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This list of frequently-asked questions (FAQs) about LexBIG is organized by subject and may include links to forum topics and other sources in addition to Knowledge Base articles. If you don't find an answer to your specific question, please email the VKC:Vocabulary Knowledge Centeror post a question in the LexBIG User forums.

General

Question: Can you explain the interaction with LexBIG?

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Answer: A "Coding Scheme Manifest" (or simply "manifest" as used interchangeably in this document) encapsulates the user-supplied values to set for a coding scheme while loading or converting an OWL (currently it a manifest is supported only for OWL type of files) source to LexGrid format.

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Answer: When a terminology is being converted to the LexGrid data model from its native format (in this case OWL), Coding Scheme information is read from the source file. Sometimes values may be missing (not provided or invalid) or the author/user of the terminology wants to override or set default values despite (or in addition to) what is provided in the source file. This can be accomplished using "manifest" files along with the source file.

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Question: Can I deploy LexBIG to operating systems other than Windows or Linux?

Answer: 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, in the package's Admin and Example folders, 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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Answer: Searching can be accomplished by a graphical user interface or a general purpose end-user interface such as the NCI Term Browser. 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.

User Interface

Question: How are Vocabularies Loaded into LexBIG?

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Answer: LexBIG is distributed with an older version of the Java MySQL driver due to licensing concerns. If LexBIG reports an error concerning establishing a connection to the MySQL server yet the MySQL CLI is able to connect, a new version of Connector/J may be required. To update the driver, download the latest version from the MySQL site and place the mysql connector .jar file in the <install-root>/runtime/sqldrivers directory.

Also, be sure to rename or remove the older mm.mysql-2.0.6.jar to prevent any classpath issues.

The older jar file was sufficient to work with older mySQL environments, but has problems working with the latest MySQL 4.x and 5.x releases. Note that we cannot redistribute the latest driver due to license restrictions. It is likely that future LexBIG/LexEVS releases of the Java API will removethis remove this older jar entirely, and require download as a separate step taken by
the administrator as part of install.

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The download location and reference to 'RELEASE_INFO.RRF' (also misspelled in the guide) are outdated and no longer correct. .

Regarding the RELEASE_INFO file - notes dating to early 2006 indicate this file was a standard part of UMLS distributions and expected by the loader. It was not a standard part of the NCI RRF distribution, however, which is why it was noted in the guide. This file is no longer referenced or required by the NCI Meta loader. We recently loaded from versions without this file present as part of recent release testing (e.g. 200802D).

This information will be updated in documentation for future releases.

Plugins

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No FAQs posted at this time

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