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 LexBIG Terminology Server

NCI EVS is the lead adopter site for the open source public domain terminology server LexBIG, which is being developed by the Mayo Clinic as part of the caBIG_^® program. Effective with the release of EVS/caCORE 4.0, LexBIG provides the base terminology server infrastructure for EVS. EVS/caCORE release version 4.1 relies on LexBIG version 2.2.0.

LexBIG is based on the LexGrid Data Modelhttp://informatics.mayo.edu/LexGrid/index.php?page=lgm, Mayo's standard data model for 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 (for example, relational database, LDAP) and an XML format. This model provides the core representation for all data managed and retrieved through the LexBIG system, and is rich enough to represent vocabularies provided in numerous source formats including:

• Open Biomedical Ontologies (OBO)
• Web Ontology Language (OWL)
• Unified Medical Language System (UMLS)
• Rich Release Format (RRF)

This common model is a critical component of the LexBIG project and EVS/caCORE 4.x. Once disparate vocabulary information can be represented in a standardized model, it becomes possible to build common repositories to store vocabulary content and to build common programming interfaces and tools to access and manipulate that content.

LexBIG has three major components:

• Service Management tools to load, index, and manage vocabulary content for the vocabulary server
• An API providing Java interfaces to various functions including lexical queries, graph representation and traversal, and NCI change event history
• A Graphical User Interface providing access to service management and restricted API functions

The LexBIG API enables querying information stored in the LexGrid model. NCI and caBIG_^® are not alone in adopting LexGrid. An essentially identical API called LexBio has been developed for the National Center for Biomedical Ontologies (NCBO). NCI EVS has adopted a variant of NCBO's BioPortal as the terminology browser for EVS/caCORE 4.x. This variant is called NCI BioPortal.

LexGrid Vocabulary Services Project

Link provided for historical purposes
If you need access to these files, please contact Application Support: ncicbiit@mail.nih.gov
https://gforge.nci.nih.gov/projects/lexbig/

This project provided externalization and support of LexGrid-based terminology software (services, persistence, tooling) developed for the

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caBIG® Vocabulary and Common Data Elements workspace.

The goal of the project

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was a vocabulary server built using standards-based and commodity technologies and accessible through a well-structured application programming interface (API) capable of accessing and distributing vocabularies as commodity resources.

Primary objectives for the project

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included:

• Provide a robust and scalable open source implementation of EVS-compliant terminology services. The API specification is based on but not limited to fulfillment of the EVS/caCORE API. The specification is further refined to accommodate changes and requirements based on prioritized needs of the

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• caBIG® community.
• Provide a flexible implementation for terminology storage and persistence, allowing for alternative mechanisms without impacting client applications or end users. Initial development focuses on delivery of open source freely available solutions, though this does not preclude the ability to introduce commercial solutions such as Oracle.
• Provide standard tooling for loading and distribution of vocabulary content. This involves support of standardized representations in UMLS Rich Release Format (RRF) and the OWL web ontology language. Vocabulary editing, vocabulary submission, and vocabulary cross-linking are out of scope for this aim.

This project

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was developed by the Division of Biomedical Informatics at the Mayo Clinic College of Medicine.