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National Cancer Institute Center for Bioinformatics
NCI Thesaurus Browser 2.0 Release Notes

Overview

NCI Term Browser provides a consistent, user-friendly tool to browse and search all of the biomedical terminologies hosted by NCI EVS, including both NCI Thesaurus (NCIt) and the NCI Metathesaurus (NCIm), which itself includes more than 70 terminologies. These terminologies normally represent each specific meaning, such as melanoma, lung, or chemotherapy, by a distinct concept with a unique, permanent code. Each concept normally provides additional information such as a preferred name, other terms and codes, definitions, and relationships with other concepts. Concepts are normally organized in parent-child hierarchies from very broad top concepts down to the most specific subcategories. All browsing and searching in this browser reflects this concept-based view of terminology.

Support:
GForge project archive; Docs archive, Files archive

Important Remaining Issues

Cart functionality behavior for multiple terminologies -  You may save visited concepts to a cart and export these concepts to a file in either LexGrid XML format or Comma Separated Values (CSV) format at a later time. Because the browser supports multiple versions of the same terminology (for example MedDRA 12.0 and 13.1), you will be prompted for the terminology version when you are ready to export concepts in carts. Please be aware that if a concept in the cart is not found in the version of the terminology you specified, then you should not expect the concept to appear in the file. For example,  the MedDRA concept Traumatic renal injury (Code 10070510) appears in MedDRA 13.1, but not in MedDRA 12.0. So, if you visit the concept, save it to the cart, then try do an export, selecting 12.0 as MedDRA version, then you won’t find this concept in the export.

Concept Code search on Mappings tab is case sensitive -The Mappings Concept Code search is case sensitive.  For example, if a user is on the Mapping tab and does a Concept Code search on go:0006200, the search will come back empty.  The user will need to do the same search using uppercase letter (GO:0006200) to get the result back. This is something we plan on fixing in a future release.

Search box on the Value Set tab Terminology View and Source View pages - Please be aware that the sole purpose of the search box on the Terminology View and Source View pages is for finding Value Sets containing at least one concept that match with your search criteria. So, search results would remain the same if no search criteria is changed when you perform a search on these pages. To search against a particular matched value set returned by the above search, you should click on a matched value set hyperlink to go to its home page and then perform search there.

Release 2.0 features

The NCI Term Browser 2.0 release provides access to the CTS 2 functionality provided in the LexEVS 6.0 terminology server including Mappings and Value Sets search and display. This release also includes an advanced search and concept cart capabilities. Additional details are listed below:

GF#24935 - Inverse association & inverse role: display should be configurable

GF#27282 - UMLS CUI - remove link for RRF sources

GF#28514 - Tree retired GO concepts

GF#26722 - Support cross-linking of individual source vocabularies with NCI Metathesaurus.

GF#23316 - Cart for concepts

GF#23935 - Be able to disable tree access

GF#24610 - Inverse roles not covered in Relationship search

GF#26761 - Display caDSR CDEs based on concepts in applicable vocabularies.

GF#27771 - Add advanced search by a specific property type or association.

GF#29301 - Support the search and display of mapping data.

GF#29369 - Convert code base to LexEVS 6.0 Alpha.

GF#29761 - Display Report Writer's generated reports

GF#29304 - Browser must be navigable by keyboard only - Section 508

GF#29316 - Pages need column headers with scope

GF#29819 - Support local extension to an existing coding scheme.

GF#29928 - Cache hierarchies after startup

GF#29966 - Handle coding schemes with multiple namespaces.

GF#30148 - Allow access to mapping data from source and target coding schemes.

GF#30154 - Add a map_rank_applicable element to mapping coding scheme metadata.

GF#30155 - Make the Map Rank column of the mapping table configurable.

GF#30156 - Add abbreviated source and target namespace names to metadata of a mapping coding scheme.

GF#30157 - Display abbreviated source and target namespace names on the mapping data table.

GF#30158 - Add a Mapping Tab to the navigation bar.

GF#28514 - Tree retired GO concepts.

GF#28640 - HUGO: Inconsistencies on Terms & Properties

GF#30457 - Redesign term browser home page using tabs.

GF#30505 - Update on-line Help page.

GF#30632 - Implement value set viewer.

GF#30699 - Merge all license pages into one

GF#30768 - Switch Relationships and Synonym Details tabs.

GF#30787 - UI changes (slight overhaul)

GF#30790 - Export NCI Definition to CSV formatted resolved value set definition file.

GF#30809 - Redesign term browser home page.

GF#30811 - Remove download from the main menubar.

GF#30828 - Develop a source coding scheme for supporting display of value set hierarchy.

GF#30829 - Display value set hierarchy.

GF#30833 - ChEBI Link

Bugs Fixed Since Last Release

GF#24618 - Defined Fully by Roles not relevant for most sources

GF#27034 - GO_Annotation in NCI Thesaurus not showing up as complex property

GF#28640 - HUGO: Inconsistencies on Terms & Properties

GF#28687 - Term browser displays OBO roles as associations

GF#28826 - Update hyperlink to Swiss Prot site

GF#28455 - OBI View Hierarchy has nothing to show

GF#28486 - GO, PDQ, UMLS Concepts "View in Hierarchy" are not treed correctly

GF#28687 - Term browser displays OBO roles as associations

GF#29667 - Alt text on Advanced Search has typo - Section 508

GF#29865 - Terms browser unable to display multiple versions of same ontology

GF#30297 - HL7 Vocabulary being identified as the HL7 RIM in the browser

GF#30298 - Failure to search in ncimeta

GF#30443 - disappearing rels in term browser

GF#30504 - Error message for no terminlogy selected worded incorrectly.

GF#30545 - View in Hierarchy shows more than 5 parent levels above the concept

GF#30727 - Problem when user does not specify a Vocabulary in Search

Known issues

GF#31019 - Bookmark return to Term Browser (using Firefox) returns Terminologies page with incorrect tab highlighted.

GF#31073 - Concept Code search on Mappings tab is case sensitive.

GF#31124 - Clicking Source Name under Mappings does not sort the concepts by name.

GF#31167 - Search against Matched Value Sets returns nothing.

GF#31169 - Property Search in Mappings tab does not return any results.

GF#31182 - Clicking on a Concept on the HL7 Hierarchy returns an Error code.

GF#31204 - Relationship Simple Search for "gene" returns a blank concept list.

GF#31210 - Target Name link does not not sort concepts in Mappings.

GF#31273 - Anonymous concepts appear in value sets.

GF#30159 - Populate the mapping tab based on the atom data contained in NCI Metathesaurus.

GF#30203 - Create a map ranking score help page.

GF#30428 - Design value set viewer.

CORE Product Dependencies

This product (internally) relies on LexEVS 6.0 APIs for access to all source terminology data. Refer to LexEVS 6.0 for details.

Release History

Release

Date

Description

NCI Thesaurus Browser v1.0

7/28/2009

Initial release

NCI Thesaurus Browser v1.2

10/19/2010

New Features and fixes

NCI Thesaurus Browser v2.0

November 2011

Access to the CTS 2 functionality provided in LexEVS 6.0

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