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As primary reference, see the Installation and Administration Guide :

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in the GForge archive.

Building the LexBIG Installer from CVS

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Development and build processes are not dependent on a particular CVS client or programming environment. However, files with the extension '.classpath' and '.project' have been inserted into each project folder to help facilitate compilation and use within the Eclipse development environmentuse within the Eclipse development environment

Folder content and purpose

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• Command line: Download and unzip the latest stable version of Ant from the [Apache site|http://ant.apache.org/bindownload.cgi.

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  . Check out all project folders from CVS, and then run the Ant command against the build.xml file provided in lbCVSDeploy. If successful, files will be created in /lbCVSDeploy/dist/.
• Eclipse: Open the build.xml file in the Eclipse Ant view and run the default task. If successful, refresh the /lbCVSDeploy folder; files will be created in /lbCVSDeploy/dist.

How to enable ydoc

• /lbCVSDeploy/dist.

How to enable ydoc

• yDoc

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  yDoc offers the capability to add UML diagrams to the generated LexBIG JavaDoc.
  If the yDoc directory is present and a valid license is located in the /yDoc/resources directory, the enhanced yDoc support is automatically enabled and used. If not, standard JavaDoc is produced.

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A coding scheme manifest file is a valid XML file, conforming to the schema defined by http://LexGrid.org/schema/LexBIG/2007/01/CodingSchemeManifestList.xsd]

This XML file can define values for one or more coding schemes you are dealing with. Some coding scheme meta-information may not easily map to information in the source file. In this case a manifest file is of great help to bridge the gap and control the information flow while mapping to the LexGrid model. A detailed model of the LexGrid Coding Scheme and its fields can be found online. Structure of the schema for the manifest file is explained in the following table (manifest components refer to the original LexGrid model schema namespaces and types):

• Coding Scheme Manifest entry field: '''id'''
  • Type: lgCommon:registeredName
  • Required: Yes
  • Override flag set: Not applicable

  • Description:
    The registered name is the key used to find a coding scheme (for example a unique URL or namespace by which other people access same coding scheme). This String value will be used to identify the manifest entry in the manifest file for the coding scheme too. For example the registered name for coding scheme "Amino-acid"

    is

    is 

    Code Block
    Historical link http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#

    .

    This string is also set as the coding scheme's registered name field in the LexGrid model.

• Coding Scheme Manifest entry field: '''codingScheme'''
  • Type: lgBuiltin:localId
  • Required: No
  • Override flag set: Yes
  • Description:
    This value will be set for 'coding scheme name' in the LexGrid format counterpart. If the override flag is set to 'true', the value provided in the source file will be replaced with this one. Otherwise, this value is treated as a default value and used only if the value is not provided in the source file.

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When generating source RRF files from the Metathesaurus, the UMLS Metamorphosys tool should be set to output versionless source abbreviations rather than versioned source abbreviations in any RRF subset to be loaded to LexGrid. Failing to do so will create an incomplete database leaving the association and concept tables empty.

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