org.sbolstandard.core2

Class EDAMOntology

java.lang.Object

org.sbolstandard.core2.EDAMOntology

public class EDAMOntology
extends Object

This class provides methods for accessing EMBRACE Data and Methods (EDAM) terms and querying about their relationships.

Version:

2.1

Author:

Zhen Zhang, Chris Myers

Field Summary

Fields

Modifier and Type	Field and Description
static URI	BIOPAX BioPAX is an exchange format for pathway data, with its data model defined in OWL (BIOPAX).
static URI	CELLML CellML, the format for mathematical models of biological and other networks (CELLML).
static URI	FORMAT A defined way or layout of representing and structuring data in a computer file, blob, string, message, or elsewhere.
static URI	NAMESPACE Namespace of the EDAM Ontology (http://identifiers.org/edam/).
static URI	SBML Systems Biology Markup Language (SBML), the standard XML format for models of biological processes such as for example metabolism, cell signaling, and gene regulation (SBML).

Constructor Summary

Constructors

Constructor and Description
EDAMOntology() Construct an EDAM ontology object and read the OBO definition file, if necessary.

Method Summary

Modifier and Type	Method and Description
Set<String>	getDescendantNamesOf(String parentId) Returns the set of child names that are descendants of the given parent ID.
Set<String>	getDescendantNamesOf(URI parentURI) Returns the set of child names that are descendants of the given parent URI.
Set<String>	getDescendantsOf(String parentId) Returns a set of child IDs that are descendants of the given parent ID.
Set<String>	getDescendantsOf(URI parentURI) Returns a set of child IDs that are descendants of the given parent URI.
Set<URI>	getDescendantURIsOf(String parentId) Returns a set of child URIs that are descendants of the given parent ID.
Set<URI>	getDescendantURIsOf(URI parentURI) Returns a set of child URIs that are descendants of the given parent URI.
String	getId(String stanzaName) Returns the ID field of the stanza whose name field matches the given name.
String	getId(URI stanzaURI) Returns the extracted ID of the given stanza's URI.
String	getName(String stanzaId) Returns the name field of the stanza matching the ID extracted from the given stanza URI.
String	getName(URI stanzaURI) Returns the name field of the stanza that matches the ID for the given stanza URI.
URI	getURIbyId(String stanzaId) Creates a new URI from the EDAM Ontology namespace with the given ID.
URI	getURIbyName(String stanzaName) Returns the URI, i.e.
boolean	isDescendantOf(String Id1, String Id2) Returns true if the stanza with Id1 is a descendant of the stanza with Id2.
boolean	isDescendantOf(URI childURI, URI parentURI) Returns true if the stanza with childURI is a descendant of the stanza with parentURI.

Methods inherited from class java.lang.Object

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

Field Detail

NAMESPACE

public static final URI NAMESPACE

Namespace of the EDAM Ontology (http://identifiers.org/edam/).

FORMAT

public static final URI FORMAT

A defined way or layout of representing and structuring data in a computer file, blob, string, message, or elsewhere. The main focus in EDAM lies on formats as means of structuring data exchanged between different tools or resources. The serialisation, compression, or encoding of concrete data formats/models is not in scope of EDAM. Format 'is format of' Data. (FORMAT).

SBML

public static final URI SBML

Systems Biology Markup Language (SBML), the standard XML format for models of biological processes such as for example metabolism, cell signaling, and gene regulation (SBML).

CELLML

public static final URI CELLML

CellML, the format for mathematical models of biological and other networks (CELLML).

BIOPAX

public static final URI BIOPAX

BioPAX is an exchange format for pathway data, with its data model defined in OWL (BIOPAX).

Constructor Detail

EDAMOntology

public EDAMOntology()

Construct an EDAM ontology object and read the OBO definition file, if necessary.

Method Detail

getId

public final String getId(URI stanzaURI)

Returns the extracted ID of the given stanza's URI.

Parameters:

stanzaURI - the given stanza's URI

Returns:

the extracted ID of the given stanza's URI.

getId

public final String getId(String stanzaName)

Returns the ID field of the stanza whose name field matches the given name. If multiple matches are found, only the first matching one is returned.

Parameters:

stanzaName - the given stanza's name

Returns:

the ID of the matching stanza, or null if no match was found

getName

public final String getName(URI stanzaURI)

Returns the name field of the stanza that matches the ID for the given stanza URI.

Parameters:

stanzaURI - the given stanza URI

Returns:

the name field of the stanza that matches the ID extracted from the given stanza URI

getName

public final String getName(String stanzaId)

Returns the name field of the stanza matching the ID extracted from the given stanza URI.

Parameters:

stanzaId - the given stanza URI

Returns:

the name field of the stanza that matches the ID in the given stanza URI, or null if no match was found

getURIbyName

public final URI getURIbyName(String stanzaName)

Returns the URI, i.e. the EDAM Ontology namespace URL followed by an ID of an EDAM ontology term, of the stanza whose name matches the given name. If multiple matches are found, only the first matching one is returned.

Parameters:

stanzaName - the given stanza's name

Returns:

the URI of the given EDAM ontology name.

getURIbyId

public final URI getURIbyId(String stanzaId)

Creates a new URI from the EDAM Ontology namespace with the given ID.

Parameters:

stanzaId - the given stanza's ID

Returns:

the created URI

isDescendantOf

public boolean isDescendantOf(String Id1,
                              String Id2)

Returns true if the stanza with Id1 is a descendant of the stanza with Id2.

Parameters:

Id1 - the given stanza's ID

Id2 - the given stanza's ID

Returns:

true if the stanza with Id1 is a descendant of the stanza with Id2, false otherwise.

isDescendantOf

public final boolean isDescendantOf(URI childURI,
                                    URI parentURI)

Returns true if the stanza with childURI is a descendant of the stanza with parentURI.

Parameters:

childURI - the given stanza's URI

parentURI - the given stanza's URI

Returns:

true if the stanza with childURI is a descendant of the stanza with parentURI, false otherwise.

getDescendantsOf

public Set<String> getDescendantsOf(String parentId)

Returns a set of child IDs that are descendants of the given parent ID. This set excludes the given parent ID.

Parameters:

parentId - the id of the parent term

Returns:

a set of child IDs that are descendants of the given parent ID.

getDescendantsOf

public final Set<String> getDescendantsOf(URI parentURI)

Returns a set of child IDs that are descendants of the given parent URI. This set excludes the given parent ID.

Parameters:

parentURI - the URI of the parent term

Returns:

a set of child IDs that are descendants of the given parent URI.

getDescendantURIsOf

public final Set<URI> getDescendantURIsOf(String parentId)

Returns a set of child URIs that are descendants of the given parent ID. This set excludes the given parent URI.

Parameters:

parentId - the ID of the parent term

Returns:

a set of child URIs that are descendants of the given parent ID.

getDescendantURIsOf

public final Set<URI> getDescendantURIsOf(URI parentURI)

Returns a set of child URIs that are descendants of the given parent URI. This set excludes the given parent URI.

Parameters:

parentURI - the URI of the parent term

Returns:

a set of child URIs that are descendants of the given parent URI.

getDescendantNamesOf

public final Set<String> getDescendantNamesOf(String parentId)

Returns the set of child names that are descendants of the given parent ID. This set excludes the given parent name.

Parameters:

parentId - the ID of the parent stanza

Returns:

the set of child names that are descendants of the given parent ID.

getDescendantNamesOf

public final Set<String> getDescendantNamesOf(URI parentURI)

Returns the set of child names that are descendants of the given parent URI. This set excludes the given parent name.

Parameters:

parentURI - the URI of the parent stanza

Returns:

the set of child names that are descendants of the given parent URI