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The LexEVS software, documentation, indexes, and system logs are located in the {LEXBIG_DIRECTORY} (e.g., /usr/local/packages/LexBIG or c:\lexbig). These files may be part of the local file system and may require backup procedures to meet servicability and recovery requirements for your organization.

LexEVS uses basic database indexes, but also includes a separate indexing facility using Apache Lucene. Lucene Index files are stored in a directory as specified in the lbconfig.props file index_location variable.

What

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Is a Coding Scheme Manifest?

A "Coding Scheme Manifest" (or simply "manifest" as used interchangeably in this document) allows the user to set values for a coding scheme while loading or converting a LexGrid "XML", "NCI MetaThesaurus", "NCI OWL","OWL", "OBO", "UMLS RRF File", or"HL7 RIM Database" source to LexGrid format.

What

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Is a Coding Scheme?

Coding Scheme is the term that is used to represent an ontology/terminology being loaded or converted. In the LexGrid data model a terminology is represented as a coding scheme and it can reference other coding schemes. An example of coding scheme is "Amino Acid" which is described in the "amino acid.owl" file.

A Coding Scheme has some meta information about it; values like 'formal name', 'local names', 'default language', 'version', 'copyright', 'sources' to name some.

Why

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Do We Need a Coding Scheme Manifest?

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.

How

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Do We Create a Coding Scheme Manifest

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File?

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 1. 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:

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• 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 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.

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• Coding Scheme Manifest entry field:

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• codingScheme

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• • 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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• Coding Scheme Manifest entry field:

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• entityDescription

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• • Type: lgCommon:entityDescription
  • Required: No
  • Override flag set: Yes
  • Description:
    This value will be set for 'coding scheme description' 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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