fr.curie.BiNoM.pathways.biopax
Interface biochemicalReaction

All Superinterfaces:

conversion, entity, interaction, physicalInteraction, com.ibm.adtech.jastor.Thing

All Known Subinterfaces:

transportWithBiochemicalReaction

All Known Implementing Classes:

biochemicalReactionImpl, transportWithBiochemicalReactionImpl

public interface biochemicalReaction
extends conversion, com.ibm.adtech.jastor.Thing

Interface for biochemicalReaction ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory to create instances of this interface.

(URI: http://www.biopax.org/release/biopax-level2.owl#biochemicalReaction)

RDF Schema Standard Properties
comment : Definition: A conversion interaction in which one or more entities (substrates) undergo covalent changes to become one or more other entities (products). The substrates of biochemical reactions are defined in terms of sums of species. This is convention in biochemistry, and, in principle, all of the EC reactions should be biochemical reactions. Examples: ATP + H2O = ADP + Pi Comment: In the example reaction above, ATP is considered to be an equilibrium mixture of several species, namely ATP4-, HATP3-, H2ATP2-, MgATP2-, MgHATP-, and Mg2ATP. Additional species may also need to be considered if other ions (e.g. Ca2+) that bind ATP are present. Similar considerations apply to ADP and to inorganic phosphate (Pi). When writing biochemical reactions, it is not necessary to attach charges to the biochemical reactants or to include ions such as H+ and Mg2+ in the equation. The reaction is written in the direction specified by the EC nomenclature system, if applicable, regardless of the physiological direction(s) in which the reaction proceeds. Polymerization reactions involving large polymers whose structure is not explicitly captured should generally be represented as unbalanced reactions in which the monomer is consumed but the polymer remains unchanged, e.g. glycogen + glucose = glycogen.^^http://www.w3.org/2001/XMLSchema#string

Field Summary

static com.hp.hpl.jena.rdf.model.Property	DELTA_DASH_GProperty The Jena Property for DELTA_DASH_G
static com.hp.hpl.jena.rdf.model.Property	DELTA_DASH_HProperty The Jena Property for DELTA_DASH_H
static com.hp.hpl.jena.rdf.model.Property	DELTA_DASH_SProperty The Jena Property for DELTA_DASH_S
static com.hp.hpl.jena.rdf.model.Property	EC_DASH_NUMBERProperty The Jena Property for EC_DASH_NUMBER
static com.hp.hpl.jena.rdf.model.Property	KEQProperty The Jena Property for KEQ
static com.hp.hpl.jena.rdf.model.Resource	TYPE The rdf:type for this ontology class

Fields inherited from interface fr.curie.BiNoM.pathways.biopax.conversion

LEFTProperty, RIGHTProperty, SPONTANEOUSProperty

Fields inherited from interface fr.curie.BiNoM.pathways.biopax.physicalInteraction

INTERACTION_DASH_TYPEProperty

Fields inherited from interface fr.curie.BiNoM.pathways.biopax.interaction

EVIDENCEProperty, PARTICIPANTSProperty

Fields inherited from interface fr.curie.BiNoM.pathways.biopax.entity

AVAILABILITYProperty, COMMENTProperty, DATA_DASH_SOURCEProperty, NAMEProperty, SHORT_DASH_NAMEProperty, SYNONYMSProperty, XREFProperty

Fields inherited from interface com.ibm.adtech.jastor.Thing

copyright

Method Summary

deltaGprimeO	addDELTA_DASH_G() Adds an anonymous value for the 'DELTA_DASH_G' property
void	addDELTA_DASH_G(deltaGprimeO DELTA_DASH_G) Adds a value for the 'DELTA_DASH_G' property
deltaGprimeO	addDELTA_DASH_G(com.hp.hpl.jena.rdf.model.Resource resource) Adds a value for the 'DELTA_DASH_G' property.
void	addDELTA_DASH_H(java.lang.Double DELTA_DASH_H) Add a 'DELTA_DASH_H' property value
void	addDELTA_DASH_S(java.lang.Double DELTA_DASH_S) Add a 'DELTA_DASH_S' property value
void	addEC_DASH_NUMBER(java.lang.String EC_DASH_NUMBER) Add a 'EC_DASH_NUMBER' property value
kPrime	addKEQ() Adds an anonymous value for the 'KEQ' property
void	addKEQ(kPrime KEQ) Adds a value for the 'KEQ' property
kPrime	addKEQ(com.hp.hpl.jena.rdf.model.Resource resource) Adds a value for the 'KEQ' property.
java.util.Iterator	getDELTA_DASH_G() Get an Iterator the 'DELTA_DASH_G' property values.
java.util.Iterator	getDELTA_DASH_H() Iterates through the 'DELTA_DASH_H' property values.
java.util.Iterator	getDELTA_DASH_S() Iterates through the 'DELTA_DASH_S' property values.
java.util.Iterator	getEC_DASH_NUMBER() Iterates through the 'EC_DASH_NUMBER' property values.
java.util.Iterator	getKEQ() Get an Iterator the 'KEQ' property values.
void	removeDELTA_DASH_G(deltaGprimeO DELTA_DASH_G) Removes a value for the 'DELTA_DASH_G' property.
void	removeDELTA_DASH_H(java.lang.Double DELTA_DASH_H) Remove a 'DELTA_DASH_H' property value.
void	removeDELTA_DASH_S(java.lang.Double DELTA_DASH_S) Remove a 'DELTA_DASH_S' property value.
void	removeEC_DASH_NUMBER(java.lang.String EC_DASH_NUMBER) Remove a 'EC_DASH_NUMBER' property value.
void	removeKEQ(kPrime KEQ) Removes a value for the 'KEQ' property.

Methods inherited from interface fr.curie.BiNoM.pathways.biopax.conversion

addLEFT, addLEFT, addLEFT, addPARTICIPANTS_asphysicalEntityParticipant, addPARTICIPANTS_asphysicalEntityParticipant, addPARTICIPANTS, addRIGHT, addRIGHT, addRIGHT, getLEFT, getPARTICIPANTS_asphysicalEntityParticipant, getRIGHT, getSPONTANEOUS, removeLEFT, removePARTICIPANTS, removeRIGHT, setSPONTANEOUS

Methods inherited from interface fr.curie.BiNoM.pathways.biopax.physicalInteraction

addINTERACTION_DASH_TYPE, addINTERACTION_DASH_TYPE, addINTERACTION_DASH_TYPE, getINTERACTION_DASH_TYPE, removeINTERACTION_DASH_TYPE

Methods inherited from interface fr.curie.BiNoM.pathways.biopax.interaction

addEVIDENCE, addEVIDENCE, addEVIDENCE, addPARTICIPANTS_asentity, addPARTICIPANTS_asentity, addPARTICIPANTS, getEVIDENCE, getPARTICIPANTS_asentity, removeEVIDENCE, removePARTICIPANTS

Methods inherited from interface fr.curie.BiNoM.pathways.biopax.entity

addAVAILABILITY, addCOMMENT, addDATA_DASH_SOURCE, addDATA_DASH_SOURCE, addDATA_DASH_SOURCE, addSYNONYMS, addXREF, addXREF, addXREF, getAVAILABILITY, getCOMMENT, getDATA_DASH_SOURCE, getNAME, getSHORT_DASH_NAME, getSYNONYMS, getXREF, removeAVAILABILITY, removeCOMMENT, removeDATA_DASH_SOURCE, removeSYNONYMS, removeXREF, setNAME, setSHORT_DASH_NAME

Methods inherited from interface com.ibm.adtech.jastor.Thing

clearCache, isRDFType, listStatements, model, registerListener, removeStatements, resource, unregisterListener, uri

Field Detail

TYPE

static final com.hp.hpl.jena.rdf.model.Resource TYPE

The rdf:type for this ontology class

DELTA_DASH_HProperty

static final com.hp.hpl.jena.rdf.model.Property DELTA_DASH_HProperty

The Jena Property for DELTA_DASH_H

(URI: http://www.biopax.org/release/biopax-level2.owl#DELTA-H)

RDF Schema Standard Properties
comment : For biochemical reactions, this property refers to the standard transformed enthalpy change for a reaction written in terms of biochemical reactants (sums of species), delta-H'^o. delta-G'^o = delta-H'^o - T delta-S'^o Units: kJ/mole (This definition from EcoCyc)^^http://www.w3.org/2001/XMLSchema#string

EC_DASH_NUMBERProperty

static final com.hp.hpl.jena.rdf.model.Property EC_DASH_NUMBERProperty

The Jena Property for EC_DASH_NUMBER

(URI: http://www.biopax.org/release/biopax-level2.owl#EC-NUMBER)

RDF Schema Standard Properties
comment : The unique number assigned to a reaction by the Enzyme Commission of the International Union of Biochemistry and Molecular Biology. Note that not all biochemical reactions currently have EC numbers assigned to them.^^http://www.w3.org/2001/XMLSchema#string

DELTA_DASH_SProperty

static final com.hp.hpl.jena.rdf.model.Property DELTA_DASH_SProperty

The Jena Property for DELTA_DASH_S

(URI: http://www.biopax.org/release/biopax-level2.owl#DELTA-S)

RDF Schema Standard Properties
comment : For biochemical reactions, this property refers to the standard transformed entropy change for a reaction written in terms of biochemical reactants (sums of species), delta-S'^o. delta-G'^o = delta-H'^o - T delta-S'^o (This definition from EcoCyc)^^http://www.w3.org/2001/XMLSchema#string

DELTA_DASH_GProperty

static final com.hp.hpl.jena.rdf.model.Property DELTA_DASH_GProperty

The Jena Property for DELTA_DASH_G

(URI: http://www.biopax.org/release/biopax-level2.owl#DELTA-G)

RDF Schema Standard Properties
comment : For biochemical reactions, this property refers to the standard transformed Gibbs energy change for a reaction written in terms of biochemical reactants (sums of species), delta-G'^o. delta-G'^o = -RT lnK' and delta-G'^o = delta-H'^o - T delta-S'^o delta-G'^o has units of kJ/mol. Like K', it is a function of temperature (T), ionic strength (I), pH, and pMg (pMg = -log₁₀[Mg²⁺]). Therefore, these quantities must be specified, and values for DELTA-G for biochemical reactions are represented as 5-tuples of the form (delta-G'^o T I pH pMg). This property may have multiple values, representing different measurements for delta-G'^o obtained under the different experimental conditions listed in the 5-tuple. (This definition from EcoCyc)^^http://www.w3.org/2001/XMLSchema#string

KEQProperty

static final com.hp.hpl.jena.rdf.model.Property KEQProperty

The Jena Property for KEQ

(URI: http://www.biopax.org/release/biopax-level2.owl#KEQ)

RDF Schema Standard Properties
comment : This quantity is dimensionless and is usually a single number. The measured equilibrium constant for a biochemical reaction, encoded by the slot KEQ, is actually the apparent equilibrium constant, K'. Concentrations in the equilibrium constant equation refer to the total concentrations of all forms of particular biochemical reactants. For example, in the equilibrium constant equation for the biochemical reaction in which ATP is hydrolyzed to ADP and inorganic phosphate: K' = [ADP][P_i]/[ATP], The concentration of ATP refers to the total concentration of all of the following species: [ATP] = [ATP^4-] + [HATP^3-] + [H₂ATP^2-] + [MgATP^2-] + [MgHATP^-] + [Mg₂ATP]. The apparent equilibrium constant is formally dimensionless, and can be kept so by inclusion of as many of the terms (1 mol/dm³) in the numerator or denominator as necessary. It is a function of temperature (T), ionic strength (I), pH, and pMg (pMg = -log₁₀[Mg²⁺]). Therefore, these quantities must be specified to be precise, and values for KEQ for biochemical reactions may be represented as 5-tuples of the form (K' T I pH pMg). This property may have multiple values, representing different measurements for K' obtained under the different experimental conditions listed in the 5-tuple. (This definition adapted from EcoCyc)^^http://www.w3.org/2001/XMLSchema#string

Method Detail

getDELTA_DASH_H

java.util.Iterator getDELTA_DASH_H()
                                   throws com.ibm.adtech.jastor.JastorException

Iterates through the 'DELTA_DASH_H' property values. This Iteartor may be used to remove all such values.

Returns:

Iterator of Double

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

DELTA_DASH_HProperty

addDELTA_DASH_H

void addDELTA_DASH_H(java.lang.Double DELTA_DASH_H)
                     throws com.ibm.adtech.jastor.JastorException

Add a 'DELTA_DASH_H' property value

Parameters:

{@link - java.lang.Double}, the value to add

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

DELTA_DASH_HProperty

removeDELTA_DASH_H

void removeDELTA_DASH_H(java.lang.Double DELTA_DASH_H)
                        throws com.ibm.adtech.jastor.JastorException

Remove a 'DELTA_DASH_H' property value. This method should not be invoked while iterator through values. In that case, the remove() method of the Iterator itself should be used.

Parameters:

{@link - java.lang.Double}, the value to remove

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

DELTA_DASH_HProperty

getEC_DASH_NUMBER

java.util.Iterator getEC_DASH_NUMBER()
                                     throws com.ibm.adtech.jastor.JastorException

Iterates through the 'EC_DASH_NUMBER' property values. This Iteartor may be used to remove all such values.

Returns:

Iterator of String

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

EC_DASH_NUMBERProperty

addEC_DASH_NUMBER

void addEC_DASH_NUMBER(java.lang.String EC_DASH_NUMBER)
                       throws com.ibm.adtech.jastor.JastorException

Add a 'EC_DASH_NUMBER' property value

Parameters:

{@link - java.lang.String}, the value to add

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

EC_DASH_NUMBERProperty

removeEC_DASH_NUMBER

void removeEC_DASH_NUMBER(java.lang.String EC_DASH_NUMBER)
                          throws com.ibm.adtech.jastor.JastorException

Remove a 'EC_DASH_NUMBER' property value. This method should not be invoked while iterator through values. In that case, the remove() method of the Iterator itself should be used.

Parameters:

{@link - java.lang.String}, the value to remove

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

EC_DASH_NUMBERProperty

getDELTA_DASH_S

java.util.Iterator getDELTA_DASH_S()
                                   throws com.ibm.adtech.jastor.JastorException

Iterates through the 'DELTA_DASH_S' property values. This Iteartor may be used to remove all such values.

Returns:

Iterator of Double

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

DELTA_DASH_SProperty

addDELTA_DASH_S

void addDELTA_DASH_S(java.lang.Double DELTA_DASH_S)
                     throws com.ibm.adtech.jastor.JastorException

Add a 'DELTA_DASH_S' property value

Parameters:

{@link - java.lang.Double}, the value to add

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

DELTA_DASH_SProperty

removeDELTA_DASH_S

void removeDELTA_DASH_S(java.lang.Double DELTA_DASH_S)
                        throws com.ibm.adtech.jastor.JastorException

Remove a 'DELTA_DASH_S' property value. This method should not be invoked while iterator through values. In that case, the remove() method of the Iterator itself should be used.

Parameters:

{@link - java.lang.Double}, the value to remove

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

DELTA_DASH_SProperty

getDELTA_DASH_G

java.util.Iterator getDELTA_DASH_G()
                                   throws com.ibm.adtech.jastor.JastorException

Get an Iterator the 'DELTA_DASH_G' property values. This Iteartor may be used to remove all such values.

Returns:

Iterator of deltaGprimeO

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

DELTA_DASH_GProperty

addDELTA_DASH_G

void addDELTA_DASH_G(deltaGprimeO DELTA_DASH_G)
                     throws com.ibm.adtech.jastor.JastorException

Adds a value for the 'DELTA_DASH_G' property

Parameters:

The - deltaGprimeO to add

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

DELTA_DASH_GProperty

addDELTA_DASH_G

deltaGprimeO addDELTA_DASH_G()
                             throws com.ibm.adtech.jastor.JastorException

Adds an anonymous value for the 'DELTA_DASH_G' property

Returns:

The anoymous deltaGprimeO created

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

DELTA_DASH_GProperty

addDELTA_DASH_G

deltaGprimeO addDELTA_DASH_G(com.hp.hpl.jena.rdf.model.Resource resource)
                             throws com.ibm.adtech.jastor.JastorException

Adds a value for the 'DELTA_DASH_G' property. This method is equivalent constructing a new instance of deltaGprimeO with the factory and calling addDELTA_DASH_G(fr.curie.BiNoM.pathways.biopax.deltaGprimeO DELTA_DASH_G) The resource argument have rdf:type http://www.biopax.org/release/biopax-level2.owl#deltaGprimeO. That is, this method should not be used as a shortcut for creating new objects in the model.

Parameters:

The - om.hp.hpl.jena.rdf.model.Resource to add

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

DELTA_DASH_GProperty

removeDELTA_DASH_G

void removeDELTA_DASH_G(deltaGprimeO DELTA_DASH_G)
                        throws com.ibm.adtech.jastor.JastorException

Removes a value for the 'DELTA_DASH_G' property. This method should not be invoked while iterator through values. In that case, the remove() method of the Iterator itself should be used.

Parameters:

The - deltaGprimeO to remove

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

DELTA_DASH_GProperty

getKEQ

java.util.Iterator getKEQ()
                          throws com.ibm.adtech.jastor.JastorException

Get an Iterator the 'KEQ' property values. This Iteartor may be used to remove all such values.

Returns:

Iterator of kPrime

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

KEQProperty

addKEQ

void addKEQ(kPrime KEQ)
            throws com.ibm.adtech.jastor.JastorException

Adds a value for the 'KEQ' property

Parameters:

The - kPrime to add

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

KEQProperty

addKEQ

kPrime addKEQ()
              throws com.ibm.adtech.jastor.JastorException

Adds an anonymous value for the 'KEQ' property

Returns:

The anoymous kPrime created

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

KEQProperty

addKEQ

kPrime addKEQ(com.hp.hpl.jena.rdf.model.Resource resource)
              throws com.ibm.adtech.jastor.JastorException

Adds a value for the 'KEQ' property. This method is equivalent constructing a new instance of kPrime with the factory and calling addKEQ(fr.curie.BiNoM.pathways.biopax.kPrime KEQ) The resource argument have rdf:type http://www.biopax.org/release/biopax-level2.owl#kPrime. That is, this method should not be used as a shortcut for creating new objects in the model.

Parameters:

The - om.hp.hpl.jena.rdf.model.Resource to add

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

KEQProperty

removeKEQ

void removeKEQ(kPrime KEQ)
               throws com.ibm.adtech.jastor.JastorException

Removes a value for the 'KEQ' property. This method should not be invoked while iterator through values. In that case, the remove() method of the Iterator itself should be used.

Parameters:

The - kPrime to remove

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

KEQProperty