Author: Traci St.Martin/Craig Stancl
Email: stmartin.traci@mayo.edu, stancl.craig@mayo.edu
Team: LexEVS
Contract: CBIIT BOA Subcontract #29XS223
Client: NCI CBIIT
National Institutes of Heath
US Department of Health and Human Services
Sign off | Date | Role | CBIIT or Stakeholder Organization |
|---|---|---|---|
Larry Wright | 5/6/2010 | NCI PO & EVS Product Manager | CBIIT: NCI EVS & Semantic Infrastructure |
Jason Lucas | 5/6/2010 | EVS Software Project Manager |
|
Sherri de Coronado | 5/7/2010 | NCI PO | CBIIT: NCI EVS & Semantic Infrastructure |
The purpose of this document is to collect, analyze, and define high-level needs and features of the National Cancer Institute Center for Biomedical Informatics and Information Technology (NCI CBIIT) caCORE LexEVS Release 6.0. This document focuses on the functionalities proposed by the product stakeholders and target users in order to make it a better product. The use-case and supplementary specifications document will detail how the framework will fulfill these needs.
Vision and Needs
The objective of this release of the LexEVS API is to design and construct a reference implementation of the CTS2 specification, leveraging LexEVS as the basis for the design and code base.
This release will address support for value sets, mappings between code sets, support for creation of local extensions to code sets and support related to content creation and editing.
Current Solution
LexEVS 5.1 currently supports much of the functionality called for by the CTS2 Specification.
Proposed Solutions
LexEVS 6.0 will provide the additional functionality to enhance LexEVS to meet the goals of a CTS2 Reference Implementation and requirements of the user communities.
Functional Requirements
Each enhancement, modification or new feature is described in detail below.
GForge number | Brief description of functional requirement | Status | Iteration |
|---|---|---|---|
| 26638 | OBO Loader update for LexEVS 6.0 | Approved | --- |
NCIt/OWL loader update for LexEVS 6.0 | Approved | --- | |
Query enhancements for CTS2 Implementation LexEVS 6.0 | Approved | --- | |
XML Exporter update for LexEVS 6.0 | Approved | --- | |
NCIm Loader updates for LexEVS 6.0 | Approved | --- | |
HL7 loader update for LexEVS 6.0 | Approved | --- | |
Coding Scheme Supplement Changes for LexEVS 6.0 | Approved | --- | |
Usage context enhancements for LexEVS 6.0 | Approved | --- | |
Associations (maps) enhancements for LexEVS 6.0 | Approved | --- | |
Concept Domain enhancements for LexEVS 6.0 | Approved | --- | |
Value Set Enhancements for LexEVS 6.0 | Approved | --- | |
Versioning enhancements for LexEVS 6.0 | Approved | --- | |
XML loader update for LexEVS 6.0 | Approved | --- | |
ICD10 loader update for LexEVS 6.0 | Approved | --- | |
ICD 9 loader update for LexEVS 6.0 | Approved | --- | |
UMLS loader update to support LexEVS 6.0 | Approved | --- | |
Database changes to support LexEVS 6.0 | Approved | --- | |
LexGrid model changes for LexEVS 6.0 | Approved | --- | |
LexBIG model changes for LexEVS 6.0 | Approved | --- | |
DAO layer changes for LexEVS 6.0 CTS2 Implementation | Approved | --- | |
Text loader update for LexEVS 6.0 | Approved | --- | |
Manifest loader update for LexEVS 6.0 | Approved | --- | |
Notification enhancements for LexEVS 6.0 | Approved | --- | |
OBO Exporter update for LexEVS 6.0 | Approved | --- | |
Associations Exporter for LexEVS 6.0 | Approved | --- | |
Protege Frames Loader update for LexEVS 6.0 | Approved | --- | |
Loader Preferences Loader update for LexEVS 6.0 | Approved | --- | |
Authoring enhancements for CTS2 Implementation LexEVS 6.0 | Approved | --- | |
ISO 21090 Data Type Support enhancements for CTS2 Implementation LexEVS 6.0 | Approved | --- | |
Grid Service enablement CTS2 Implementation LexEVS 6.0 | Approved | --- | |
GEM loader update for LexEVS 6.0 | Approved | --- | |
ClaML Loader update for LexEVS 6.0 | Approved | --- | |
Load all MRMAP data | Approved | --- | |
Java 1.6 | Approved | --- | |
Control the setting of isActive via Loader preferences | Approved | --- | |
Modify Meta Browser Extension to support browsing and searching of other applicable source hierarchies. | Approved | --- | |
Need to be able to identify all supported properties of a particular property type. | Approved | --- | |
Convert codes in entity description of anonymous class to names. | Approved | --- | |
Ability to keep database load if indexes fail. | Approved | --- | |
Page CodedNodeGraph Results | Approved | --- | |
Option to include or exclude entity types in association search. | Approved | --- | |
Examine use of LexBIG entity status | Approved | --- | |
Provide XSLT transformations for backwards compatability of LexBIG XML | Approved | --- | |
A call for requirements for the HL7.OWL loader with an emphasis on top nodes | Approved | --- | |
LexEVS 6.0 Load Balancing | Approved | --- | |
Option to include or exclude anonymous concepts. | Approved | --- | |
OWL/RDF Exporter for LexEVS 6.0 | Approved | --- |
Functional Bug Fixes
Each bug fix included in this release is described in detail below.
GForge number | Brief description of bug | Status | Iteration |
|---|---|---|---|
OWL loader processing <owl:Restriction> associations incorrectly | Approved | --- | |
Focus code data is not found when referencing external coding scheme | Approved | --- | |
Include immediate parent/children when Value Domain Definition has transitiveClosure as 'false' and referenceAssociation is present | Approved | --- | |
"Pages" links not being built correctly in LexEVS caCORE SDK Service | Approved | --- | |
OBI load shows odd has_curation_status property | Approved | --- | |
The isDefined column in the entity table should accurately reflect the source data | Approved | --- | |
Incorrect Hibernate mappings of Oracle CLOB database type in caCORE SDK functions | Approved | --- | |
PropertyLinks won't load without namespace being supplied | Approved | --- | |
Loader should not shut down on a duplicate property | Approved | --- | |
Loader should not shut down on missing propertylink reference | Approved | --- | |
OWL loader does not load concepts with paranthesis | Approved | --- | |
Problem loading MeSH and Spanish version of SNOMED | Approved | --- | |
Null-Pointer Exception Thrown when no value-Domain content loaded. | Approved | --- | |
OBI.owl loading - missing property "has curation status" for concepts | Approved | --- | |
OBI.owl loading - Incorrect infromation as value to the property "imported from" | Approved | --- | |
Results not Deserializing Properly when using QueryModifiers on CQL Queries | Approved | --- | |
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Non-Functional Requirements
This section describes in detail all the related requirements which must be met for this release but do not add functionality. These requirements are included in the scope and project plan due to level of effort or relative importance to the overall success of delivery of the release.
GForge number (hyperlinked) | Brief description of non-functional requirement | Status | Iteration |
|---|---|---|---|
LexEVS 6.0 Project Charter | Approved | --- | |
BDA Compliance Package update for LexEVS 6.0 | Approved | --- | |
Release Notes for LexEVS 6.0 | Approved | --- | |
LexEVS Product Documentation (Wiki Guides) for LexEVS 6.0 | Approved | --- | |
LexEVS NCI/NCICB website updates for LexEVS 6.0 | Approved | --- | |
LexEVS 6.0 ECCF Documentation | Approved | --- | |
LexEVS 6.0 System and Software Design Document | Approved | --- | |
LexEVS 6.0 Design Review Package | Approved | --- | |
LexEVS 6.0 Deliverable Readiness Review Package | Approved | --- | |
6.0 Deployment to Dev Tier | Approved | --- | |
6.0 Deployment to QA Tier | Approved | --- | |
6.0 Deployment to Stage Tier | Approved | --- | |
Project plan for 6.0 | Approved | --- | |
6.0 Test Plan & Test Results | Approved | --- | |
6.0 Use Case Document | Approved | --- | |
6.0 ARC Document | Approved | --- | |
6.0 Prototype 1 | Approved | --- | |
6.0 Prototype 2 | Approved | --- | |
6.0 Prototype 3 | Approved | --- | |
6.0 Alpha 1 | Approved | --- | |
6.0 Alpha 2 | Approved | --- | |
6.0 Deployment to Production Tier | Approved | --- | |
6.0 Production Announcements | Approved | --- |
General Support Activities
This section describes in detail all the related activities which must be performed for this release but do not add functionality. These activities are included in the scope and project plan due to level of effort or relative importance to the overall success of delivery of the release.
GForge number (hyperlinked) | Brief description of general support activity | Status | Iteration |
|---|---|---|---|
| LexEVS Level 2 Support - integration of help and training to the user community. | Approved | --- |
Stakeholder Summary
CBIIT Staff/Contractor Name | Role | Responsibilities |
|---|---|---|
George Komatsoulis | NCICB Application Infrastructure | Oversees NCICB Application Infrastructure |
Avinash Shanbhag | NCICB Application Infrastructure | Oversees NCICB caCORE Software Engineering |
Larry Wright/ Sherri de Coronado | EVS Product Managers | Directs EVS Projects |
Denise Warzel | CORE Product Line Manager | Trans-CORE requirement coordination |
Gilberto Fragoso | Associate Director EVS Infrastructure | Technical Direction |
Jason Lucas | EVS Software Project Manager | Project schedule and task management for EVS team |
Craig Stancl | Mayo Clinic Technical Lead | Technical Direction and Implementation |
Traci St.Martin | Mayo Clinic Project Manager | Project schedule and task management |
Larry Brem | SAIC caBIG ARCH and VCDE Technical Program Manager | Contract governance |
Technical Environment
This product uses the following technical components which have been derived from the current NCICB Technology Stack.
Component | Description |
|---|---|
Client Interface |
|
Application Server |
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Database Server |
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Operating System |
|
[EVS:Other] | --- |
Product Dependencies
This release is dependent on the caCORE components or products documented in the CORE Product Dependency Matrix.
Out of Scope Items
Items that are out of scope were evaluated as part of the initial scoping activities for this release, and subsequently not included in the final approved scope. These items are also documented in the cumulative backlog of requirements found on the product GForge site. They include out-of-scope functional requirements (enhancements or new features), bug fixes, non-functional requirements, and general support activities.
GForge number (hyperlinked) | Brief description of item moved from the in-scope section | Iteration during which the item |
|---|---|---|
Make sample programs (in the examples folder) runnable under both local and distributed modes. Deferred due to low priority. | Inception | |
Need to be abe to uniquely identify the coding scheme to which a concept belongs. Deferred due to low priority. | Inception | |
MedDRA loading into LexEVS. Deferred due to low priority. | Inception | |
Spruce up MetaDataLoader GUI. Deferred due to low priority. | Inception | |
Enhance LexBIG query API to fetch AssociationData objects. Deferred due to low priority. | Inception | |
Better validation on restrictions. Deferred due to low priority. | Inception | |
Need an option to exclude the focused node itself from ResolvedConceptReferenceList when resolving a CNG. Deferred due to low priority. | Inception | |
Ontology for Genetic Interval hierarchy does not match up Protege. Deferred - This item has been discussed and is not an issue for 6.0. | Inception | |
ECG Ontology missing Description, Date, Source and Creator fields. Deferred - This item has been discussed and is not an issue for 6.0. | Inception | |
Can not compute root node for OBI version v1.0.1423. Deferred - This item has been discussed and is not an issue for 6.0. | Inception | |
Lucene Max Clause Count exceeded on broad NCI MetaThesaurus RegExp Restrictions. Deferred - This item has been discussed and is not an issue for 6.0. | Inception | |
CodedNodeGraph resolveAsList distributed method encountered Java heap space error. Deferred - This item has been discussed and is not an issue for 6.0. | Inception | |
Heap space error on Doubpe Metaphone MetaThesaurus query. Deferred - This item has been discussed and is not an issue for 6.0. | Inception | |
REST API Features. Deferred - This item has been discussed and is not an issue for 6.0. | Inception | |
LexEVS Value Domain Support to include persistance of resolved value domain content. Deferred - This item has been discussed and is not an issue for 6.0. | Inception | |
Add methods to ResolvedConceptReferencesIterator for supporting communications with client applications. Deferred - This item has been discussed and is not an issue for 6.0. | Inception | |
Ability to query for inferred data - implement ability to reason. Deferred - This item has been discussed and is not an issue for 6.0. | Inception | |
Anonymous class hierarchy with unions not showing up correctly. Deferred due to priority. | Inception | |
LexEVS 5.0 Silver Level Review. Out of Scope - Compatibility Review process change. | Inception | |
LexEVS 6.0 Silver Level Compatibility Review Submission Package. Out of Scope - Compatibility Review process change. | Inception | |
| CTS2 Semantic Profiles: Developing Terminology Profile, HL7 Terminology Profile | Inception |
Document History
Item | Information |
|---|---|
Document Version: | Click the Info tab. View the Recent Changes or click the link to view the page history. |
Last Modified: | Refer to the first line displayed in the document window. |
Project GForge site: | LexEVS GForge project Docs archive, Files archive |
Most current version: | Unless the display includes a notice that you are viewing a previous version, you are viewing the most current version of this Scope Document for the release indicated in the title. |
Revision history: | Click the Info tab. In the Recent Changes area, click the link to view the page history. |
Review history: | Click the Info tab. In the Recent Changes area, note the developer who made each change and the date and time. Refer to the Key People Directory for their roles. Click the link to view any page or to view the page history, and then click the link for a page. When the page opens, view the comments and changes made in that version. |
Related documents: | Confluence Wiki documents: LexEVS 6.0 Development Documents |
Project Information
CBIIT Management | Role | Responsibilities |
|---|---|---|
Larry Wright/ Sherri de Coronado | Co-Product Managers | Oversees development of the product: features, functions, definition of stakeholders, priorities within the scope, timeframe for release |
Avinash Shanbhag | Engineering Manager | Oversees NCICB caCORE software engineering practices, conducts design reviews, guides technical development |
Denise Warzel | Product Line Manager | Oversees NCICB caCORE product line. Responsible for overall product integration, major and minor release cycles. Supports Product Manager. |
