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Page History
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- caDSR Team represented by Sima, Natalia, Vikram
- caDSR Applications that use EVS
- Sentinel - Alerts for concepts, job that does concept clean up (compares concepts)
- Curation tooling - links to concepts, and search results.
- CDE Browser - Concepts used from search results.
- Semantic integration workbench - concepts used from search results
- CDEs
- Utilize the NCIT, NCI meta,
- Look into NCIT - will use the concept to describe the CDE.
- Organizing concepts to build CDE terminology.
- CDEs are used for forms (permissible values on forms)
- Tooling hasn't changed or been replaced.
- Currently use JARS and put in /lib
- Using Remote API today.
- Recently removed EJB
- Need to consider architecture in the future.
- MDR is planning to architect a solution moving forward.
- Currently searches are restricted to preferred terms.
- Building data element - definitional information, preferred name
- Existing CDE - pull back perferred name.
- Current Tooling Issues
- Need to have a data load completed to PROD.
- Confirmed data load and ready once things move to production.
- New LexEVS Jars will be included in next release.
- Remote API Architecture
- Issues
- Replacement of JARS
- Serialization of objects.
- Issues
- Proposed Architecture?
- REST-ful API
Decision Points:
- Identify current JAVA API usage by caDSR caDSR to provide list of what is currently used in the Java API
- EVS team to provide feedback as to how to do things better.
- EVS team to ensure that if REST-ful API is created, functionality to be prioritized.
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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.
| Time | Location | Topics | Participants |
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| 2:00 PM - 3:00 PM | 5E030 | LexEVS Mapping DiscussionDetermine requirements and propose solution for mapping.
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- Investigate the MRMAP load and determine why that work wasn't completed.
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| Time | Location |
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| Time | Location | Topics | Participants |
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| 3:00 PM - 4:30 PM | 5E030 | Lucene DiscussionPropose additional features of Lucene to be used within LexEVS.
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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.
| Time | Location | Topics | Participants | Resources |
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| 4:30 PM - 5:00 PM | 5E030 | Overflow/Additional Topics |
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| Time | Location | Topics | Participants |
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| 1:00 PM - 3:30 PM | 3W030 | NCI Systems Discussions
| Sara, Shireesha, Phil
Jacob, Yeon (Systems Team) |
Attendees: Larry, Sherri, Rob, Tracy, Jacob, Sarah, Scott, Cory, Craig, Kwan, Yeon, Sherri, Tin, Sana, ShireshaShireseha, 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
Decision Points:
- 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.
| Time | Location | Topics | Participants |
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| Time | Location | Topics | Participants |
|---|---|---|---|
| 3:30 PM - 4:00 PM | 3W030 | FHIR and terminology services (CTS2)
| Harold |
Attendees:
Discussion Points:
Decision Points:
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:
Discussion Points:
Decision Points:
Overflow/Additional Topics
Attendees:
Discussion Points:
Decision Points:
Friday, December 2nd, 2016
Topic:
Attendees:
Discussion Points:
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:
| Time | Location | Topics | Participants |
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| 4:00 |
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| 5:00 |
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| PM |
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| 3W030 | OWL Restrictions in LexGrid Model |
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- GUI
- Consider a web based tool. A simple way to look at the data.
- Command Line loader requirements
- Other considerations
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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.
| Time | Location | Topics | Participants |
|---|---|---|---|
| 5:00 PM - 5:30 PM | 3W030 | 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:
- Implement fix for Value Set Loader to not load value set with no content.
Jira server NCI Tracker serverId 7954a81f-12da-3366-a0ef-97c806660e7c key LEXEVS-2510
Friday, December 2nd, 2016
| Time | Location | Topics | Participants |
|---|---|---|---|
| 9:00 AM - 10:00 AM | 1W030 | LexEVS AdminDiscuss current and future requirements.
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Attendees: Larry, Rob, Tracy, Cory, Craig, Scott, Tin
Discussion Points:
- Ability to look at data in a graphical way would be important.
- Command Line usage - List Schemes - can return 700+, so prefer to use the UI.
- Usage of the UI for troubleshooting to review the data in the database.
- Minimal ability to look at data would be preferred (fully graphical is not required)
- Administrative tasks not required in the GUI (only in the cmd line tooling)
- Ability to load metadata at the same time as the load.
- Web based tool.
- We need to replace based on functionality used by Browser
- graphical hierarchy representation (tree extension?)
- Optimal or best practice as an alternative
- providing code snippets for end users as options
- Secure any admin code (Loading, changing code systems) on a web based gui is a concern
- Could be potentially be used as a browser for technical users on an NCI Production server (Discussed)
- There is a request for admin ability for editing the preferences and manifest.
- Currently, there is no way to view what metadata is loaded.
- Investigate ability to combine data from the metadata and manifest files into one file.
- This would make administration/loading easier.
- Post load options may be an issue.
- History loader creates multiple errors when loading - there is an existing JIRA item.
- May be caused by DB timeout.
- Investigate what is causing.
- LG xml Loader is used to load maps. However, it doesn't take in account of the type of maps (it could). Not sure the rankings can be applied.
- No existing issues, but may find some loading additional maps
- SY relationships and Ranking are provided.
- Monthly changes are applied.
- GUI Performance during x-forwarding noted by Rob.
- File system preferences - lock?
- UI is good for Tagging to Production
- UI is good for Removing a Coding Scheme
- Listing Schemes in CMD - ListSchemes.sh - formatting is limited to column width.
- Default, do not show entire width.
- Minimailly add 10 chars to URL
- Minimally add 5 chars to Versions
- Add option to see full length's of all fields.
- Add option to see minimal information.
Decision Points:
| Time | Location | Topics | Participants |
|---|---|---|---|
| 10:00 AM - 12:00 PM | 1W030 | Prioritization and Debrief
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Attendees: Kumar, Larry, Jason, Sherri, Rob, Tracy, Cory, Scott, Craig
Discussion Points:
Architecture
- Future considerations.
- Smaller services -
- For example, Coding List listing service as a separate service.
- Concerns around ability to deploy up the tiers
- Current requirements will prohibit how quickly services can be exposed.
- Concerns about tech stack upgrades across services. Micro Services may or may not be impacted by upgrades (some or all).
- If addressed well, we can get rid of silos and duplication.
- Resources are a concern,
- Containers, JETTY, and how to balance.
- Security
- Scanning will take nearly as long as the large service.
- Instead of re-architecting all, focus on new and additional functionality (along side existing LexEVS)
- No longer would need clients to include jars, dependencies.
- Smaller services -
Decision Points:
- Investigate services architecture to support new and additional functionality.
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Attendees:
Discussion Points:
Decision Points:
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Prioritization and Debrief
- Discuss OWL2, RRF, LexEVS, CTS2, Browser, and all previous topics
- Discuss future architecture
- Determine next steps/road map and priorities
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Attendees:
Discussion Points:
Decision Points:
| Time | Location | Topics | Participants |
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| 1:00 PM - 2:00 PM | 1W030 | Prioritization and Debrief (Continued if needed) |
Attendees:
Discussion Points:
Strategic direction - RESTful services
- Moving to micro architecture in new areas in functionality for LexEVS
- Integrated REST services across LexEVS, Triple Store, Clinical Trials (Integrated REST Services)
- Future MDR redesign effort - areas of service support of terminologies.
- Future CTRP support
Decision Points:
