Package org.obolibrary.robot

Class TemplateOperation

  • public class TemplateOperation
extends Object
    Generate OWL from tables. Based on "Overcoming the ontology enrichment bottleneck with Quick Term Templates" (link). See template.md for details.
    Author:
    James A. Overton

    • Constructor Detail

      • TemplateOperation

        public TemplateOperation()

    • Method Detail

      • getDefaultOptions

        public static Map<String,​String> getDefaultOptions()
        Get the default template options.
        Returns:
        map of template options

      • template

        public static org.semanticweb.owlapi.model.OWLOntology template​(org.semanticweb.owlapi.model.OWLOntology inputOntology,
                                                                IOHelper ioHelper,
                                                                String tableName,
                                                                List<List<String>> table)
                                                         throws Exception
        Given an OWLOntology, an IOHelper, a table name, and the table contents, use the table as the template to generate an output OWLOntology.
        Parameters:
        inputOntology - OWLOntology to use to get existing entities
        ioHelper - IOHelper to resolve prefixes
        tableName - name of the table for error reporting
        table - List of rows (lists of cells) in the template
        Returns:
        new OWLOntology created from the template
        Throws:
        Exception - on any issue

      • template

        public static org.semanticweb.owlapi.model.OWLOntology template​(org.semanticweb.owlapi.model.OWLOntology inputOntology,
                                                                IOHelper ioHelper,
                                                                String tableName,
                                                                List<List<String>> table,
                                                                Map<String,​String> options)
                                                         throws Exception
        Given an OWLOntology, an IOHelper, a table name, the table contents, and a map of template options, use the table as the template to generate an output OWLOntology.
        Parameters:
        inputOntology - OWLOntology to use to get existing entities
        ioHelper - IOHelper to resolve prefixes
        tableName - name of the table for error reporting
        table - List of rows (lists of cells) in the template
        options - map of template options
        Returns:
        new OWLOntology created from the template
        Throws:
        Exception - on any issue

      • template

        public static org.semanticweb.owlapi.model.OWLOntology template​(org.semanticweb.owlapi.model.OWLOntology inputOntology,
                                                                IOHelper ioHelper,
                                                                Map<String,​List<List<String>>> tables,
                                                                Map<String,​String> options)
                                                         throws Exception
        Given an OWLOntology, an IOHelper, a map of table names to table contents, and a map of template options, use the tables as templates to generate a merged output ontology.
        Parameters:
        inputOntology - OWLOntology to use to get existing entities
        ioHelper - IOHelper to resolve prefixes
        tables - table names to table contents
        options - map of template options
        Returns:
        new OWLOntology created from merged template ontologies
        Throws:
        Exception - on any issue

      • getAnnotationProperty

        @Deprecated
public static org.semanticweb.owlapi.model.OWLAnnotationProperty getAnnotationProperty​(QuotedEntityChecker checker,
                                                                                       String name)
                                                                                throws Exception
        Deprecated.
        Find an annotation property with the given name or create one.
        Parameters:
        checker - used to search by rdfs:label (for example)
        name - the name to search for
        Returns:
        an annotation property
        Throws:
        Exception - if the name cannot be resolved

      • getDatatype

        @Deprecated
public static org.semanticweb.owlapi.model.OWLDatatype getDatatype​(QuotedEntityChecker checker,
                                                                   String name)
                                                            throws Exception
        Deprecated.
        Find a datatype with the given name or create one.
        Parameters:
        checker - used to search by rdfs:label (for example)
        name - the name to search for
        Returns:
        a datatype
        Throws:
        Exception - if the name cannot be resolved

      • getStringAnnotation

        @Deprecated
public static org.semanticweb.owlapi.model.OWLAnnotation getStringAnnotation​(QuotedEntityChecker checker,
                                                                             String template,
                                                                             String value)
                                                                      throws Exception
        Deprecated.
        Return a string annotation for the given template string and value.
        Parameters:
        checker - used to resolve the annotation property
        template - the template string
        value - the value for the annotation
        Returns:
        a new annotation with property and string literal value
        Throws:
        Exception - if the annotation property cannot be found

      • getTypedAnnotation

        @Deprecated
public static org.semanticweb.owlapi.model.OWLAnnotation getTypedAnnotation​(QuotedEntityChecker checker,
                                                                            String template,
                                                                            String value)
                                                                     throws Exception
        Deprecated.
        Return a typed annotation for the given template string and value. The template string format is "AT [name]^^[datatype]" and the value is any string.
        Parameters:
        checker - used to resolve the annotation property and datatype
        template - the template string
        value - the value for the annotation
        Returns:
        a new annotation axiom with property and typed literal value
        Throws:
        Exception - if the annotation property cannot be found

      • getLanguageAnnotation

        @Deprecated
public static org.semanticweb.owlapi.model.OWLAnnotation getLanguageAnnotation​(QuotedEntityChecker checker,
                                                                               String template,
                                                                               String value)
                                                                        throws Exception
        Deprecated.
        Return a language tagged annotation for the given template and value. The template string format is "AL [name]@[lang]" and the value is any string.
        Parameters:
        checker - used to resolve the annotation property
        template - the template string
        value - the value for the annotation
        Returns:
        a new annotation axiom with property and language tagged literal
        Throws:
        Exception - if the annotation property cannot be found

      • getIRIAnnotation

        @Deprecated
public static org.semanticweb.owlapi.model.OWLAnnotation getIRIAnnotation​(QuotedEntityChecker checker,
                                                                          String template,
                                                                          org.semanticweb.owlapi.model.IRI value)
                                                                   throws Exception
        Deprecated.
        Return an IRI annotation for the given template string and value. The template string format is "AI [name]" and the value is a string that can be interpreted as an IRI.
        Parameters:
        checker - used to resolve the annotation property
        template - the template string
        value - the IRI value for the annotation
        Returns:
        a new annotation axiom with property and an IRI value
        Throws:
        Exception - if the annotation property cannot be found

      • getEntity

        @Deprecated
public static org.semanticweb.owlapi.model.OWLEntity getEntity​(QuotedEntityChecker checker,
                                                               org.semanticweb.owlapi.model.IRI type,
                                                               String id,
                                                               String label)
        Deprecated.
        Use type, id, and label information to get an entity from the data in a row. Requires either: an id (default type is owl:Class); an id and type; or a label.
        Parameters:
        checker - for looking up labels
        type - the IRI of the type for this entity, or null
        id - the ID for this entity, or null
        label - the label for this entity, or null
        Returns:
        the entity or null

      • getIRIs

        @Deprecated
public static List<org.semanticweb.owlapi.model.IRI> getIRIs​(Map<String,​List<List<String>>> tables,
                                                             IOHelper ioHelper)
                                                      throws Exception
        Deprecated.
        Get a list of the IRIs defined in a set of template tables.
        Parameters:
        tables - a map from table names to tables
        ioHelper - used to find entities by name
        Returns:
        a list of IRIs
        Throws:
        Exception - when names or templates cannot be handled

      • getIRIs

        @Deprecated
public static List<org.semanticweb.owlapi.model.IRI> getIRIs​(String tableName,
                                                             List<List<String>> rows,
                                                             IOHelper ioHelper)
                                                      throws Exception
        Deprecated.
        Get a list of the IRIs defined in a template table.
        Parameters:
        tableName - the name of the table
        rows - the table of data
        ioHelper - used to find entities by name
        Returns:
        a list of IRIs
        Throws:
        Exception - when names or templates cannot be handled

      • template

        @Deprecated
public static org.semanticweb.owlapi.model.OWLOntology template​(Map<String,​List<List<String>>> tables)
                                                         throws Exception
        Deprecated.
        Use a table to generate an ontology. With this signature we use all defaults.
        Parameters:
        tables - a map from names to tables of data
        Returns:
        a new ontology generated from the table
        Throws:
        Exception - when names or templates cannot be handled

      • template

        @Deprecated
public static org.semanticweb.owlapi.model.OWLOntology template​(Map<String,​List<List<String>>> tables,
                                                                org.semanticweb.owlapi.model.OWLOntology inputOntology)
                                                         throws Exception
        Deprecated.
        Use tables to generate an ontology.
        Parameters:
        tables - a map from names to tables of data
        inputOntology - the ontology to use to resolve names
        Returns:
        a new ontology generated from the table
        Throws:
        Exception - when names or templates cannot be handled

      • template

        @Deprecated
public static org.semanticweb.owlapi.model.OWLOntology template​(Map<String,​List<List<String>>> tables,
                                                                org.semanticweb.owlapi.model.OWLOntology inputOntology,
                                                                QuotedEntityChecker checker)
                                                         throws Exception
        Deprecated.
        Use tables to generate an ontology.
        Parameters:
        tables - a map from names to tables of data
        inputOntology - the ontology to use to resolve names
        checker - used to find entities by name
        Returns:
        a new ontology generated from the table
        Throws:
        Exception - when names or templates cannot be handled

      • template

        @Deprecated
public static org.semanticweb.owlapi.model.OWLOntology template​(Map<String,​List<List<String>>> tables,
                                                                org.semanticweb.owlapi.model.OWLOntology inputOntology,
                                                                IOHelper ioHelper)
                                                         throws Exception
        Deprecated.
        Use tables to generate an ontology.
        Parameters:
        tables - a map from names to tables of data
        inputOntology - the ontology to use to resolve names
        ioHelper - used to find entities by name
        Returns:
        a new ontology generated from the table
        Throws:
        Exception - when names or templates cannot be handled

      • template

        @Deprecated
public static org.semanticweb.owlapi.model.OWLOntology template​(Map<String,​List<List<String>>> tables,
                                                                org.semanticweb.owlapi.model.OWLOntology inputOntology,
                                                                QuotedEntityChecker checker,
                                                                IOHelper ioHelper)
                                                         throws Exception
        Deprecated.
        Use tables to generate an ontology. Input is a map from table names to tables. The first row of each table must be header names. The second row of each table must be template strings, including ID and CLASS_TYPE columns. The new ontology is created in two passes: first terms are declared and annotations added, then logical axioms are added. This allows annotations from the first pass to be used as names in the logical axioms.
        Parameters:
        tables - a map from names to tables of data
        inputOntology - the ontology to use to resolve names
        checker - used to find entities by name
        ioHelper - used to find entities by name
        Returns:
        a new ontology generated from the table
        Throws:
        Exception - when names or templates cannot be handled

      • validateTemplateString

        @Deprecated
public static boolean validateTemplateString​(String template)
        Deprecated.
        Return true if the template string is valid, false otherwise.
        Parameters:
        template - the template string to check
        Returns:
        true if valid, false otherwise