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The Lexical Grid
Currently, there are many terminologies and ontological resources available (ICD-9, NCI Thesaurus, SNOMED-CT). However, many of these resources involve incompatible formats, tooling, and programming interfaces. This can make it difficult to use these resources to their full potential. The Lexical Grid (LexGrid) project is an initiative of the Mayo Clinic Division of Biomedical Informatics (BMI) designed to bridge this gap using common tools, data formats, and read/update mechanisms. Resources on the Lexical Grid are intended to be:
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In short, LexGrid provides the standardized building blocks and tools to take advantage of vocabulary and ontology content where and when needed, thereby providing the infrastructure necessary to support large-scale terminology adoption and use. Additional information for LexGrid is available on the LexGrid page.
LexGrid Features
- Accommodation of multiple vocabulary and ontology distribution formats
- Support of multiple data stores to accommodate federated vocabulary distribution
- Consistent and standardized access across multiple vocabularies
- Rich API for supporting lexical and graph search and traversal
- Fully compatible with HL7-CTS implementation
- Support for programmatic access via Java, .NET, and web services
- Open source tooling and code to facilitate adoption and use
LexGrid Users
LexGrid is intended to meet the needs of the following groups:
- Vocabulary service providers - Describes organizations currently supporting externalized API-level interfaces to vocabulary content
- Vocabulary integrators - Describes organizations that desire to integrate new vocabulary content or relations to be served locally
- Vocabulary users - Describes persons and organizations desiring common, consistent access to vocabulary content for a supporting multiple application development uses
LexGrid Principles
LexGrid software is based on a model-driven architecture. The LexGrid model (further described below) is maintained in XML-Schema format and represents a core component of design. The LexBIG API, a Java-based API to LexGrid content (also described below) is formally modeled and accommodates registration of additional load, index, and search functions. The LexBIG API also provides a conscious separation of service and data classes in order to support deferred query resolution and software iterators.
LexGrid Model
The LexGrid Model is Mayo's proposal for standard storage of controlled vocabularies and ontologies. The LexGrid Model defines how vocabularies should be formatted and represented programmatically, and is intended to be flexible enough to accurately represent a wide variety of vocabularies and other lexically-based resources. The model also defines several different server storage mechanisms (e.g., relational database, LDAP) and a XML format. This model provides the core representation for all data managed and retrieved through the LexBIG system, and is now rich enough to represent vocabularies provided in numerous source formats including:
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Implementation or technology-specific renderings of the model also exist. These include relational database schema (MySQL, PostgreSQL, DB2, Oracle, etc.) and Lightweight Directory Access Protocol (LDAP) schema. Programming interfaces generated from the formal representation include Java bean interfaces based on the Eclipse Modeling Framework (EMF) and Castor frameworks.
LexGrid Components
This section provides a basic description of the building blocks, interfaces, and tools comprising the LexGrid project.
LexGrid Node
A LexGrid Node represents both software and a backing data store that provide a logical persistence layer for accessing, storing, and managing vocabulary content according to a formalized information model (described above). LexGrid nodes typically utilize relational database management systems for management of data and indexing functions. Implementations include but are not limited to MySQL, PostgreSQL, UDB/DB2, Oracle, Hypersonic, and LDAP/BDB.
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The *LexGrid Registry Service provides a mechanism to locate available vocabularies that are stored on one or more LexGrid nodes.
LexGrid Projects
LexGrid technologies are integrated and play an essential role in many vocabulary and ontology projects, meeting the needs of both the Mayo Clinic and external organizations. Some projects include the following:
- LexCTS - HL7 Common Terminology Services reference implementation
- LexBIG - LexGrid Vocabulary Services for caBIG®
- LexBIO - LexGrid Vocabulary Services for NCBO
- Mayo Clinic Life Sciences vocabulary services
- Mayo Surgical Index Retrieval Services ICD-9 codebook
LexBIG
Of these projects, perhaps the most significant and influential to LexGrid architecture, has been the LexBIG (LexGrid Vocabulary Services for caBIG®) project, which in turn provides the core infrastructure for the LexBIO and LexPHIN projects.
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LexBIG Graphical User Interface - Browse Query Results
LexBIG API
This section provides a brief introduction to the LexBIG application programming interface.
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Note: Additional information regarding API options and invocation is provided by the LexBIG Programmer's Guide (provided with the software distribution).
Links to Translated Versions of this page
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