org.molgenis.omx.observ.target

Class Ontology

java.lang.Object

org.molgenis.util.AbstractEntity

org.molgenis.omx.observ.target.Ontology

All Implemented Interfaces:

Serializable, Autoid, Identifiable, Entity

@Entity
public class Ontology
extends AbstractEntity
implements Identifiable

Ontology: Ontology defines a reference to an ontology or controlled vocabulary from which well-defined and stable (ontology) terms can be obtained. Each Ontology should have a unique identifer, for instance: Gene Ontology, Mammalian Phenotype, Human Phenotype Ontology, Unified Medical Language System, Medical Subject Headings, etc. Also a abbreviation is required, for instance: GO, MP, HPO, UMLS, MeSH, etc. Use of existing ontologies/vocabularies is recommended to harmonize phenotypic feature and value descriptions. But one can also create a 'local' Ontology. The Ontology class maps to FuGE::Ontology, MAGE-TAB::TermSourceREF. .

Author:

MOLGENIS generator

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static String	ID
static String	IDENTIFIER
static String	NAME
static String	ONTOLOGYACCESSION
static String	ONTOLOGYURI

Constructor Summary

Constructors

Constructor and Description
Ontology()
Ontology(Ontology copyMe) copy constructor

Method Summary

Methods

Modifier and Type	Method and Description
Ontology	create(Entity entity)
boolean	equals(Object obj)
static List<? extends Ontology>	find(Database db, QueryRule... rules) Shorthand for db.find(Ontology.class, org.molgenis.framework.db.QueryRule ...
static Ontology	findById(Database db, Integer id)
static Ontology	findByIdentifier(Database db, String identifier)
Object	get(String name) Generic getter.
Vector<String>	getFields()
Vector<String>	getFields(boolean skipAutoIds) Get the names of all public properties of Ontology.
String	getFields(String sep) Deprecated.
Integer	getId() Get the automatically generated internal id, only for internal use..
String	getIdentifier() Get the user supplied or automatically assigned (using a decorator) unique and short identifier, e.g.
String	getIdentifier(Database db) Deprecated.
String	getIdField()
Object	getIdValue()
List<String>	getLabelFields()
String	getName() Get the human readible name, not necessary unique..
String	getName(Database db) Deprecated.
String	getOntologyAccession() Get the A accession that uniquely identifies the ontology (typically an acronym).
String	getOntologyAccession(Database db) Deprecated.
String	getOntologyURI() Get the (Optional) A URI that references the location of the ontology..
String	getOntologyURI(Database db) Deprecated.
String	getValues(String sep) Deprecated.
String	getXrefIdFieldName(String fieldName)
int	hashCode()
static Query<? extends Ontology>	query(Database db) Shorthand for db.query(Ontology.class).
void	set(Entity entity, boolean strict)
void	setId(Integer id) Set the automatically generated internal id, only for internal use..
void	setIdentifier(String identifier) Set the user supplied or automatically assigned (using a decorator) unique and short identifier, e.g.
void	setName(String name) Set the human readible name, not necessary unique..
void	setOntologyAccession(String ontologyAccession) Set the A accession that uniquely identifies the ontology (typically an acronym).
void	setOntologyURI(String ontologyURI) Set the (Optional) A URI that references the location of the ontology..
String	toString()
String	toString(boolean verbose)
void	validate()

Methods inherited from class org.molgenis.util.AbstractEntity

get__Type, get__TypeLabel, get__TypeOptions, getLabelValue, getValues, isObjectRepresentation, isReadonly, set__Type, set, set, setReadonly, setValuesFromString, string2date

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.molgenis.util.Entity

getLabelValue, getValues, isReadonly, set, set, setReadonly

Field Detail

ID

public static final String ID

See Also:

Constant Field Values

IDENTIFIER

public static final String IDENTIFIER

See Also:

Constant Field Values

NAME

public static final String NAME

See Also:

Constant Field Values

ONTOLOGYACCESSION

public static final String ONTOLOGYACCESSION

See Also:

Constant Field Values

ONTOLOGYURI

public static final String ONTOLOGYURI

See Also:

Constant Field Values

Constructor Detail

Ontology

public Ontology()

Ontology

public Ontology(Ontology copyMe)
         throws Exception

copy constructor

Throws:

Exception

Method Detail

query

public static Query<? extends Ontology> query(Database db)

Shorthand for db.query(Ontology.class).

find

public static List<? extends Ontology> find(Database db,
                            QueryRule... rules)
                                     throws DatabaseException

Shorthand for db.find(Ontology.class, org.molgenis.framework.db.QueryRule ... rules).

Throws:

DatabaseException

findById

public static Ontology findById(Database db,
                Integer id)
                         throws DatabaseException

Throws:

DatabaseException

findByIdentifier

public static Ontology findByIdentifier(Database db,
                        String identifier)
                                 throws DatabaseException

Throws:

DatabaseException

getId

public Integer getId()

Get the automatically generated internal id, only for internal use..

Specified by:

getId in interface Autoid

Returns:

id.

setId

public void setId(Integer id)

Set the automatically generated internal id, only for internal use..

Specified by:

setId in interface Autoid

Parameters:

id -

getIdentifier

public String getIdentifier()

Get the user supplied or automatically assigned (using a decorator) unique and short identifier, e.g. MA1234.

Specified by:

getIdentifier in interface Identifiable

Returns:

identifier.

getIdentifier

@Deprecated
public String getIdentifier(Database db)

Deprecated.

setIdentifier

public void setIdentifier(String identifier)

Set the user supplied or automatically assigned (using a decorator) unique and short identifier, e.g. MA1234.

Specified by:

setIdentifier in interface Identifiable

Parameters:

identifier -

getName

public String getName()

Get the human readible name, not necessary unique..

Specified by:

getName in interface Identifiable

Returns:

name.

getName

@Deprecated
public String getName(Database db)

Deprecated.

setName

public void setName(String name)

Set the human readible name, not necessary unique..

Specified by:

setName in interface Identifiable

Parameters:

name -

getOntologyAccession

public String getOntologyAccession()

Get the A accession that uniquely identifies the ontology (typically an acronym). E.g. GO, MeSH, HPO..

Returns:

ontologyAccession.

getOntologyAccession

@Deprecated
public String getOntologyAccession(Database db)

Deprecated.

setOntologyAccession

public void setOntologyAccession(String ontologyAccession)

Set the A accession that uniquely identifies the ontology (typically an acronym). E.g. GO, MeSH, HPO..

Parameters:

ontologyAccession -

getOntologyURI

public String getOntologyURI()

Get the (Optional) A URI that references the location of the ontology..

Returns:

ontologyURI.

getOntologyURI

@Deprecated
public String getOntologyURI(Database db)

Deprecated.

setOntologyURI

public void setOntologyURI(String ontologyURI)

Set the (Optional) A URI that references the location of the ontology..

Parameters:

ontologyURI -

get

public Object get(String name)

Generic getter. Get the property by using the name.

Specified by:

get in interface Entity

validate

public void validate()
              throws DatabaseException

Specified by:

validate in interface Entity

Throws:

DatabaseException

set

public void set(Entity entity,
       boolean strict)
         throws Exception

Specified by:

set in interface Entity

Throws:

Exception

toString

public String toString()

Overrides:

toString in class Object

toString

public String toString(boolean verbose)

getFields

public Vector<String> getFields(boolean skipAutoIds)

Get the names of all public properties of Ontology.

Specified by:

getFields in interface Entity

getFields

public Vector<String> getFields()

Specified by:

getFields in interface Entity

getIdField

public String getIdField()

Specified by:

getIdField in interface Entity

getLabelFields

public List<String> getLabelFields()

Specified by:

getLabelFields in interface Entity

getFields

@Deprecated
public String getFields(String sep)

Deprecated.

Specified by:

getFields in interface Entity

getIdValue

public Object getIdValue()

Specified by:

getIdValue in interface Entity

getXrefIdFieldName

public String getXrefIdFieldName(String fieldName)

Specified by:

getXrefIdFieldName in interface Entity

getValues

@Deprecated
public String getValues(String sep)

Deprecated.

Specified by:

getValues in interface Entity

Overrides:

getValues in class AbstractEntity

create

public Ontology create(Entity entity)
                throws Exception

Specified by:

create in interface Entity

Throws:

Exception

equals

public boolean equals(Object obj)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object