Author: Craig Stancl, Scott Bauer, Cory Endle Email: craig.stancl2@nih.gov, scott.bauer@nih.gov, Team: LexEVS Contract: 16X237 Client: NCI CBIIT National Institutes of Heath US Department of Health and Human Services |
The purpose of this document is to document the technical face to face meeting details between the NCI and the LexEVS Team.
2016 November/December Face-to-Face Meeting Notes
Wednesday, November 30th, 2016
Time | Location | Topics | Participants |
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9:00 AM - 10:00 AM | 4W030 | User Group Discussion- Team to share how they are using LexEVS and additional usage requirements they may have.
- What components of LexEVS do you currently use?
LexEVS API LexEVS Remote API CTS2 RESTful services
Are there LexEVS services that you would like to use, but they don't meet your requirements? Are there any other road blocks preventing you from using LexEVS? What version of LexEVS are you currently using?
| CTRP, caDSR, GDC |
Attendees: Larry, Jason, Kim, Craig, Scott, Cory, John, Liz, Sima, Rui, Natalia, Tracy, Sana, Tin, Gilberto
Discussion Points:
- 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.
- Proposed Architecture?
Decision Points:
- 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.
Time | Location | Topics | Participants |
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10:00 AM - 11:00 AM | 4W030 | RESTful API Discussion- Discuss requirements for continued development of REST services. This will include both CTS2 and separate REST-ful API.
- Browser: Discuss requirements for remote API and CTS2 REST-ful API.
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Attendees: Larry, Jason, Kim, Craig, Scott, Cory, John, Liz, Sima, Rui, Natalia, Tracy, Sana, Tin, Gilberto, Jacob
Discussion Points:
- Browser use cases reviewed.
- Additional cases
- History - the browser currently uses.
- Security - for Medra or other licensed vocabularies.
- May be able to use CTS2 APIs, but may need to have separate REST-ful services for customized/specialized content.
- Current browser wouldn't use REST services.
- Unknown coverage for REST possibilities. So additional investigation required.
- Previous F2F considerations.
- Custom Lucene may need to be provided for clinical trials.
- Group Value Sets - may be useful.
- Restrict to Properties - need to better understand this usecase.
- History - suggested by the CTRP but has some requirements in scope of the Browser.
- Graph and Association
- Additional requirements
- Bulk Download
- ability to download full or part of a complete terminology.
- Align rest calls to support Moonshot API services.
- Make others aware services are available.
- Tracy suggested to look at Data.gov
- Browser team not going to use REST at this time
- caDSR not going to use REST at this time.
Decision Points:
- Identify Moonshot Clinical Trial API services to be supported by REST services.
- Identify ways to promote REST services.
- Identify possibilities of participating in Data.gov
Time | Location | Topics | Participants |
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11:00 AM - 12:00 PM | 4W030 | Triple store/RDF Discussion- Discuss what triple stores would be used for in parallel and in conjunction with LexEVS
- Text searching
- NCBO SPARQL white paper and it's implications
- Searching on Roles (Gilberto, Kim)
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Attendees:
Discussion Points:
- There is a pilot ongoing to review triple stores
- selected 3 triple stores (StarDog, Allegrograph (http://allegrograph.com/), Viritouso) and have been working for the past 6 months
- evaluations covering restricting operations, loading data, performance testing, examine security (secured and anonymous access via proxies)
- nature of queries haven't been as representative of what is needed for production.
- more focus on real use queries.
- operations - hosting model not supported by CBIIT - so no support. (ie, patching support not provided)
- all can be queried with standard SPARQL
- will still want REST services available to the end users.
- Transition to SPAQRL gives raw access to the data (unlike API)
- However, you need to understand the data - and this could differ from endpoint to endpoint.
- What do TripleStores provide - that differ (better than) LexEVS
- Representation of Hierarchy
- Level of expressivity
- 3 use cases for triplestore evaluation:
- Expressivity (reasoning support)
- Linked open data
- use vocabulary as a "glue" between different data repositories. Ability to "join" distributed repositories.
- Closer integration of vocabulary and meta data (part of the MDR).
- Report writer now uses the triple store
- Loading of Value sets take much less time
- Access of Value Sets is better, but not hugely different.
- Need to determine where Triple Store is better and where LexEVS is better.
Decision Points:
Time | Location | Topics | Participants |
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1:00 PM - 2:00 PM | 5E030 | EVS Project Group Discussion (During regular call-in time)
- User/content priorities for value set, mapping, and other services.
- Specialized search and other capabilities for complex chemical names and genetic names.
- Current capabilities and browser implementation
- Possible expert system extension
| EVS project meeting |
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Time | Location | Topics | Participants |
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2:00 PM - 3:00 PM | 5E030 | LexEVS Mapping DiscussionDetermine requirements and propose solution for mapping. - User requirement: One terminology to many terminologies mapping.
- Other topics: Current, conditional, external relationships
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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. - Discuss specialized search use cases.
- Possible Lucene enhancements for coding scheme categorizations, auto complete aids, Lucene services.
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Time | Location | Topics | Participants | Resources |
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4:30 PM - 5:00 PM | 5E030 | Overflow/Additional Topics | | |
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Thursday, December 1st, 2016
Time | Location | Topics | Participants |
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9:00 AM - 11:00 AM | 3W030 | Value Set management and workflow- Discuss requirements for value set version management and workflow management and supporting technology.
- Rob to give a demo of their current workflow and the scripts they use.
| Rob, Tracy |
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Time | Location | Topics | Participants |
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11:00 AM - 12:00 PM | 3W030 | Value Set and Mapping Data with Hierarchical structure Discussion- Determine requirements and propose options to hierarchical structure and mapping.
- Discuss how VS could retain their multiple hierarchical structure that it came from.
- Discuss what changes would be needed to CTS2 for this.
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1:00 PM - 3:30 PM | 3W030 | 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) |
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3:30 PM - 4:00 PM | 3W030 | FHIR and terminology services (CTS2)- Harold to provide update on CTS2 and FHIR.
| Harold |
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4:00 PM - 5:00 PM | 3W030 | 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
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5:00 PM - 5:30 PM | 3W030 | Overflow/Additional Topics | |
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Friday, December 2nd, 2016
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Time | Location | Topics | Participants |
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9:00 AM - 10:00 AM | 1W030 | LexEVS AdminDiscuss current and future requirements. - GUI
- Consider a web based tool. A simple way to look at the data.
- Command Line loader requirements
- Other considerations
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Time | Location | Topics | Participants |
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10:00 AM - 12:00 PM | 1W030 | 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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1:00 PM - 2:00 PM | 1W030 | Prioritization and Debrief (Continued if needed)
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