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StepAction
1

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

2

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
languagexml
    <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
languagexml
titleCoding Scheme
   <supportedCodingScheme isImported="false" localId="OBIobi" 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
languagexml
titleCoding Scheme
 <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
languagexml
titleCoding Scheme
        <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>

OBI_Apr2015_With_NamespaceToCS_MF.xml

OBI_StrictOWL_PF.xml

3Load source with options using option files

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