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Contents

Q. What is LexBIG?

LexBIG is a project that applies LexGrid vision and technologies to requirements of the caBIG™ community. The goal of the project is to build a vocabulary server accessed through a well-structured application programming interface (API) capable of accessing and distributing vocabularies as commodity resources. Primary objectives for the project include:

  • Provide a robust and scalable open source implementation of EVS-compliant vocabulary services. The API specification is based on but not limited to fulfillment of the caCORE EVS API. The specification also accommodates changes and requirements based on prioritized needs of the caBIG™ community.
  • Provide a flexible implementation for vocabulary storage and persistence, allowing for alternative mechanisms without impacting client applications or end users. Initial development will focus on delivery of open source freely available solutions, though this does not preclude the ability to introduce commercial solutions (e.g. Oracle).
  • Provide standard tooling for load and distribution of vocabulary content. This includes but is not limited to support of standardized representations such as UMLS Rich Release Format (RRF), the OWL web ontology language, and Open Biomedical Ontologies (OBO).

The LexBIG package represents a compressive set of software and services to load, publish, and access vocabulary. Cancer Centers can use the LexBIG package to install the NCI Thesaurus and NCI Metathesaurus and query content via a rich application programming interface (API). LexBIG services can also be incorporated into numerous applications wherever vocabulary content is needed.

Q. How do I install the software?

Refer to the Installation and Administration Guide, which can be downloaded from the Files tab of the LexBIG GForge project.

Q. How do I load vocabularies

Content can be loaded using either the administrative functions provided by the LexBIG Graphical User Interface (GUI) or counterpart command-line scripts. Refer to the Installation and Administration Guide, which can be downloaded from the Files tab of the LexBIG GForge project or referenced in the /doc folder of the installed materials.

Q. How do I access vocabularies in my programs?

Refer to the Programmer Guide, which can be downloaded from the Files tab of the LexBIG GForge project or found in the /doc folder of the installed materials.

Q. Once LexBIG is deployed onto the server and content is loaded, what is the best way to interact with it?

LexBIG services are delivered as middleware. Refer to the previous question if the goal is to interact through a client program.

  • If the goal is to interact through a graphical user interface, other options are available. The LexBIG GUI, as described in the programmer and administration guides, provides a basic API-centric way to query and visualize content. It is a development time tool written for audiences that are both technical and somewhat familiar with the LexBIG API.
  • If the goal is to provide a general purpose end-user interface, other options are available. One browser-based front end to LexBIG is BioPortal. The BioPortal code base originates as part of work done by the National Center for Biomedical Ontology (NCBO), and provides the basis for the NCI BioPortal. The NCI BioPortal is available from NCI at (http://gforge.nci.nih.gov/projects/lex-browser/).

Q. Do I need to develop my own application client to create/update/search a concept and for imports/exports?

Searching can be accomplished by one of the browser interfaces described above. However, content creation and maintenance are considered out of scope for the current LexBIG API which addresses load, publish, and query of fully versioned ontologies. LexBIG can consume many types of file formats (e.g. XML, OBO, RRF, OWL) as versioned ontologies. Given any structured source, it should be possible to review these files and create a transform for load into the LexGrid repository.

Q. Can I deploy LexBIG to operating systems other than Windows or Linux?

While you shouldn't need a separate installer, you will need to have the correct Java JDK installed for the system you are on. Some limitations will automatically apply. The GUI installer and a GUI browser may have problems with operating systems other than Windows or Linux. If the browser has options, note that we do have a fair amount of command line demonstration code that you might exercise in the package's Admin and Example folders.

Note that environments other than Windows or Linux are not tested or formally supported.

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