public class SBO
extends java.lang.Object
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 also be
obtained using the method getOntology()
.
The values of 'id' attributes on SBML components allow the components to
be crossreferenced 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 firstorder 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.,
HenriMichaelisMenten 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).
SBO
Labeling model components with terms from shared controlled vocabularies allows a software tool to identify each component using identifiers that are not toolspecific. 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., 'MichaelisMenten'), 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 isa 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 'firstorder irreversible massaction 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 firstorder irreversible massaction
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/), PSIMI (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.
SBO
and SBMLThe 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 hierarchicallystructured 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 SBMLcompliant.
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<Term> 
terms 
Constructor and Description 

SBO() 
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 
getActivator() 
static int 
getAllostericActivator()
Describes an activator (ligand) which binds at a site other than the active site, resulting in a conformational change, enhancing the activity of the enzyme.

static int 
getAllostericInhibitor()
An inhibitor whose binding to an enzyme results in a conformational change, resulting in a loss of enzymatic activity.

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 noncovalent complex

static int 
getBindingActivator()
An essential activator that affects the apparent value of the Michaelis
constant(s).

static int 
getBiochemicalReaction()
An event involving one or more chemical entities that modifies the electrochemical structure of at least one of the participants.

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 
getCompetitiveInhibitor()
Substance that decreases the probability of a chemical reaction, without itself being consumed or transformed by the reaction, by stericaly hindering the interaction between reactants.

static int 
getCompleteInhibitor() 
static int 
getComplex() 
static int 
getComplexAssembly()
Interaction between several biochemical entities that results in the formation of a noncovalent complex
Also known as noncovalent binding

static int 
getConservationLaw() 
static int 
getConsumption()
Decrease in amount of a material or conceptual entity.

static int 
getContinuousFramework() 
static int 
getConversion()
Biochemical reaction that results in the modification of some covalent bonds.

static java.util.Set<java.lang.Integer> 
getDefaultPossibleEnzymes()
Creates and returns a list of molecule types accepted as an enzyme by
default.

static int 
getDegradation()
Complete disappearance of a physical entity.

static int 
getDiscreteFramework() 
static int 
getDissociation()
Transformation of a noncovalent complex that results in the formation of
several independent biochemical entities.

static int 
getDNA()
Polymer composed of nucleotides containing deoxyribose and linked by phosphodiester bonds.

static int 
getDNASegment()
Fragment or region of a DNA macromolecule.

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 
getEnthalpyChange()
Change in enthalpy observed in the constituents of a thermodynamic system when undergoing
a transformation or chemical reaction.

static int 
getEntity() 
static int 
getEntropyChange()
The increase or decrease of the entropy of a system.

static int 
getEnzymaticCatalysis() 
static int 
getEquilibriumConstant()
Quantity characterizing a chemical equilibrium in a chemical reaction, which is a useful tool to
determine the concentration of various reactants or products in a system where chemical equilibrium
occurs.

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 
getGeneticInteraction()
A phenomenon whereby an observed phenotype, qualitative or quantative, is not explainable by the simple additive effects of the individual gene pertubations alone.

static int 
getGibbsFreeEnergyChange()
The increase or decrease of the Gibbs free energy of a system.

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 
getIonicStrength()
A combined (weighted) measure of the concentration of all electrolytes present in a
solution.

static int 
getIrreversibleInhibitor()
An inhibitor which binds irreversibly with the enzyme such that it cannot be removed, and abolishes enzymatic function.

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 
getModifierUnknownActivity()
A modifier whose activity is not known or has not been specified.

static int 
getModulation()
Modification of the execution of an event or a process.

static int 
getMolecularInteraction()
Relationship between molecular entities, based on contacts, direct or indirect.

static int 
getNecessaryStimulation()
Control that is necessary to the execution of a process.

static int 
getNonAllostericActivator()
Describes an activator (ligand) which binds to the enzyme, which does not result in a conformational change, but which enhances the enzyme's activity.

static int 
getNonCompetitiveInhibitor()
Substance that decreases the probability of a chemical reaction, without itself being consumed or transformed by the reaction, and without sterically hindering the interaction between reactants.

static int 
getNonCovalentComplex()
Entity composed of several independant components that are not linked by covalent bonds.

static int 
getNonEssentialActivator()
An activator which is not necessary for an enzymatic reaction, but whose presence will further increase enzymatic activity.

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 
getpH()
"A measure of acidity and alkalinity of a solution that is a number on a scale on
which a value of 7 represents neutrality and lower numbers indicate increasing acidity
and higher numbers increasing alkalinity and on which each unit of change represents a
tenfold change in acidity or alkalinity and that is the negative logarithm of the
effective hydrogenion concentration or hydrogenion activity in gram equivalents per
liter of the solution.

static int 
getPhenotype() 
static int 
getPhysicalCompartment() 
static int 
getPhysicalParticipant() 
static int 
getPMg()
An enumeration of the concentration of magnesium (Mg) in solution (pMg = log10[Mg2+]).

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 
getPotentiator()
Substance that increases the probability of a chemical reaction without itself being consumed or transformed by the reaction.

static int 
getProcess() 
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 int 
getRNASegment()
Fragment or region of an RNA macromolecule.

static Term 
getSBORoot()
Returns the root element of the SBO Ontology (SBO:0000000).

static int 
getSideProduct()
Returns the side product SBO term

static int 
getSideSubstrate()
Returns the side substrate SBO term

static int 
getSimpleMolecule() 
static int 
getSmallMolecule()
Simple, nonrepetitive chemical entity.

static int 
getSpecificActivator() 
static int 
getStateTransition() 
static int 
getSteadyStateExpression() 
static int 
getStimulation()
Positive modulation of the execution of a process.

static int 
getStimulator() 
static int 
getTemplateReaction()
A composite biochemical process through which a gene sequence is fully converted into
mature gene products.

static int 
getTemplateReactionRegulation()
A phenomenon whereby an observed phenotype, qualitative or quantative, is not explainable by the simple additive effects of the individual gene pertubations alone.

static Term 
getTerm(int sboTerm)
Gets the SBO term with the id 'sboTerm'.

static Term 
getTerm(java.lang.String sboTerm)
Gets the SBO term with the id 'sboTerm'.

static java.util.Set<Term> 
getTerms()
Return the set of terms of the SBO Ontology.

static int 
getThermodynamicTemperature()
Temperature is the physical property of a system which underlies the common notions of
"hot" and "cold"; the material with the higher temperature is said to be hotter.

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 
getTransportWithBiochemicalReaction()
An event involving one or more physical entities that modifies the structure, location or free energy of at least one of the participants.

static int 
getTrigger()
Returns the SBO id corresponding to the alias 'TRIGGER'

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 int 
getTruncated()
Returns the SBO id corresponding to the alias 'TRUNCATED'

static int 
getUncompetitiveInhibitor()
An inhibitor which binds only to the complex formed between the enzyme and substrate (ES complex).

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'

boolean 
hasTerm(int sboTerm)
This method will test if a term for the given SBO code number exists and
returns
true if this is the case. 
boolean 
hasTerm(java.lang.String sboTerm)
This method will test if a term for the given SBO code number exists and
returns
true if this is the case. 
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 
isAssociation(int sboTerm) 
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(Term subject,
Term object)

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 isa conservation law, false otherwise 
static boolean 
isContinuousFramework(int sboTerm)
Returns
true if the term isa continuous framework, false otherwise 
static boolean 
isDiscreteFramework(int sboTerm)
Returns
true if the term isa discrete framework, false otherwise 
static boolean 
isDissociation(int sboTerm) 
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 isa 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 
isProcess(int sboTerm) 
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 void 
main(java.lang.String[] args)
For testing purposes.

static java.lang.String 
sboNumberString(int sboTerm)
Creates and returns a 7 digit SBO number for the given
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.

private static java.util.Properties alias2sbo
private static final java.lang.String prefix
private static Ontology sbo
private static java.util.Properties sbo2alias
private static java.util.Set<Term> terms
public static boolean checkTerm(int sboTerm)
sboTerm
 true
if sboTerm is in the range {0,.., 9999999}, false
otherwise.public static boolean checkTerm(java.lang.String sboTerm)
sboTerm
 true
if sboTerm is in the correct format (a zeropadded, seven
digit string), false
otherwise.public static int convertAlias2SBO(java.lang.String alias)
alias
 public static java.lang.String convertSBO2Alias(int sboterm)
sboterm
 public static int getAntisenseRNA()
public static int getAssociation()
public static int getAllostericActivator()
public static int getAllostericInhibitor()
public static int getBindingActivator()
public static int getCatalysis()
public static int getBiochemicalReaction()
public static int getCatalyst()
public static int getCatalyticActivator()
public static int getCompartment()
public static int getCompetitiveInhibitor()
public static int getCompleteInhibitor()
public static int getComplex()
public static int getComplexAssembly()
public static int getConservationLaw()
public static int getConsumption()
public static int getContinuousFramework()
public static int getConversion()
public static final java.util.Set<java.lang.Integer> getDefaultPossibleEnzymes()
public static int getDegradation()
public static int getDiscreteFramework()
public static int getDissociation()
public static int getDNA()
public static int getDNASegment()
public static int getDrug()
public static int getEmptySet()
public static int getEnthalpyChange()
public static int getEntity()
public static int getEntropyChange()
public static int getEnzymaticCatalysis()
public static int getEquilibriumConstant()
public static int getEssentialActivator()
public static int getEvent()
public static int getFunctionalCompartment()
public static int getFunctionalEntity()
public static int getGene()
public static int getGeneticInteraction()
public static int getGeneCodingRegion()
public static int getGeneric()
public static int getGibbsFreeEnergyChange()
public static int getHillEquation()
public static int getInhibition()
public static int getInhibitor()
public static int getInteraction()
public static int getIrreversibleInhibitor()
public static int getActivator()
public static int getIon()
public static int getIonicStrength()
public static int getIonChannel()
public static int getKineticConstant()
public static int getLogicalFramework()
public static int getMacromolecule()
public static int getMaterialEntity()
public static int getMathematicalExpression()
public static int getMessengerRNA()
public static int getModellingFramework()
public static int getModifier()
public static int getModifierUnknownActivity()
public static int getModulation()
public static int getMolecularInteraction()
public static int getNecessaryStimulation()
public static int getNonAllostericActivator()
public static int getNonCompetitiveInhibitor()
public static int getNonCovalentComplex()
public static int getNonEssentialActivator()
public static Ontology getOntology()
Ontology
form BioJava.public static int getPartialInhibitor()
Term
with
the name "partial inhibitor".public static int getParticipant()
public static int getParticipantRole()
public static int getPertubingAgent()
public static int getpH()
public static int getPhenotype()
public static int getPhysicalCompartment()
public static int getPMg()
public static int getPhysicalParticipant()
public static int getProcess()
public static final java.util.Set<java.lang.Integer> getPossibleEnzymes(java.lang.String... types)
types
 public static int getPotentiator()
public static int getProduct()
public static int getProduction()
public static int getProtein()
public static int getQuantitativeParameter()
public static int getRateLaw()
public static int getReactant()
public static int getReceptor()
public static int getRNA()
public static int getRNASegment()
public static Term getSBORoot()
public static int getSideProduct()
public static int getSideSubstrate()
public static int getSimpleMolecule()
public static int getSmallMolecule()
public static int getSpecificActivator()
public static int getStateTransition()
public static int getSteadyStateExpression()
public static int getStimulation()
public static int getStimulator()
public static int getTemplateReaction()
public static int getTemplateReactionRegulation()
public static Term getTerm(int sboTerm)
sboTerm
 the id of the SBO term to search for.java.util.NoSuchElementException
 if the id is not found.public static Term getTerm(java.lang.String sboTerm)
The id need to be of the form 'SBO:XXXXXXX' where X is a digit number.
sboTerm
 the id of the SBO 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 org.biojava.nbio.ontology.Term
containing also the org.biojava.nbio.ontology.Triple
, use getOntology()
to get the underlying biojava object.
public static int getThermodynamicTemperature()
public static int getTranscription()
public static int getTranscriptionalActivation()
public static int getTranscriptionalInhibitor()
public static int getTransitionOmitted()
public static int getTranslation()
public static int getTranslationalActivation()
public static int getTranslationalInhibitor()
public static int getTransport()
public static int getTransportWithBiochemicalReaction()
public static int getTrigger()
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. For example:
getTriples(SBO.getTerm("SBO:0000002"), SBO.getTerm("is_a"), null);will returned all the parent Terms of
SBO:0000002
and
getTriples(null, SBO.getTerm("is_a"), SBO.getTerm(188));will returned all the children Terms of
SBO:0000188
subject
 the subject to search for, or null
.predicate
 the relationship to search for, or null
.object
 the object to search for, or null
.org.biojava.nbio.ontology.Ontology#getTriples(org.biojava.nbio.ontology.Term,
org.biojava.nbio.ontology.Term, org.biojava.nbio.ontology.Term)
public static int getTruncated()
public static int getUncompetitiveInhibitor()
public static int getUnknownMolecule()
public static int getUnknownTransition()
public boolean hasTerm(int sboTerm)
true
if this is the case. It is recommended to call this
method before trying to retrieve an actual Term
object, because
this could result in a NoSuchElementException
.sboTerm
 the SBO identifier for which a term is to be retrieved.true
if an SBO Term
object can be safely retrieved
for the given identifier.hasTerm(String)
public boolean hasTerm(java.lang.String sboTerm)
true
if this is the case. It is recommended to call this
method before trying to retrieve an actual Term
object, because
this could result in a NoSuchElementException
.sboTerm
 the SBO identifier for which a term is to be retrieved.true
if an SBO Term
object can be safely retrieved
for the given identifier.hasTerm(int)
public static java.lang.String intToString(int sboTerm)
sboTerm
 public static boolean isAntisenseRNA(int sboTerm)
true
if the given term identifier comes from the stated branch of SBO.
sboTerm
 true
if term
isa SBO 'product', false
otherwise.public static boolean isAssociation(int sboTerm)
sboTerm
 public static boolean isBindingActivator(int sboTerm)
true
if the given term identifier comes from the stated branch of SBO.
sboTerm
 true
if term
isa SBO 'product', false
otherwise.public static boolean isCatalyst(int sboTerm)
true
if the given term identifier comes from the stated branch of SBO.
sboTerm
 true
if term
isa SBO 'product', false
otherwise.public static boolean isCatalyticActivator(int sboTerm)
true
if the given term identifier comes from the stated branch of SBO.
sboTerm
 true
if term
isa SBO 'product', false
otherwise.public static boolean isChildOf(int sboTerm, int parent)
sboTerm
 An SBO term.parent
 An SBO term that is the root of a certain subgraph within the
SBO.true
if the subgraph of the SBO rooted at the term parent
contains a term with the id corresponding to sboTerm.private static boolean isChildOf(Term subject, Term object)
Term
subject until
either the root (SBO:0000000) or the Term
object is reached.subject
 Childobject
 Parenttrue
if subject is a child of object.public static boolean isCompetetiveInhibitor(int sboTerm)
true
if the given term identifier comes from the stated branch of SBO.
sboTerm
 true
if term
isa SBO 'product', false
otherwise.public static boolean isCompleteInhibitor(int sboTerm)
true
if the given term identifier comes from the stated branch of SBO.
sboTerm
 true
if term
isa SBO 'product', false
otherwise.public static boolean isComplex(int sboTerm)
true
if the given term identifier comes from the stated branch of SBO.
sboTerm
 true
if term
isa SBO 'product', false
otherwise.public static boolean isConservationLaw(int sboTerm)
true
if the term isa conservation law, false
otherwisesboTerm
 true
if the term isa conservation law, false
otherwisepublic static boolean isContinuousFramework(int sboTerm)
true
if the term isa continuous framework, false
otherwisesboTerm
 true
if the term isa continuous framework, false
otherwisepublic static boolean isDiscreteFramework(int sboTerm)
true
if the term isa discrete framework, false
otherwisesboTerm
 true
if the term isa discrete framework, false
otherwisepublic static boolean isDissociation(int sboTerm)
sboTerm
 public static boolean isDrug(int sboTerm)
true
if the given term identifier comes from the stated branch of SBO.
sboTerm
 true
if term
isa SBO 'product', false
otherwise.public static boolean isEmptySet(int sboTerm)
true
if the given term identifier comes from the stated branch of SBO.
sboTerm
 true
if term
isa SBO 'product', false
otherwise.public static boolean isEntity(int sboTerm)
true
if the term isa Entity, false
otherwisesboTerm
 true
if the term isa Entity, false
otherwisepublic static boolean isEnzymaticCatalysis(int sboTerm)
true
if the given term identifier comes from the stated branch of SBO.
sboTerm
 true
if term
isa SBO 'product', false
otherwise.public static boolean isEssentialActivator(int sboTerm)
true
if the given term identifier comes from the stated branch of SBO.
sboTerm
 true
if term
isa SBO 'product', false
otherwise.public static boolean isEvent(int sboTerm)
sboTerm
 true
if the term isan Event, false
otherwisepublic static boolean isFunctionalCompartment(int sboTerm)
sboTerm
 true
if the term isa functional compartment, false
otherwisepublic static boolean isFunctionalEntity(int sboTerm)
sboTerm
 true
if the term isa functional entity, false
otherwisepublic static boolean isGene(int sboTerm)
true
if the given term identifier comes from the stated branch of SBO.
sboTerm
 true
if term
isa SBO 'product', false
otherwise.public static boolean isGeneCodingRegion(int sboTerm)
true
if the sboTerm stands for a gene coding region, false
otherwisesboTerm
 true
if the sboTerm stands for a gene coding region, false
otherwisepublic static boolean isGeneOrGeneCodingRegion(int sboTerm)
true
if the sboTerm stands for a gene coding region or a gene,
false otherwisesboTerm
 true
if the sboTerm stands for a gene coding region or a gene,
false otherwisepublic static boolean isGeneric(int sboTerm)
true
if the given term identifier comes from the stated branch of SBO.
sboTerm
 true
if term
isa SBO 'product', false
otherwise.public static boolean isHillEquation(int sboTerm)
true
if the given term identifier comes from the stated branch of SBO.
sboTerm
 true
if term
isa SBO 'product', false
otherwise.public static boolean isInhibitor(int sboTerm)
true
if the given term identifier comes from the stated branch of SBO.
sboTerm
 true
if term
isa SBO 'product', false
otherwise.public static boolean isInteraction(int sboTerm)
sboTerm
 true
if the term isan interaction, false
otherwisepublic static boolean isIon(int sboTerm)
true
if the given term identifier comes from the stated branch of SBO.
sboTerm
 true
if term
isa SBO 'product', false
otherwise.public static boolean isIonChannel(int sboTerm)
true
if the given term identifier comes from the stated branch of SBO.
sboTerm
 true
if term
isa SBO 'product', false
otherwise.public static boolean isKineticConstant(int sboTerm)
sboTerm
 true
if the term isa kinetic constant, false
otherwisepublic static boolean isLogicalFramework(int sboTerm)
sboTerm
 true
if the term isa logical framework, false
otherwisepublic static boolean isMaterialEntity(int sboTerm)
sboTerm
 true
if the term isa material entity, false
otherwisepublic static boolean isMathematicalExpression(int sboTerm)
sboTerm
 true
if the term isa mathematical expression, false
otherwisepublic static boolean isMessengerRNA(int sboTerm)
true
if the given term identifier comes from the stated branch of SBO.
sboTerm
 true
if term
isa SBO 'product', false
otherwise.public static boolean isModellingFramework(int sboTerm)
sboTerm
 true
if the term isa modelling framework, false
otherwisepublic static boolean isModifier(int sboTerm)
sboTerm
 true
if the term isa modifier, false
otherwisepublic static boolean isNonCompetetiveInhibitor(int sboTerm)
true
if the given term identifier comes from the stated branch of SBO.
sboTerm
 true
if term
isa SBO 'product', false
otherwise.public static boolean isNonEssentialActivator(int sboTerm)
true
if the given term identifier comes from the stated branch of SBO.
sboTerm
 true
if term
isa SBO 'product', false
otherwise.public static boolean isObsolete(int sboTerm)
sboTerm
 true
if the term isan obsolete term, false
otherwisepublic static boolean isPartialInhibitor(int sboTerm)
true
if the given term identifier comes from the stated branch of SBO.
sboTerm
 true
if term
isa SBO 'product', false
otherwise.public static boolean isParticipant(int sboTerm)
sboTerm
 true
if the term isa participant, false
otherwisepublic static boolean isParticipantRole(int sboTerm)
sboTerm
 true
if the term isa participant role, false
otherwisepublic static boolean isPhenotype(int sboTerm)
true
if the given term identifier comes from the stated branch of SBO.
sboTerm
 true
if term
isa SBO 'product', false
otherwise.public static boolean isPhysicalCompartment(int sboTerm)
true
if the given term identifier comes from the stated branch of SBO.
sboTerm
 true
if term
isa SBO 'product', false
otherwise.public static boolean isPhysicalParticipant(int sboTerm)
sboTerm
 true
if the term isa physical participant, false
otherwisepublic static boolean isProcess(int sboTerm)
sboTerm
 public static boolean isProduct(int sboTerm)
sboTerm
 true
if the term isa product, false
otherwisepublic static boolean isProtein(int sboTerm)
true
if the given term identifier comes from the stated branch of SBO.
sboTerm
 true
if term
isa SBO 'product', false
otherwise.public static boolean isQuantitativeParameter(int sboTerm)
sboTerm
 true
if the term isa quantitative parameter, false
otherwisepublic static boolean isRateLaw(int sboTerm)
sboTerm
 true
if the term isa rate law, false
otherwisepublic static boolean isReactant(int sboTerm)
sboTerm
 true
if the term isa reactant, false
otherwisepublic static boolean isReceptor(int sboTerm)
true
if the given term identifier comes from the stated branch of SBO.
sboTerm
 true
if term
isa SBO 'product', false
otherwise.public static boolean isRNA(int sboTerm)
true
if the given term identifier comes from the stated branch of SBO.
sboTerm
 true
if term
isa SBO 'product', false
otherwise.public static boolean isRNAOrMessengerRNA(int sboTerm)
true
if the given term identifier comes from the stated branch of SBO.
sboTerm
 true
if term
isa SBO 'product', false
otherwise.public static boolean isSimpleMolecule(int sboTerm)
true
if the given term identifier comes from the stated branch of SBO.
sboTerm
 true
if term
isa SBO 'product', false
otherwise.public static boolean isSpecificActivator(int sboTerm)
true
if the given term identifier comes from the stated branch of SBO.
sboTerm
 true
if term
isa SBO 'product', false
otherwise.public static boolean isStateTransition(int sboTerm)
true
if the given term identifier comes from the stated branch of SBO.
sboTerm
 true
if term
isa SBO 'product', false
otherwise.public static boolean isSteadyStateExpression(int sboTerm)
sboTerm
 true
if the term isa steady state expression, false
otherwisepublic static boolean isStimulator(int sboTerm)
true
if the given term identifier comes from the stated branch of SBO.
sboTerm
 true
if term
isa SBO 'product', false
otherwise.public static boolean isTranscription(int sboTerm)
true
if the given term identifier comes from the stated branch of SBO.
sboTerm
 true
if term
isa SBO 'product', false
otherwise.public static boolean isTranscriptionalActivation(int sboTerm)
true
if the given term identifier comes from the stated branch of SBO.
sboTerm
 true
if term
isa SBO 'product', false
otherwise.public static boolean isTranscriptionalInhibitor(int sboTerm)
true
if the given term identifier comes from the stated branch of SBO.
sboTerm
 true
if term
isa SBO 'product', false
otherwise.public static boolean isTransitionOmitted(int sboTerm)
true
if the given term identifier comes from the stated branch of SBO.
sboTerm
 true
if term
isa SBO 'product', false
otherwise.public static boolean isTranslation(int sboTerm)
true
if the given term identifier comes from the stated branch of SBO.
sboTerm
 true
if term
isa SBO 'product', false
otherwise.public static boolean isTranslationalActivation(int sboTerm)
true
if the given term identifier comes from the stated branch of SBO.
sboTerm
 true
if term
isa SBO 'product', false
otherwise.public static boolean isTranslationalInhibitor(int sboTerm)
true
if the given term identifier comes from the stated branch of SBO.
sboTerm
 true
if term
isa SBO 'product', false
otherwise.public static boolean isTransport(int sboTerm)
true
if the given term identifier comes from the stated branch of SBO.
sboTerm
 true
if term
isa SBO 'product', false
otherwise.public static boolean isTrigger(int sboTerm)
true
if the given term identifier comes from the stated branch of SBO.
sboTerm
 true
if term
isa SBO 'product', false
otherwise.public static boolean isTruncated(int sboTerm)
true
if the given term identifier comes from the stated branch of SBO.
sboTerm
 true
if term
isa SBO 'product', false
otherwise.public static boolean isUnknownMolecule(int sboTerm)
true
if the given term identifier comes from the stated branch of SBO.
sboTerm
 true
if term
isa SBO 'product', false
otherwise.public static boolean isUnknownTransition(int sboTerm)
true
if the given term identifier comes from the stated branch of SBO.
sboTerm
 true
if term
isa SBO 'product', false
otherwise.public static java.lang.String sboNumberString(int sboTerm)
Term
identifier (if
this is a valid identifier). The returned String
will not contain the
SBO prefix.sboTerm
 Term
identifier (if
this is a valid identifier). The returned String
will not contain the
SBO prefix.java.lang.IllegalArgumentException
 if the given value is no valid SBO term number.public static int stringToInt(java.lang.String sboTerm)
sboTerm
 public static void main(java.lang.String[] args)
args
