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title

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titleContents of this Page
Table of Contents
minLevel2
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titleDocument Information
Author:
Traci St.Martin/
Craig Stancl
Email:
stmartin.traci@mayo.edu, stancl.

Team: LexEVS
Contract:

CBIIT BOA Subcontract #29XS223

ST12-1106
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 6.01. 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.

...

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
(hyperlinked)

Brief description of functional requirement
(enhancement or new feature)

Status
(Approved or Proposed)

Iteration

26638

OBO Loader update for LexEVS 6.0

Approved

---

26640

NCIt/OWL loader update for LexEVS 6.0

Approved

---

26641

Query enhancements for CTS2 Implementation LexEVS 6.0

Approved

---

26642

XML Exporter update for LexEVS 6.0

Approved

---

26643

NCIm Loader updates for LexEVS 6.0

Approved

---

26644

HL7 loader update for LexEVS 6.0

Approved

---

26645

Coding Scheme Supplement Changes for LexEVS 6.0

Approved

---

26646

Usage context enhancements for LexEVS 6.0

Approved

---

26648

Associations (maps) enhancements for LexEVS 6.0

Approved

---

26649

Concept Domain enhancements for LexEVS 6.0

Approved

---

26650

Value Set Enhancements for LexEVS 6.0

Approved

---

26651

Versioning enhancements for LexEVS 6.0

Approved

---

26652

XML loader update for LexEVS 6.0

Approved

---

26653

ICD10 loader update for LexEVS 6.0

Approved

---

26654

ICD 9 loader update for LexEVS 6.0

Approved

---

26655

UMLS loader update to support LexEVS 6.0

Approved

---

26656

Database changes to support LexEVS 6.0

Approved

---

26657

LexGrid model changes for LexEVS 6.0

Approved

---

26658

LexBIG model changes for LexEVS 6.0

Approved

---

26659

DAO layer changes for LexEVS 6.0 CTS2 Implementation

Approved

---

27829

Text loader update for LexEVS 6.0

Approved

---

27831

Manifest loader update for LexEVS 6.0

Approved

---

27838

Notification enhancements for LexEVS 6.0

Approved

---

27839

OBO Exporter update for LexEVS 6.0

Approved

---

27840

Associations Exporter for LexEVS 6.0

Approved

---

27841

Protege Frames Loader update for LexEVS 6.0

Approved

---

27842

Loader Preferences Loader update for LexEVS 6.0

Approved

---

27843

Authoring enhancements for CTS2 Implementation LexEVS 6.0

Approved

---

27844

ISO 21090 Data Type Support enhancements for CTS2 Implementation LexEVS 6.0

Approved

---

27845

Grid Service enablement CTS2 Implementation LexEVS 6.0

Approved

---

28166

GEM loader update for LexEVS 6.0

Approved

---

28167

ClaML Loader update for LexEVS 6.0

Approved

---

21720

Load all MRMAP data

Approved

---

23643

Java 1.6

Approved

---

26329

Control the setting of isActive via Loader preferences

Approved

---

27026

Modify Meta Browser Extension to support browsing and searching of other applicable source hierarchies.

Approved

---

24699

Need to be able to identify all supported properties of a particular property type.

Approved

---

25509

Convert codes in entity description of anonymous class to names.

Approved

---

26627

Ability to keep database load if indexes fail.

Approved

---

26637

Page CodedNodeGraph Results

Approved

---

26683

Option to include or exclude entity types in association search.

Approved

---

26709

Examine use of LexBIG entity status

Approved

---

28120

Provide XSLT transformations for backwards compatability of LexBIG XML

Approved

---

24191

A call for requirements for the HL7.OWL loader with an emphasis on top nodes

Approved

---

28369

LexEVS 6.0 Load Balancing

Approved

---

23324

Option to include or exclude anonymous concepts.

Approved

---

28420

OWL/RDF Exporter for LexEVS 6.0

Approved

---

LEXEVS-539CTS2 REST CodeSystemVersionCatalogEntry  
LEXEVS-540CTS2 REST EntityDescription  
LEXEVS-541CTS2 REST Association  
LEXEVS-542CTS2 REST ValueSetDefinition  
LEXEVS-543CTS2 REST ResolvedValueSet  
LEXEVS-544CTS2 REST MapCatalogEntry  
LEXEVS-545CTS2 REST MapVersionCatalogEntry  
LEXEVS-546CTS2 REST MapEntry  
LEXEVS-547LexEVS Enhancement for CTS2 - Entity Query Across Code System  
LEXEVS-548LexEVS Performance Enhancement - Implement a persistance mechanism for resolved Value Sets  
LEXEVS-549LexEVS Performance Enhancement - Performace Improvement of Hierarchy Traversal  
LEXEVS-550LexEVS Performance Enhancement - Search Performance (Contains)  
LEXEVS-551LexEVS Loader Enhancement - MedDRA Loader  
LEXEVS-552LexEVS Loader Enhancement - OWL2 Loader  
LEXEVS-553LexEVS Loader Enhancement - HL7 MIF Loader  

Functional Bug Fixes

Each bug fix included in this release is described in detail below.

GForge JIRA number
(hyperlinked)

Brief description of bug

Status
(Approved or Proposed)

Iteration

21935

OWL loader processing <owl:Restriction> associations incorrectly

Approved

---

22036

Focus code data is not found when referencing external coding scheme

Approved

---

24037

Include immediate parent/children when Value Domain Definition has transitiveClosure as 'false' and referenceAssociation is present

Approved

---

24538

"Pages" links not being built correctly in LexEVS caCORE SDK Service

Approved

---

25042

OBI load shows odd has_curation_status property

Approved

---

25325

The isDefined column in the entity table should accurately reflect the source data

Approved

---

26072

Incorrect Hibernate mappings of Oracle CLOB database type in caCORE SDK functions

Approved

---

26975

PropertyLinks won't load without namespace being supplied

Approved

---

26976

Loader should not shut down on a duplicate property

Approved

---

26977

Loader should not shut down on missing propertylink reference

Approved

---

22296

OWL loader does not load concepts with paranthesis

Approved

---

25681

Problem loading MeSH and Spanish version of SNOMED

Approved

---

24967

Null-Pointer Exception Thrown when no value-Domain content loaded.

Approved

---

23770

OBI.owl loading - missing property "has curation status" for concepts

Approved

---

23806

OBI.owl loading - Incorrect infromation as value to the property "imported from"

Approved

---

19406

Results not Deserializing Properly when using QueryModifiers on CQL Queries

Approved

---

 

 

 

---

LEXEVS-444Trying to load NCIt to ICD9 MRMAP file, get error  
LEXEVS-495ICD9 GEMS map throws java.lang.NullPointerException  
LEXEVS-506Missing database index for Metathesaurus  
LEXEVS-527LoadMetaBatch throws illegal character error  
LEXEVS-514OWL loader puts property comments on every property value  
LEXEVS-533SNOMED Loader does not build Transitivity Table  
LEXEVS-526Metathesaurus unable to load or Resume  
LEXEVS-522Excessive SQL Query crashes server  
LEXEVS-492Unable 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
(Approved or Proposed)

Iteration

26660 LEXEVS-555LexEVS 6.0 Project Charter

Approved

---

27856

BDA Compliance Package update for LexEVS 6.0

Approved

---

27857

Release Notes for LexEVS 6.0

Approved

---

27859

LexEVS Product Documentation (Wiki Guides) for LexEVS 6.0

Approved

---

27860

LexEVS NCI/NCICB website updates for LexEVS 6.0

Approved

---

27861

LexEVS 6.0 ECCF Documentation

Approved

---

27862

LexEVS 6.0 System and Software Design Document

Approved

---

27863

LexEVS 6.0 Design Review Package

Approved

---

27864

LexEVS 6.0 Deliverable Readiness Review Package

Approved

---

28159

6.0 Deployment to Dev Tier

Approved

---

28161

6.0 Deployment to QA Tier

Approved

---

28162

6.0 Deployment to Stage Tier

Approved

---

28163

Project plan for 6.0

Approved

---

28164

6.0 Test Plan & Test Results

Approved

---

28165

6.0 Use Case Document

Approved

---

28168

6.0 ARC Document

Approved

---

28169

6.0 Prototype 1

Approved

---

28170

6.0 Prototype 2

Approved

---

28172

6.0 Prototype 3

Approved

---

28173

6.0 Alpha 1

Approved

---

28174

6.0 Alpha 2

Approved

---

28175

6.0 Deployment to Production Tier

Approved

---

28177

6.0 Production Announcements

Approved

---

1 Software Design Document  
LEXEVS-556LexEVS 6.1 Information Systems Security Plan Document  
LEXEVS-557LexEVS 6.1 Technical/Product Documentation (Wiki)  
LEXEVS-559LexEVS 6.1 Design Review Package  
LEXEVS-558LexEVS 6.1 Release Notes  
LEXEVS-560LexEVS 6.1 Readiness Review Package  
LEXEVS-561LexEVS 6.1 Technical Project Plan  
LEXEVS-562LexEVS 6.1 Deployment to NCI Dev Tier  
LEXEVS-563LexEVS 6.1 Deployment to NCI QA Tier  
LEXEVS-564LexEVS 6.1 Deployment to NCI Stage Tier  
LEXEVS-565LexEVS 6.1 Deployment to NCI Production Tier  
LEXEVS-566LexEVS 6.1 Production Announcements  
LEXEVS-554LexEVS 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
(Approved or Proposed)

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.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

Client Interface

  • NCI Browsers

Application Server

  • JBoss 4.0.5.GA

Database Server

  • MySQL 5.0.51b

Operating System

  • Red Hat Enterprise Linux AS release 4 (Nahant Update 8)

[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.

26628 . Deferred - This item has been discussed and is not an issue for 6.0.

GForge JIRA number (hyperlinked)

Brief description of item moved from the in-scope section
with brief explanation added of why it was not included in this release

Iteration during which the item
was removed from in-scope

21880

Make sample programs (in the examples folder) runnable under both local and distributed modes. Deferred due to low priority.

Inception

22644

Need to be abe to uniquely identify the coding scheme to which a concept belongs. Deferred due to low priority.

Inception

22877

MedDRA loading into LexEVS. Deferred due to low priority.

Inception

24812

Spruce up MetaDataLoader GUI. Deferred due to low priority.

Inception

25071

Enhance LexBIG query API to fetch AssociationData objects. Deferred due to low priority.

Inception

27164

Better validation on restrictions. Deferred due to low priority.

Inception

28147

Need an option to exclude the focused node itself from ResolvedConceptReferenceList when resolving a CNG. Deferred due to low priority.

Inception

20661

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

20665

ECG Ontology missing Description, Date, Source and Creator fields. Deferred - This item has been discussed and is not an issue for 6.0.

Inception

20684

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-505Case-insensitive concept code search support.Inception
LEXEVS-239OBO loaded data with roots that delcare disjointness do not display in hierarchyInception
LEXEVS-236OBO optional synonym type nameInception
LEXEVS-370Export the content of ResolvedValueSetDefinition to StringBuffer in LexGrid XML formatInception
LEXEVS-372Extensions should be able to add properties to existing conceptsInception
LEXEVS-369Add a label or description member variable to EntityDescription.Inception
LEXEVS-367Support retrieval of ValueSetDefinition by multiple coding schemes.Inception
LEXEVS-366Modify output parameter of the getCodingSchemesInValueSetDefinition method in LexEVSValueSetDefinitionServices.Inception
LEXEVS-368Support retrieval of ValueSetDefinition by multiple concept domains.Inception
LEXEVS-365Resolve nested value set definition through distributed Value Set API.Inception
LEXEVS-363Extend MappingExtension functionalities to support restrictions.Inception
LEXEVS-354Load source qualifiers for generic properties in NCI-META RRF loaderInception
LEXEVS-350Examine use of LexBIG entity statusInception
LEXEVS-531Build scripts do not have path for dataqaInception
LEXEVS-255Linux gui does not workInception
LEXEVS-233SNOMED Role Groups not loading from RRF filesInception
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

21739

CodedNodeGraph resolveAsList distributed method encountered Java heap space error. Deferred - This item has been discussed and is not an issue for 6.0.

Inception

21740

Heap space error on Doubpe Metaphone MetaThesaurus query. Deferred - This item has been discussed and is not an issue for 6.0.

Inception

23598

REST API Features. Deferred - This item has been discussed and is not an issue for 6.0.

Inception

23611

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

25945

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-371Make it easy to do retrieval of only active concepts in a terminology through the/ a serviceInception
LEXEVS-362Owl/rdf exporter limitationInception
LEXEVS-345Convert codes in entity description of anonymous class to names.Inception
LEXEVS-512LexEVSValueSetDefinitionServices.getCodedNodeSetForValueSetDefinition method can be extremely slow.Inception
LEXEVS-508Mapping concepts don't always have a suitable targetInception
LEXEVS-507Inefficient query when trying to filter Metathesaurus by Source.Inception
LEXEVS-496LexEVS api calls do not populate directionalName in the associationInception
LEXEVS-515Caching of value sets don't always workInception
LEXEVS-518Trying to load ICD10 results in errorInception
LEXEVS-516LexEVSValueSetDefinitionServices getValueSetDefinitionEntitiesForTerm fails on inactive coding schemes.Inception
LEXEVS-519Inconsistant package namingInception
LEXEVS-461Necessity to rebuild indexes after loadInception
LEXEVS-538Loader should support unicodeInception
LEXEVS-521Transition table hangs in UMLS loader on large vocabsInception
LEXEVS-244Unqueryable classes are registered by the grid serviceInception
LEXEVS-232The codedNodeGraph is not displaying the top nodes correctlyInception
LEXEVS-235PDQ load shows multiple LT : TRD properties in browserInception
LEXEVS-234RRF Snomed Loader not interpreting SNOMED status codes correctlyInception
LEXEVS-230The contains algorithm fails on search strings starting with a single character word such as 'a'.Inception
LEXEVS-442NCIt Loader preferences file with defaultsInception
LEXEVS-361Unregister coding scheme supplement through the LexBIG GUI application.Inception
LEXEVS-360Add a Boolean-Valued member variable applyToSubconcepts to EntityReference.Inception
LEXEVS-359Need an effective way of counting the size of a CNG.Inception
LEXEVS-356GUI should reflect administrative nomenclatureInception
LEXEVS-358Authoring Tool / Graphical User Interface (GUI)Inception
LEXEVS-353Need an option to exclude the focused node itself from ResolvedConceptReferenceList when resolving a CNG.Inception
LEXEVS-352Better validation on restrictionsInception
LEXEVS-347Control the setting of isActive via Loader preferencesInception
LEXEVS-348Ability to query for inferred data - implement ability to reason

Inception

Inception
LEXEVS-344Enhance LexBIG query API to fetch AssociationData objects.Inception
LEXEVS-269Demonstrate cross ontology relationshipsInception
LEXEVS-264Validation of UTF-8 subsetInception
LEXEVS-250Duplicate alias &quot;_value&quot; when quering LexEVSDataServiceInception
LEXEVS-510Documentation location in the installerInception
LEXEVS-511UMLS meta loader script is in the wrong formatInception
LEXEVS-509Sorting in Mapping tab in Term Browser can lead to 500 errorsInception
LEXEVS-500Load Progress indicatorsInception
LEXEVS-517LexEVSAuthoringServiceImpl 'getEntity' restricts to types of 'concept'Inception
LEXEVS-469Attempted load of a MRMAP mapping failed with inscrutable errorInception
LEXEVS-482Ability to load metadata and mapping in one operationInception
LEXEVS-481Ability to load metadata and coding scheme in one operationInception
LEXEVS-475Enhancement to versioning of Mapping loadsInception
LEXEVS-480Better support for "Metathesaurus" data structures (e.g. accessing source hierarchies in NCI-META)Inception
LEXEVS-478Clean up GUI - functionality should match documentaion/presentationInception
LEXEVS-476Ability to load MRMAP without a MRSAT entryInception
LEXEVS-474Ability to add metadata to value set definitionsInception
LEXEVS-473Concept Sorting in Mappings when using local APIInception
LEXEVS-446UMLS loader should give an error if the SAB is not specifiedInception
LEXEVS-454OWL Export exhibits memory leak.Inception
LEXEVS-493Search SNOMEDCT for '<' using the contains algorithm returns no matches.Inception
LEXEVS-464The NCI OWL loader is loading the "type" property inconsistentlyInception
LEXEVS-463The NCI OWL loader is loading Metadata properties inconsistently.Inception
LEXEVS-462NCI OWL loader for LexBIG 6.0 is creating extraneous "label" property qualifiersInception
LEXEVS-460Enable use of ALT keys in LexEVS Developer GUIsInception
LEXEVS-459Batch Loader for LexEVS Value SetInception
LEXEVS-529ValueSetDefinition getDefinitionEntryCount() returns incorrect numberInception
LEXEVS-537JIRA task - Unable to assign issues to QA person, and not Ready For QA statusInception
LEXEVS-536The ResolvedConceptReferencesIterator numberRemaining method can be quite inaccurate.Inception
LEXEVS-535Term Browser "View In Hierarchy" function fails for ICD10 root nodesInception
LEXEVS-534Reduce error volume for hibernate issuesInception
LEXEVS-525Metathesaurus does not load completelyInception
LEXEVS-528Suppressable CUIs in RRF loaderInception
LEXEVS-22320653Anonymous class hierarchy with unions not showing up correctly. Deferred due to priority.Inception
LEXEVS-341REST API Features

27849

LexEVS 5.0 Silver Level Review. Out of Scope - Compatibility Review process change.Inception

27854

LexEVS 6.0 Silver Level Compatibility Review Submission Package. Out of Scope - Compatibility Review process change.

Inception

LEXEVS-339MedDRA loading into LexEVSInception
LEXEVS-497Documentation IssueInception
LEXEVS-502Spelling error in loader

 

CTS2 Semantic Profiles:  Developing Terminology Profile, HL7 Terminology ProfileInception

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 JIRA site:

[https://gforge.nci.nih.gov/projects/lexevs/
]

 

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
GForge documents (deliverables)

 

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.

...