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National Cancer Institute Center for Bioinformatics
Product LexEVS 5.

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1 Release Notes

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December 18 2009

Product Changes

• New Feature: Removed convenience methods for codeToName
  CF#15222
• New Feature: Update to work with SDK 4.1
  CF#15942
• New Feature: Javadocs should open in new window
  CF#16686
• New Feature: LexBIG GUI launch support for OSX environment
  CF#16989
• New Feature: Import RRF Representation of Relationship Groups
  CF#17019
• New Feature: CodingSchemeId not present in exported LexGrid XML
  CF#17183
• New Feature: OWL Loader Enhancements
  CF#17233
• New Feature: Finalize BDA for 5.0 release
  CF#17508
• New Feature: Model revisions & readiness for Silver/Gold Compatibility
  (scope modified & approved 1/14/09)
  CF#17509
• New Feature: 5.0 Data Services/SDK
  CF#17511
• New Feature: 2009/01 model changes
  (please see Gforge tracker for more detail on the nature of the changes and further descriptions)
  CF#18449
• New Feature: Add 'namespace' to the Lucene Indexes
  CF#19883
• New Feature: Change name of ProtegeFramesLoader to RadlexProtegeFramesLoader
  CF#19888
• New Feature: Rename getParentsOf() and getChildrenOf()
  CF#19889
• New Feature: Support query of non-concept entities
  CF#19890
• New Feature: Creation of XSL stylesheets for transformation of LexBig data to n-1 LexBig versions
  CF#20043

• Bug: Implement getAssociation for EVS API web service
  CF#15091
• Bug: Two constructors create ConceptReferenceList methods throw exceptions
  CF#15976
• Bug: Example to dump/query auxiliary metadata
  CF#16508
• Bug: Better error handling for invalid search criteria in http interface
  CF#16579
• Bug: Users should have the ability to request Search results be sorted
  CF#17161
• Bug: Remove JUnit test dependency on 'Automobiles' vocab for LexEVS Grid Services
  CF#17405
• Bug: Change -nf option to -fe (fail on error)
  CF#17410
• Bug: EntityDescription not assigned to the NCI PT (rdfs:label) using Scrubber output
  CF#17421
• Bug: LexBIG History 'getEditActionList' Error
  CF#19411
• Bug: Owl loader fails when duplicate objectProperty is loaded from two namespaces
  CF#19462
• Bug: Supported Coding Scheme default is set even when coding scheme name is specified in manifest
  CF#19484
• Bug: Applying manifest with only an association forward/reverse name receives 'String index out of range' exception.
  CF#19485
• Bug: CodedNodeGraph not resolving across ontology boundary
  CF#19492
• Bug: Entity 'isActive' not being indexed correctly on Postgresql and MS Access
  CF#19573
• Bug: Problem applying supportedNamespace
  CF#19586
• Bug: Unable to load NCIT v9.01d and other large ontologies
  CF#19600
• Bug: Equivalent CodingScheme on SupportedNamespace default value not being set correctly.
  CF#19628
• Bug: Relationships not resolving that contain a Namespace that has a localId that does not match the CodingScheme.
  CF#19629
• Bug: CodingSchemeProperties not being persisted to the database.
  CF#19702
• Bug: LexBIG property behavior does not match EA model
  CF#19716
• Bug: Transitivity Table not being built
  CF#19741
• Bug: Supported Hierarchies not being fully populated in 2.3 - 5.0 Compatibility Test
  CF#19864
• Bug: LexBIG 2.3 xml import command fails
  CF#19900
• Bug: Metathesaurus history accessing wrong column name
  CF#20032
• Bug: Owl loader ClassCast Exception while loading OWLObjectProperties
  CF#20037
• Bug: Lucene Indexer fails with empty EntityDescription
  CF#20068
• Bug: EMF loaders fail while inserting CodingScheme Properties
  CF#20070
• Bug: Exception entering null into BIGINT column on PostgreSQL database.
  CF#20193
• Bug: Blank description in the Service Context on grid portal
  CF#20419

Important Remaining Issues

Make use of logging consistent - elminate system out. We will address this if time permits
CF#14971
The NCI_Thesaurus association Has_Salt_Form and Has_Free_Acid_Or_Base needs reverse name. We will address this if time permits.
CF#15975
gov.nih.nci.evs.domain.Atom.getLUI does not return value. We will address this if time permits.
CF#15667
Serializer Exception on org.apach.lucene.search.regenex. We will address this if time permits.
CF#16678
Results not Deserializing Properly when using QueryModifiers on CQL Queries
CF#19406
Root concepts found by ListHierarchyMetaBySource when running against NCI MetaThesaurus with source set to NCI are different from root concepts in NCI Thesaurus.
CF#20354

Fixed Since Last Release - Bugs

21567 - ResourceManager cache not Thread-safe
21923 - Connection Leak on SQLImplementedMethods 'mapToCodingSchemeName'
22355 - LexGrid XML exporter not writing correctly if there are two Enitities with the same code but different namespace
22743 - Unable to resolve GO and CTCAE hierarchy roots.
23278 - CodedNodeGraph restrictToAssociations fails with Qualifier containing null value
23359 - Supported Attributes missing from 5.1 NCI Thesaurus 09.08e
23456 - Loaded MedDRA - unable to see Code System Details
23755 - Semantic_Type Property not being loaded by Meta Loader
23761 - Delay advancing a ResolvedConceptReferencesIterator in Distributred mode
23858 - Duplicate results returned on CodedNodeSet resolve
24148 - PathToRoot over-protecting for looping hierarchy paths

Feature Requests

21716 - Add data from MRSAT file to NCI Meta data
21717 - MRSAB conifgured to load for NCI Meta data
21718 - MRREL data for NCi Meta - needs more data loaded
21719 - Load MRRANK data for NCI Meta
21721 - Add some additional data from MRHIER
21722 - Make sure MRDOC data for NCI Meta is loaded
21723 - Add more data from MRDEF file for NCI Meta
21724 - Add data from MRCONSO file to NCI Meta data
21849 - Add an algorithm for supporting case-insensitive substring search.
21850 - Add a search algorithm for supporting case-insensitive substring search with an additional spelling-error tolerant feature.
21879 - Improve error messages (e.g., CNS.resolve, CNS.resolveToList, CNG.resolveToList)
21881 - Improve ResolvedConceptReferencesIterator performance by reducing client-server network traffic in distributed mode.
21882 - LexEVS 5.1 Value Domain Support
21976 - Improve LexEVS Loading Framework
21980 - Optimize Lucene code to improve search performance
21982 - Implement a server side sort to improve performance
22006 - General SQL optimization
22565 - Add special character search
22893 - Add asserted relations into the transitive table
23053 - Load TUI as a Property in UMLS loader
23071 - Allow multiple CUI Properties per UMLS Entity

Important Remaining Issues / Limitations

• Value Domain (CTS 2 Value Set) support in the 5.1 release is not fully implemented and is offered as a capability that developers of LexEVS dependent applications and services can use to familiarize themselves with value domains in a non-production setting. Production use of Value Domain fuctionality should be delayed until the release of the 6.0 build of LexEVS.
• LexBIGServiceConvenienceMethods in the 5.1 release are not all adapted for use in distributed mode and should not be attempted to be used distributed. These include getHierarchyOrphanedConcepts(), getHierarchyLevelNextCount(), getHierarchyLevelPrevCount(), addEntityLuceneIndexes(), removeEntityLuceneIndexes(), modifyEntityLuceneIndexes().

Deferred/Deprecated Items

Bugs

19406 - Results not Deserializing Properly when using QueryModifiers on CQL Queries
20590 - Not all concept status property values are accessible through the API.
20653 - Anonymous class hierarchy with unions not showing up correctly.
20661 - Ontology for Genetic Interval hierarchy does not match up Protege
20665 - ECG Ontology missing Description, Date, Source and Creator fields
20684 - Can not compute root node for OBI version v1.0.1423
20797 - Strict Owl Processing
23770 - OBI.owl loading - missing property "has curation status" for concepts
23806 - OBI.owl loading - Incorrect infromation as value to the property "imported from"
24967 - Null-Pointer Exception Thrown when no value-Domain content loaded.

Feature Requests

21720 - Load all MRMAP data
22877 - MedDRA loading into LexEVS
22887 - BDA Certification
23324 - Option to include or exclude anonymous concepts.
23598 - REST API Features
23611 - LexEVS Value Domain Support to include persistance of resolved value domain content
23643 - Java 1.6

CORE Product Dependencies

Refer to the CORE Product Dependency Matrix for the caCORE SDK and other software technologies on which this release of this product relies.

Release History