public class CBO
extends java.lang.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 Term
s and Triple
s 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
Object
s 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.
Constructor | Description |
---|---|
CBO() |
Modifier and Type | Method | Description |
---|---|---|
static boolean |
checkTerm(java.lang.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(java.lang.String cboTerm) |
Gets the CBO term with the id 'cboTerm'.
|
static java.util.Set<Term> |
getTerms() |
Return the set of terms of the CBO.
|
static java.util.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(java.lang.String[] args) |
Test main class
|
public static boolean checkTerm(java.lang.String cboTerm)
cboTerm
- true
if cboTerm is in the correct format (starts with
right header), false
otherwise.public static org.biojava.nbio.ontology.Ontology getOntology()
Ontology
form BioJava.public static Term getTerm(java.lang.String cboTerm)
cboTerm
- the id of the CBO term to search for.java.util.NoSuchElementException
- if the id is not found or null.public static java.util.Set<Term> getTerms()
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.
public static java.util.Set<Triple> getTriples(Term subject, Term predicate, Term object)
If any of the parameters of this method are null, they are treated as wildcards.
subject
- the subject to search for, or null
.predicate
- the relationship to search for, or null
.object
- the object to search for, or null
.Ontology.getTriples(org.biojava.nbio.ontology.Term,
org.biojava.nbio.ontology.Term, org.biojava.nbio.ontology.Term)
public static void main(java.lang.String[] args)
args
-