org.molgenis.omx.observ.target

Class OntologyTerm

java.lang.Object

org.molgenis.data.support.AbstractEntity

org.molgenis.omx.observ.Characteristic

org.molgenis.omx.observ.target.OntologyTerm

All Implemented Interfaces:

java.io.Serializable, Entity, Autoid, Identifiable

Direct Known Subclasses:

Accession, PersonRole, Species

@Entity
public class OntologyTerm
extends Characteristic
implements Entity

OntologyTerm: OntologyTerm defines a single entry (term) from an ontology or a controlled vocabulary (defined by Ontology). The identifier is the ontology term is unique. E.g. 'NCI:Antigen Gene'. Other data entities can reference to this OntologyTerm to harmonize naming of concepts. If no suitable ontology term exists then one can define new terms locally (in which case there is no formal accession for the term limiting its use for cross-Investigation queries). .

Author:

MOLGENIS generator

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	DEFINITION
static java.lang.String	ENTITY_NAME
static java.lang.String	ID
static java.lang.String	ONTOLOGY
static java.lang.String	TERMACCESSION

Fields inherited from class org.molgenis.omx.observ.Characteristic

__TYPE, DESCRIPTION, IDENTIFIER, NAME

Constructor Summary

Constructors

Constructor and Description
OntologyTerm()

Method Summary

Methods

Modifier and Type	Method and Description
boolean	equals(java.lang.Object obj)
java.lang.Object	get(java.lang.String name) Generic getter.
java.lang.Iterable<java.lang.String>	getAttributeNames()
java.lang.String	getDefinition() Get the (Optional) The definition of the term..
java.util.Collection<ObservableFeature>	getDefinitionsObservableFeatureCollection()
EntityMetaData	getEntityMetaData()
java.lang.String	getEntityName()
java.lang.Integer	getIdValue()
java.util.List<java.lang.String>	getLabelAttributeNames()
Ontology	getOntology() Get the (Optional) The source ontology or controlled vocabulary list that ontology terms have been obtained from..
java.lang.String	getTermAccession() Get the (Optional) The accession number assigned to the ontology term in its source ontology.
int	hashCode()
void	set(Entity entity, boolean strict)
void	set(java.lang.String attributeName, java.lang.Object value)
void	setDefinition(java.lang.String definition) Set the (Optional) The definition of the term..
void	setDefinitionsObservableFeatureCollection(java.util.Collection<ObservableFeature> collection)
void	setOntology(Ontology ontology) Set the (Optional) The source ontology or controlled vocabulary list that ontology terms have been obtained from..
void	setTermAccession(java.lang.String termAccession) Set the (Optional) The accession number assigned to the ontology term in its source ontology.
java.lang.String	toString()
java.lang.String	toString(boolean verbose)

Methods inherited from class org.molgenis.omx.observ.Characteristic

get__Type, get__TypeLabel, get__TypeOptions, getDescription, getId, getIdentifier, getName, getValueMrefValueCollection, set__Type, setDescription, setId, setIdentifier, setName, setValueMrefValueCollection

Methods inherited from class org.molgenis.data.support.AbstractEntity

getBoolean, getDate, getDouble, getEntities, getEntities, getEntity, getEntity, getInt, getIntList, getLabelValue, getList, getLong, getString, getTimestamp, getUtilDate, isObjectRepresentation, set, setValuesFromString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.molgenis.data.Entity

getBoolean, getDate, getDouble, getEntities, getEntities, getEntity, getEntity, getInt, getIntList, getLabelValue, getList, getLong, getString, getTimestamp, getUtilDate, set

Field Detail

ENTITY_NAME

public static final java.lang.String ENTITY_NAME

See Also:

Constant Field Values

ONTOLOGY

public static final java.lang.String ONTOLOGY

See Also:

Constant Field Values

TERMACCESSION

public static final java.lang.String TERMACCESSION

See Also:

Constant Field Values

DEFINITION

public static final java.lang.String DEFINITION

See Also:

Constant Field Values

ID

public static final java.lang.String ID

See Also:

Constant Field Values

Constructor Detail

OntologyTerm

public OntologyTerm()

Method Detail

getEntityName

public java.lang.String getEntityName()

Overrides:

getEntityName in class Characteristic

getOntology

public Ontology getOntology()

Get the (Optional) The source ontology or controlled vocabulary list that ontology terms have been obtained from..

Returns:

ontology.

setOntology

public void setOntology(Ontology ontology)

Set the (Optional) The source ontology or controlled vocabulary list that ontology terms have been obtained from..

Parameters:

ontology -

getTermAccession

public java.lang.String getTermAccession()

Get the (Optional) The accession number assigned to the ontology term in its source ontology. If empty it is assumed to be a locally defined term..

Returns:

termAccession.

setTermAccession

public void setTermAccession(java.lang.String termAccession)

Set the (Optional) The accession number assigned to the ontology term in its source ontology. If empty it is assumed to be a locally defined term..

Parameters:

termAccession -

getDefinition

public java.lang.String getDefinition()

Get the (Optional) The definition of the term..

Returns:

definition.

setDefinition

public void setDefinition(java.lang.String definition)

Set the (Optional) The definition of the term..

Parameters:

definition -

get

public java.lang.Object get(java.lang.String name)

Generic getter. Get the property by using the name.

Specified by:

get in interface Entity

Overrides:

get in class Characteristic

set

public void set(Entity entity,
       boolean strict)

Specified by:

set in interface Entity

Overrides:

set in class Characteristic

toString

public java.lang.String toString()

Overrides:

toString in class Characteristic

toString

public java.lang.String toString(boolean verbose)

Overrides:

toString in class Characteristic

getIdValue

public java.lang.Integer getIdValue()

Specified by:

getIdValue in interface Entity

Overrides:

getIdValue in class Characteristic

getDefinitionsObservableFeatureCollection

public java.util.Collection<ObservableFeature> getDefinitionsObservableFeatureCollection()

setDefinitionsObservableFeatureCollection

public void setDefinitionsObservableFeatureCollection(java.util.Collection<ObservableFeature> collection)

getAttributeNames

public java.lang.Iterable<java.lang.String> getAttributeNames()

Specified by:

getAttributeNames in interface Entity

Overrides:

getAttributeNames in class Characteristic

getLabelAttributeNames

public java.util.List<java.lang.String> getLabelAttributeNames()

Specified by:

getLabelAttributeNames in interface Entity

Overrides:

getLabelAttributeNames in class Characteristic

set

public void set(java.lang.String attributeName,
       java.lang.Object value)

Specified by:

set in interface Entity

Overrides:

set in class Characteristic

equals

public boolean equals(java.lang.Object obj)

Overrides:

equals in class Characteristic

hashCode

public int hashCode()

Overrides:

hashCode in class Characteristic

getEntityMetaData

public EntityMetaData getEntityMetaData()

Specified by:

getEntityMetaData in interface Entity

Overrides:

getEntityMetaData in class Characteristic