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Document Information

Author: Traci St.Martin/Craig Stancl
Email: stmartin.traci@mayo.edu, stancl.craig@mayo.edu
Team: LexEVS
Contract: RFP 10-ST1099
Client: NCI CBIIT
National Institutes of Heath
US Department of Health and Human Services

Contents

Sign off

Date

Role

CBIIT or Stakeholder Organization

 


 


 


 


 


 


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
(hyperlinked)

Brief description of functional requirement
(enhancement or new feature)

Status
(Approved or Proposed)

Iteration

26638

OBO Loader update for LexEVS 6.0

Proposed

 

26640

NCIt/OWL loader update for LexEVS 6.0

Proposed

 

26641

Query enhancements for CTS2 Implementation LexEVS 6.0

Proposed

 

26642

XML Exporter update for LexEVS 6.0

Proposed

 

26643

NCIm Loader updates for LexEVS 6.0

Proposed

 

26644

HL7 loader update for LexEVS 6.0

Proposed

 

26645

Coding Scheme Supplement Changes for LexEVS 6.0

Proposed

 

26646

Usage context enhancements for LexEVS 6.0

Proposed

 

26648

Associations (maps) enhancements for LexEVS 6.0

Proposed

 

26649

Concept Domain enhancements for LexEVS 6.0

Proposed

 

26650

Value Set Enhancements for LexEVS 6.0

Proposed

 

26651

Versioning enhancements for LexEVS 6.0

Proposed

 

26652

XML loader update for LexEVS 6.0

Proposed

 

26653

ICD10 loader update for LexEVS 6.0

Proposed

 

26654

ICD 9 loader update for LexEVS 6.0

Proposed

 

26655

UMLS loader update to support LexEVS 6.0

Proposed

 

26656

Database changes to support LexEVS 6.0

Proposed

 

26657

LexGrid model changes for LexEVS 6.0

Proposed

 

26658

LexBIG model changes for LexEVS 6.0

Proposed

 

26659

DAO layer changes for LexEVS 6.0 CTS2 Implementation

Proposed

 

27829

Text loader update for LexEVS 6.0

Proposed

 

27831

Manifest loader update for LexEVS 6.0

Proposed

 

27838

Notification enhancements for LexEVS 6.0

Proposed

 

27839

OBO Exporter update for LexEVS 6.0

Proposed

 

27840

Associations Exporter for LexEVS 6.0

Proposed

 

27841

Protege Frames Loader update for LexEVS 6.0

Proposed

 

27842

Loader Preferences Loader update for LexEVS 6.0

Proposed

 

27843

Authoring enhancements for CTS2 Implementation LexEVS 6.0

Proposed

 

27844

ISO 21090 Data Type Support enhancements for CTS2 Implementation LexEVS 6.0

Proposed

 

27845

Grid Service enablement CTS2 Implementation LexEVS 6.0

Proposed

 

28166

GEM loader update for LexEVS 6.0

Proposed

 

28167

ClaML Loader update for LexEVS 6.0

Proposed

 

21720

Load all MRMAP data

Proposed

 

23643

Java 1.6

Proposed

 

26329

Control the setting of isActive via Loader preferences

Proposed

 

27026

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

Proposed

 

24699

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

Proposed

 

25509

Convert codes in entity description of anonymous class to names.

Proposed

 

26627

Ability to keep database load if indexes fail.

Proposed

 

26637

Page CodedNodeGraph Results

Proposed

 

26683

Option to include or exclude entity types in association search.

Proposed

 

26709

Examine use of LexBIG entity status

Proposed

 

28120

Provide XSLT transformations for backwards compatability of LexBIG XML

Proposed

 

24191

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

Proposed

 

 

 

 

 

Functional Bug Fixes

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

GForge number
(hyperlinked)

Brief description of bug

Status
(Approved or Proposed)

Iteration

21935

OWL loader processing <owl:Restriction> associations incorrectly

Proposed

 

22036

Focus code data is not found when referencing external coding scheme

Proposed

 

24037

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

Proposed

 

24538

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

Proposed

 

25042

OBI load shows odd has_curation_status property

Proposed

 

25325

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

Proposed

 

26072

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

Proposed

 

26975

PropertyLinks won't load without namespace being supplied

Proposed

 

26976

Loader should not shut down on a duplicate property

Proposed

 

26977

Loader should not shut down on missing propertylink reference

Proposed

 

22296

OWL loader does not load concepts with paranthesis

Proposed

 

25681

Problem loading MeSH and Spanish version of SNOMED

Proposed

 

24967

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

Proposed

 

23770

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

Proposed

 

23806

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

Proposed

 

19406

Results not Deserializing Properly when using QueryModifiers on CQL Queries

Proposed

 

 

 

 

 

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
(Approved or Proposed)

Iteration

26660

LexEVS 6.0 Project Charter

Proposed

 

27849

LexEVS 5.0 Silver Level Review

Proposed

 

27854

LexEVS 6.0 Silver Level Compatibility Review Submission Package

Proposed

 

27856

BDA Compliance Package update for LexEVS 6.0

Proposed

 

27857

Release Notes for LexEVS 6.0

Proposed

 

27859

LexEVS Product Documentation (Wiki Guides) for LexEVS 6.0

Proposed

 

27860

LexEVS NCI/NCICB website updates for LexEVS 6.0

Proposed

 

27861

LexEVS 6.0 ECCF Documentation

Proposed

 

27862

LexEVS 6.0 System and Software Design Document

Proposed

 

27863

LexEVS 6.0 Design Review Package

Proposed

 

27864

LexEVS 6.0 Deliverable Readiness Review Package

Proposed

 

28159

6.0 Deployment to Dev Tier

Proposed

 

28161

6.0 Deployment to QA Tier

Proposed

 

28162

6.0 Deployment to Stage Tier

Proposed

 

28163

Project plan for 6.0

Proposed

 

28164

6.0 Test Plan & Test Results

Proposed

 

28165

6.0 Use Case Document

Proposed

 

28168

6.0 ARC Document

Proposed

 

28169

6.0 Prototype 1

Proposed

 

28170

6.0 Prototype 2

Proposed

 

28172

6.0 Prototype 3

Proposed

 

28173

6.0 Alpha 1

Proposed

 

28174

6.0 Alpha 2

Proposed

 

28175

6.0 Deployment to Production Tier

Proposed

 

28177

6.0 Production Announcements

Proposed

 

 

 

 

 

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
(Approved or Proposed)

Iteration

 

LexEVS Level 2 Support -  integration of help and training to the user community.

 

 

 

 

 

 

Stakeholder Summary

Customer Name

Role

Interest/Need

Jason Lucas

NCI Metathesaurus Browser Project Manager

Project schedule and task management for browser team

 

 

 

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

NCI EVS 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.

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)

<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="2378e4a7-10bb-4f29-a935-7f6098c44971"><ac:plain-text-body><![CDATA[

[Other]

 

]]></ac:plain-text-body></ac:structured-macro>

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
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

21336

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

26628

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

23324

Option to include or exclude anonymous concepts. Deferred due to priority.

Inception

20653

Anonymous class hierarchy with unions not showing up correctly. Deferred due to priority.

Inception

 

 

 

Document History

Document Version:

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Last Modified:

Refer to the first line displayed in the document window.

Project GForge 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:  https://wiki.nci.nih.gov/display/EVS/LexEVS+6.0;jsessionid=FC91B299FBF01E1498CDCDAE6D3975F6&nbsp;
Gforge documents (deliverables):  https://gforge.nci.nih.gov/docman/index.php?group_id=491&selected_doc_group_id=5428&language_id=1

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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