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 |
---|---|---|---|
9:00 AM - 10:00 AM | 4W030 | User Group Discussion
| 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.
- Issues
- Proposed Architecture?
- REST-ful API
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
|
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.
- Additional cases
- 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
- No need from caDSR
- Additional requirements
- Bulk Download
- ability to download full or part of a complete terminology.
- Bulk Download
- 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 |
---|---|---|---|
11:00 AM - 12:00 PM | 4W030 | Triple store/RDF Discussion
|
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:
- Investigate where Triple Store usage may augment LexEVS.
Time | Location | Topics | Participants |
---|---|---|---|
1:00 PM - 2:00 PM | 5E030 | EVS Project Group Discussion (During regular call-in time)
| EVS project meeting |
Attendees: Larry, Kim, Craig, Scott, Cory, John, Liz, Gilberto, Lori, Tin, Teri, Sharon, Sana, Nick, Nels, Margaret, George, Brenda, Abigail, Erin, Joanne
Discussion Points:
- 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:
- Revisit the mapping discussion during a future project meeting.
Time | Location | Topics | Participants |
---|---|---|---|
2:00 PM - 3:00 PM | 5E030 | LexEVS Mapping DiscussionDetermine requirements and propose solution for mapping.
|
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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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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
| Rob, Tracy |
Attendees:
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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
|
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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) |
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Time | Location | Topics | Participants |
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3:30 PM - 4:00 PM | 3W030 | FHIR and terminology services (CTS2)
| Harold |
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4:00 PM - 5:00 PM | 3W030 | OWL Restrictions in LexGrid Model
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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.
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Time | Location | Topics | Participants |
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10:00 AM - 12:00 PM | 1W030 | Prioritization and Debrief
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Time | Location | Topics | Participants |
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1:00 PM - 2:00 PM | 1W030 | Prioritization and Debrief (Continued if needed) |
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