapping
    • On a mapping page, you can download an excel or cvs file.  
    • ie, chebi has mapping.  
    • For GDC - ICD9 or 10 coding - to be able to use NCIT coding, there needs to be way to translate between ICD9 and NCIT codes.  There currently isn't a good way to do that today.  
      • ie ICD9 - Brest cancer - corresponds to ABC in NCIT
      • Determine how such a map could be published (browser and LexEVS)
  • Other Services
    • IUPAC - there are 2 flavors to be considered - but can be managed.
    • HUGO - the slash and hyphens have been problematic, but have been mostly resolved in the NCI Browser.
    • Review of 4 identified searching issues (differences between results in LexEVS and Protege).
    • NGram tokenizers may provide solution if we implement an Expert System.

Decision Points:

  • Identify additional mapping requirements from the EVS Project group.
  • Investigate the use of
  • Revisit the mapping discussion during a future project meeting.
  • Consider and prioritize the expert system solution to support specialized search capabilities for complex chemical and genetic names. 
  • Review Investigate the usage of NGrams in Lucene to support specialized search.

 

TimeLocationTopicsParticipants
2:00 PM - 3:00 PM5E030

LexEVS Mapping Discussion

Determine requirements and propose solution for mapping.

  • User requirement: One terminology to many terminologies mapping.
  • Other topics:  Current, conditional, external relationships
 

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  • Investigate the MRMAP load and determine why that work wasn't completed.  Investigate the ability to capture non-synonymous

 

TimeLocationTopicsParticipants
3:00 PM - 4:30 PM5E030

Lucene Discussion

Propose additional features of Lucene to be used within LexEVS.

  • Discuss specialized search use cases.
  • Possible Lucene enhancements for coding scheme categorizations, auto complete aids, Lucene services.
 

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  • Investigate ability to use Lucene Facets and identify where it could be used. 
  • Investigate ability to design a usable auto complete and where it could be used.  

 

TimeLocationTopicsParticipantsResources
4:30 PM - 5:00 PM5E030

Overflow/Additional Topics

  

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TimeLocationTopicsParticipants
1:00 PM - 3:30 PM3W030

NCI Systems Discussions

  • Nexus Deployment Discussion
    • Current status of LexEVS artifacts on NCI Nexus server
    • Discuss current technical challenges.
  • CI and Docker Status/Roadmap
    • Discuss the current status of the Docker scripts used to build/test LexEVS components.
    • Discuss NCI's current status and future plans to use Docker.
    • Discuss security challenges associated with NCI's environment and Docker.
  • Discuss a separate DEV environment for CI server deployment
  • Tech Stack Upgrades
    • Discuss DB upgrade: 
      • MySQL 5.6 vs. MariaDB (10.1 Supported 2017.01)
    • Discuss CentOS 7 upgrade
  • Tier Deployment testing responsibilities
    • Mayo development team responsibilities
    • NCI development team responsibilities

Sara, Shireesha, Phil

 

 

Jacob, Yeon (Systems Team)

Attendees:  Larry, Sherri, Rob, Tracy, Jacob, Sarah, Scott, Cory, Craig, Kwan, Yeon, Sherri, Tin, Sana, Shireseha, Jason

Discussion Points:

Nexus Server Configuration

  • Testing on DEV tier - config of security permissions
  • Manual publishing until configured
  • CTS2 - Maven build was the simplest case, so that's the focus.
  • ANT publishing not currently available.  Will need to look at public and private key possibilities.  Sara's team should be able to support. (LexEVS requires ANT build).

Tech Stack Updates

  • DB
    • Currently at 5.5 
    • Tech stack is moving to 5.6 and migration has started. 
    • Preliminary tests show that we can support 5.6.
    • 5.6.33 is the current version.  Yeon can update each tier for EVS team.
    • No plan for 5.7, but MarieDB (in 6 months to year)
    • Need to move to 5.6 as soon as we can.
  • CentOS 7
    • LexEVS is ready to upgrade to CentOS 7
    • CentOS 7 is available.
    • Blade servers would need to be ordered or current blades would need to be re-imaged.
    • May be able to shuffle the upgrade and swap servers so it moves up.  
  • Java 1.8
    • LexEVS is ready with 1.8
    • Waiting on other tooling to support 1.8

Dev Environment

  • Set up secondary Dev instance for Jenkins and application servers.  
  • Need to consider what database connection is needed. 
  • Suggested - set up a VM for this Dev 
  • Can submit tickets to Jacob to get this started.  

Docker and CI Discussion

  • Overview of Mayo usage and configuration.
    • NCI uses Jenkins 2.19
    • Docker differences between what NCI has and Mac version.
    • Would require move from Ubuntu.  
    • Image repository not ready, testing Nexus 3.x for Docker Image Storage.  
  • NCI can support Docker configuration. 
  • Need to negotiate timelines.  

Decision Points:

  • Plan to migrate to 5.6.33 as soon as possible.
  • Plan to migrate to CentOS7 (work with Jacob).
  • Plan configuration of DEV instance (work with Jacob).
  • Plan to further investigate Docker configuration. (with Kwan)

 

TimeLocationTopicsParticipants
3:30 PM - 4:00 PM3W030

FHIR and terminology services (CTS2)

  • Harold to provide update on CTS2 and FHIR.
Harold

Attendees: Tin, Jason, Rob, Tracy, Scott, Craig, Cory, Larry, Sherri, Harold, Gilberto

Discussion Points:

  • Harold noted that the OMG process stalled by no further participation by Mayo.
  • Remaining issues:
    • SOAP WSDL
    • Miscellaneous issues
  • Additional Features:
    • Columnar Format
    • Cannonical RDF
    • SNOMED CT implementation guide 
  • FHIR and CTS2 are similar in that both are complex but much is not required - only use what you need.
  • Clinical Research and Biomedical informatics groups are taking note of FHIR and beginning participation in FHIR.
  • FHIR Terminology - possible integration of CTS2 services. 
  • Grahm Grieve (HL7 FHIR) is in support of CTS2 services for FHIR.  
  • Current Planning
    • Plan on implementing entity description in native FHIR to demonstrate the differences and begin discussing with the FHIR community.
    • Review FHIR terminology and CTS2 terminology to describe overlap and gaps.  A paper will be written and published.  
  • Other project - CIMI HSP - Determined that CTS2 wasn't a candidate for services.
  • FHIR does offer:
    • Provides extensibility
    • Not to be fully implemented.
  • HL7 and OMG HSSP process was not successful in that the standard wasn't successfully integrated back to HL7.
  • A better model would have been what FHIR is doing within HL7 - collaborative within HL7.  
  • Harold to be at the January HL7 meeting to listen in on the FHIR sessions.  

Decision Points:

 

TimeLocationTopicsParticipants
4:00 PM - 5:00 PM3W030

OWL Restrictions in LexGrid Model

  • Discuss approach and propose additional features.
  • Determine if there are LexEVS model changes needed.
  • Loader considerations.
  • Additional problems and solutions
 

Attendees:  Larry, Sherri, Jason, Rob, Tracy, Cory, Scott, Craig, Harold, Gilberto, Kim

Discussion Points:

  • Much of OWL2 is similar to OWL1.
  • OWL2 includes property chains, but thy aren't being used.
  • The entire semantic meaning in LexEVS isn't required for OWL2.  For example, reasoners would use OWL2 source - not out of a terminology server. 
  • There is no requirement to include additional OWL2 representation in LexEVS.  Instead, use triple store and expand RESTful services.  
  • Current OWL2 issues have been resolved.  
  • Need to revisit the OBO JIRA item - and close it. 

Decision Points:

  • No additional OWL2 representation needed in LexEVS.
  • Review OBO JIRA issue and resolve.

 

TimeLocationTopicsParticipants
5:00 PM - 5:30 PM3W030

Overflow/Additional Topics

 

Attendees:   Larry, Sherri, Jason, Rob, Tracy, Cory, Scott, Craig, Harold, Gilberto, Kim

Discussion Points:

  • Browser issue - search issue when value sets don't return content.  
  • Noted that QA could be done in Protege before publishing
  • Value Set Loader should not load a value set with no content.  

Decision Points:

  • Create JIRA item Implement fix for Value Set Loader and link to the browser issueto not load value set with no content.  

Friday, December 2nd, 2016

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