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Obtain or write an OWL2 source

An example is the OBI Ontology described here:

http://obi-ontology.org/page/Main_Page

With source currently available here:

http://svn.code.sf.net/p/obi/code/releases/2015-09-15/obi.owl

Create a manifest and preferences file for this source

Manifests are XML files formatted to an XML schema. They are easiest to create when using an XML editor that can reference an XML schema. The manifest schema is hosted here:

http://LexGrid.org/schema/2010/01/LexOnt/CodingSchemeManifest

For OWL2 the user can create one like the example for regular OWL above but add a tag for mappings that will help define namespaces in the OBI load:

Code Block

theme	Eclipse
language	xml
title	Mappings Tag

    <owldef:mappings dc="mappings" xmlns="http://LexGrid.org/schema/2009/01/LexGrid/codingSchemes">

As tag content supply a supported coding scheme for the enclosing coding scheme OBI.

Code Block

theme	Eclipse
language	xml
title	Coding Scheme

   <supportedCodingScheme isImported="false" localId="obi" urn="http://purl.obolibrary.org/obo/obi.owl#" xmlns="http://LexGrid.org/schema/2008/01/LexGrid/codingSchemes"/>

After this tag define the namespace for the enclosing coding scheme with a reference to the enclosing coding scheme in the equivalent coding scheme attribute

Code Block

theme	Eclipse
language	xml
title	Enclosing Scheme Namespace

 <supportedNamespace localId="obi" uri="http://purl.obolibrary.org/obo/obi.owl#" equivalentCodingScheme="obi">obi</supportedNamespace>

All other namespaces can be defined in the same way with references from the original OWL source which are found in the xmlns attributes of the "<rdf:RDF tag." Each with a reference to the enclosing coding scheme using the equivalentCodingScheme attribute

Code Block

theme	Eclipse
language	xml
title	Supported Namespace

        <supportedNamespace localId="dc" uri="http://purl.org/dc/elements/1.1/" equivalentCodingScheme="obi">dc</supportedNamespace>
        <supportedNamespace localId="doap" uri="http://usefulinc.com/ns/doap#" equivalentCodingScheme="obi">doap</supportedNamespace>
        <supportedNamespace localId="foaf" uri="http://xmlns.com/foaf/0.1/" equivalentCodingScheme="obi">foaf</supportedNamespace>
        <supportedNamespace localId="obo" uri="http://purl.obolibrary.org/obo/" equivalentCodingScheme="obi">obo</supportedNamespace>
        <supportedNamespace localId="oboInOwl" uri="http://www.geneontology.org/formats/oboInOwl#" equivalentCodingScheme="obi">oboInOwl</supportedNamespace>
        <supportedNamespace localId="owl" uri="http://www.w3.org/2002/07/owl" equivalentCodingScheme="obi">owl</supportedNamespace>     
        <supportedNamespace localId="protege" uri="http://protege.stanford.edu/plugins/owl/protege#" equivalentCodingScheme="obi">protege</supportedNamespace>
        <supportedNamespace localId="rdf" uri="http://www.w3.org/1999/02/22-rdf-syntax-ns" equivalentCodingScheme="obi">rdf</supportedNamespace>
        <supportedNamespace localId="rdfs" uri="http://www.w3.org/2000/01/rdf-schema" equivalentCodingScheme="obi">rdfs</supportedNamespace>
        <supportedNamespace localId="xsd" uri="http://www.w3.org/2001/XMLSchema" equivalentCodingScheme="obi">xsd</supportedNamespace>
        <supportedNamespace localId="xml" uri="http://www.w3.org/XML/1998/namespace" equivalentCodingScheme="obi">xml</supportedNamespace>

Attached is a full example of a working manifest for OBI

OBI_Apr2015_With_NamespaceToCS_MF.xml

Preferences files work in a similar way to the manifest. Instead of updating coding scheme data, they initiate programmatic switches determining how a variety of source definitions can be loaded. The preferences XML scheme is defined here:

http://LexGrid.org/schema/LexBIG/2009/01/Preferences/load/OWLLoadPreferences

This includes setting nodes designated as root, i.e. without relational parent codes of any kind.

Code Block

theme	Eclipse
language	xml
title	Match Root Name

   <MatchRootName>(BFO_0000001|Project|SVNRepository|ObsoleteClass|Version)</MatchRootName>

Other applications for OWL2 include loading Annotation Properties and their restrictions as a variety of relationships. This is accomplished by setting the strict owl tag value to true:

Code Block

theme	Eclipse
language	xml
title	Strict OWL

<StrictOWLImplementation>true</StrictOWLImplementation>

A full working preferences file is attached below

OBI_StrictOWL_PF.xml

Load source with options using option files

Code Block

./LoadOWL2.sh -in "file:///data/phont/LexEVS/test/resources/testData/obi.owl" -mf "file:///data/phont/LexEVS/test/resources/testData/OBI_Apr2015_With_NamespaceToCS_MF.xml" -lp "file:///data/phont/LexEVS/test/resources/testData/OBI_StrictOWL_PF.xml"

Load source with options using option files

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