SystemsBiologyOntology

java.lang.Object
- org.sbolstandard.core2.SystemsBiologyOntology

```
public class SystemsBiologyOntology
extends Object
```
This class provides methods for accessing Systems Biology Ontology (SBO) terms and querying about their relationships.

Version:

2.1

Author:

Zhen Zhang, Tramy Nguyen, Nicholas Roehner, Chris Myers

Field Summary

Fields
Modifier and Type	Field and Description
`static URI`	`ABSOLUTE_INHIBITION` Control that precludes the execution of a process (SBO:0000407).
`static URI`	`ABSOLUTE_STIMULATION` Control that always triggers the controlled process (SBO:0000411).
`static URI`	`ACETYLATION` Addition of an acetyl group (-COCH3) to a chemical entity (SBO:0000215).
`static URI`	`ACID_BASE_REACTION` Chemical reaction where a proton is given by a compound, the acid, to another one, the base (Brønsted-Lowry definition) (SBO:0000208).
`static URI`	`ADDITION_OF_A_CHEMICAL_GROUP` Covalent reaction that results in the addition of a chemical group on a molecule (SBO:0000210).
`static URI`	`ALLOSTERIC_CONTROL` Regulation of the influence of a reaction participant by binding an effector to a binding site of the participant different of the site of the participant conveying the influence (SBO:0000239).
`static URI`	`AND` All the preceding events or participating entities are necessary to perform the control (SBO:0000173).
`static URI`	`BINDING_ACTIVATOR` An essential activator that affects the apparent value of the Michaelis constant(s) (SBO:0000535).
`static URI`	`BIOCHEMICAL_OR_TRANSPORT_REACTION` An event involving one or more physical entities that modifies the structure, location or free energy of at least one of the participants (SBO:0000167).
`static URI`	`BIOCHEMICAL_REACTION` An event involving one or more chemical entities that modifies the electrochemical structure of at least one of the participants.
`static URI`	`BIOLOGICAL_ACTIVITY` The potential action that a biological entity has on other entities (SBO:0000412).
`static URI`	`BIOLOGICAL_EFFECT_OF_A_PERTURBATION` Biochemical networks can be affected by external influences (SBO:0000357).
`static URI`	`BOOLEAN_LOGICAL_FRAMEWORK` Equationally defined algebraic framework usually interpreted as a two-valued logic using the basic Boolean operations (conjunction, disjunction and negation), together with the constants '0' and '1' denoting false and true values, respectively (SBO:0000547).
`static URI`	`CATALYSIS` Modification of the velocity of a reaction by lowering the energy of the transition state (SBO:0000172).
`static URI`	`CATALYST` Substance that accelerates the velocity of a chemical reaction without itself being consumed or transformed (SBO:0000013).
`static URI`	`CATALYTIC_ACTIVATOR` An essential activator that affects the apparent value of the catalytic constant (SBO:0000534).
`static URI`	`CIS` Positional relationship between entities on the same strand (e.g.
`static URI`	`CLEAVAGE` Rupture of a covalent bond resulting in the conversion of one physical entity into several physical entities (SBO:0000178).
`static URI`	`COMPETITIVE_INHIBITOR` 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 (SBO:0000206).
`static URI`	`COMPOSITE_BIOCHEMICAL_PROCESS` Process that involves the participation of chemical or biological entities and is composed of several elementary steps or reactions (SBO:0000205).
`static URI`	`CONFORMATIONAL_TRANSITION` Biochemical reaction that does not result in the modification of covalent bonds of reactants, but rather modifies the conformation of some reactants, that is the relative position of their atoms in space (SBO:0000181).
`static URI`	`CONSUMPTION` Decrease in amount of a material or conceptual entity (SBO:0000394).
`static URI`	`CONTAINMENT` An entity that is a subset of another entity or object (SBO:0000469).
`static URI`	`CONTINUOUS_FRAMEWORK` Modelling approach where the quantities of participants are considered continuous, and represented by real values (SBO:0000062).
`static URI`	`CONTROL` Modification of the execution of an event or a process (SBO:0000168).
`static URI`	`CONVERSION` Biochemical reaction that results in the modification of some covalent bonds (SBO:0000182).
`static URI`	`DEAMINATION` Removal of an amine group from a molecule, often under the addition of water (SBO:0000401).
`static URI`	`DECARBONYLATION` Removal of a carbonyl group (-C-O-) from a molecule, usually as carbon monoxide (SBO:0000400).
`static URI`	`DECARBOXYLATION` A process in which a carboxyl group (COOH) is removed from a molecule as carbon dioxide (SBO:0000399).
`static URI`	`DEGRADATION` Complete disappearance of a physical entity (SBO:0000179).
`static URI`	`DEPHOSPHORYLATION` Removal of a phosphate group (-H2PO4) from a chemical entity (SBO:0000330).
`static URI`	`DEPROTONATION` Removal of a proton (hydrogen ion H+) from a chemical entity (SBO:0000213).
`static URI`	`DISCRETE_FRAMEWORK` Modelling approach where the quantities of participants are considered discrete, and represented by integer values (SBO:0000063).
`static URI`	`DISSOCIATION` Transformation of a non-covalent complex that results in the formation of several independent biochemical entities (SBO:0000180).
`static URI`	`DNA_REPLICATION` Process in which a DNA duplex is transformed into two identical DNA duplexes (SBO:0000204).
`static URI`	`DUAL_ACTIVITY_MODIFIER` A modifier that can exhibit either inhibitory or stimulatory effects on a process depending on the context in which it occurs (SBO:0000595).
`static URI`	`ENCAPSULATING_PROCESS` An aggregation of interactions and entities into a single process (SBO:0000395).
`static URI`	`ENZYMATIC_CATALYST` A substance that accelerates the velocity of a chemical reaction without itself being consumed or transformed, by lowering the free energy of the transition state (SBO:0000460).
`static URI`	`EQUIVALENCE` Term to signify those material or conceptual entities that are identical in some respect within a frame of reference (SBO:0000392).
`static URI`	`ESSENTIAL_ACTIVATOR` A substance that is absolutely required for occurrence and stimulation of a reaction (SBO:0000461).
`static URI`	`FARNESYLATION` Addition of a farnesyl group (CH2-CH=C(CH3)-CH2-CH2-CH=C(CH3)-CH2-CH2-CH=C(CH3)2) to a chemical entity (SBO:0000222).
`static URI`	`FLUX_BALANCE_FRAMEWORK` Modelling approach, typically used for metabolic models, where the flow of metabolites (flux) through a network can be calculated (SBO:0000624).
`static URI`	`FUNCTIONAL_COMPARTMENT` Logical or physical subset of the event space that contains pools, that is sets of participants considered identical when it comes to the event they are involved into (SBO:0000289).
`static URI`	`GENETIC_ENHANCEMENT` Genetic enhancement is said to have occurred when the phenotypic effect of an initial mutation in a gene is made increasingly severe by a subsequent mutation (SBO:0000501).
`static URI`	`GENETIC_INTERACTION` A phenomenon whereby an observed phenotype, qualitative or quantative, is not explainable by the simple additive effects of the individual gene pertubations alone (SBO:0000343).
`static URI`	`GENETIC_PRODUCTION` A composite biochemical process through which a gene sequence is fully converted into mature gene products (SBO:0000589).
`static URI`	`GENETIC_SUPPRESSION` Genetic suppression is said to have occurred when the phenotypic effect of an initial mutation in a gene is less severe, or entirely negated, by a subsequent mutation (SBO:0000500).
`static URI`	`GERANYLGERANYLATION` Addition of a geranylgeranyl group (CH2-CH=C(CH3)-CH2-CH2-CH=C(CH3)-CH2-CH2-CH=C(CH3)-CH2-CH2-CH=C(CH3)2) to a chemical entity (SBO:0000223).
`static URI`	`GLYCOSYLATION` Addition of a saccharide group to a chemical entity (SBO:0000217).
`static URI`	`GROWTH_RATE` A measure of the rate of growth of an organism, usually in culture.
`static URI`	`HYDROLYSIS` Decomposition of a compound by reaction with water, where the hydroxyl and H groups are incorporated into different products (SBO:0000376).
`static URI`	`HYDROXYLATION` Addition of an hydroxyl group (-OH) to a chemical entity (SBO:0000233).
`static URI`	`INHIBITED` Conceptual or material entity that is the object of an inhibition process, and is acted upon by an inhibitor (SBO:0000642).
`static URI`	`INHIBITION` Negative modulation of the execution of a process (SBO:0000169).
`static URI`	`INHIBITOR` Substance that decreases the probability of a chemical reaction without itself being consumed or transformed by the reaction (SBO:0000020).
`static URI`	`INTERACTOR` Entity participating in a physical or functional interaction (SBO:0000336).
`static URI`	`IONISATION` Ionization is the physical process of converting an atom or molecule into an ion by changing the difference between the number of protons and electrons (SBO:0000209).
`static URI`	`ISOMERISATION` A reaction in which the principal reactant and principal product are isomers of each other (SBO:0000377).
`static URI`	`LOGICAL_COMBINATION` Combining the influence of several entities or events in a unique influence (SBO:0000237).
`static URI`	`LOGICAL_FRAMEWORK` Modelling approach, pioneered by Rene Thomas and Stuart Kaufman, where the evolution of a system is described by the transitions between discrete activity states of "genes" that control each other (SBO:0000234).
`static URI`	`LOGICAL_RELATIONSHIP` Relationship between entities (material or conceptual) and logical operators, or between logical operators themselves (SBO:0000398).
`static URI`	`METHYLATION` Addition of a methyl group (-CH3) to a chemical entity (SBO:0000214).
`static URI`	`MODELING_FRAMEWORK` Set of assumptions that underlay a mathematical description (SBO:0000004).
`static URI`	`MODIFIED` Conceptual or material entity that is the object of a modification process, and is acted upon by a modifier (SBO:0000644).
`static URI`	`MODIFIER` Substance that changes the velocity of a process without itself being consumed or transformed by the reaction (SBO:0000019).
`static URI`	`MODIFIER_OF_UNKNOWN_ACTIVITY` A modifier whose activity is not known or has not been specified (SBO:0000596).
`static URI`	`MOLECULAR_INTERACTION` Relationship between molecular entities, based on contacts, direct or indirect (SBO:0000344).
`static URI`	`MOLECULAR_OR_GENETIC_INTERACTION` Mutual or reciprocal action or influence between molecular entities (SBO:0000342).
`static URI`	`MYRISTOYLATION` Addition of a myristoyl (CH3-[CH2]12-CO-) to a chemical entity (SBO:0000219).
`static URI`	`NAMESPACE` Namespace of the Systems Biology Ontology (http://identifiers.org/biomodels.sbo/).
`static URI`	`NECESSARY_STIMULATION` Control that is necessary to the execution of a process (SBO:0000171).
`static URI`	`NEUTRAL_PARTICIPANT` A participant whose presence does not alter the velocity of a process or event (SBO:0000594).
`static URI`	`NON_COMPETITIVE_INHIBITOR` 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 (SBO:0000207).
`static URI`	`NON_COVALENT_BINDING` Interaction between several biochemical entities that results in the formation of a non-covalent complex (SBO:0000177).
`static URI`	`NON_ESSENTIAL_ACTIVATOR` An activator which is not necessary for an enzymatic reaction, but whose presence will further increase enzymatic activity (SBO:0000462).
`static URI`	`NON_SPATIAL_CONTINUOUS_FRAMEWORK` Modelling approach where the quantities of participants are considered continuous, and represented by real values (SBO:0000293).
`static URI`	`NON_SPATIAL_DISCRETE_FRAMEWORK` Modelling approach where the quantities of participants are considered discrete, and represented by integer values (SBO:0000295).
`static URI`	`NOT` The preceding event or participating entity cannot participate to the control (SBO:0000238).
`static URI`	`OCCURRING_ENTITY_REPRESENTATION` Representation of an entity that manifests, unfolds or develops through time, such as a discrete event, or a mutual or reciprocal action or influence that happens between participating physical entities, and/or other occurring entities (SBO:0000231).
`static URI`	`OMITTED_PROCESS` One or more processes that are not represented in certain representations or interpretations of a model (SBO:0000397).
`static URI`	`OR` Any of the preceding events or participating entities are necessary to perform the control (SBO:0000174).
`static URI`	`OXIDATION` Chemical process during which a molecular entity loses electrons (SBO:0000201).
`static URI`	`PALMITOYLATION` Addition of a palmitoyl group (CH3-[CH2]14-CO-) to a chemical entity (SBO:0000218).
`static URI`	`PARTICIPANT_ROLE` The function of a physical or conceptual entity, that is its role, in the execution of an event or process (SBO:0000003).
`static URI`	`PETRI_NET_TRANSITION` A process that can modify the state of petri net 'places' (SBO:0000591).
`static URI`	`PHENOTYPE` A biochemical network can generate phenotypes or affects biological processes (SBO:0000358).
`static URI`	`PHOSPHORYLATION` Addition of a phosphate group (-H2PO4) to a chemical entity (SBO:0000216).
`static URI`	`POSITIONAL_RELATIONSHIP` The connectedness between entities as related by their position (SBO:0000413).
`static URI`	`POTENTIATOR` Substance that increases the probability of a chemical reaction without itself being consumed or transformed by the reaction (SBO:0000021).
`static URI`	`PRENYLATION` Addition of a prenyl group (generic sense) to a chemical entity (SBO:0000221).
`static URI`	`PROCESS` A sequential series of actions, motions, or occurrences, such as chemical reactions, that affect one or more entities in a phenomenologically characteristic manner (SBO:0000375).
`static URI`	`PRODUCT` Substance that is produced in a reaction (SBO:0000011).
`static URI`	`PRODUCTION` Generation of a material or conceptual entity (SBO:0000393).
`static URI`	`PROMOTER` A region of DNA to which various transcription factors and RNA polymerase must bind in order to initiate transcription for a gene (SBO:0000598).
`static URI`	`PROTEIN_COMPLEX_FORMATION` The process by which two or more proteins interact non-covalently to form a protein complex (SBO:0000526).
`static URI`	`PROTONATION` Addition of a proton (H+) to a chemical entity (SBO:0000212).
`static URI`	`REACTANT` Substance consumed by a chemical reaction (SBO:0000010).
`static URI`	`REDOX_REACTION` Chemical process in which atoms have their oxidation number (oxidation state) changed (SBO:0000200).
`static URI`	`REDUCTION` Chemical process in which a molecular entity gain electrons (SBO:0000202).
`static URI`	`RELATIONSHIP` Connectedness between entities and/or interactions representing their relatedness or influence (SBO:0000374).
`static URI`	`REMOVAL_OF_A_CHEMICAL_GROUP` Covalent reaction that results in the removal of a chemical group from a molecule (SBO:0000211).
`static URI`	`SIDE_PRODUCT` A substance that is produced in a chemical reaction but is not itself the primary product or focus of that reaction (SBO:0000603).
`static URI`	`SIDE_SUBSTRATE` A substance that is consumed in a chemical reaction but is not itself the primary substrate or focus of that reaction (SBO:0000604).
`static URI`	`SILENCER` A silencer is a modifier which acts in a manner that completely prevents an event or process from occurring (SBO:0000597).
`static URI`	`SPATIAL_CONTINUOUS_FRAMEWORK` Modelling approach where the quantities of participants are considered continuous, and represented by real values (SBO:0000292).
`static URI`	`SPATIAL_DISCRETE_FRAMEWORK` Modelling approach where the quantities of participants are considered discrete, and represented by integer values (SBO:0000294).
`static URI`	`SPECIFIC_ACTIVATOR` An essential activator that affects the apparent value of the specificity constant (SBO:0000533).
`static URI`	`STATE_VARIABLE_ASSIGNMENT` Assignment of a state or a value to a state variable, characteristic or property, of a biological entity (SBO:0000464).
`static URI`	`STIMULATED` Conceptual or material entity that is the object of a stimulation process, and is acted upon by a stimulator (SBO:0000643).
`static URI`	`STIMULATION` Positive modulation of the execution of a process (SBO:0000170).
`static URI`	`STIMULATOR` Substance that accelerates the velocity of a chemical reaction without itself being consumed or transformed (SBO:0000459).
`static URI`	`SUBSTRATE` Molecule which is acted upon by an enzyme (SBO:0000015).
`static URI`	`SULFATION` Addition of a sulfate group (SO4--) to a chemical entity (SBO:0000220).
`static URI`	`SYNTHETIC_LETHALITY` Synthetic lethality is said to have occurred where gene mutations, each of which map to a separate locus, fail to complement in an offspring to correct a phenotype, as would be expected (SBO:0000502).
`static URI`	`SYSTEMS_DESCRIPTION_PARAMETER` A value, numerical or symbolic, that defines certain characteristics of systems or system functions, or is necessary in their derivation.
`static URI`	`TEMPLATE` An entity that acts as the starting material for genetic production (SBO:0000645).
`static URI`	`TRANS` Positional relationship between entities on different sides, or strands (SBO:0000415).
`static URI`	`TRANSAMINATION` The transfer of an amino group between two molecules (SBO:0000403).
`static URI`	`TRANSCELLULAR_MEMBRANE_EFFLUX_REACTION` A transport reaction which results in the removal of the transported entity from the cell (SBO:0000588).
`static URI`	`TRANSCELLULAR_MEMBRANE_INFLUX_REACTION` A transport reaction which results in the entry of the transported entity, into the cell (SBO:0000587).
`static URI`	`TRANSCRIPTION` Process through which a DNA sequence is copied to produce a complementary RNA (SBO:0000183).
`static URI`	`TRANSFER_OF_A_CHEMICAL_GROUP` Covalent reaction that results in the transfer of a chemical group from one molecule to another (SBO:0000402).
`static URI`	`TRANSLATION` Process in which a polypeptide chain is produced from a messenger RNA (SBO:0000184).
`static URI`	`TRANSPORT_REACTION` Movement of a physical entity without modification of the structure of the entity (SBO:0000185).
`static URI`	`UBIQUITINATION` Covalent linkage to the protein ubiquitin (SBO:0000224).
`static URI`	`UNCERTAIN_PROCESS` An equivocal or conjectural process, whose existence is assumed but not proven (SBO:0000396).
`static URI`	`XOR` Only one of the preceding events or participating entities can perform the control at one time (SBO:0000175).

Constructor Summary

Constructors
Constructor and Description

SystemsBiologyOntology()
Construct an SBO ontology object and read the OBO definition file, if it has not been constructed.

Constructors
Constructor and Description
`SystemsBiologyOntology()` Construct an SBO ontology object and read the OBO definition file, if it has not been constructed.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`Set<String>`	`getDescendantNamesOf(String parentId)` Returns the set of child names that are descendants of a given parent ID.
`Set<String>`	`getDescendantNamesOf(URI parentURI)` Returns the set of child names that are descendants of a given parent URI.
`Set<String>`	`getDescendantsOf(String parentId)` Returns the set of child IDs that are descendants of the given parent ID.
`Set<String>`	`getDescendantsOf(URI parentURI)` Returns the set of child IDs that are descendants of the given parent URI.
`Set<URI>`	`getDescendantURIsOf(String parentId)` Returns the set of child URIs that are descendants of the given parent ID.
`Set<URI>`	`getDescendantURIsOf(URI parentURI)` Returns the set of child URIs that are descendants of the given parent URI.
`String`	`getId(String stanzaName)` Returns the ID of the stanza whose name matches the given stanza name.
`String`	`getId(URI termURI)` Returns the extracted ID of the given term's URI.
`String`	`getName(String stanzaId)` Returns the name field of the stanza that matches the ID referred by the given stanza URI.
`String`	`getName(URI termURI)` Returns the name field of the stanza that matches the ID for the given term URI.
`URI`	`getURIbyId(String stanzaId)` Creates a URI by appending the given stanza ID to the end of the Systems Biology Ontology (SBO) namespace，i.e.
`URI`	`getURIbyName(String stanzaName)` Returns the URI that is composed of the Systems Biology Ontology (SBO) namespace, "http://identifiers.org/biomodels.sbo/", followed by the ID of an SBO term, of the stanza whose name matches the given name.
`boolean`	`isDescendantOf(String Id1, String Id2)` Returns `true` if the stanza with Id1 is a descendant of the stanza with Id2.
`boolean`	`isDescendantOf(URI childURI, URI parentURI)` Returns `true` if the stanza with childURI is a descendant of the stanza with parentURI.

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

- Field Detail
  - NAMESPACE
```
public static final URI NAMESPACE
```
    Namespace of the Systems Biology Ontology (http://identifiers.org/biomodels.sbo/).
  - MODELING_FRAMEWORK
```
public static final URI MODELING_FRAMEWORK
```
    Set of assumptions that underlay a mathematical description (SBO:0000004).
  - CONTINUOUS_FRAMEWORK
```
public static final URI CONTINUOUS_FRAMEWORK
```
    Modelling approach where the quantities of participants are considered continuous, and represented by real values (SBO:0000062). The associated simulation methods make use of differential equations.
  - NON_SPATIAL_CONTINUOUS_FRAMEWORK
```
public static final URI NON_SPATIAL_CONTINUOUS_FRAMEWORK
```
    Modelling approach where the quantities of participants are considered continuous, and represented by real values (SBO:0000293). The associated simulation methods make use of differential equations. The models do not take into account the distribution of the entities and describe only the temporal fluxes.
  - SPATIAL_CONTINUOUS_FRAMEWORK
```
public static final URI SPATIAL_CONTINUOUS_FRAMEWORK
```
    Modelling approach where the quantities of participants are considered continuous, and represented by real values (SBO:0000292). The associated simulation methods make use of differential equations. The models take into account the distribution of the entities and describe the spatial fluxes.
  - DISCRETE_FRAMEWORK
```
public static final URI DISCRETE_FRAMEWORK
```
    Modelling approach where the quantities of participants are considered discrete, and represented by integer values (SBO:0000063). The associated simulation methods can be deterministic or stochastic.
  - NON_SPATIAL_DISCRETE_FRAMEWORK
```
public static final URI NON_SPATIAL_DISCRETE_FRAMEWORK
```
    Modelling approach where the quantities of participants are considered discrete, and represented by integer values (SBO:0000295). The associated simulation methods can be deterministic or stochastic.The models do not take into account the distribution of the entities and describe only the temporal fluxes.
  - SPATIAL_DISCRETE_FRAMEWORK
```
public static final URI SPATIAL_DISCRETE_FRAMEWORK
```
    Modelling approach where the quantities of participants are considered discrete, and represented by integer values (SBO:0000294). The associated simulation methods can be deterministic or stochastic. The models take into account the distribution of the entities and describe the spatial fluxes.
  - FLUX_BALANCE_FRAMEWORK
```
public static final URI FLUX_BALANCE_FRAMEWORK
```
    Modelling approach, typically used for metabolic models, where the flow of metabolites (flux) through a network can be calculated (SBO:0000624). This approach will generally produce a set of solutions (solution space), which may be reduced using objective functions and constraints on individual fluxes.
  - LOGICAL_FRAMEWORK
```
public static final URI LOGICAL_FRAMEWORK
```
    Modelling approach, pioneered by Rene Thomas and Stuart Kaufman, where the evolution of a system is described by the transitions between discrete activity states of "genes" that control each other (SBO:0000234).
  - BOOLEAN_LOGICAL_FRAMEWORK
```
public static final URI BOOLEAN_LOGICAL_FRAMEWORK
```
    Equationally defined algebraic framework usually interpreted as a two-valued logic using the basic Boolean operations (conjunction, disjunction and negation), together with the constants '0' and '1' denoting false and true values, respectively (SBO:0000547).
  - OCCURRING_ENTITY_REPRESENTATION
```
public static final URI OCCURRING_ENTITY_REPRESENTATION
```
    Representation of an entity that manifests, unfolds or develops through time, such as a discrete event, or a mutual or reciprocal action or influence that happens between participating physical entities, and/or other occurring entities (SBO:0000231).
  - BIOLOGICAL_ACTIVITY
```
public static final URI BIOLOGICAL_ACTIVITY
```
    The potential action that a biological entity has on other entities (SBO:0000412). Example are enzymatic activity, binding activity etc.
  - PROCESS
```
public static final URI PROCESS
```
    A sequential series of actions, motions, or occurrences, such as chemical reactions, that affect one or more entities in a phenomenologically characteristic manner (SBO:0000375).
  - BIOCHEMICAL_OR_TRANSPORT_REACTION
```
public static final URI BIOCHEMICAL_OR_TRANSPORT_REACTION
```
    An event involving one or more physical entities that modifies the structure, location or free energy of at least one of the participants (SBO:0000167).
  - BIOCHEMICAL_REACTION
```
public static final URI BIOCHEMICAL_REACTION
```
    An event involving one or more chemical entities that modifies the electrochemical structure of at least one of the participants. (SBO:0000176)
  - ACID_BASE_REACTION
```
public static final URI ACID_BASE_REACTION
```
    Chemical reaction where a proton is given by a compound, the acid, to another one, the base (Brønsted-Lowry definition) (SBO:0000208). An alternative, more general, definition is a reaction where a compound, the base, gives a pair of electrons to another, the acid (Lewis definition).
  - DEPROTONATION
```
public static final URI DEPROTONATION
```
    Removal of a proton (hydrogen ion H+) from a chemical entity (SBO:0000213).
  - PROTONATION
```
public static final URI PROTONATION
```
    Addition of a proton (H+) to a chemical entity (SBO:0000212).
  - CONFORMATIONAL_TRANSITION
```
public static final URI CONFORMATIONAL_TRANSITION
```
    Biochemical reaction that does not result in the modification of covalent bonds of reactants, but rather modifies the conformation of some reactants, that is the relative position of their atoms in space (SBO:0000181).
  - CONVERSION
```
public static final URI CONVERSION
```
    Biochemical reaction that results in the modification of some covalent bonds (SBO:0000182).
  - ADDITION_OF_A_CHEMICAL_GROUP
```
public static final URI ADDITION_OF_A_CHEMICAL_GROUP
```
    Covalent reaction that results in the addition of a chemical group on a molecule (SBO:0000210).
  - ACETYLATION
```
public static final URI ACETYLATION
```
    Addition of an acetyl group (-COCH3) to a chemical entity (SBO:0000215).
  - GLYCOSYLATION
```
public static final URI GLYCOSYLATION
```
    Addition of a saccharide group to a chemical entity (SBO:0000217).
  - HYDROXYLATION
```
public static final URI HYDROXYLATION
```
    Addition of an hydroxyl group (-OH) to a chemical entity (SBO:0000233).
  - METHYLATION
```
public static final URI METHYLATION
```
    Addition of a methyl group (-CH3) to a chemical entity (SBO:0000214).
  - MYRISTOYLATION
```
public static final URI MYRISTOYLATION
```
    Addition of a myristoyl (CH3-[CH2]12-CO-) to a chemical entity (SBO:0000219).
  - PALMITOYLATION
```
public static final URI PALMITOYLATION
```
    Addition of a palmitoyl group (CH3-[CH2]14-CO-) to a chemical entity (SBO:0000218).
  - PHOSPHORYLATION
```
public static final URI PHOSPHORYLATION
```
    Addition of a phosphate group (-H2PO4) to a chemical entity (SBO:0000216).
  - PRENYLATION
```
public static final URI PRENYLATION
```
    Addition of a prenyl group (generic sense) to a chemical entity (SBO:0000221).
  - FARNESYLATION
```
public static final URI FARNESYLATION
```
    Addition of a farnesyl group (CH2-CH=C(CH3)-CH2-CH2-CH=C(CH3)-CH2-CH2-CH=C(CH3)2) to a chemical entity (SBO:0000222).
  - GERANYLGERANYLATION
```
public static final URI GERANYLGERANYLATION
```
    Addition of a geranylgeranyl group (CH2-CH=C(CH3)-CH2-CH2-CH=C(CH3)-CH2-CH2-CH=C(CH3)-CH2-CH2-CH=C(CH3)2) to a chemical entity (SBO:0000223).
  - SULFATION
```
public static final URI SULFATION
```
    Addition of a sulfate group (SO4--) to a chemical entity (SBO:0000220).
  - UBIQUITINATION
```
public static final URI UBIQUITINATION
```
    Covalent linkage to the protein ubiquitin (SBO:0000224).
  - CLEAVAGE
```
public static final URI CLEAVAGE
```
    Rupture of a covalent bond resulting in the conversion of one physical entity into several physical entities (SBO:0000178).
  - REMOVAL_OF_A_CHEMICAL_GROUP
```
public static final URI REMOVAL_OF_A_CHEMICAL_GROUP
```
    Covalent reaction that results in the removal of a chemical group from a molecule (SBO:0000211).
  - DEAMINATION
```
public static final URI DEAMINATION
```
    Removal of an amine group from a molecule, often under the addition of water (SBO:0000401).
  - DECARBONYLATION
```
public static final URI DECARBONYLATION
```
    Removal of a carbonyl group (-C-O-) from a molecule, usually as carbon monoxide (SBO:0000400).
  - DECARBOXYLATION
```
public static final URI DECARBOXYLATION
```
    A process in which a carboxyl group (COOH) is removed from a molecule as carbon dioxide (SBO:0000399).
  - DEPHOSPHORYLATION
```
public static final URI DEPHOSPHORYLATION
```
    Removal of a phosphate group (-H2PO4) from a chemical entity (SBO:0000330).
  - TRANSFER_OF_A_CHEMICAL_GROUP
```
public static final URI TRANSFER_OF_A_CHEMICAL_GROUP
```
    Covalent reaction that results in the transfer of a chemical group from one molecule to another (SBO:0000402).
  - TRANSAMINATION
```
public static final URI TRANSAMINATION
```
    The transfer of an amino group between two molecules (SBO:0000403). Commonly in biology this is restricted to reactions between an amino acid and an alpha-keto carbonic acid, whereby the reacting amino acid is converted into an alpha-keto acid, and the alpha-keto acid reactant into an amino acid.
  - DEGRADATION
```
public static final URI DEGRADATION
```
    Complete disappearance of a physical entity (SBO:0000179).
  - DISSOCIATION
```
public static final URI DISSOCIATION
```
    Transformation of a non-covalent complex that results in the formation of several independent biochemical entities (SBO:0000180).
  - HYDROLYSIS
```
public static final URI HYDROLYSIS
```
    Decomposition of a compound by reaction with water, where the hydroxyl and H groups are incorporated into different products (SBO:0000376).
  - IONISATION
```
public static final URI IONISATION
```
    Ionization is the physical process of converting an atom or molecule into an ion by changing the difference between the number of protons and electrons (SBO:0000209).
  - ISOMERISATION
```
public static final URI ISOMERISATION
```
    A reaction in which the principal reactant and principal product are isomers of each other (SBO:0000377).
  - NON_COVALENT_BINDING
```
public static final URI NON_COVALENT_BINDING
```
    Interaction between several biochemical entities that results in the formation of a non-covalent complex (SBO:0000177).
  - REDOX_REACTION
```
public static final URI REDOX_REACTION
```
    Chemical process in which atoms have their oxidation number (oxidation state) changed (SBO:0000200).
  - OXIDATION
```
public static final URI OXIDATION
```
    Chemical process during which a molecular entity loses electrons (SBO:0000201).
  - REDUCTION
```
public static final URI REDUCTION
```
    Chemical process in which a molecular entity gain electrons (SBO:0000202).
  - TRANSPORT_REACTION
```
public static final URI TRANSPORT_REACTION
```
    Movement of a physical entity without modification of the structure of the entity (SBO:0000185).
  - TRANSCELLULAR_MEMBRANE_EFFLUX_REACTION
```
public static final URI TRANSCELLULAR_MEMBRANE_EFFLUX_REACTION
```
    A transport reaction which results in the removal of the transported entity from the cell (SBO:0000588).
  - TRANSCELLULAR_MEMBRANE_INFLUX_REACTION
```
public static final URI TRANSCELLULAR_MEMBRANE_INFLUX_REACTION
```
    A transport reaction which results in the entry of the transported entity, into the cell (SBO:0000587).
  - BIOLOGICAL_EFFECT_OF_A_PERTURBATION
```
public static final URI BIOLOGICAL_EFFECT_OF_A_PERTURBATION
```
    Biochemical networks can be affected by external influences (SBO:0000357). Those influences can be well-defined physical perturbations, such as a light pulse, or a change in temperature but also more complex of not well defined phenomena, for instance a biological process, an experimental setup, or a mutation.
  - COMPOSITE_BIOCHEMICAL_PROCESS
```
public static final URI COMPOSITE_BIOCHEMICAL_PROCESS
```
    Process that involves the participation of chemical or biological entities and is composed of several elementary steps or reactions (SBO:0000205).
  - DNA_REPLICATION
```
public static final URI DNA_REPLICATION
```
    Process in which a DNA duplex is transformed into two identical DNA duplexes (SBO:0000204).
  - GENETIC_PRODUCTION
```
public static final URI GENETIC_PRODUCTION
```
    A composite biochemical process through which a gene sequence is fully converted into mature gene products (SBO:0000589). These gene products may include RNA species as well as proteins, and the process encompasses all intermediate steps required to generate the active form of the gene product.
  - TRANSCRIPTION
```
public static final URI TRANSCRIPTION
```
    Process through which a DNA sequence is copied to produce a complementary RNA (SBO:0000183).
  - TRANSLATION
```
public static final URI TRANSLATION
```
    Process in which a polypeptide chain is produced from a messenger RNA (SBO:0000184).
  - ENCAPSULATING_PROCESS
```
public static final URI ENCAPSULATING_PROCESS
```
    An aggregation of interactions and entities into a single process (SBO:0000395).
  - MOLECULAR_OR_GENETIC_INTERACTION
```
public static final URI MOLECULAR_OR_GENETIC_INTERACTION
```
    Mutual or reciprocal action or influence between molecular entities (SBO:0000342).
  - GENETIC_INTERACTION
```
public static final URI GENETIC_INTERACTION
```
    A phenomenon whereby an observed phenotype, qualitative or quantative, is not explainable by the simple additive effects of the individual gene pertubations alone (SBO:0000343). Genetic interaction between perturbed genes is usually expected to generate a 'defective' phenotype. The level of defectiveness is often used to sub-classify this phenomenon.
  - GENETIC_ENHANCEMENT
```
public static final URI GENETIC_ENHANCEMENT
```
    Genetic enhancement is said to have occurred when the phenotypic effect of an initial mutation in a gene is made increasingly severe by a subsequent mutation (SBO:0000501).
  - GENETIC_SUPPRESSION
```
public static final URI GENETIC_SUPPRESSION
```
    Genetic suppression is said to have occurred when the phenotypic effect of an initial mutation in a gene is less severe, or entirely negated, by a subsequent mutation (SBO:0000500).
  - SYNTHETIC_LETHALITY
```
public static final URI SYNTHETIC_LETHALITY
```
    Synthetic lethality is said to have occurred where gene mutations, each of which map to a separate locus, fail to complement in an offspring to correct a phenotype, as would be expected (SBO:0000502).
  - MOLECULAR_INTERACTION
```
public static final URI MOLECULAR_INTERACTION
```
    Relationship between molecular entities, based on contacts, direct or indirect (SBO:0000344).
  - PROTEIN_COMPLEX_FORMATION
```
public static final URI PROTEIN_COMPLEX_FORMATION
```
    The process by which two or more proteins interact non-covalently to form a protein complex (SBO:0000526).
  - OMITTED_PROCESS
```
public static final URI OMITTED_PROCESS
```
    One or more processes that are not represented in certain representations or interpretations of a model (SBO:0000397).
  - PHENOTYPE
```
public static final URI PHENOTYPE
```
    A biochemical network can generate phenotypes or affects biological processes (SBO:0000358). Such processes can take place at different levels and are independent of the biochemical network itself.
  - STATE_VARIABLE_ASSIGNMENT
```
public static final URI STATE_VARIABLE_ASSIGNMENT
```
    Assignment of a state or a value to a state variable, characteristic or property, of a biological entity (SBO:0000464).
  - PETRI_NET_TRANSITION
```
public static final URI PETRI_NET_TRANSITION
```
    A process that can modify the state of petri net 'places' (SBO:0000591).
  - UNCERTAIN_PROCESS
```
public static final URI UNCERTAIN_PROCESS
```
    An equivocal or conjectural process, whose existence is assumed but not proven (SBO:0000396).
  - RELATIONSHIP
```
public static final URI RELATIONSHIP
```
    Connectedness between entities and/or interactions representing their relatedness or influence (SBO:0000374).
  - CONTROL
```
public static final URI CONTROL
```
    Modification of the execution of an event or a process (SBO:0000168).
  - ALLOSTERIC_CONTROL
```
public static final URI ALLOSTERIC_CONTROL
```
    Regulation of the influence of a reaction participant by binding an effector to a binding site of the participant different of the site of the participant conveying the influence (SBO:0000239).
  - CONSUMPTION
```
public static final URI CONSUMPTION
```
    Decrease in amount of a material or conceptual entity (SBO:0000394).
  - INHIBITION
```
public static final URI INHIBITION
```
    Negative modulation of the execution of a process (SBO:0000169).
  - ABSOLUTE_INHIBITION
```
public static final URI ABSOLUTE_INHIBITION
```
    Control that precludes the execution of a process (SBO:0000407).
  - PRODUCTION
```
public static final URI PRODUCTION
```
    Generation of a material or conceptual entity (SBO:0000393).
  - STIMULATION
```
public static final URI STIMULATION
```
    Positive modulation of the execution of a process (SBO:0000170).
  - ABSOLUTE_STIMULATION
```
public static final URI ABSOLUTE_STIMULATION
```
    Control that always triggers the controlled process (SBO:0000411).
  - CATALYSIS
```
public static final URI CATALYSIS
```
    Modification of the velocity of a reaction by lowering the energy of the transition state (SBO:0000172).
  - NECESSARY_STIMULATION
```
public static final URI NECESSARY_STIMULATION
```
    Control that is necessary to the execution of a process (SBO:0000171).
  - EQUIVALENCE
```
public static final URI EQUIVALENCE
```
    Term to signify those material or conceptual entities that are identical in some respect within a frame of reference (SBO:0000392).
  - LOGICAL_COMBINATION
```
public static final URI LOGICAL_COMBINATION
```
    Combining the influence of several entities or events in a unique influence (SBO:0000237).
  - AND
```
public static final URI AND
```
    All the preceding events or participating entities are necessary to perform the control (SBO:0000173).
  - NOT
```
public static final URI NOT
```
    The preceding event or participating entity cannot participate to the control (SBO:0000238).
  - OR
```
public static final URI OR
```
    Any of the preceding events or participating entities are necessary to perform the control (SBO:0000174).
  - XOR
```
public static final URI XOR
```
    Only one of the preceding events or participating entities can perform the control at one time (SBO:0000175).
  - LOGICAL_RELATIONSHIP
```
public static final URI LOGICAL_RELATIONSHIP
```
    Relationship between entities (material or conceptual) and logical operators, or between logical operators themselves (SBO:0000398).
  - POSITIONAL_RELATIONSHIP
```
public static final URI POSITIONAL_RELATIONSHIP
```
    The connectedness between entities as related by their position (SBO:0000413).
  - CIS
```
public static final URI CIS
```
    Positional relationship between entities on the same strand (e.g. in DNA), or on the same side (SBO:0000414).
  - CONTAINMENT
```
public static final URI CONTAINMENT
```
    An entity that is a subset of another entity or object (SBO:0000469).
  - TRANS
```
public static final URI TRANS
```
    Positional relationship between entities on different sides, or strands (SBO:0000415).
  - PARTICIPANT_ROLE
```
public static final URI PARTICIPANT_ROLE
```
    The function of a physical or conceptual entity, that is its role, in the execution of an event or process (SBO:0000003).
  - FUNCTIONAL_COMPARTMENT
```
public static final URI FUNCTIONAL_COMPARTMENT
```
    Logical or physical subset of the event space that contains pools, that is sets of participants considered identical when it comes to the event they are involved into (SBO:0000289). A compartment can have any number of dimensions, including 0, and be of any size including null.
  - MODIFIER
```
public static final URI MODIFIER
```
    Substance that changes the velocity of a process without itself being consumed or transformed by the reaction (SBO:0000019).
  - DUAL_ACTIVITY_MODIFIER
```
public static final URI DUAL_ACTIVITY_MODIFIER
```
    A modifier that can exhibit either inhibitory or stimulatory effects on a process depending on the context in which it occurs (SBO:0000595). For example, the observed effect may be dependent upon the concentration of the modifier.
  - INHIBITOR
```
public static final URI INHIBITOR
```
    Substance that decreases the probability of a chemical reaction without itself being consumed or transformed by the reaction (SBO:0000020).
  - COMPETITIVE_INHIBITOR
```
public static final URI COMPETITIVE_INHIBITOR
```
    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 (SBO:0000206).
  - NON_COMPETITIVE_INHIBITOR
```
public static final URI NON_COMPETITIVE_INHIBITOR
```
    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 (SBO:0000207).
  - SILENCER
```
public static final URI SILENCER
```
    A silencer is a modifier which acts in a manner that completely prevents an event or process from occurring (SBO:0000597). For example, a silencer in gene expression is usually a transcription factor that binds a DNA sequence in such a way as to completely prevent the binding of RNA polymerase, and thus fully suppresses transcription.
  - MODIFIER_OF_UNKNOWN_ACTIVITY
```
public static final URI MODIFIER_OF_UNKNOWN_ACTIVITY
```
    A modifier whose activity is not known or has not been specified (SBO:0000596).
  - STIMULATOR
```
public static final URI STIMULATOR
```
    Substance that accelerates the velocity of a chemical reaction without itself being consumed or transformed (SBO:0000459).
  - CATALYST
```
public static final URI CATALYST
```
    Substance that accelerates the velocity of a chemical reaction without itself being consumed or transformed (SBO:0000013). This effect is achieved by lowering the free energy of the transition state.
  - ENZYMATIC_CATALYST
```
public static final URI ENZYMATIC_CATALYST
```
    A substance that accelerates the velocity of a chemical reaction without itself being consumed or transformed, by lowering the free energy of the transition state (SBO:0000460). The substance acting as a catalyst is an enzyme.
  - ESSENTIAL_ACTIVATOR
```
public static final URI ESSENTIAL_ACTIVATOR
```
    A substance that is absolutely required for occurrence and stimulation of a reaction (SBO:0000461).
  - BINDING_ACTIVATOR
```
public static final URI BINDING_ACTIVATOR
```
    An essential activator that affects the apparent value of the Michaelis constant(s) (SBO:0000535).
  - CATALYTIC_ACTIVATOR
```
public static final URI CATALYTIC_ACTIVATOR
```
    An essential activator that affects the apparent value of the catalytic constant (SBO:0000534).
  - SPECIFIC_ACTIVATOR
```
public static final URI SPECIFIC_ACTIVATOR
```
    An essential activator that affects the apparent value of the specificity constant (SBO:0000533). Mechanistically, the activator would need to be bound before reactant and product binding can take place.
  - NON_ESSENTIAL_ACTIVATOR
```
public static final URI NON_ESSENTIAL_ACTIVATOR
```
    An activator which is not necessary for an enzymatic reaction, but whose presence will further increase enzymatic activity (SBO:0000462).
  - POTENTIATOR
```
public static final URI POTENTIATOR
```
    Substance that increases the probability of a chemical reaction without itself being consumed or transformed by the reaction (SBO:0000021). This effect is achieved by increasing the difference of free energy between the reactant(s) and the product(s).
  - NEUTRAL_PARTICIPANT
```
public static final URI NEUTRAL_PARTICIPANT
```
    A participant whose presence does not alter the velocity of a process or event (SBO:0000594).
  - PRODUCT
```
public static final URI PRODUCT
```
    Substance that is produced in a reaction (SBO:0000011). 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.
  - SIDE_PRODUCT
```
public static final URI SIDE_PRODUCT
```
    A substance that is produced in a chemical reaction but is not itself the primary product or focus of that reaction (SBO:0000603). Examples include, but are not limited to, currency compounds such as ATP, NADPH and protons.
  - PROMOTER
```
public static final URI PROMOTER
```
    A region of DNA to which various transcription factors and RNA polymerase must bind in order to initiate transcription for a gene (SBO:0000598).
  - REACTANT
```
public static final URI REACTANT
```
    Substance consumed by a chemical reaction (SBO:0000010). 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.
  - INTERACTOR
```
public static final URI INTERACTOR
```
    Entity participating in a physical or functional interaction (SBO:0000336).
  - SUBSTRATE
```
public static final URI SUBSTRATE
```
    Molecule which is acted upon by an enzyme (SBO:0000015). The substrate binds with the enzyme's active site, and the enzyme catalyzes a chemical reaction involving the substrate.
  - SIDE_SUBSTRATE
```
public static final URI SIDE_SUBSTRATE
```
    A substance that is consumed in a chemical reaction but is not itself the primary substrate or focus of that reaction (SBO:0000604). Examples include, but are not limited to, currency compounds such as ATP, NADPH and protons.
  - INHIBITED
```
public static final URI INHIBITED
```
    Conceptual or material entity that is the object of an inhibition process, and is acted upon by an inhibitor (SBO:0000642).
  - STIMULATED
```
public static final URI STIMULATED
```
    Conceptual or material entity that is the object of a stimulation process, and is acted upon by a stimulator (SBO:0000643).
  - MODIFIED
```
public static final URI MODIFIED
```
    Conceptual or material entity that is the object of a modification process, and is acted upon by a modifier (SBO:0000644).
  - TEMPLATE
```
public static final URI TEMPLATE
```
    An entity that acts as the starting material for genetic production (SBO:0000645).
  - SYSTEMS_DESCRIPTION_PARAMETER
```
public static final URI SYSTEMS_DESCRIPTION_PARAMETER
```
    A value, numerical or symbolic, that defines certain characteristics of systems or system functions, or is necessary in their derivation. (SBO:0000545).
  - GROWTH_RATE
```
public static final URI GROWTH_RATE
```
    A measure of the rate of growth of an organism, usually in culture. This can be expressed as increase in cell number or, more usually as an increase in dry weight of cells (grams), measured over a unit time period. Usually expressed as hour -1. (SBO:0000610).
- Constructor Detail
  - SystemsBiologyOntology
```
public SystemsBiologyOntology()
```
    Construct an SBO ontology object and read the OBO definition file, if it has not been constructed.
- Method Detail
  - getId
```
public final String getId(URI termURI)
```
    Returns the extracted ID of the given term's URI.
    
    Parameters:
    
    termURI - the identity URI of a term
    
    Returns:
    
    the extracted ID of the given term's URI
  - getId
```
public final String getId(String stanzaName)
```
    Returns the ID of the stanza whose name matches the given stanza name. If multiple matches are found, only the first matching one is returned.
    
    Parameters:
    
    stanzaName - the name of a stanza
    
    Returns:
    
    the matching stanza ID, or null if no match is found.
  - getName
```
public final String getName(URI termURI)
```
    Returns the name field of the stanza that matches the ID for the given term URI.
    
    Parameters:
    
    termURI - the identity URI of a term
    
    Returns:
    
    the name field of the stanza whose ID is referred to by the given term URI.
  - getName
```
public final String getName(String stanzaId)
```
    Returns the name field of the stanza that matches the ID referred by the given stanza URI.
    
    Parameters:
    
    stanzaId - the ID of a stanza
    
    Returns:
    
    the name field of the stanza that matches the ID referred by the given stanza URI, or null if this no match was found
  - getURIbyName
```
public final URI getURIbyName(String stanzaName)
```
    Returns the URI that is composed of the Systems Biology Ontology (SBO) namespace, "http://identifiers.org/biomodels.sbo/", followed by the ID of an SBO term, of the stanza whose name matches the given name. If multiple matches are found, only the first matching one is returned.
    
    Parameters:
    
    stanzaName - the name of a term
    
    Returns:
    
    the URI of the given SBO name
  - getURIbyId
```
public final URI getURIbyId(String stanzaId)
```
    Creates a URI by appending the given stanza ID to the end of the Systems Biology Ontology (SBO) namespace，i.e. "http://identifiers.org/biomodels.sbo/".
    
    Parameters:
    
    stanzaId - the ID of a stanza
    
    Returns:
    
    the created URI
  - isDescendantOf
```
public final boolean isDescendantOf(URI childURI,
                                    URI parentURI)
```
    Returns true if the stanza with childURI is a descendant of the stanza with parentURI. This method first extracts IDs for the child and parent, and then passes them to isDescendantOf(String, String).
    
    Parameters:
    
    childURI - the URI of the child stanza
    
    parentURI - the URI of the parent stanza
    
    Returns:
    
    true if the stanza with childURI is a descendant of the stanza with parentURI, or false otherwise
  - isDescendantOf
```
public final boolean isDescendantOf(String Id1,
                                    String Id2)
```
    Returns true if the stanza with Id1 is a descendant of the stanza with Id2.
    
    Parameters:
    
    Id1 - ID of the first stanza
    
    Id2 - ID of the second stanza
    
    Returns:
    
    true if the stanza with Id1 is a descendant of the stanza with Id2, or false otherwise
  - getDescendantsOf
```
public Set<String> getDescendantsOf(String parentId)
```
    Returns the set of child IDs that are descendants of the given parent ID. This set excludes the given parent ID.
    
    Parameters:
    
    parentId - the ID of the parent stanza
    
    Returns:
    
    the set of child IDs that are descendants of the given parent ID
  - getDescendantsOf
```
public final Set<String> getDescendantsOf(URI parentURI)
```
    Returns the set of child IDs that are descendants of the given parent URI. This set excludes the given parent ID.
    
    Parameters:
    
    parentURI - the URI of the parent stanza
    
    Returns:
    
    the set of child IDs that are descendants of the given parent URI
  - getDescendantURIsOf
```
public final Set<URI> getDescendantURIsOf(String parentId)
```
    Returns the set of child URIs that are descendants of the given parent ID. This set excludes the given parent URI.
    
    Parameters:
    
    parentId - the ID of the parent stanza
    
    Returns:
    
    the set of child URIs that are descendants of the given parent ID.
  - getDescendantURIsOf
```
public final Set<URI> getDescendantURIsOf(URI parentURI)
```
    Returns the set of child URIs that are descendants of the given parent URI. This set excludes the given parent URI.
    
    Parameters:
    
    parentURI - the URI of the parent stanza
    
    Returns:
    
    the set of child URIs that are descendants of the given parent URI
  - getDescendantNamesOf
```
public final Set<String> getDescendantNamesOf(String parentId)
```
    Returns the set of child names that are descendants of a given parent ID. This set excludes the given parent name.
    
    Parameters:
    
    parentId - the ID of the parent stanza
    
    Returns:
    
    the set of child names that are descendants of a given parent ID.
  - getDescendantNamesOf
```
public final Set<String> getDescendantNamesOf(URI parentURI)
```
    Returns the set of child names that are descendants of a given parent URI. This set excludes the given parent name.
    
    Parameters:
    
    parentURI - the URI of the parent stanza
    
    Returns:
    
    the set of child names that are descendants of a given parent URI

Class SystemsBiologyOntology

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

NAMESPACE

MODELING_FRAMEWORK

CONTINUOUS_FRAMEWORK

NON_SPATIAL_CONTINUOUS_FRAMEWORK

SPATIAL_CONTINUOUS_FRAMEWORK

DISCRETE_FRAMEWORK

NON_SPATIAL_DISCRETE_FRAMEWORK

SPATIAL_DISCRETE_FRAMEWORK

FLUX_BALANCE_FRAMEWORK

LOGICAL_FRAMEWORK

BOOLEAN_LOGICAL_FRAMEWORK

OCCURRING_ENTITY_REPRESENTATION

BIOLOGICAL_ACTIVITY

PROCESS

BIOCHEMICAL_OR_TRANSPORT_REACTION

BIOCHEMICAL_REACTION

ACID_BASE_REACTION

DEPROTONATION

PROTONATION

CONFORMATIONAL_TRANSITION

CONVERSION

ADDITION_OF_A_CHEMICAL_GROUP

ACETYLATION

GLYCOSYLATION

HYDROXYLATION

METHYLATION

MYRISTOYLATION

PALMITOYLATION

PHOSPHORYLATION

PRENYLATION

FARNESYLATION

GERANYLGERANYLATION

SULFATION

UBIQUITINATION

CLEAVAGE

REMOVAL_OF_A_CHEMICAL_GROUP

DEAMINATION

DECARBONYLATION

DECARBOXYLATION

DEPHOSPHORYLATION

TRANSFER_OF_A_CHEMICAL_GROUP

TRANSAMINATION

DEGRADATION

DISSOCIATION

HYDROLYSIS

IONISATION

ISOMERISATION

NON_COVALENT_BINDING

REDOX_REACTION

OXIDATION

REDUCTION

TRANSPORT_REACTION

TRANSCELLULAR_MEMBRANE_EFFLUX_REACTION

TRANSCELLULAR_MEMBRANE_INFLUX_REACTION

BIOLOGICAL_EFFECT_OF_A_PERTURBATION

COMPOSITE_BIOCHEMICAL_PROCESS

DNA_REPLICATION

GENETIC_PRODUCTION

TRANSCRIPTION

TRANSLATION

ENCAPSULATING_PROCESS

MOLECULAR_OR_GENETIC_INTERACTION

GENETIC_INTERACTION

GENETIC_ENHANCEMENT

GENETIC_SUPPRESSION

SYNTHETIC_LETHALITY

MOLECULAR_INTERACTION

PROTEIN_COMPLEX_FORMATION

OMITTED_PROCESS

PHENOTYPE

STATE_VARIABLE_ASSIGNMENT

PETRI_NET_TRANSITION

UNCERTAIN_PROCESS

RELATIONSHIP