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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

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. 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):

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• 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 http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#

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

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• Primary Key Strategy - see (DB_PRIMARY_KEY_STRATEGY Config Setting)
  • Sequential Integer Primary Key (SEQUENTIAL_INTEGER) is the best strategy for large loads. This allows the database to insert records into the index in a sequential manner, which is more efficient. If GUID strategy is used, records will be inserted into the index tree at random locations, resulting in index re-balancing after every insert.
• Hardware is very important to large content loads.
  • RRF Loads are loaded in a multi-threaded manner. Multi-processor servers will give the best performance.
  • If possible, seperate the database server and the loader server.
• Monitoring a load
  • Monitor all LexEVS logs (both 'load' and 'full' log).
  • If using MySQL, use INNODB tools to monitor Inserts per second. (SHOW INNODB STATUS)

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Load Time Preferences

Preferences for loading elements of sources such as OWL can be done at load time.

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This value can be adjusted by creating an XML file that resolves against this schema: http://LexGrid.org/schema/LexBIG/2009/01/Preferences/load/LoadPreferences

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XMLMetadataFilePath

Any xml document can be assigned as metadata to a newly loaded coding scheme. The xml document is broken down into individual tags and values, which are then searchable through the LexBIG Service Metadata interface. This parameter indicates the path of xml metadata assigned during the current load operation. For most loaders, the given path serves strictly as an option to input user-specified data. For The NCI Metathesaurus loader, metadata is automatically generated and assigned to the coding scheme. In these cases, the generated xml will be output to the given file, overwriting any existing content.

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These values can be adjusted by creating an XML file that resolves against this schema: http://LexGrid.org/schema/LexBIG/2009/01/Preferences/load/OWLLoadPreferences

PropnamePrimitive

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PropnamePrimitive

Entities can be assigned a property that Entities can be assigned a property that indicates whether or not it is considered primitive (having no equivalent classes). This preference controls
the name of the property that is created; the property value will indicate true or false. If not specified, the name 'primitive' is assumed.

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This value can be adjusted by creating an XML file that resolves against this schema: http://LexGrid.org/schema/LexBIG/2009/01/Preferences/load/SemNetLoadPreferences

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SemNetLoaderPreferences

The load parameter controls which inherited relationships are loaded and navigable within LexBIG. When selecting the option not to load inherited relationships, all associations are extracted from the source file SRSTR (stated relations). When loading all inherited relations, associations are extracted from the source file SRSTRE1 (classified relations).

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A Revision Overview

CodingSchemes

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can be extensively revised by loading a Revision

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object in LexGrid XML format. A coding scheme Revision can be created to resolve against a "revision" schema URL and loaded to a coding scheme current in the service. This revision is tracked within the service history. Revision function centers around LexGrid model elements that inherit from the Versionable

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element. Versionable classes and attributes include those "types" of Versionable and any attributes inherited from this element. Whenever a Versionable element appears in a revision it is accompanied by an EntryState accompanied by an EntryState

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element which helps define it's role in the revision process.

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For instance, the following revision defines a new association for the coding scheme AutomobilesAD. The AssociationTarget

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class is a Versionable type, but the AssociationSource

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is not. So the AssociationTarget revision is defined by an EntryState element with a changeType value "NEW".

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Notice that even though an AssociationSource contains a collection of targets, it is not a Versionable element itself, so the revision definition for an association is in the association target. A collection of sources is contained in another unversioned element the AssociationPredicate

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. The predicate's container, Relations is a Versionable element but it is already defined in the coding scheme so it is defined as a "DEPENDENT" revision. Similarly the containing CodingScheme itself is a Versionable element also defined as a "DEPENDENT" revision. Notice the revisionId attribute of the the top level Revision element and how it corresponds to the containingRevision attribute value on all the EntryState elements. This value must differ from the current revisionId of the coding scheme being revised.

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Revisions in LexGrid are discussed in more detail here:

• Authoring Design Document

Post Processing Options

Post load processing algorithms allow users to access information about the source that may only be available post load and apply to coding scheme meta-data.

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1. Start from an installed LexEVS local API.
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2. Load from <LexEVS root>/test/resources/testData/ the coding scheme Automobiles.xml (You should be able to do this using a source in any format supported for loading)
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3. Activate this scheme and view it's contents by getting a coded node set and resolving it.
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4. Load from <LexEVS root>/test/resources/testData/ the coding scheme testExtension.xml selecting the option to extend by selecting the Automobiles terminology from the drop down list by it's URN and version.
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5. View the concept codes for the extension and see both the original code set and the supplemental code set.
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Keep in mind that the testExtension.xml's file format can be used to extend any coding scheme currently loaded to LexEVS.

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• Requirements:
  • Address of the latest LexGrid model xsd: http://LexGrid.org/schema/2010/01/LexGrid/codingSchemes.xsd

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  • An XML editor like oXygen.

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