org.wandora.application.tools.importers

Class OBO

java.lang.Object

org.wandora.application.tools.importers.OBO

public class OBO
extends java.lang.Object

This class is a static library for OBOImport, OBOExport, and OBORoundtrip tools. Library contains shared constants and services used to map OBO (Open Biological Ontologies) elements to Topic Maps and vice versa.

Author:

akivela

Field Summary

Fields

Modifier and Type	Field and Description
static boolean	COLLATE_SIMILAR_SYNONYMS
static java.lang.String	DBXREF_SI
static java.lang.String	HEADER_SI
static java.lang.String	LANG
static boolean	MAKE_DESCRIPTION_TOPICS
static boolean	MAKE_SIS_FROM_ALT_IDS
static java.lang.String	optionPrefix
static boolean	PROCESS_HEADER_IMPORTS
static java.lang.String	QUOTE_STRING_PATTERN
static java.lang.String	SCHEMA_SI
static java.lang.String	SCHEMA_TERM_ADJACENT_TO
static java.lang.String	SCHEMA_TERM_AGENT_IN
static java.lang.String	SCHEMA_TERM_ALTERNATIVE_ID
static java.lang.String	SCHEMA_TERM_ASSOCIATION_TYPE
static java.lang.String	SCHEMA_TERM_CATEGORY
static java.lang.String	SCHEMA_TERM_COMMENT
static java.lang.String	SCHEMA_TERM_CONSIDER_USING
static java.lang.String	SCHEMA_TERM_CONTAINED_IN
static java.lang.String	SCHEMA_TERM_CONTAINS
static java.lang.String	SCHEMA_TERM_CREATED_BY
static java.lang.String	SCHEMA_TERM_CREATION_DATE
static java.lang.String	SCHEMA_TERM_DEFINITION
static java.lang.String	SCHEMA_TERM_DEFINITION_ORIGIN
static java.lang.String	SCHEMA_TERM_DERIVES_FROM
static java.lang.String	SCHEMA_TERM_DERIVES_INTO
static java.lang.String	SCHEMA_TERM_DESCRIPTION
static java.lang.String	SCHEMA_TERM_DISJOINT_FROM
static java.lang.String	SCHEMA_TERM_DOMAIN
static java.lang.String	SCHEMA_TERM_EXPAND_ASSERTION
static java.lang.String	SCHEMA_TERM_HAS_AGENT
static java.lang.String	SCHEMA_TERM_HAS_PART
static java.lang.String	SCHEMA_TERM_HAS_PARTICIPANT
static java.lang.String	SCHEMA_TERM_HOLS_CHAIN_OVER
static java.lang.String	SCHEMA_TERM_ID
static java.lang.String	SCHEMA_TERM_INSTANCE
static java.lang.String	SCHEMA_TERM_INSTANCE_OF
static java.lang.String	SCHEMA_TERM_INTERSECTION_OF
static java.lang.String	SCHEMA_TERM_INVERSE_OF
static java.lang.String	SCHEMA_TERM_IS_ANONYMOUS
static java.lang.String	SCHEMA_TERM_IS_ANTISYMMETRIC
static java.lang.String	SCHEMA_TERM_IS_CLASS_LEVEL
static java.lang.String	SCHEMA_TERM_IS_CYCLIC
static java.lang.String	SCHEMA_TERM_IS_METADATA_TAG
static java.lang.String	SCHEMA_TERM_IS_REFLEXIVE
static java.lang.String	SCHEMA_TERM_IS_SYMMETRIC
static java.lang.String	SCHEMA_TERM_IS_TRANSITIVE
static java.lang.String	SCHEMA_TERM_IS_TRANSITIVE_OVER
static java.lang.String	SCHEMA_TERM_LOCATED_IN
static java.lang.String	SCHEMA_TERM_LOCATION_OF
static java.lang.String	SCHEMA_TERM_MEMBER
static java.lang.String	SCHEMA_TERM_MODIFIER
static java.lang.String	SCHEMA_TERM_NAMESPACE
static java.lang.String	SCHEMA_TERM_PART_OF
static java.lang.String	SCHEMA_TERM_PARTICIPATES_IN
static java.lang.String	SCHEMA_TERM_PRECEDED_BY
static java.lang.String	SCHEMA_TERM_PRECEDES
static java.lang.String	SCHEMA_TERM_PROPERTY_VALUE
static java.lang.String	SCHEMA_TERM_PROPERTY_VALUE_TYPE
static java.lang.String	SCHEMA_TERM_RANGE
static java.lang.String	SCHEMA_TERM_RELATED_TO
static java.lang.String	SCHEMA_TERM_RELATIONSHIP
static java.lang.String	SCHEMA_TERM_REPLACED_BY
static java.lang.String	SCHEMA_TERM_SUBCLASS
static java.lang.String	SCHEMA_TERM_SUPERCLASS
static java.lang.String	SCHEMA_TERM_SUPERCLASS_SUBCLASS
static java.lang.String	SCHEMA_TERM_SYNONYM
static java.lang.String	SCHEMA_TERM_SYNONYM_ORIGIN
static java.lang.String	SCHEMA_TERM_SYNONYM_SCOPE
static java.lang.String	SCHEMA_TERM_SYNONYM_TEXT
static java.lang.String	SCHEMA_TERM_SYNONYM_TYPE
static java.lang.String	SCHEMA_TERM_TERM
static java.lang.String	SCHEMA_TERM_TRANSFORMATION_INTO
static java.lang.String	SCHEMA_TERM_TRANSFORMATION_OF
static java.lang.String	SCHEMA_TERM_TYPEDEF
static java.lang.String	SCHEMA_TERM_UNION_OF
static java.lang.String	SCHEMA_TERM_XREF
static java.lang.String	SCHEMA_TERM_XREF_SCOPE
static java.lang.String	SI
static boolean	USE_SCOPED_XREFS

Constructor Summary

Constructors

Constructor and Description
OBO()

Method Summary

Modifier and Type	Method and Description
static Topic	createAuthorTopic(TopicMap tm, java.lang.String namespace)
static Topic	createCategoryTopic(TopicMap tm, java.lang.String namespace)
static Topic	createDescriptionTopic(TopicMap tm, java.lang.String namespace)
static Topic	createHeaderTopic(TopicMap tm, java.lang.String namespace)
static Topic	createInstanceTopic(TopicMap tm, java.lang.String namespace)
static Topic	createISARootTopic(TopicMap tm, java.lang.String namespace)
static Topic	createObsoleteTopic(TopicMap tm, java.lang.String namespace)
static Topic	createPropertyDatatypeTopic(TopicMap tm)
static Topic	createPropertyRelationshipTopic(TopicMap tm)
static Topic	createPropertyValueTopic(TopicMap tm)
static Topic	createRootTopic(TopicMap tm, java.lang.String namespace)
static Topic	createSchemaTopic(TopicMap tm)
static Topic	createSynonymTopic(TopicMap tm, java.lang.String namespace)
static Topic	createTermTopic(TopicMap tm, java.lang.String namespace)
static Topic	createTopicForAssertionExpansion(TopicMap tm, java.lang.String exp)
static Topic	createTopicForAuthor(TopicMap tm, java.lang.String name, java.lang.String namespace)
static Topic	createTopicForCategory(TopicMap tm, java.lang.String id)
static Topic	createTopicForCategory(TopicMap tm, java.lang.String id, java.lang.String description)
static Topic	createTopicForDbxref(TopicMap tm, java.lang.String id)
static Topic	createTopicForDbxref(TopicMap tm, java.lang.String id, java.lang.String description)
static Topic	createTopicForDescription(TopicMap tm, java.lang.String description, java.lang.String namespace)
static Topic	createTopicForInstance(TopicMap tm, java.lang.String id)
static Topic	createTopicForInstance(TopicMap tm, java.lang.String id, java.lang.String name, java.lang.String namespace)
static Topic	createTopicForModifier(TopicMap tm, java.lang.String id)
static Topic	createTopicForModifier(TopicMap tm, java.lang.String id, java.lang.String name)
static Topic	createTopicForPropertyDatatype(TopicMap tm, java.lang.String str)
static Topic	createTopicForPropertyRelationship(TopicMap tm, java.lang.String id)
static Topic	createTopicForPropertyValue(TopicMap tm, java.lang.String value)
static Topic	createTopicForRelation(TopicMap tm, java.lang.String id, java.lang.String namespace)
static Topic	createTopicForRelation(TopicMap tm, java.lang.String id, java.lang.String name, java.lang.String namespace)
static Topic	createTopicForSchemaTerm(TopicMap tm, java.lang.String schemaTerm)
static Topic	createTopicForSynonym(TopicMap tm, java.lang.String name, java.lang.String namespace)
static Topic	createTopicForTerm(TopicMap tm, java.lang.String id)
static Topic	createTopicForTerm(TopicMap tm, java.lang.String id, java.lang.String name, java.lang.String namespace)
static Topic	createTopicForTypedef(TopicMap tm, java.lang.String id)
static Topic	createTopicForTypedef(TopicMap tm, java.lang.String id, java.lang.String name, java.lang.String namespace)
static Topic	createTypedefTopic(TopicMap tm, java.lang.String namespace)
static Topic	getCategoryTopic(TopicMap tm, java.lang.String namespace)
static Topic	getDescriptionTopic(TopicMap tm, java.lang.String namespace)
static Topic	getHeaderTopic(TopicMap tm, java.lang.String namespace)
static Topic	getInstanceTopic(TopicMap tm, java.lang.String namespace)
static Topic	getObsoleteTopic(TopicMap tm, java.lang.String namespace)
static int	getOptions()
private static Topic	getOrCreateTopic(TopicMap tm, Locator si, java.lang.String basename)
private static Topic	getOrCreateTopic(TopicMap tm, java.lang.String si)
private static Topic	getOrCreateTopic(TopicMap tm, java.lang.String si, java.lang.String basename)
static Topic	getRootTopic(TopicMap tm, java.lang.String namespace)
static Topic	getTermTopic(TopicMap tm, java.lang.String namespace)
private static Topic	getTopic(TopicMap tm, java.lang.String si)
static Topic	getTopicForSchemaTerm(TopicMap tm, java.lang.String schemaTerm)
static Topic	getTypedefTopic(TopicMap tm, java.lang.String namespace)
static void	importExport(java.io.File[] importFiles)
static void	importExport(java.lang.String dir)
static java.lang.String	Java2OBO(java.lang.String str)
static java.lang.String	Java2OBOLite(java.lang.String str)
static java.lang.String	makeBasename(java.lang.String termid)
static Locator	makeLocator(java.lang.String id)
static java.lang.String	makeSI(java.lang.String id)
static java.lang.String	makeSI(java.lang.String prefix, java.lang.String str)
static java.lang.String	makeSICarefully(java.lang.String id)
private static void	makeSubclassOf(TopicMap tm, Topic t, Topic superclass)
static java.lang.String	makeTermSI(java.lang.String termId)
static java.lang.String	OBO2Java(java.lang.String str)
private static void	setData(Topic t, Topic type, java.lang.String lang, java.lang.String text)
static void	setOptions(boolean collateSysnonyms, boolean descriptionTopics, boolean altIdSIs, boolean scopedXrefs, java.lang.String lang)
static void	setOptions(int options)
static java.lang.String	solveOBODescription(Association a, Topic t)
static java.lang.String	solveOBODescription(Topic t)
static java.lang.String	solveOBOId(Locator l)
static java.lang.String	solveOBOId(Topic t)
static java.lang.String	solveOBOName(Topic t)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

optionPrefix

public static final java.lang.String optionPrefix

See Also:

Constant Field Values

COLLATE_SIMILAR_SYNONYMS

public static boolean COLLATE_SIMILAR_SYNONYMS

MAKE_DESCRIPTION_TOPICS

public static boolean MAKE_DESCRIPTION_TOPICS

MAKE_SIS_FROM_ALT_IDS

public static boolean MAKE_SIS_FROM_ALT_IDS

USE_SCOPED_XREFS

public static boolean USE_SCOPED_XREFS

PROCESS_HEADER_IMPORTS

public static boolean PROCESS_HEADER_IMPORTS

QUOTE_STRING_PATTERN

public static final java.lang.String QUOTE_STRING_PATTERN

See Also:

Constant Field Values

LANG

public static java.lang.String LANG

SI

public static final java.lang.String SI

See Also:

Constant Field Values

SCHEMA_SI

public static final java.lang.String SCHEMA_SI

See Also:

Constant Field Values

HEADER_SI

public static final java.lang.String HEADER_SI

See Also:

Constant Field Values

DBXREF_SI

public static final java.lang.String DBXREF_SI

See Also:

Constant Field Values

SCHEMA_TERM_ID

public static final java.lang.String SCHEMA_TERM_ID

See Also:

Constant Field Values

SCHEMA_TERM_ALTERNATIVE_ID

public static final java.lang.String SCHEMA_TERM_ALTERNATIVE_ID

See Also:

Constant Field Values

SCHEMA_TERM_DEFINITION

public static final java.lang.String SCHEMA_TERM_DEFINITION

See Also:

Constant Field Values

SCHEMA_TERM_DEFINITION_ORIGIN

public static final java.lang.String SCHEMA_TERM_DEFINITION_ORIGIN

See Also:

Constant Field Values

SCHEMA_TERM_COMMENT

public static final java.lang.String SCHEMA_TERM_COMMENT

See Also:

Constant Field Values

SCHEMA_TERM_ASSOCIATION_TYPE

public static final java.lang.String SCHEMA_TERM_ASSOCIATION_TYPE

See Also:

Constant Field Values

SCHEMA_TERM_DESCRIPTION

public static final java.lang.String SCHEMA_TERM_DESCRIPTION

See Also:

Constant Field Values

SCHEMA_TERM_MEMBER

public static final java.lang.String SCHEMA_TERM_MEMBER

See Also:

Constant Field Values

SCHEMA_TERM_CATEGORY

public static final java.lang.String SCHEMA_TERM_CATEGORY

See Also:

Constant Field Values

SCHEMA_TERM_SUPERCLASS_SUBCLASS

public static final java.lang.String SCHEMA_TERM_SUPERCLASS_SUBCLASS

See Also:

Constant Field Values

SCHEMA_TERM_SUPERCLASS

public static final java.lang.String SCHEMA_TERM_SUPERCLASS

See Also:

Constant Field Values

SCHEMA_TERM_SUBCLASS

public static final java.lang.String SCHEMA_TERM_SUBCLASS

See Also:

Constant Field Values

SCHEMA_TERM_TERM

public static final java.lang.String SCHEMA_TERM_TERM

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Constant Field Values

SCHEMA_TERM_TYPEDEF

public static final java.lang.String SCHEMA_TERM_TYPEDEF

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Constant Field Values

SCHEMA_TERM_INSTANCE

public static final java.lang.String SCHEMA_TERM_INSTANCE

See Also:

Constant Field Values

SCHEMA_TERM_NAMESPACE

public static final java.lang.String SCHEMA_TERM_NAMESPACE

See Also:

Constant Field Values

SCHEMA_TERM_IS_ANONYMOUS

public static final java.lang.String SCHEMA_TERM_IS_ANONYMOUS

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Constant Field Values

SCHEMA_TERM_CONSIDER_USING

public static final java.lang.String SCHEMA_TERM_CONSIDER_USING

See Also:

Constant Field Values

SCHEMA_TERM_REPLACED_BY

public static final java.lang.String SCHEMA_TERM_REPLACED_BY

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Constant Field Values

SCHEMA_TERM_RELATIONSHIP

public static final java.lang.String SCHEMA_TERM_RELATIONSHIP

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Constant Field Values

SCHEMA_TERM_RELATED_TO

public static final java.lang.String SCHEMA_TERM_RELATED_TO

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Constant Field Values

SCHEMA_TERM_INTERSECTION_OF

public static final java.lang.String SCHEMA_TERM_INTERSECTION_OF

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Constant Field Values

SCHEMA_TERM_PART_OF

public static final java.lang.String SCHEMA_TERM_PART_OF

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Constant Field Values

SCHEMA_TERM_HAS_PART

public static final java.lang.String SCHEMA_TERM_HAS_PART

See Also:

Constant Field Values

SCHEMA_TERM_AGENT_IN

public static final java.lang.String SCHEMA_TERM_AGENT_IN

See Also:

Constant Field Values

SCHEMA_TERM_HAS_AGENT

public static final java.lang.String SCHEMA_TERM_HAS_AGENT

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Constant Field Values

SCHEMA_TERM_PARTICIPATES_IN

public static final java.lang.String SCHEMA_TERM_PARTICIPATES_IN

See Also:

Constant Field Values

SCHEMA_TERM_HAS_PARTICIPANT

public static final java.lang.String SCHEMA_TERM_HAS_PARTICIPANT

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Constant Field Values

SCHEMA_TERM_PRECEDED_BY

public static final java.lang.String SCHEMA_TERM_PRECEDED_BY

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Constant Field Values

SCHEMA_TERM_PRECEDES

public static final java.lang.String SCHEMA_TERM_PRECEDES

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Constant Field Values

SCHEMA_TERM_DERIVES_FROM

public static final java.lang.String SCHEMA_TERM_DERIVES_FROM

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Constant Field Values

SCHEMA_TERM_DERIVES_INTO

public static final java.lang.String SCHEMA_TERM_DERIVES_INTO

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Constant Field Values

SCHEMA_TERM_TRANSFORMATION_OF

public static final java.lang.String SCHEMA_TERM_TRANSFORMATION_OF

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Constant Field Values

SCHEMA_TERM_TRANSFORMATION_INTO

public static final java.lang.String SCHEMA_TERM_TRANSFORMATION_INTO

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Constant Field Values

SCHEMA_TERM_CONTAINS

public static final java.lang.String SCHEMA_TERM_CONTAINS

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Constant Field Values

SCHEMA_TERM_CONTAINED_IN

public static final java.lang.String SCHEMA_TERM_CONTAINED_IN

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Constant Field Values

SCHEMA_TERM_LOCATION_OF

public static final java.lang.String SCHEMA_TERM_LOCATION_OF

See Also:

Constant Field Values

SCHEMA_TERM_LOCATED_IN

public static final java.lang.String SCHEMA_TERM_LOCATED_IN

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Constant Field Values

SCHEMA_TERM_DISJOINT_FROM

public static final java.lang.String SCHEMA_TERM_DISJOINT_FROM

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Constant Field Values

SCHEMA_TERM_ADJACENT_TO

public static final java.lang.String SCHEMA_TERM_ADJACENT_TO

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Constant Field Values

SCHEMA_TERM_UNION_OF

public static final java.lang.String SCHEMA_TERM_UNION_OF

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Constant Field Values

SCHEMA_TERM_MODIFIER

public static final java.lang.String SCHEMA_TERM_MODIFIER

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Constant Field Values

SCHEMA_TERM_DOMAIN

public static final java.lang.String SCHEMA_TERM_DOMAIN

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Constant Field Values

SCHEMA_TERM_RANGE

public static final java.lang.String SCHEMA_TERM_RANGE

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Constant Field Values

SCHEMA_TERM_INVERSE_OF

public static final java.lang.String SCHEMA_TERM_INVERSE_OF

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Constant Field Values

SCHEMA_TERM_IS_TRANSITIVE

public static final java.lang.String SCHEMA_TERM_IS_TRANSITIVE

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Constant Field Values

SCHEMA_TERM_IS_TRANSITIVE_OVER

public static final java.lang.String SCHEMA_TERM_IS_TRANSITIVE_OVER

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Constant Field Values

SCHEMA_TERM_IS_REFLEXIVE

public static final java.lang.String SCHEMA_TERM_IS_REFLEXIVE

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Constant Field Values

SCHEMA_TERM_IS_CYCLIC

public static final java.lang.String SCHEMA_TERM_IS_CYCLIC

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Constant Field Values

SCHEMA_TERM_IS_SYMMETRIC

public static final java.lang.String SCHEMA_TERM_IS_SYMMETRIC

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Constant Field Values

SCHEMA_TERM_IS_ANTISYMMETRIC

public static final java.lang.String SCHEMA_TERM_IS_ANTISYMMETRIC

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Constant Field Values

SCHEMA_TERM_IS_METADATA_TAG

public static final java.lang.String SCHEMA_TERM_IS_METADATA_TAG

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Constant Field Values

SCHEMA_TERM_INSTANCE_OF

public static final java.lang.String SCHEMA_TERM_INSTANCE_OF

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Constant Field Values

SCHEMA_TERM_PROPERTY_VALUE

public static final java.lang.String SCHEMA_TERM_PROPERTY_VALUE

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Constant Field Values

SCHEMA_TERM_PROPERTY_VALUE_TYPE

public static final java.lang.String SCHEMA_TERM_PROPERTY_VALUE_TYPE

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Constant Field Values

SCHEMA_TERM_SYNONYM

public static final java.lang.String SCHEMA_TERM_SYNONYM

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Constant Field Values

SCHEMA_TERM_SYNONYM_TEXT

public static final java.lang.String SCHEMA_TERM_SYNONYM_TEXT

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Constant Field Values

SCHEMA_TERM_SYNONYM_TYPE

public static final java.lang.String SCHEMA_TERM_SYNONYM_TYPE

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Constant Field Values

SCHEMA_TERM_SYNONYM_SCOPE

public static final java.lang.String SCHEMA_TERM_SYNONYM_SCOPE

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Constant Field Values

SCHEMA_TERM_SYNONYM_ORIGIN

public static final java.lang.String SCHEMA_TERM_SYNONYM_ORIGIN

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Constant Field Values

SCHEMA_TERM_XREF

public static final java.lang.String SCHEMA_TERM_XREF

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Constant Field Values

SCHEMA_TERM_XREF_SCOPE

public static final java.lang.String SCHEMA_TERM_XREF_SCOPE

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Constant Field Values

SCHEMA_TERM_CREATED_BY

public static final java.lang.String SCHEMA_TERM_CREATED_BY

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Constant Field Values

SCHEMA_TERM_CREATION_DATE

public static final java.lang.String SCHEMA_TERM_CREATION_DATE

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Constant Field Values

SCHEMA_TERM_EXPAND_ASSERTION

public static final java.lang.String SCHEMA_TERM_EXPAND_ASSERTION

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Constant Field Values

SCHEMA_TERM_IS_CLASS_LEVEL

public static final java.lang.String SCHEMA_TERM_IS_CLASS_LEVEL

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Constant Field Values

SCHEMA_TERM_HOLS_CHAIN_OVER

public static final java.lang.String SCHEMA_TERM_HOLS_CHAIN_OVER

See Also:

Constant Field Values

Constructor Detail

OBO

public OBO()

Method Detail

setOptions

public static void setOptions(boolean collateSysnonyms,
                              boolean descriptionTopics,
                              boolean altIdSIs,
                              boolean scopedXrefs,
                              java.lang.String lang)

setOptions

public static void setOptions(int options)

getOptions

public static int getOptions()

createRootTopic

public static Topic createRootTopic(TopicMap tm,
                                    java.lang.String namespace)
                             throws TopicMapException

Throws:

TopicMapException

createHeaderTopic

public static Topic createHeaderTopic(TopicMap tm,
                                      java.lang.String namespace)
                               throws TopicMapException

Throws:

TopicMapException

createTermTopic

public static Topic createTermTopic(TopicMap tm,
                                    java.lang.String namespace)
                             throws TopicMapException

Throws:

TopicMapException

createTypedefTopic

public static Topic createTypedefTopic(TopicMap tm,
                                       java.lang.String namespace)
                                throws TopicMapException

Throws:

TopicMapException

createInstanceTopic

public static Topic createInstanceTopic(TopicMap tm,
                                        java.lang.String namespace)
                                 throws TopicMapException

Throws:

TopicMapException

createObsoleteTopic

public static Topic createObsoleteTopic(TopicMap tm,
                                        java.lang.String namespace)
                                 throws TopicMapException

Throws:

TopicMapException

createCategoryTopic

public static Topic createCategoryTopic(TopicMap tm,
                                        java.lang.String namespace)
                                 throws TopicMapException

Throws:

TopicMapException

createDescriptionTopic

public static Topic createDescriptionTopic(TopicMap tm,
                                           java.lang.String namespace)
                                    throws TopicMapException

Throws:

TopicMapException

createSynonymTopic

public static Topic createSynonymTopic(TopicMap tm,
                                       java.lang.String namespace)
                                throws TopicMapException

Throws:

TopicMapException

createSchemaTopic

public static Topic createSchemaTopic(TopicMap tm)
                               throws TopicMapException

Throws:

TopicMapException

createISARootTopic

public static Topic createISARootTopic(TopicMap tm,
                                       java.lang.String namespace)
                                throws TopicMapException

Throws:

TopicMapException

createAuthorTopic

public static Topic createAuthorTopic(TopicMap tm,
                                      java.lang.String namespace)
                               throws TopicMapException

Throws:

TopicMapException

getRootTopic

public static Topic getRootTopic(TopicMap tm,
                                 java.lang.String namespace)
                          throws TopicMapException

Throws:

TopicMapException

getHeaderTopic

public static Topic getHeaderTopic(TopicMap tm,
                                   java.lang.String namespace)
                            throws TopicMapException

Throws:

TopicMapException

getTermTopic

public static Topic getTermTopic(TopicMap tm,
                                 java.lang.String namespace)
                          throws TopicMapException

Throws:

TopicMapException

getTypedefTopic

public static Topic getTypedefTopic(TopicMap tm,
                                    java.lang.String namespace)
                             throws TopicMapException

Throws:

TopicMapException

getInstanceTopic

public static Topic getInstanceTopic(TopicMap tm,
                                     java.lang.String namespace)
                              throws TopicMapException

Throws:

TopicMapException

getObsoleteTopic

public static Topic getObsoleteTopic(TopicMap tm,
                                     java.lang.String namespace)
                              throws TopicMapException

Throws:

TopicMapException

getCategoryTopic

public static Topic getCategoryTopic(TopicMap tm,
                                     java.lang.String namespace)
                              throws TopicMapException

Throws:

TopicMapException

getDescriptionTopic

public static Topic getDescriptionTopic(TopicMap tm,
                                        java.lang.String namespace)
                                 throws TopicMapException

Throws:

TopicMapException

solveOBOId

public static java.lang.String solveOBOId(Topic t)
                                   throws TopicMapException

Throws:

TopicMapException

solveOBOName

public static java.lang.String solveOBOName(Topic t)
                                     throws TopicMapException

Throws:

TopicMapException

solveOBODescription

public static java.lang.String solveOBODescription(Association a,
                                                   Topic t)
                                            throws TopicMapException

Throws:

TopicMapException

solveOBODescription

public static java.lang.String solveOBODescription(Topic t)
                                            throws TopicMapException

Throws:

TopicMapException

createTopicForTypedef

public static Topic createTopicForTypedef(TopicMap tm,
                                          java.lang.String id)
                                   throws TopicMapException

Throws:

TopicMapException

createTopicForTypedef

public static Topic createTopicForTypedef(TopicMap tm,
                                          java.lang.String id,
                                          java.lang.String name,
                                          java.lang.String namespace)
                                   throws TopicMapException

Throws:

TopicMapException

createTopicForTerm

public static Topic createTopicForTerm(TopicMap tm,
                                       java.lang.String id)
                                throws TopicMapException

Throws:

TopicMapException

createTopicForTerm

public static Topic createTopicForTerm(TopicMap tm,
                                       java.lang.String id,
                                       java.lang.String name,
                                       java.lang.String namespace)
                                throws TopicMapException

Throws:

TopicMapException

createTopicForInstance

public static Topic createTopicForInstance(TopicMap tm,
                                           java.lang.String id)
                                    throws TopicMapException

Throws:

TopicMapException

createTopicForInstance

public static Topic createTopicForInstance(TopicMap tm,
                                           java.lang.String id,
                                           java.lang.String name,
                                           java.lang.String namespace)
                                    throws TopicMapException

Throws:

TopicMapException

createTopicForAssertionExpansion

public static Topic createTopicForAssertionExpansion(TopicMap tm,
                                                     java.lang.String exp)
                                              throws TopicMapException

Throws:

TopicMapException

createTopicForAuthor

public static Topic createTopicForAuthor(TopicMap tm,
                                         java.lang.String name,
                                         java.lang.String namespace)
                                  throws TopicMapException

Throws:

TopicMapException

createTopicForSynonym

public static Topic createTopicForSynonym(TopicMap tm,
                                          java.lang.String name,
                                          java.lang.String namespace)
                                   throws TopicMapException

Throws:

TopicMapException

createTopicForDescription

public static Topic createTopicForDescription(TopicMap tm,
                                              java.lang.String description,
                                              java.lang.String namespace)
                                       throws TopicMapException

Throws:

TopicMapException

createTopicForRelation

public static Topic createTopicForRelation(TopicMap tm,
                                           java.lang.String id,
                                           java.lang.String namespace)
                                    throws TopicMapException

Throws:

TopicMapException

createTopicForRelation

public static Topic createTopicForRelation(TopicMap tm,
                                           java.lang.String id,
                                           java.lang.String name,
                                           java.lang.String namespace)
                                    throws TopicMapException

Throws:

TopicMapException

createTopicForModifier

public static Topic createTopicForModifier(TopicMap tm,
                                           java.lang.String id)
                                    throws TopicMapException

Throws:

TopicMapException

createTopicForModifier

public static Topic createTopicForModifier(TopicMap tm,
                                           java.lang.String id,
                                           java.lang.String name)
                                    throws TopicMapException

Throws:

TopicMapException

getTopicForSchemaTerm

public static Topic getTopicForSchemaTerm(TopicMap tm,
                                          java.lang.String schemaTerm)
                                   throws TopicMapException

Throws:

TopicMapException

createTopicForSchemaTerm

public static Topic createTopicForSchemaTerm(TopicMap tm,
                                             java.lang.String schemaTerm)
                                      throws TopicMapException

Throws:

TopicMapException

createTopicForDbxref

public static Topic createTopicForDbxref(TopicMap tm,
                                         java.lang.String id)
                                  throws TopicMapException

Throws:

TopicMapException

createTopicForDbxref

public static Topic createTopicForDbxref(TopicMap tm,
                                         java.lang.String id,
                                         java.lang.String description)
                                  throws TopicMapException

Throws:

TopicMapException

createTopicForCategory

public static Topic createTopicForCategory(TopicMap tm,
                                           java.lang.String id)
                                    throws TopicMapException

Throws:

TopicMapException

createTopicForCategory

public static Topic createTopicForCategory(TopicMap tm,
                                           java.lang.String id,
                                           java.lang.String description)
                                    throws TopicMapException

Throws:

TopicMapException

createTopicForPropertyRelationship

public static Topic createTopicForPropertyRelationship(TopicMap tm,
                                                       java.lang.String id)
                                                throws TopicMapException

Throws:

TopicMapException

createPropertyRelationshipTopic

public static Topic createPropertyRelationshipTopic(TopicMap tm)
                                             throws TopicMapException

Throws:

TopicMapException

createTopicForPropertyValue

public static Topic createTopicForPropertyValue(TopicMap tm,
                                                java.lang.String value)
                                         throws TopicMapException

Throws:

TopicMapException

createPropertyValueTopic

public static Topic createPropertyValueTopic(TopicMap tm)
                                      throws TopicMapException

Throws:

TopicMapException

createTopicForPropertyDatatype

public static Topic createTopicForPropertyDatatype(TopicMap tm,
                                                   java.lang.String str)
                                            throws TopicMapException

Throws:

TopicMapException

createPropertyDatatypeTopic

public static Topic createPropertyDatatypeTopic(TopicMap tm)
                                         throws TopicMapException

Throws:

TopicMapException

getOrCreateTopic

private static Topic getOrCreateTopic(TopicMap tm,
                                      java.lang.String si,
                                      java.lang.String basename)
                               throws TopicMapException

Throws:

TopicMapException

getOrCreateTopic

private static Topic getOrCreateTopic(TopicMap tm,
                                      java.lang.String si)
                               throws TopicMapException

Throws:

TopicMapException

getOrCreateTopic

private static Topic getOrCreateTopic(TopicMap tm,
                                      Locator si,
                                      java.lang.String basename)
                               throws TopicMapException

Throws:

TopicMapException

getTopic

private static Topic getTopic(TopicMap tm,
                              java.lang.String si)
                       throws TopicMapException

Throws:

TopicMapException

setData

private static void setData(Topic t,
                            Topic type,
                            java.lang.String lang,
                            java.lang.String text)
                     throws TopicMapException

Throws:

TopicMapException

makeSubclassOf

private static void makeSubclassOf(TopicMap tm,
                                   Topic t,
                                   Topic superclass)
                            throws TopicMapException

Throws:

TopicMapException

solveOBOId

public static java.lang.String solveOBOId(Locator l)
                                   throws TopicMapException

Throws:

TopicMapException

makeLocator

public static Locator makeLocator(java.lang.String id)

makeSI

public static java.lang.String makeSI(java.lang.String id)

makeSICarefully

public static java.lang.String makeSICarefully(java.lang.String id)

makeSI

public static java.lang.String makeSI(java.lang.String prefix,
                                      java.lang.String str)

makeTermSI

public static java.lang.String makeTermSI(java.lang.String termId)

makeBasename

public static java.lang.String makeBasename(java.lang.String termid)

OBO2Java

public static java.lang.String OBO2Java(java.lang.String str)

Java2OBO

public static java.lang.String Java2OBO(java.lang.String str)

Java2OBOLite

public static java.lang.String Java2OBOLite(java.lang.String str)

importExport

public static void importExport(java.lang.String dir)

importExport

public static void importExport(java.io.File[] importFiles)