SBO

java.lang.Object
- org.sbml.jsbml.SBO

```
public class SBO
extends java.lang.Object
```
Methods for interacting with Systems Biology Ontology (SBO) terms.
This class uses the BioJava classes for working with ontologies and contains static classes to represent single SBO.Terms and SBO.Triples of subject, predicate, and object, where each of these three entities is again an instance of SBO.Term. The classes SBO.Term and SBO.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 also be obtained using the method getOntology().
The values of 'id' attributes on SBML components allow the components to be cross-referenced within a model. The values of 'name' attributes on SBML components provide the opportunity to assign them meaningful labels suitable for display to humans. The specific identifiers and labels used in a model necessarily must be unrestricted by SBML, so that software and users are free to pick whatever they need. However, this freedom makes it more difficult for software tools to determine, without additional human intervention, the semantics of models more precisely than the semantics provided by the SBML object classes defined in other sections of this document. For example, there is nothing inherent in a parameter with identifier k that would indicate to a software tool it is a first-order rate constant (if that's what k happened to be in some given model). However, one may need to convert a model between different representations (e.g., Henri-Michaelis-Menten versus elementary steps), or to use it with different modeling approaches (discrete or continuous). One may also need to relate the model components with other description formats such as SBGN (http://www.sbgn.org/) using deeper semantics. Although an advanced software tool might be able to deduce the semantics of some model components through detailed analysis of the kinetic rate expressions and other parts of the model, this quickly becomes infeasible for any but the simplest of models.
An approach to solving this problem is to associate model components with terms from carefully curated controlled vocabularies (CVs). This is the purpose of the optional 'sboTerm' attribute provided on the SBML class SBase. The 'sboTerm' attribute always refers to terms belonging to the Systems Biology Ontology (SBO).

Use of SBO

Labeling model components with terms from shared controlled vocabularies allows a software tool to identify each component using identifiers that are not tool-specific. An example of where this is useful is the desire by many software developers to provide users with meaningful names for reaction rate equations. Software tools with editing interfaces frequently provide these names in menus or lists of choices for users. However, without a standardized set of names or identifiers shared between developers, a given software package cannot reliably interpret the names or identifiers of reactions used in models written by other tools.
The first solution that might come to mind is to stipulate that certain common reactions always have the same name (e.g., 'Michaelis-Menten'), but this is simply impossible to do: not only do humans often disagree on the names themselves, but it would not allow for correction of errors or updates to the list of predefined names except by issuing new releases of the SBML specification—to say nothing of many other limitations with this approach. Moreover, the parameters and variables that appear in rate expressions also need to be identified in a way that software tools can interpret mechanically, implying that the names of these entities would also need to be regulated.
The Systems Biology Ontology (SBO) provides terms for identifying most elements of SBML. The relationship implied by an 'sboTerm' on an SBML model component is is-a between the characteristic of the component meant to be described by SBO on this element and the SBO term identified by the value of the 'sboTerm'. By adding SBO term references on the components of a model, a software tool can provide additional details using independent, shared vocabularies that can enable other software tools to recognize precisely what the component is meant to be. Those tools can then act on that information. For example, if the SBO identifier 'SBO:0000049' is assigned to the concept of 'first-order irreversible mass-action kinetics, continuous framework', and a given KineticLaw object in a model has an 'sboTerm' attribute with this value, then regardless of the identifier and name given to the reaction itself, a software tool could use this to inform users that the reaction is a first-order irreversible mass-action reaction. This kind of reverse engineering of the meaning of reactions in a model would be difficult to do otherwise, especially for more complex reaction types.
The presence of SBO labels on Compartment, Species, and Reaction objects in SBML can help map those entities to equivalent concepts in other standards, such as (but not limited to) BioPAX (http://www.biopax.org/), PSI-MI (http://www.psidev.info), or the Systems Biology Graphical Notation (SBGN, http://www.sbgn.org/). Such mappings can be used in conversion procedures, or to build interfaces, with SBO becoming a kind of 'glue' between standards of representation.
The presence of the label on a kinetic expression can also allow software tools to make more intelligent decisions about reaction rate expressions. For example, an application could recognize certain types of reaction formulas as being ones it knows how to solve with optimized procedures. The application could then use internal, optimized code implementing the rate formula indexed by identifiers such as 'SBO:0000049' appearing in SBML models.
Finally, SBO labels may be very valuable when it comes to model integration, by helping identify interfaces, convert mathematical expressions and parameters etc.
Although the use of SBO can be beneficial, it is critical to keep in mind that the presence of an 'sboTerm' value on an object must not change the fundamental mathematical meaning of the model. An SBML model must be defined such that it stands on its own and does not depend on additional information added by SBO terms for a correct mathematical interpretation. SBO term definitions will not imply any alternative mathematical semantics for any SBML object labeled with that term. Two important reasons motivate this principle. First, it would be too limiting to require all software tools to be able to understand the SBO vocabularies in addition to understanding SBML. Supporting SBO is not only additional work for the software developer; for some kinds of applications, it may not make sense. If SBO terms on a model are optional, it follows that the SBML model must remain unambiguous and fully interpretable without them, because an application reading the model may ignore the terms. Second, we believe allowing the use of 'sboTerm' to alter the mathematical meaning of a model would allow too much leeway to shoehorn inconsistent concepts into SBML objects, ultimately reducing the interoperability of the models.

Relationships between SBO and SBML

The goal of SBO labeling for SBML is to clarify to the fullest extent possible the nature of each element in a model. The approach taken in SBO begins with a hierarchically-structured set of controlled vocabularies with six main divisions: (1) entity, (2) participant role, (3) quantitative parameter, (4) modeling framework, (5) mathematical expression, and (6) interaction. The web site for SBO (http://biomodels.net) should be consulted for the current version of the ontology.
The Systems Biology Ontology (SBO) is not part of SBML; it is being developed separately, to allow the modeling community to evolve the ontology independently of SBML. However, the terms in the ontology are being designed keeping SBML components in mind, and are classified into subsets that can be directly related with SBML components such as reaction rate expressions, parameters, and others. The use of 'sboTerm' attributes is optional, and the presence of 'sboTerm' on an element does not change the way the model is interpreted. Annotating SBML elements with SBO terms adds additional semantic information that may be used to convert the model into another model, or another format. Although SBO support provides an important source of information to understand the meaning of a model, software does not need to support 'sboTerm' to be considered SBML-compliant.

Since:

0.8

Version:

$Rev: 1639 $

Author:

Andreas Dräger, Nicolas Rodriguez

Nested Class Summary

Nested Classes
Modifier and Type	Class and Description
`static class`	`SBO.Term` This is a convenient wrapper class for the corresponding implementation of `org.biojava.ontology.Term` in BioJava as it provides specialized methods to obtain the information from the SBO OBO file directly and under the same name as the keys are given in that file.
`static class`	`SBO.Triple` This is a wrapper class for the corresponding BioJava class `org.biojava.ontology.Triple`, to allow for simplified access to the properties of a subject-predicate-object triple in this ontology.

Field Summary

Fields
Modifier and Type	Field and Description
`private static java.util.Properties`	`alias2sbo`
`private static java.lang.String`	`prefix` the prefix of all SBO ids.
`private static Ontology`	`sbo`
`private static java.util.Properties`	`sbo2alias`
`private static java.util.Set<SBO.Term>`	`terms`

Constructor Summary

Constructors
Constructor and Description

SBO()

Constructors
Constructor and Description
`SBO()`

Method Summary

Methods
Modifier and Type	Method and Description
`static boolean`	`checkTerm(int sboTerm)` Checks the format of the given SBO integer portion.
`static boolean`	`checkTerm(java.lang.String sboTerm)` Checks the format of the given SBO string.
`static int`	`convertAlias2SBO(java.lang.String alias)` Returns an SBO id corresponding to the given alias.
`static java.lang.String`	`convertSBO2Alias(int sboterm)` Returns an alias corresponding to the given SBO id.
`static int`	`getAntisenseRNA()` Returns the SBO id for antisense RNA.
`static int`	`getAssociation()` Interaction between several biochemical entities that results in the formation of a non-covalent complex
`static int`	`getBindingActivator()` An essential activator that affects the apparent value of the Michaelis constant(s).
`static int`	`getCatalysis()` Modification of the velocity of a reaction by lowering the energy of the transition state.
`static int`	`getCatalyst()` Substance that accelerates the velocity of a chemical reaction without itself being consumed or transformed.
`static int`	`getCatalyticActivator()`
`static int`	`getCompartment()` Physical compartment.
`static int`	`getCompetetiveInhibitor()`
`static int`	`getCompleteInhibitor()`
`static int`	`getComplex()`
`static int`	`getConservationLaw()`
`static int`	`getConsumption()` Decrease in amount of a material or conceptual entity.
`static int`	`getContinuousFramework()`
`static java.util.Set<java.lang.Integer>`	`getDefaultPossibleEnzymes()` Creates and returns a list of molecule types accepted as an enzyme by default.
`static int`	`getDiscreteFramework()`
`static int`	`getDissociation()` Transformation of a non-covalent complex that results in the formation of several independent biochemical entities.
`static int`	`getDrug()`
`static int`	`getEmptySet()` Empty set is used to represent the source of a creation process or the result of a degradation process.
`static int`	`getEntity()`
`static int`	`getEnzymaticCatalysis()`
`static int`	`getEssentialActivator()`
`static int`	`getEvent()`
`static int`	`getFunctionalCompartment()`
`static int`	`getFunctionalEntity()`
`static int`	`getGene()` A gene is an informational molecule segment.
`static int`	`getGeneCodingRegion()`
`static int`	`getGeneric()`
`static int`	`getHillEquation()`
`static int`	`getInhibition()` Negative modulation of the execution of a process.
`static int`	`getInhibitor()` Substance that decreases the probability of a chemical reaction without itself being consumed or transformed by the reaction.
`static int`	`getInteraction()`
`static int`	`getIon()`
`static int`	`getIonChannel()`
`static int`	`getKineticConstant()`
`static int`	`getLogicalFramework()`
`static int`	`getMacromolecule()` Returns the SBO term id for macromolecule.
`static int`	`getMaterialEntity()`
`static int`	`getMathematicalExpression()`
`static int`	`getMessengerRNA()`
`static int`	`getModellingFramework()`
`static int`	`getModifier()` Substance that changes the velocity of a process without itself being consumed or transformed by the reaction.
`static int`	`getModulation()` Modification of the execution of an event or a process.
`static int`	`getNecessaryStimulation()` Control that is necessary to the execution of a process.
`static int`	`getNonCompetetiveInhibitor()`
`static int`	`getNonCovalentComplex()`
`static int`	`getNonEssentialActivator()`
`static Ontology`	`getOntology()` Grants access to the underlying `Ontology` form BioJava.
`static int`	`getPartialInhibitor()`
`static int`	`getParticipant()`
`static int`	`getParticipantRole()` The function of a physical or conceptual entity, that is its role, in the execution of an event or process.
`static int`	`getPertubingAgent()` Perturbing agent.
`static int`	`getPhenotype()`
`static int`	`getPhysicalCompartment()`
`static int`	`getPhysicalParticipant()`
`static java.util.Set<java.lang.Integer>`	`getPossibleEnzymes(java.lang.String... types)` Creates and returns a list of molecule types that are accepted as an enzyme for the given type names.
`static int`	`getProduct()` Substance that is produced in a reaction.
`static int`	`getProduction()` Generation of a material or conceptual entity.
`static int`	`getProtein()`
`static int`	`getQuantitativeParameter()`
`static int`	`getRateLaw()`
`static int`	`getReactant()` Substance consumed by a chemical reaction.
`static int`	`getReceptor()`
`static int`	`getRNA()`
`static SBO.Term`	`getSBORoot()` Returns the root element of the SBO Ontology (SBO:0000000).
`static int`	`getSimpleMolecule()`
`static int`	`getSpecificActivator()`
`static int`	`getStateTransition()`
`static int`	`getSteadyStateExpression()`
`static int`	`getStimulation()` Positive modulation of the execution of a process.
`static int`	`getStimulator()`
`static SBO.Term`	`getTerm(int sboTerm)` Gets the SBO term with the id 'sboTerm'.
`static SBO.Term`	`getTerm(java.lang.String sboTerm)` Gets the SBO term with the id 'sboTerm'.
`static java.util.Set<SBO.Term>`	`getTerms()` Return the set of terms of the SBO Ontology.
`static int`	`getTranscription()` Returns the SBO id corresponding to the alias 'TRANSCRIPTION'
`static int`	`getTranscriptionalActivation()` Returns the SBO id corresponding to the alias 'TRANSCRIPTIONAL_ACTIVATION'
`static int`	`getTranscriptionalInhibitor()` Returns the SBO id corresponding to the alias 'TRANSCRIPTIONAL_INHIBITION'
`static int`	`getTransitionOmitted()` Returns the SBO id corresponding to the alias 'KNOWN_TRANSITION_OMITTED'
`static int`	`getTranslation()` Returns the SBO id corresponding to the alias 'TRANSLATION'
`static int`	`getTranslationalActivation()` Returns the SBO id corresponding to the alias 'TRANSLATIONAL_ACTIVATION'
`static int`	`getTranslationalInhibitor()` Returns the SBO id corresponding to the alias 'TRANSLATIONAL_INHIBITION'
`static int`	`getTransport()` Returns the SBO id corresponding to the alias 'TRANSPORT'
`static int`	`getTrigger()` Returns the SBO id corresponding to the alias 'TRIGGER'
`static java.util.Set<SBO.Triple>`	`getTriples(SBO.Term subject, SBO.Term predicate, SBO.Term object)` Returns a set of Triple which match the supplied subject, predicate and object.
`static int`	`getTruncated()` Returns the SBO id corresponding to the alias 'TRUNCATED'
`static int`	`getUnknownMolecule()` Returns the SBO id corresponding to the alias 'UNKNOWN'
`static int`	`getUnknownTransition()` Returns the SBO id corresponding to the alias 'UNKNOWN_TRANSITION'
`static java.lang.String`	`intToString(int sboTerm)` Returns the integer as a correctly formatted SBO string.
`static boolean`	`isAntisenseRNA(int sboTerm)` Returns `true` if the given term identifier comes from the stated branch of SBO.
`static boolean`	`isBindingActivator(int sboTerm)` Returns `true` if the given term identifier comes from the stated branch of SBO.
`static boolean`	`isCatalyst(int sboTerm)` Returns `true` if the given term identifier comes from the stated branch of SBO.
`static boolean`	`isCatalyticActivator(int sboTerm)` Returns `true` if the given term identifier comes from the stated branch of SBO.
`static boolean`	`isChildOf(int sboTerm, int parent)` Checks whether the given sboTerm is a member of the SBO subgraph rooted at parent.
`private static boolean`	`isChildOf(SBO.Term subject, SBO.Term object)` Traverses the systems biology ontology starting at `SBO.Term` subject until either the root (SBO:0000000) or the `SBO.Term` object is reached.
`static boolean`	`isCompetetiveInhibitor(int sboTerm)` Returns `true` if the given term identifier comes from the stated branch of SBO.
`static boolean`	`isCompleteInhibitor(int sboTerm)` Returns `true` if the given term identifier comes from the stated branch of SBO.
`static boolean`	`isComplex(int sboTerm)` Returns `true` if the given term identifier comes from the stated branch of SBO.
`static boolean`	`isConservationLaw(int sboTerm)` Returns `true` if the term is-a conservation law, `false` otherwise
`static boolean`	`isContinuousFramework(int sboTerm)` Returns `true` if the term is-a continuous framework, `false` otherwise
`static boolean`	`isDiscreteFramework(int sboTerm)` Returns `true` if the term is-a discrete framework, `false` otherwise
`static boolean`	`isDrug(int sboTerm)` Returns `true` if the given term identifier comes from the stated branch of SBO.
`static boolean`	`isEmptySet(int sboTerm)` Returns `true` if the given term identifier comes from the stated branch of SBO.
`static boolean`	`isEntity(int sboTerm)` Returns `true` if the term is-a Entity, `false` otherwise
`static boolean`	`isEnzymaticCatalysis(int sboTerm)` Returns `true` if the given term identifier comes from the stated branch of SBO.
`static boolean`	`isEssentialActivator(int sboTerm)` Returns `true` if the given term identifier comes from the stated branch of SBO.
`static boolean`	`isEvent(int sboTerm)` Function for checking the SBO term is from correct part of SBO.
`static boolean`	`isFunctionalCompartment(int sboTerm)` Function for checking the SBO term is from correct part of SBO.
`static boolean`	`isFunctionalEntity(int sboTerm)` Function for checking the SBO term is from correct part of SBO.
`static boolean`	`isGene(int sboTerm)` Returns `true` if the given term identifier comes from the stated branch of SBO.
`static boolean`	`isGeneCodingRegion(int sboTerm)` Returns `true` if the sboTerm stands for a gene coding region, false otherwise
`static boolean`	`isGeneOrGeneCodingRegion(int sboTerm)` Returns `true` if the sboTerm stands for a gene coding region or a gene, false otherwise
`static boolean`	`isGeneric(int sboTerm)` Returns `true` if the given term identifier comes from the stated branch of SBO.
`static boolean`	`isHillEquation(int sboTerm)` Returns `true` if the given term identifier comes from the stated branch of SBO.
`static boolean`	`isInhibitor(int sboTerm)` Returns `true` if the given term identifier comes from the stated branch of SBO.
`static boolean`	`isInteraction(int sboTerm)` Function for checking the SBO term is from correct part of SBO.
`static boolean`	`isIon(int sboTerm)` Returns `true` if the given term identifier comes from the stated branch of SBO.
`static boolean`	`isIonChannel(int sboTerm)` Returns `true` if the given term identifier comes from the stated branch of SBO.
`static boolean`	`isKineticConstant(int sboTerm)` Function for checking the SBO term is from correct part of SBO.
`static boolean`	`isLogicalFramework(int sboTerm)` Function for checking the SBO term is from correct part of SBO.
`static boolean`	`isMaterialEntity(int sboTerm)` Function for checking the SBO term is from correct part of SBO.
`static boolean`	`isMathematicalExpression(int sboTerm)` Function for checking the SBO term is from correct part of SBO.
`static boolean`	`isMessengerRNA(int sboTerm)` Returns `true` if the given term identifier comes from the stated branch of SBO.
`static boolean`	`isModellingFramework(int sboTerm)` Function for checking the SBO term is from correct part of SBO.
`static boolean`	`isModifier(int sboTerm)` Function for checking the SBO term is from correct part of SBO.
`static boolean`	`isNonCompetetiveInhibitor(int sboTerm)` Returns `true` if the given term identifier comes from the stated branch of SBO.
`static boolean`	`isNonEssentialActivator(int sboTerm)` Returns `true` if the given term identifier comes from the stated branch of SBO.
`static boolean`	`isObsolete(int sboTerm)` Function for checking whether the SBO term is obsolete.
`static boolean`	`isPartialInhibitor(int sboTerm)` Returns `true` if the given term identifier comes from the stated branch of SBO.
`static boolean`	`isParticipant(int sboTerm)` Function for checking the SBO term is from correct part of SBO.
`static boolean`	`isParticipantRole(int sboTerm)` Function for checking the SBO term is from correct part of SBO.
`static boolean`	`isPhenotype(int sboTerm)` Returns `true` if the given term identifier comes from the stated branch of SBO.
`static boolean`	`isPhysicalCompartment(int sboTerm)` Returns `true` if the given term identifier comes from the stated branch of SBO.
`static boolean`	`isPhysicalParticipant(int sboTerm)` Function for checking the SBO term is from correct part of SBO.
`static boolean`	`isProduct(int sboTerm)` Function for checking the SBO term is from correct part of SBO.
`static boolean`	`isProtein(int sboTerm)` Returns `true` if the given term identifier comes from the stated branch of SBO.
`static boolean`	`isQuantitativeParameter(int sboTerm)` Function for checking the SBO term is from correct part of SBO.
`static boolean`	`isRateLaw(int sboTerm)` Function for checking the SBO term is from correct part of SBO.
`static boolean`	`isReactant(int sboTerm)` Function for checking the SBO term is from correct part of SBO.
`static boolean`	`isReceptor(int sboTerm)` Returns `true` if the given term identifier comes from the stated branch of SBO.
`static boolean`	`isRNA(int sboTerm)` Returns `true` if the given term identifier comes from the stated branch of SBO.
`static boolean`	`isRNAOrMessengerRNA(int sboTerm)` Returns `true` if the given term identifier comes from the stated branch of SBO.
`static boolean`	`isSimpleMolecule(int sboTerm)` Returns `true` if the given term identifier comes from the stated branch of SBO.
`static boolean`	`isSpecificActivator(int sboTerm)` Returns `true` if the given term identifier comes from the stated branch of SBO.
`static boolean`	`isStateTransition(int sboTerm)` Returns `true` if the given term identifier comes from the stated branch of SBO.
`static boolean`	`isSteadyStateExpression(int sboTerm)` Function for checking the SBO term is from correct part of SBO.
`static boolean`	`isStimulator(int sboTerm)` Returns `true` if the given term identifier comes from the stated branch of SBO.
`static boolean`	`isTranscription(int sboTerm)` Returns `true` if the given term identifier comes from the stated branch of SBO.
`static boolean`	`isTranscriptionalActivation(int sboTerm)` Returns `true` if the given term identifier comes from the stated branch of SBO.
`static boolean`	`isTranscriptionalInhibitor(int sboTerm)` Returns `true` if the given term identifier comes from the stated branch of SBO.
`static boolean`	`isTransitionOmitted(int sboTerm)` Returns `true` if the given term identifier comes from the stated branch of SBO.
`static boolean`	`isTranslation(int sboTerm)` Returns `true` if the given term identifier comes from the stated branch of SBO.
`static boolean`	`isTranslationalActivation(int sboTerm)` Returns `true` if the given term identifier comes from the stated branch of SBO.
`static boolean`	`isTranslationalInhibitor(int sboTerm)` Returns `true` if the given term identifier comes from the stated branch of SBO.
`static boolean`	`isTransport(int sboTerm)` Returns `true` if the given term identifier comes from the stated branch of SBO.
`static boolean`	`isTrigger(int sboTerm)` Returns `true` if the given term identifier comes from the stated branch of SBO.
`static boolean`	`isTruncated(int sboTerm)` Returns `true` if the given term identifier comes from the stated branch of SBO.
`static boolean`	`isUnknownMolecule(int sboTerm)` Returns `true` if the given term identifier comes from the stated branch of SBO.
`static boolean`	`isUnknownTransition(int sboTerm)` Returns `true` if the given term identifier comes from the stated branch of SBO.
`static java.lang.String`	`sboNumberString(int sboTerm)` Creates and returns a 7 digit SBO number for the given `SBO.Term` identifier (if this is a valid identifier).
`static int`	`stringToInt(java.lang.String sboTerm)` Returns the string as a correctly formatted SBO integer portion.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - alias2sbo
```
private static java.util.Properties alias2sbo
```
  - prefix
```
private static final java.lang.String prefix
```
    the prefix of all SBO ids.
    
    See Also:
    Constant Field Values
  - sbo
```
private static Ontology sbo
```
  - sbo2alias
```
private static java.util.Properties sbo2alias
```
  - terms
```
private static java.util.Set<SBO.Term> terms
```
- Constructor Detail
  - SBO
```
public SBO()
```
- Method Detail
  - checkTerm
```
public static boolean checkTerm(int sboTerm)
```
    Checks the format of the given SBO integer portion.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if sboTerm is in the range {0,.., 9999999}, false otherwise.
  - checkTerm
```
public static boolean checkTerm(java.lang.String sboTerm)
```
    Checks the format of the given SBO string.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if sboTerm is in the correct format (a zero-padded, seven digit string), false otherwise.
  - convertAlias2SBO
```
public static int convertAlias2SBO(java.lang.String alias)
```
    Returns an SBO id corresponding to the given alias.
    
    Parameters:
    alias -
    
    Returns:
    an SBO id corresponding to the given alias.
  - convertSBO2Alias
```
public static java.lang.String convertSBO2Alias(int sboterm)
```
    Returns an alias corresponding to the given SBO id.
    
    Parameters:
    sboterm -
    
    Returns:
    an alias corresponding to the given SBO id.
  - getAntisenseRNA
```
public static int getAntisenseRNA()
```
    Returns the SBO id for antisense RNA.
    
    Returns:
    the SBO id for antisense RNA.
  - getAssociation
```
public static int getAssociation()
```
    Interaction between several biochemical entities that results in the formation of a non-covalent complex
    
    Returns:
    177
  - getBindingActivator
```
public static int getBindingActivator()
```
    An essential activator that affects the apparent value of the Michaelis constant(s).
    
    Returns:
    535
  - getCatalysis
```
public static int getCatalysis()
```
    Modification of the velocity of a reaction by lowering the energy of the transition state.
    
    Returns:
    172
  - getCatalyst
```
public static int getCatalyst()
```
    Substance that accelerates the velocity of a chemical reaction without itself being consumed or transformed. This effect is achieved by lowering the free energy of the transition state.
    
    Returns:
    the SBO id corresponding to the alias 'CATALYSIS'
  - getCatalyticActivator
```
public static int getCatalyticActivator()
```
    Returns:
  - getCompartment
```
public static int getCompartment()
```
    Physical compartment.
    
    Returns:
  - getCompetetiveInhibitor
```
public static int getCompetetiveInhibitor()
```
    Returns:
  - getCompleteInhibitor
```
public static int getCompleteInhibitor()
```
    Returns:
  - getComplex
```
public static int getComplex()
```
    Returns:
  - getConservationLaw
```
public static int getConservationLaw()
```
    Returns:
  - getConsumption
```
public static int getConsumption()
```
    Decrease in amount of a material or conceptual entity.
    
    Returns:
    394
  - getContinuousFramework
```
public static int getContinuousFramework()
```
    Returns:
  - getDefaultPossibleEnzymes
```
public static final java.util.Set<java.lang.Integer> getDefaultPossibleEnzymes()
```
    Creates and returns a list of molecule types accepted as an enzyme by default. These are:
    - ANTISENSE_RNA
    - SIMPLE_MOLECULE
    - UNKNOWN
    - COMPLEX
    - TRUNCATED
    - GENERIC
    - RNA
    - RECEPTOR
    Returns:
  - getDiscreteFramework
```
public static int getDiscreteFramework()
```
    Returns:
  - getDissociation
```
public static int getDissociation()
```
    Transformation of a non-covalent complex that results in the formation of several independent biochemical entities.
    
    Returns:
    180
  - getDrug
```
public static int getDrug()
```
    Returns:
  - getEmptySet
```
public static int getEmptySet()
```
    Empty set is used to represent the source of a creation process or the result of a degradation process.
    
    Returns:
  - getEntity
```
public static int getEntity()
```
    Returns:
  - getEnzymaticCatalysis
```
public static int getEnzymaticCatalysis()
```
    Returns:
  - getEssentialActivator
```
public static int getEssentialActivator()
```
    Returns:
  - getEvent
```
public static int getEvent()
```
    Returns:
  - getFunctionalCompartment
```
public static int getFunctionalCompartment()
```
    Returns:
  - getFunctionalEntity
```
public static int getFunctionalEntity()
```
    Returns:
  - getGene
```
public static int getGene()
```
    A gene is an informational molecule segment. The Nucleic acid feature construct in SBGN is meant to represent a fragment of a macro- molecule carrying genetic information. A common use for this construct is to represent a gene or transcript. The label of this EPN and its units of information are often important for making the purpose clear to the reader of a map.
    
    Returns:
  - getGeneCodingRegion
```
public static int getGeneCodingRegion()
```
    Returns:
  - getGeneric
```
public static int getGeneric()
```
    Returns:
  - getHillEquation
```
public static int getHillEquation()
```
    Returns:
  - getInhibition
```
public static int getInhibition()
```
    Negative modulation of the execution of a process.
    
    Returns:
    169
  - getInhibitor
```
public static int getInhibitor()
```
    Substance that decreases the probability of a chemical reaction without itself being consumed or transformed by the reaction.
    
    Returns:
    the SBO id corresponding to the alias 'INHIBITION'
  - getInteraction
```
public static int getInteraction()
```
    Returns:
  - getIon
```
public static int getIon()
```
    Returns:
  - getIonChannel
```
public static int getIonChannel()
```
    Returns:
  - getKineticConstant
```
public static int getKineticConstant()
```
    Returns:
  - getLogicalFramework
```
public static int getLogicalFramework()
```
    Returns:
  - getMacromolecule
```
public static int getMacromolecule()
```
    Returns the SBO term id for macromolecule.
    
    Returns:
  - getMaterialEntity
```
public static int getMaterialEntity()
```
    Returns:
  - getMathematicalExpression
```
public static int getMathematicalExpression()
```
    Returns:
  - getMessengerRNA
```
public static int getMessengerRNA()
```
    Returns:
  - getModellingFramework
```
public static int getModellingFramework()
```
    Returns:
  - getModifier
```
public static int getModifier()
```
    Substance that changes the velocity of a process without itself being consumed or transformed by the reaction.
    
    Returns:
    the SBO id corresponding to the alias 'MODULATION'
  - getModulation
```
public static int getModulation()
```
    Modification of the execution of an event or a process.
    
    Returns:
    168
  - getNecessaryStimulation
```
public static int getNecessaryStimulation()
```
    Control that is necessary to the execution of a process.
    
    Returns:
    171
  - getNonCompetetiveInhibitor
```
public static int getNonCompetetiveInhibitor()
```
    Returns:
  - getNonCovalentComplex
```
public static int getNonCovalentComplex()
```
    Returns:
  - getNonEssentialActivator
```
public static int getNonEssentialActivator()
```
    Returns:
  - getOntology
```
public static Ontology getOntology()
```
    Grants access to the underlying Ontology form BioJava.
    
    Returns:
  - getPartialInhibitor
```
public static int getPartialInhibitor()
```
    Returns:
    The SBO term identifier corresponding to the SBO.Term with the name "partial inhibitor".
  - getParticipant
```
public static int getParticipant()
```
    Returns:
  - getParticipantRole
```
public static int getParticipantRole()
```
    The function of a physical or conceptual entity, that is its role, in the execution of an event or process.
    
    Returns:
    3
  - getPertubingAgent
```
public static int getPertubingAgent()
```
    Perturbing agent.
    
    Returns:
  - getPhenotype
```
public static int getPhenotype()
```
    Returns:
  - getPhysicalCompartment
```
public static int getPhysicalCompartment()
```
    Returns:
  - getPhysicalParticipant
```
public static int getPhysicalParticipant()
```
    Returns:
  - getPossibleEnzymes
```
public static final java.util.Set<java.lang.Integer> getPossibleEnzymes(java.lang.String... types)
```
    Creates and returns a list of molecule types that are accepted as an enzyme for the given type names.
    
    Parameters:
    types -
    
    Returns:
  - getProduct
```
public static int getProduct()
```
    Substance that is produced in a reaction. In a chemical equation the Products are the elements or compounds on the right hand side of the reaction equation. A product can be produced and consumed by the same reaction, its global quantity remaining unchanged.
    
    Returns:
    the SBO id corresponding to the alias 'product'
  - getProduction
```
public static int getProduction()
```
    Generation of a material or conceptual entity.
    
    Returns:
    393
  - getProtein
```
public static int getProtein()
```
    Returns:
  - getQuantitativeParameter
```
public static int getQuantitativeParameter()
```
    Returns:
  - getRateLaw
```
public static int getRateLaw()
```
    Returns:
  - getReactant
```
public static int getReactant()
```
    Substance consumed by a chemical reaction. Reactants react with each other to form the products of a chemical reaction. In a chemical equation the Reactants are the elements or compounds on the left hand side of the reaction equation. A reactant can be consumed and produced by the same reaction, its global quantity remaining unchanged.
    
    Returns:
    the SBO id corresponding to the alias 'reactant'
  - getReceptor
```
public static int getReceptor()
```
    Returns:
  - getRNA
```
public static int getRNA()
```
    Returns:
  - getSBORoot
```
public static SBO.Term getSBORoot()
```
    Returns the root element of the SBO Ontology (SBO:0000000).
    
    Returns:
    the root element of the SBO Ontology (SBO:0000000).
  - getSimpleMolecule
```
public static int getSimpleMolecule()
```
    Returns:
  - getSpecificActivator
```
public static int getSpecificActivator()
```
    Returns:
  - getStateTransition
```
public static int getStateTransition()
```
    Returns:
  - getSteadyStateExpression
```
public static int getSteadyStateExpression()
```
    Returns:
  - getStimulation
```
public static int getStimulation()
```
    Positive modulation of the execution of a process.
    
    Returns:
    170
  - getStimulator
```
public static int getStimulator()
```
    Returns:
  - getTerm
```
public static SBO.Term getTerm(int sboTerm)
```
    Gets the SBO term with the id 'sboTerm'.
    
    Parameters:
    sboTerm - the id of the SBO term to search for.
    
    Returns:
    the SBO term with the id 'sboTerm'.
    
    Throws:
    
    java.util.NoSuchElementException - if the id is not found.
  - getTerm
```
public static SBO.Term getTerm(java.lang.String sboTerm)
```
    Gets the SBO term with the id 'sboTerm'.
    The id need to be of the form 'SBO:XXXXXXX' where X is a digit number.
    
    Parameters:
    sboTerm - the id of the SBO term to search for.
    
    Returns:
    the SBO term with the id 'sboTerm'.
    
    Throws:
    
    java.util.NoSuchElementException - if the id is not found or null.
  - getTerms
```
public static java.util.Set<SBO.Term> getTerms()
```
    Return the set of terms of the SBO Ontology.
    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 org.biojava.ontology.Term containing also the org.biojava.ontology.Triple, use getOntology() to get the underlying biojava object.
    
    Returns:
    the set of terms of the SBO Ontology.
  - getTranscription
```
public static int getTranscription()
```
    Returns the SBO id corresponding to the alias 'TRANSCRIPTION'
    
    Returns:
    the SBO id corresponding to the alias 'TRANSCRIPTION'
  - getTranscriptionalActivation
```
public static int getTranscriptionalActivation()
```
    Returns the SBO id corresponding to the alias 'TRANSCRIPTIONAL_ACTIVATION'
    
    Returns:
    the SBO id corresponding to the alias 'TRANSCRIPTIONAL_ACTIVATION'
  - getTranscriptionalInhibitor
```
public static int getTranscriptionalInhibitor()
```
    Returns the SBO id corresponding to the alias 'TRANSCRIPTIONAL_INHIBITION'
    
    Returns:
    the SBO id corresponding to the alias 'TRANSCRIPTIONAL_INHIBITION'
  - getTransitionOmitted
```
public static int getTransitionOmitted()
```
    Returns the SBO id corresponding to the alias 'KNOWN_TRANSITION_OMITTED'
    
    Returns:
    the SBO id corresponding to the alias 'KNOWN_TRANSITION_OMITTED'
  - getTranslation
```
public static int getTranslation()
```
    Returns the SBO id corresponding to the alias 'TRANSLATION'
    
    Returns:
    the SBO id corresponding to the alias 'TRANSLATION'
  - getTranslationalActivation
```
public static int getTranslationalActivation()
```
    Returns the SBO id corresponding to the alias 'TRANSLATIONAL_ACTIVATION'
    
    Returns:
    the SBO id corresponding to the alias 'TRANSLATIONAL_ACTIVATION'
  - getTranslationalInhibitor
```
public static int getTranslationalInhibitor()
```
    Returns the SBO id corresponding to the alias 'TRANSLATIONAL_INHIBITION'
    
    Returns:
    the SBO id corresponding to the alias 'TRANSLATIONAL_INHIBITION'
  - getTransport
```
public static int getTransport()
```
    Returns the SBO id corresponding to the alias 'TRANSPORT'
    
    Returns:
    the SBO id corresponding to the alias 'TRANSPORT'
  - getTrigger
```
public static int getTrigger()
```
    Returns the SBO id corresponding to the alias 'TRIGGER'
    
    Returns:
    the SBO id corresponding to the alias 'TRIGGER'
  - getTriples
```
public static java.util.Set<SBO.Triple> getTriples(SBO.Term subject,
                                   SBO.Term predicate,
                                   SBO.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.
```
 for example :
    getTriples(SBO.getTerm("SBO:0000002"), SBO.getTerm("is_a"), null);
    will returned all the parent Terms of SBO:0000002
 
    getTriples(null, SBO.getTerm("is_a"), SBO.getTerm(188));
    will returned all the children Terms of SBO:0000188
 
  
```
    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:
    org.biojava.ontology.Ontology#getTriples(org.biojava.ontology.Term, org.biojava.ontology.Term, org.biojava.ontology.Term)
  - getTruncated
```
public static int getTruncated()
```
    Returns the SBO id corresponding to the alias 'TRUNCATED'
    
    Returns:
    the SBO id corresponding to the alias 'TRUNCATED'
  - getUnknownMolecule
```
public static int getUnknownMolecule()
```
    Returns the SBO id corresponding to the alias 'UNKNOWN'
    
    Returns:
    the SBO id corresponding to the alias 'UNKNOWN'
  - getUnknownTransition
```
public static int getUnknownTransition()
```
    Returns the SBO id corresponding to the alias 'UNKNOWN_TRANSITION'
    
    Returns:
    the SBO id corresponding to the alias 'UNKNOWN_TRANSITION'
  - intToString
```
public static java.lang.String intToString(int sboTerm)
```
    Returns the integer as a correctly formatted SBO string. If the sboTerm is not in the correct range ({0,.., 9999999}), an empty string is returned.
    
    Parameters:
    sboTerm -
    
    Returns:
    the given integer sboTerm as a zero-padded seven digit string.
  - isAntisenseRNA
```
public static boolean isAntisenseRNA(int sboTerm)
```
    Returns true if the given term identifier comes from the stated branch of SBO.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if term is-a SBO 'product', false otherwise.
  - isBindingActivator
```
public static boolean isBindingActivator(int sboTerm)
```
    Returns true if the given term identifier comes from the stated branch of SBO.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if term is-a SBO 'product', false otherwise.
  - isCatalyst
```
public static boolean isCatalyst(int sboTerm)
```
    Returns true if the given term identifier comes from the stated branch of SBO.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if term is-a SBO 'product', false otherwise.
  - isCatalyticActivator
```
public static boolean isCatalyticActivator(int sboTerm)
```
    Returns true if the given term identifier comes from the stated branch of SBO.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if term is-a SBO 'product', false otherwise.
  - isChildOf
```
public static boolean isChildOf(int sboTerm,
                int parent)
```
    Checks whether the given sboTerm is a member of the SBO subgraph rooted at parent.
    
    Parameters:
    sboTerm - An SBO term.
    parent - An SBO term that is the root of a certain subgraph within the SBO.
    
    Returns:
    true if the subgraph of the SBO rooted at the term parent contains a term with the id corresponding to sboTerm.
  - isChildOf
```
private static boolean isChildOf(SBO.Term subject,
                SBO.Term object)
```
    Traverses the systems biology ontology starting at SBO.Term subject until either the root (SBO:0000000) or the SBO.Term object is reached.
    
    Parameters:
    subject - Child
    object - Parent
    
    Returns:
    true if subject is a child of object.
  - isCompetetiveInhibitor
```
public static boolean isCompetetiveInhibitor(int sboTerm)
```
    Returns true if the given term identifier comes from the stated branch of SBO.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if term is-a SBO 'product', false otherwise.
  - isCompleteInhibitor
```
public static boolean isCompleteInhibitor(int sboTerm)
```
    Returns true if the given term identifier comes from the stated branch of SBO.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if term is-a SBO 'product', false otherwise.
  - isComplex
```
public static boolean isComplex(int sboTerm)
```
    Returns true if the given term identifier comes from the stated branch of SBO.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if term is-a SBO 'product', false otherwise.
  - isConservationLaw
```
public static boolean isConservationLaw(int sboTerm)
```
    Returns true if the term is-a conservation law, false otherwise
    
    Parameters:
    sboTerm -
    
    Returns:
    true if the term is-a conservation law, false otherwise
  - isContinuousFramework
```
public static boolean isContinuousFramework(int sboTerm)
```
    Returns true if the term is-a continuous framework, false otherwise
    
    Parameters:
    sboTerm -
    
    Returns:
    true if the term is-a continuous framework, false otherwise
  - isDiscreteFramework
```
public static boolean isDiscreteFramework(int sboTerm)
```
    Returns true if the term is-a discrete framework, false otherwise
    
    Parameters:
    sboTerm -
    
    Returns:
    true if the term is-a discrete framework, false otherwise
  - isDrug
```
public static boolean isDrug(int sboTerm)
```
    Returns true if the given term identifier comes from the stated branch of SBO.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if term is-a SBO 'product', false otherwise.
  - isEmptySet
```
public static boolean isEmptySet(int sboTerm)
```
    Returns true if the given term identifier comes from the stated branch of SBO.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if term is-a SBO 'product', false otherwise.
  - isEntity
```
public static boolean isEntity(int sboTerm)
```
    Returns true if the term is-a Entity, false otherwise
    
    Parameters:
    sboTerm -
    
    Returns:
    true if the term is-a Entity, false otherwise
  - isEnzymaticCatalysis
```
public static boolean isEnzymaticCatalysis(int sboTerm)
```
    Returns true if the given term identifier comes from the stated branch of SBO.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if term is-a SBO 'product', false otherwise.
  - isEssentialActivator
```
public static boolean isEssentialActivator(int sboTerm)
```
    Returns true if the given term identifier comes from the stated branch of SBO.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if term is-a SBO 'product', false otherwise.
  - isEvent
```
public static boolean isEvent(int sboTerm)
```
    Function for checking the SBO term is from correct part of SBO.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if the term is-an Event, false otherwise
  - isFunctionalCompartment
```
public static boolean isFunctionalCompartment(int sboTerm)
```
    Function for checking the SBO term is from correct part of SBO.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if the term is-a functional compartment, false otherwise
  - isFunctionalEntity
```
public static boolean isFunctionalEntity(int sboTerm)
```
    Function for checking the SBO term is from correct part of SBO.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if the term is-a functional entity, false otherwise
  - isGene
```
public static boolean isGene(int sboTerm)
```
    Returns true if the given term identifier comes from the stated branch of SBO.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if term is-a SBO 'product', false otherwise.
  - isGeneCodingRegion
```
public static boolean isGeneCodingRegion(int sboTerm)
```
    Returns true if the sboTerm stands for a gene coding region, false otherwise
    
    Parameters:
    sboTerm -
    
    Returns:
    true if the sboTerm stands for a gene coding region, false otherwise
  - isGeneOrGeneCodingRegion
```
public static boolean isGeneOrGeneCodingRegion(int sboTerm)
```
    Returns true if the sboTerm stands for a gene coding region or a gene, false otherwise
    
    Parameters:
    sboTerm -
    
    Returns:
    true if the sboTerm stands for a gene coding region or a gene, false otherwise
  - isGeneric
```
public static boolean isGeneric(int sboTerm)
```
    Returns true if the given term identifier comes from the stated branch of SBO.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if term is-a SBO 'product', false otherwise.
  - isHillEquation
```
public static boolean isHillEquation(int sboTerm)
```
    Returns true if the given term identifier comes from the stated branch of SBO.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if term is-a SBO 'product', false otherwise.
  - isInhibitor
```
public static boolean isInhibitor(int sboTerm)
```
    Returns true if the given term identifier comes from the stated branch of SBO.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if term is-a SBO 'product', false otherwise.
  - isInteraction
```
public static boolean isInteraction(int sboTerm)
```
    Function for checking the SBO term is from correct part of SBO.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if the term is-an interaction, false otherwise
  - isIon
```
public static boolean isIon(int sboTerm)
```
    Returns true if the given term identifier comes from the stated branch of SBO.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if term is-a SBO 'product', false otherwise.
  - isIonChannel
```
public static boolean isIonChannel(int sboTerm)
```
    Returns true if the given term identifier comes from the stated branch of SBO.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if term is-a SBO 'product', false otherwise.
  - isKineticConstant
```
public static boolean isKineticConstant(int sboTerm)
```
    Function for checking the SBO term is from correct part of SBO.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if the term is-a kinetic constant, false otherwise
  - isLogicalFramework
```
public static boolean isLogicalFramework(int sboTerm)
```
    Function for checking the SBO term is from correct part of SBO.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if the term is-a logical framework, false otherwise
  - isMaterialEntity
```
public static boolean isMaterialEntity(int sboTerm)
```
    Function for checking the SBO term is from correct part of SBO.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if the term is-a material entity, false otherwise
  - isMathematicalExpression
```
public static boolean isMathematicalExpression(int sboTerm)
```
    Function for checking the SBO term is from correct part of SBO.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if the term is-a mathematical expression, false otherwise
  - isMessengerRNA
```
public static boolean isMessengerRNA(int sboTerm)
```
    Returns true if the given term identifier comes from the stated branch of SBO.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if term is-a SBO 'product', false otherwise.
  - isModellingFramework
```
public static boolean isModellingFramework(int sboTerm)
```
    Function for checking the SBO term is from correct part of SBO.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if the term is-a modelling framework, false otherwise
  - isModifier
```
public static boolean isModifier(int sboTerm)
```
    Function for checking the SBO term is from correct part of SBO.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if the term is-a modifier, false otherwise
  - isNonCompetetiveInhibitor
```
public static boolean isNonCompetetiveInhibitor(int sboTerm)
```
    Returns true if the given term identifier comes from the stated branch of SBO.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if term is-a SBO 'product', false otherwise.
  - isNonEssentialActivator
```
public static boolean isNonEssentialActivator(int sboTerm)
```
    Returns true if the given term identifier comes from the stated branch of SBO.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if term is-a SBO 'product', false otherwise.
  - isObsolete
```
public static boolean isObsolete(int sboTerm)
```
    Function for checking whether the SBO term is obsolete.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if the term is-an obsolete term, false otherwise
  - isPartialInhibitor
```
public static boolean isPartialInhibitor(int sboTerm)
```
    Returns true if the given term identifier comes from the stated branch of SBO.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if term is-a SBO 'product', false otherwise.
  - isParticipant
```
public static boolean isParticipant(int sboTerm)
```
    Function for checking the SBO term is from correct part of SBO. This term is actually obsolete.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if the term is-a participant, false otherwise
  - isParticipantRole
```
public static boolean isParticipantRole(int sboTerm)
```
    Function for checking the SBO term is from correct part of SBO.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if the term is-a participant role, false otherwise
  - isPhenotype
```
public static boolean isPhenotype(int sboTerm)
```
    Returns true if the given term identifier comes from the stated branch of SBO.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if term is-a SBO 'product', false otherwise.
  - isPhysicalCompartment
```
public static boolean isPhysicalCompartment(int sboTerm)
```
    Returns true if the given term identifier comes from the stated branch of SBO.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if term is-a SBO 'product', false otherwise.
  - isPhysicalParticipant
```
public static boolean isPhysicalParticipant(int sboTerm)
```
    Function for checking the SBO term is from correct part of SBO. Obsolete term.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if the term is-a physical participant, false otherwise
  - isProduct
```
public static boolean isProduct(int sboTerm)
```
    Function for checking the SBO term is from correct part of SBO.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if the term is-a product, false otherwise
  - isProtein
```
public static boolean isProtein(int sboTerm)
```
    Returns true if the given term identifier comes from the stated branch of SBO.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if term is-a SBO 'product', false otherwise.
  - isQuantitativeParameter
```
public static boolean isQuantitativeParameter(int sboTerm)
```
    Function for checking the SBO term is from correct part of SBO.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if the term is-a quantitative parameter, false otherwise
  - isRateLaw
```
public static boolean isRateLaw(int sboTerm)
```
    Function for checking the SBO term is from correct part of SBO.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if the term is-a rate law, false otherwise
  - isReactant
```
public static boolean isReactant(int sboTerm)
```
    Function for checking the SBO term is from correct part of SBO.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if the term is-a reactant, false otherwise
  - isReceptor
```
public static boolean isReceptor(int sboTerm)
```
    Returns true if the given term identifier comes from the stated branch of SBO.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if term is-a SBO 'product', false otherwise.
  - isRNA
```
public static boolean isRNA(int sboTerm)
```
    Returns true if the given term identifier comes from the stated branch of SBO.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if term is-a SBO 'product', false otherwise.
  - isRNAOrMessengerRNA
```
public static boolean isRNAOrMessengerRNA(int sboTerm)
```
    Returns true if the given term identifier comes from the stated branch of SBO.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if term is-a SBO 'product', false otherwise.
  - isSimpleMolecule
```
public static boolean isSimpleMolecule(int sboTerm)
```
    Returns true if the given term identifier comes from the stated branch of SBO.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if term is-a SBO 'product', false otherwise.
  - isSpecificActivator
```
public static boolean isSpecificActivator(int sboTerm)
```
    Returns true if the given term identifier comes from the stated branch of SBO.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if term is-a SBO 'product', false otherwise.
  - isStateTransition
```
public static boolean isStateTransition(int sboTerm)
```
    Returns true if the given term identifier comes from the stated branch of SBO.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if term is-a SBO 'product', false otherwise.
  - isSteadyStateExpression
```
public static boolean isSteadyStateExpression(int sboTerm)
```
    Function for checking the SBO term is from correct part of SBO.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if the term is-a steady state expression, false otherwise
  - isStimulator
```
public static boolean isStimulator(int sboTerm)
```
    Returns true if the given term identifier comes from the stated branch of SBO.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if term is-a SBO 'product', false otherwise.
  - isTranscription
```
public static boolean isTranscription(int sboTerm)
```
    Returns true if the given term identifier comes from the stated branch of SBO.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if term is-a SBO 'product', false otherwise.
  - isTranscriptionalActivation
```
public static boolean isTranscriptionalActivation(int sboTerm)
```
    Returns true if the given term identifier comes from the stated branch of SBO.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if term is-a SBO 'product', false otherwise.
  - isTranscriptionalInhibitor
```
public static boolean isTranscriptionalInhibitor(int sboTerm)
```
    Returns true if the given term identifier comes from the stated branch of SBO.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if term is-a SBO 'product', false otherwise.
  - isTransitionOmitted
```
public static boolean isTransitionOmitted(int sboTerm)
```
    Returns true if the given term identifier comes from the stated branch of SBO.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if term is-a SBO 'product', false otherwise.
  - isTranslation
```
public static boolean isTranslation(int sboTerm)
```
    Returns true if the given term identifier comes from the stated branch of SBO.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if term is-a SBO 'product', false otherwise.
  - isTranslationalActivation
```
public static boolean isTranslationalActivation(int sboTerm)
```
    Returns true if the given term identifier comes from the stated branch of SBO.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if term is-a SBO 'product', false otherwise.
  - isTranslationalInhibitor
```
public static boolean isTranslationalInhibitor(int sboTerm)
```
    Returns true if the given term identifier comes from the stated branch of SBO.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if term is-a SBO 'product', false otherwise.
  - isTransport
```
public static boolean isTransport(int sboTerm)
```
    Returns true if the given term identifier comes from the stated branch of SBO.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if term is-a SBO 'product', false otherwise.
  - isTrigger
```
public static boolean isTrigger(int sboTerm)
```
    Returns true if the given term identifier comes from the stated branch of SBO.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if term is-a SBO 'product', false otherwise.
  - isTruncated
```
public static boolean isTruncated(int sboTerm)
```
    Returns true if the given term identifier comes from the stated branch of SBO.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if term is-a SBO 'product', false otherwise.
  - isUnknownMolecule
```
public static boolean isUnknownMolecule(int sboTerm)
```
    Returns true if the given term identifier comes from the stated branch of SBO.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if term is-a SBO 'product', false otherwise.
  - isUnknownTransition
```
public static boolean isUnknownTransition(int sboTerm)
```
    Returns true if the given term identifier comes from the stated branch of SBO.
    
    Parameters:
    sboTerm -
    
    Returns:
    true if term is-a SBO 'product', false otherwise.
  - sboNumberString
```
public static java.lang.String sboNumberString(int sboTerm)
```
    Creates and returns a 7 digit SBO number for the given SBO.Term identifier (if this is a valid identifier). The returned String will not contain the SBO prefix.
    
    Parameters:
    sboTerm -
    
    Returns:
    a 7 digit SBO number for the given SBO.Term identifier (if this is a valid identifier). The returned String will not contain the SBO prefix.
    
    Throws:
    
    java.lang.IllegalArgumentException - if the given value is no valid SBO term number.
  - stringToInt
```
public static int stringToInt(java.lang.String sboTerm)
```
    Returns the string as a correctly formatted SBO integer portion.
    
    Parameters:
    sboTerm -
    
    Returns:
    the given string sboTerm as an integer. If the sboTerm is not in the correct format (a zero-padded, seven digit string), -1 is returned.

Class SBO

Use of SBO

Relationships between SBO and SBML

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

alias2sbo

prefix

sbo

sbo2alias

terms

Constructor Detail

SBO

Method Detail

checkTerm

checkTerm

convertAlias2SBO

convertSBO2Alias

getAntisenseRNA

getAssociation

getBindingActivator

getCatalysis

getCatalyst

getCatalyticActivator

getCompartment

getCompetetiveInhibitor

getCompleteInhibitor

getComplex

getConservationLaw

getConsumption

getContinuousFramework

getDefaultPossibleEnzymes

getDiscreteFramework

getDissociation

getDrug

getEmptySet

getEntity

getEnzymaticCatalysis

getEssentialActivator

getEvent

getFunctionalCompartment

getFunctionalEntity

getGene

getGeneCodingRegion

getGeneric

getHillEquation

getInhibition

getInhibitor

getInteraction

getIon

getIonChannel

getKineticConstant

getLogicalFramework

getMacromolecule

getMaterialEntity

getMathematicalExpression

getMessengerRNA

getModellingFramework

getModifier

getModulation

getNecessaryStimulation

getNonCompetetiveInhibitor

getNonCovalentComplex

getNonEssentialActivator

getOntology

getPartialInhibitor

getParticipant

getParticipantRole

getPertubingAgent

getPhenotype

getPhysicalCompartment

getPhysicalParticipant

getPossibleEnzymes

getProduct

getProduction

getProtein

getQuantitativeParameter

Use of `SBO`

Relationships between `SBO` and SBML