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Author: Craig Stancl Email: Team: LexEVS ST12-1106 |
Sign off | Date | Role | CBIIT or Stakeholder Organization | ||||
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Larry Wright | 5/6/2010 | NCI PO & EVS Product Manager | CBIIT: NCI EVS & Semantic Infrastructure | ||||
Jason Lucas | 5/6/2010 | EVS Software Project Manager |
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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 6.01. This document focuses on the functionalities functions 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.
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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 communitiesprovide a CTS2 compliant REST API, Enhanced Performance and new loaders.
Functional Requirements
Each enhancement, modification or new feature is described in detail below.
GForge JIRA number | Brief description of functional requirement | Status | Iteration |
---|---|---|---|
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 | --- | |
LEXEVS-539 | CTS2 REST CodeSystemVersionCatalogEntry | ||
LEXEVS-540 | CTS2 REST EntityDescription | ||
LEXEVS-541 | CTS2 REST Association | ||
LEXEVS-542 | CTS2 REST ValueSetDefinition | ||
LEXEVS-543 | CTS2 REST ResolvedValueSet | ||
LEXEVS-544 | CTS2 REST MapCatalogEntry | ||
LEXEVS-545 | CTS2 REST MapVersionCatalogEntry | ||
LEXEVS-546 | CTS2 REST MapEntry | ||
LEXEVS-547 | LexEVS Enhancement for CTS2 - Entity Query Across Code System | ||
LEXEVS-548 | LexEVS Performance Enhancement - Implement a persistance mechanism for resolved Value Sets | ||
LEXEVS-549 | LexEVS Performance Enhancement - Performace Improvement of Hierarchy Traversal | ||
LEXEVS-550 | LexEVS Performance Enhancement - Search Performance (Contains) | ||
LEXEVS-551 | LexEVS Loader Enhancement - MedDRA Loader | ||
LEXEVS-552 | LexEVS Loader Enhancement - OWL2 Loader | ||
LEXEVS-553 | LexEVS Loader Enhancement - HL7 MIF Loader |
Functional Bug Fixes
Each bug fix included in this release is described in detail below.
GForge JIRA 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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LEXEVS-444 | Trying to load NCIt to ICD9 MRMAP file, get error | ||
LEXEVS-495 | ICD9 GEMS map throws java.lang.NullPointerException | ||
LEXEVS-506 | Missing database index for Metathesaurus | ||
LEXEVS-527 | LoadMetaBatch throws illegal character error | ||
LEXEVS-514 | OWL loader puts property comments on every property value | ||
LEXEVS-533 | SNOMED Loader does not build Transitivity Table | ||
LEXEVS-526 | Metathesaurus unable to load or Resume | ||
LEXEVS-522 | Excessive SQL Query crashes server | ||
LEXEVS-492 | Unable to export NCI Thesaurus 11.10e |
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 JIRA number (hyperlinked) | Brief description of non-functional requirement | Status | Iteration |
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26660 LEXEVS-555 | 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 | --- | |
1 Software Design Document | |||
LEXEVS-556 | LexEVS 6.1 Information Systems Security Plan Document | ||
LEXEVS-557 | LexEVS 6.1 Technical/Product Documentation (Wiki) | ||
LEXEVS-559 | LexEVS 6.1 Design Review Package | ||
LEXEVS-558 | LexEVS 6.1 Release Notes | ||
LEXEVS-560 | LexEVS 6.1 Readiness Review Package | ||
LEXEVS-561 | LexEVS 6.1 Technical Project Plan | ||
LEXEVS-562 | LexEVS 6.1 Deployment to NCI Dev Tier | ||
LEXEVS-563 | LexEVS 6.1 Deployment to NCI QA Tier | ||
LEXEVS-564 | LexEVS 6.1 Deployment to NCI Stage Tier | ||
LEXEVS-565 | LexEVS 6.1 Deployment to NCI Production Tier | ||
LEXEVS-566 | LexEVS 6.1 Production Announcements | ||
LEXEVS-554 | LexEVS GitHub Migration |
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 JIRA 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 | |||
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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.MartinMandy Ager | 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 |
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Client Interface |
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Application Server |
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Database Server |
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Operating System |
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[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 JIRA number (hyperlinked) | Brief description of item moved from the in-scope section | Iteration during which the item | |||
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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 | ||||
LEXEVS-505 | Case-insensitive concept code search support. | Inception | |||
LEXEVS-239 | OBO loaded data with roots that delcare disjointness do not display in hierarchy | Inception | |||
LEXEVS-236 | OBO optional synonym type name | Inception | |||
LEXEVS-370 | Export the content of ResolvedValueSetDefinition to StringBuffer in LexGrid XML format | Inception | |||
LEXEVS-372 | Extensions should be able to add properties to existing concepts | Inception | |||
LEXEVS-369 | Add a label or description member variable to EntityDescription. | Inception | |||
LEXEVS-367 | Support retrieval of ValueSetDefinition by multiple coding schemes. | Inception | |||
LEXEVS-366 | Modify output parameter of the getCodingSchemesInValueSetDefinition method in LexEVSValueSetDefinitionServices. | Inception | |||
LEXEVS-368 | Support retrieval of ValueSetDefinition by multiple concept domains. | Inception | |||
LEXEVS-365 | Resolve nested value set definition through distributed Value Set API. | Inception | |||
LEXEVS-363 | Extend MappingExtension functionalities to support restrictions. | Inception | |||
LEXEVS-354 | Load source qualifiers for generic properties in NCI-META RRF loader | Inception | |||
LEXEVS-350 | Examine use of LexBIG entity status | Inception | |||
LEXEVS-531 | Build scripts do not have path for dataqa | Inception | |||
LEXEVS-255 | Linux gui does not work | Inception | |||
LEXEVS-233 | SNOMED Role Groups not loading from RRF files | Inception | |||
LEXEVS-22721336 | 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 | ||||
Inception | |||||
LEXEVS-371 | Make it easy to do retrieval of only active concepts in a terminology through the/ a service | Inception | |||
LEXEVS-362 | Owl/rdf exporter limitation | Inception | |||
LEXEVS-345 | Convert codes in entity description of anonymous class to names. | Inception | |||
LEXEVS-512 | LexEVSValueSetDefinitionServices.getCodedNodeSetForValueSetDefinition method can be extremely slow. | Inception | |||
LEXEVS-508 | Mapping concepts don't always have a suitable target | Inception | |||
LEXEVS-507 | Inefficient query when trying to filter Metathesaurus by Source. | Inception | |||
LEXEVS-496 | LexEVS api calls do not populate directionalName in the association | Inception | |||
LEXEVS-515 | Caching of value sets don't always work | Inception | |||
LEXEVS-518 | Trying to load ICD10 results in error | Inception | |||
LEXEVS-516 | LexEVSValueSetDefinitionServices getValueSetDefinitionEntitiesForTerm fails on inactive coding schemes. | Inception | |||
LEXEVS-519 | Inconsistant package naming | Inception | |||
LEXEVS-461 | Necessity to rebuild indexes after load | Inception | |||
LEXEVS-538 | Loader should support unicode | Inception | |||
LEXEVS-521 | Transition table hangs in UMLS loader on large vocabs | Inception | |||
LEXEVS-244 | Unqueryable classes are registered by the grid service | Inception | |||
LEXEVS-232 | The codedNodeGraph is not displaying the top nodes correctly | Inception | |||
LEXEVS-235 | PDQ load shows multiple LT : TRD properties in browser | Inception | |||
LEXEVS-234 | RRF Snomed Loader not interpreting SNOMED status codes correctly | Inception | |||
LEXEVS-230 | The contains algorithm fails on search strings starting with a single character word such as 'a'. | Inception | |||
LEXEVS-442 | NCIt Loader preferences file with defaults | Inception | |||
LEXEVS-361 | Unregister coding scheme supplement through the LexBIG GUI application. | Inception | |||
LEXEVS-360 | Add a Boolean-Valued member variable applyToSubconcepts to EntityReference. | Inception | |||
LEXEVS-359 | Need an effective way of counting the size of a CNG. | Inception | |||
LEXEVS-356 | GUI should reflect administrative nomenclature | Inception | |||
LEXEVS-358 | Authoring Tool / Graphical User Interface (GUI) | Inception | |||
LEXEVS-353 | Need an option to exclude the focused node itself from ResolvedConceptReferenceList when resolving a CNG. | Inception | |||
LEXEVS-352 | Better validation on restrictions | Inception | |||
LEXEVS-347 | Control the setting of isActive via Loader preferences | Inception | |||
LEXEVS-348 | 26628Ability to query for inferred data - implement ability to reason | . Deferred - This item has been discussed and is not an issue for 6.0.Inception | Inception | ||
LEXEVS-344 | Enhance LexBIG query API to fetch AssociationData objects. | Inception | |||
LEXEVS-269 | Demonstrate cross ontology relationships | Inception | |||
LEXEVS-264 | Validation of UTF-8 subset | Inception | |||
LEXEVS-250 | Duplicate alias "_value" when quering LexEVSDataService | Inception | |||
LEXEVS-510 | Documentation location in the installer | Inception | |||
LEXEVS-511 | UMLS meta loader script is in the wrong format | Inception | |||
LEXEVS-509 | Sorting in Mapping tab in Term Browser can lead to 500 errors | Inception | |||
LEXEVS-500 | Load Progress indicators | Inception | |||
LEXEVS-517 | LexEVSAuthoringServiceImpl 'getEntity' restricts to types of 'concept' | Inception | |||
LEXEVS-469 | Attempted load of a MRMAP mapping failed with inscrutable error | Inception | |||
LEXEVS-482 | Ability to load metadata and mapping in one operation | Inception | |||
LEXEVS-481 | Ability to load metadata and coding scheme in one operation | Inception | |||
LEXEVS-475 | Enhancement to versioning of Mapping loads | Inception | |||
LEXEVS-480 | Better support for "Metathesaurus" data structures (e.g. accessing source hierarchies in NCI-META) | Inception | |||
LEXEVS-478 | Clean up GUI - functionality should match documentaion/presentation | Inception | |||
LEXEVS-476 | Ability to load MRMAP without a MRSAT entry | Inception | |||
LEXEVS-474 | Ability to add metadata to value set definitions | Inception | |||
LEXEVS-473 | Concept Sorting in Mappings when using local API | Inception | |||
LEXEVS-446 | UMLS loader should give an error if the SAB is not specified | Inception | |||
LEXEVS-454 | OWL Export exhibits memory leak. | Inception | |||
LEXEVS-493 | Search SNOMEDCT for '<' using the contains algorithm returns no matches. | Inception | |||
LEXEVS-464 | The NCI OWL loader is loading the "type" property inconsistently | Inception | |||
LEXEVS-463 | The NCI OWL loader is loading Metadata properties inconsistently. | Inception | |||
LEXEVS-462 | NCI OWL loader for LexBIG 6.0 is creating extraneous "label" property qualifiers | Inception | |||
LEXEVS-460 | Enable use of ALT keys in LexEVS Developer GUIs | Inception | |||
LEXEVS-459 | Batch Loader for LexEVS Value Set | Inception | |||
LEXEVS-529 | ValueSetDefinition getDefinitionEntryCount() returns incorrect number | Inception | |||
LEXEVS-537 | JIRA task - Unable to assign issues to QA person, and not Ready For QA status | Inception | |||
LEXEVS-536 | The ResolvedConceptReferencesIterator numberRemaining method can be quite inaccurate. | Inception | |||
LEXEVS-535 | Term Browser "View In Hierarchy" function fails for ICD10 root nodes | Inception | |||
LEXEVS-534 | Reduce error volume for hibernate issues | Inception | |||
LEXEVS-525 | Metathesaurus does not load completely | Inception | |||
LEXEVS-528 | Suppressable CUIs in RRF loader | Inception | |||
LEXEVS-22320653 | Anonymous class hierarchy with unions not showing up correctly. Deferred due to priority. | Inception | |||
LEXEVS-341 | REST API Features | 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 | ||||
LEXEVS-339 | MedDRA loading into LexEVS | Inception | |||
LEXEVS-497 | Documentation Issue | Inception | |||
LEXEVS-502 | Spelling error in loader |
| CTS2 Semantic Profiles: Developing Terminology Profile, HL7 Terminology Profile | Inception |
Document History
Item | Information | |
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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 JIRA site: | [https://gforge.nci.nih.gov/projects/lexevs/ |
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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. |
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