org.sbml.jsbml.ext.dyn

Class CBO

java.lang.Object

org.sbml.jsbml.ext.dyn.CBO

public class CBO
extends Object

Methods for interacting with Cell Behavior Ontology (CBO) terms. This class uses the BioJava classes for working with ontologies and contains static classes to represent single Terms and Triples of subject, predicate, and object, where each of these three entities is again an instance of Term. The classes Term and Triple basically wrap the underlying functions from BioJava, but the original Objects can be accessed via dedicated get methods. Furthermore, the Ontology from BioJava, which is used in this class, can be obtained using the method getOntology().

Cell Behavior Ontology and the cboTerm attribute It is difficult to determine the semantics of Event constructs used to model intrinsic cellular behavior from SBML attributes alone. The id attribute on Event objects allows for unique identification and cross-referencing while the name attribute allows the assignment of human readable labels to Events. Possible values for these attributes are unrestricted so that modelers can choose whichever fits their modeling framework and preference best. However, this means that without any additional human intervention, software tools are unable to discern the semantics of an extended Event element modeling dynamic behavior. For instance, it would be inadvisable to interpret that an Event is modeling the process of cellular death even if the id and name of such Event have the string “Cell Death” as value. Additionally, as one may need to convert a dynamic Event between different representations (e.g., Cellular PottsModel vs. Center-based off-latticeModel), there is a need to provide a standard, framework-independent, way of associating Event components with given cellular processes. A solution inspired by SBML Level 3 Version 1 Core is to associate model components with terms from carefully curated controlled vocabularies (CVs) such as CBO. This is the purpose of the cboTerm provided through the extended SBase class in this package.

Since:

1.0

Author:

Harold Gómez

Constructor Summary

Constructors

Constructor and Description
CBO()

Method Summary

Modifier and Type	Method and Description
static boolean	checkTerm(String cboTerm) Checks the format of the given CBO string.
static org.biojava.nbio.ontology.Ontology	getOntology() Grants access to the underlying Ontology form BioJava.
static Term	getTerm(String cboTerm) Gets the CBO term with the id 'cboTerm'.
static Set<Term>	getTerms() Return the set of terms of the CBO.
static Set<Triple>	getTriples(Term subject, Term predicate, Term object) Returns a set of Triple which match the supplied subject, predicate and object.
static void	main(String[] args) Test main class

Methods inherited from class java.lang.Object

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

Constructor Detail

CBO

public CBO()

Method Detail

checkTerm

public static boolean checkTerm(String cboTerm)

Checks the format of the given CBO string.

Parameters:

cboTerm -

Returns:

true if cboTerm is in the correct format (starts with right header), false otherwise.

getOntology

public static org.biojava.nbio.ontology.Ontology getOntology()

Grants access to the underlying Ontology form BioJava.

Returns:

getTerm

public static Term getTerm(String cboTerm)

Gets the CBO term with the id 'cboTerm'.

Parameters:

cboTerm - the id of the CBO term to search for.

Returns:

the CBO term with the id 'cboTerm'.

Throws:

NoSuchElementException - if the id is not found or null.

Warning:

The methods will throw NoSuchElementException if the id is not found or null.

getTerms

public static Set<Term> getTerms()

Return the set of terms of the CBO.

This methods return only Term object and no Triple object that represent the relationship between terms. If you want to access the full set of Term containing also the Triple, use getOntology() to get the underlying biojava object.

Returns:

the set of terms of the CBO.

getTriples

public static Set<Triple> getTriples(Term subject,
                                     Term predicate,
                                     Term object)

Returns a set of Triple which match the supplied subject, predicate and object.

If any of the parameters of this method are null, they are treated as wildcards.

Parameters:

subject - the subject to search for, or null.

predicate - the relationship to search for, or null.

object - the object to search for, or null.

Returns:

a set of Triple which match the supplied subject, predicate and object.

See Also:

Ontology.getTriples(org.biojava.nbio.ontology.Term, org.biojava.nbio.ontology.Term, org.biojava.nbio.ontology.Term)

main

public static void main(String[] args)

Test main class

Parameters:

args -