(:OCELOT-KB :NAME ECOCYC::BIOPAX :PACKAGE "BIO" :WRITE-DATE
 "10:59:04 on Wed Sep 24, 2003" :WRITE-UTIME 3273404344 :USER
 "Windows-user")

(CLASS-DESIGN-RATIONALE NIL (
(:INHERITANCE-TYPE :UNIQUE)
(:VALUE-TYPE :STRING)
(:DOMAIN OCELOT::FRAMES)
(:DOCUMENTATION
 "Describes the design rationale for this frame or slot.")
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(REVERSIBILITY NIL (
(:DOCUMENTATION
 "This slot describes the reversibility and directionality of the reaction.
Possible values are:

  :REVERSIBLE -- The reaction can proceed in either direction.
  :IR-L-R         -- The reaction is known to be effectively irreversible, proceeding only in the left-to-right direction.
  :IR-R-L         -- The reaction is known to be effectively irreversible, proceeding only in the right-to-left direction.
  :L-R              -- The reaction may or may not be technically irreversible, but in biological situations occurs effectively only in the left-to-right direction.
  :R-L              -- The reaction may or may not be technically irreversible, but in biological situations occurs effectively only in the right-to-left direction.")
(:MAXIMUM-CARDINALITY 1)
(:VALUE-TYPE (:ONE-OF :REVERSIBLE :L-R :R-L :IR-L-R :IR-R-L))
(:DOMAIN |conversion|)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(CHOICE.2 NIL (
(:DOCUMENTATION "A choice of sequence location")
(:VALUE-TYPE (:ONE-OF |positionType| |intervalType|))
(:DOMAIN |baseLocationType.BeginEnd|)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(CHOICE.1 NIL (
(:DOCUMENTATION "A choice of sequence location")
(:VALUE-TYPE (:ONE-OF |positionType| |intervalType|))
(:DOMAIN |baseLocationType.BeginEnd|)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(|baseLocationType.BeginEnd| T (
(:CREATOR |Gary Bader|)
(:CREATION-DATE 3266926876)
(OCELOT::PARENTS |utilityClasses|) )
NIL)

(END NIL (
(:DOCUMENTATION "The end of a sequence interval.")
(:VALUE-TYPE :INTEGER)
(:CARDINALITY 1)
(:DOMAIN |intervalType|)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(BEGIN NIL (
(:DOCUMENTATION "The start of a sequence interval.")
(:VALUE-TYPE :INTEGER)
(:CARDINALITY 1)
(:DOMAIN |intervalType|)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(POSITION NIL (
(:DOCUMENTATION
 "The position on a sequence (e.g. amino acid position 76)")
(:CARDINALITY 1)
(:VALUE-TYPE :INTEGER)
(:DOMAIN |positionType|)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(|intervalType| T (
(COMMENT "A sequence interval")
(:CREATOR |Gary Bader|)
(:CREATION-DATE 3266925187)
(OCELOT::PARENTS |utilityClasses|) )
NIL)

(|positionType| T (
(:CREATOR |Gary Bader|)
(:CREATION-DATE 3266925179)
(OCELOT::PARENTS |utilityClasses|) )
NIL)

(BASELOCATIONCHOICE NIL (
(:DOCUMENTATION "A choice of sequence location")
(:VALUE-TYPE
 (:ONE-OF |positionType| |intervalType| |baseLocationType.BeginEnd|))
(:DOMAIN |baseLocationType|)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(|baseLocationType| T (
(:CREATOR |Gary Bader|)
(:CREATION-DATE 3266924968)
(OCELOT::PARENTS |utilityClasses|) )
NIL)

(FEATUREDESCRIPTION NIL (
(:DOCUMENTATION
 "The description of a feature.  A feature is some part of a physicalEntity (e.g. a domain on a protein, a functional group on a small molecule)")
(:MAXIMUM-CARDINALITY 1)
(:MINIMUM-CARDINALITY 0)
(:VALUE-TYPE |cvType|)
(:DOMAIN |feature|)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(|feature| T (
(THOUGHT
 "Currently the feature description system is only implemented for sequences.")
(COMMENT
 "A feature is some part of a physicalEntity (e.g. a domain on a protein, a functional group on a small molecule)")
(:CREATOR |Gary Bader|)
(:CREATION-DATE 3266924823)
(OCELOT::PARENTS |utilityClasses|) )
NIL)

(SEQUENCE NIL (
(:DOCUMENTATION "Amino acid or nucleotide sequence in uppercase")
(:MAXIMUM-CARDINALITY 1)
(:MINIMUM-CARDINALITY 0)
(:VALUE-TYPE :STRING)
(:DOMAIN |dna| |rna| |protein|)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(ORGANISM NIL (
(:DOCUMENTATION "The organismal source")
(:VALUE-TYPE |bioSourceType|)
(:MAXIMUM-CARDINALITY 1)
(:MINIMUM-CARDINALITY 0)
(:DOMAIN |dna| |rna| |protein|)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(EXPERIMENTLIST NIL (
(:DOCUMENTATION "A list of supporting experiments")
(:DOMAIN |interaction|)
(:VALUE-TYPE |experiment|)
(:MINIMUM-CARDINALITY 1)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(|utilityClasses| T (
(COMMENT
 "These classes are taken directly from PSI-MI and are named as closely as possible to the PSI naming scheme.")
(:CREATOR |Gary Bader|)
(:CREATION-DATE 3266875111)
(OCELOT::PARENTS OCELOT::FRAMES) )
NIL)

(INTERACTIONLIST NIL (
(:VALUE-TYPE |interaction|)
(:DOCUMENTATION "A list of interactions")
(:MINIMUM-CARDINALITY 1)
(:DOMAIN |entry|)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(NCBITAXID NIL (
(:DOCUMENTATION "The NCBI taxonomy ID for this organism")
(:VALUE-TYPE :INTEGER)
(:CARDINALITY 1)
(:DOMAIN |bioSourceType|)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(VALUE NIL (
(:DOCUMENTATION "Value of confidence")
(:VALUE-TYPE :STRING)
(:CARDINALITY 1)
(:DOMAIN |confidenceContainer|)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(UNIT NIL (
(:DOCUMENTATION "Unit of confidence")
(:VALUE-TYPE :STRING)
(:CARDINALITY 1)
(:DOMAIN |confidenceContainer|)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(|confidenceContainer| T (
(COMMENT "A statistical confidence value.")
(:CREATOR |Gary Bader|)
(:CREATION-DATE 3266874785)
(OCELOT::PARENTS |utilityClasses|) )
NIL)

(NAMES.REQ NIL (
(:DOCUMENTATION "Name(s)")
(:CARDINALITY 1)
(:VALUE-TYPE |namesType|)
(:DOMAIN |openCvType| |cvType|)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(XREF.REQ NIL (
(:DOCUMENTATION "An external cross-reference")
(:CARDINALITY 1)
(:VALUE-TYPE |xrefType|)
(:DOMAIN |cvType|)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(|cvType| T (
(COMMENT "A controlled vocabulary that is included in the ontology.")
(:CREATOR |Gary Bader|)
(:CREATION-DATE 3266873369)
(OCELOT::PARENTS |utilityClasses|) )
NIL)

(FEATUREDETECTION NIL (
(:DOCUMENTATION "Experimental method used to detect this feature")
(:VALUE-TYPE |cvType|)
(:MAXIMUM-CARDINALITY 1)
(:MINIMUM-CARDINALITY 0)
(:DOMAIN |feature| |experiment|)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(PARTICIPANTDETECTION NIL (
(:DOCUMENTATION
 "Experimental method used to detect the participant in the interaction")
(:VALUE-TYPE |cvType|)
(:MAXIMUM-CARDINALITY 1)
(:MINIMUM-CARDINALITY 0)
(:DOMAIN |experiment|)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(INTERACTIONDETECTION NIL (
(:DOCUMENTATION
 "The experimental method used to detect this interaction")
(:VALUE-TYPE |cvType|)
(:CARDINALITY 1)
(:DOMAIN |experiment|)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(HOSTORGANISM NIL (
(:DOCUMENTATION "The host organism this experiment was performed in")
(:VALUE-TYPE |bioSourceType|)
(:MAXIMUM-CARDINALITY 1)
(:MINIMUM-CARDINALITY 0)
(:DOMAIN |experiment|)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(|openCvType| T (
(COMMENT "A controlled vocabulary that is external to the ontology.")
(:CREATOR |Gary Bader|)
(:CREATION-DATE 3266873052)
(OCELOT::PARENTS |utilityClasses|) )
NIL)

(TISSUE NIL (
(:DOCUMENTATION "An external controlled vocabulary of tissue types")
(:VALUE-TYPE |openCvType|)
(:MAXIMUM-CARDINALITY 1)
(:MINIMUM-CARDINALITY 0)
(:DOMAIN |bioSourceType|)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(COMPARTMENT NIL (
(:DOCUMENTATION
 "A cellular compartment.  The Gene Ontology cellular component controlled vocabulary should be used here.")
(:VALUE-TYPE |openCvType|)
(:MAXIMUM-CARDINALITY 1)
(:MINIMUM-CARDINALITY 0)
(:DOMAIN |bioSourceType|)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(CELLTYPE NIL (
(:DOCUMENTATION "A cell type")
(:VALUE-TYPE |openCvType|)
(:MAXIMUM-CARDINALITY 1)
(:MINIMUM-CARDINALITY 0)
(:DOMAIN |bioSourceType|)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(|bioSourceType| T (
(COMMENT "A biological source")
(:CREATOR |Gary Bader|)
(:CREATION-DATE 3266872777)
(OCELOT::PARENTS |utilityClasses|) )
NIL)

(BIBREF NIL (
(:DOCUMENTATION "A bibliographic reference")
(:MAXIMUM-CARDINALITY 1)
(:MINIMUM-CARDINALITY 0)
(:VALUE-TYPE |bibrefType|)
(:DOMAIN |experiment| |source|)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(|experiment| T (
(COMMENT "Describes an experiment.")
(THOUGHT
 "This class is directly copied from the PSI-MI definition.  Because of this, only describes experiments related to proteins and protein interactions.")
(:CREATOR |Gary Bader|)
(:CREATION-DATE 3266872518)
(OCELOT::PARENTS |utilityClasses|) )
NIL)

(AVAILABILITY NIL (
(:DOCUMENTATION
 "Describes the availability of this data (e.g. a copyright statement)")
(:VALUE-TYPE :STRING)
(:MINIMUM-CARDINALITY 0)
(:DOMAIN |entity| |entry|)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(SOURCE NIL (
(:DOCUMENTATION "The source of this data")
(:MAXIMUM-CARDINALITY 1)
(:MINIMUM-CARDINALITY 0)
(:VALUE-TYPE |source|)
(:DOMAIN |entry|)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(ATTRIBUTELIST NIL (
(:DOCUMENTATION "A list of user defined attributes for experiment")
(:VALUE-TYPE |attributeListContainer|)
(:MAXIMUM-CARDINALITY 1)
(:MINIMUM-CARDINALITY 0)
(:DOMAIN |entity| |entry| |openCvType| |experiment| |source|)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(|attributeListContainer| T (
(COMMENT "A container for the list of attributes.")
(:CREATOR |Gary Bader|)
(:CREATION-DATE 3266871817)
(OCELOT::PARENTS |utilityClasses|) )
NIL)

(NAME NIL (
(:DOCUMENTATION "The name of this attribute")
(:CARDINALITY 1)
(:VALUE-TYPE :STRING)
(:DOMAIN |attributeListType|)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(ATTRIBUTE NIL (
(:DOCUMENTATION "A user-defined attribute")
(:CARDINALITY 1)
(:VALUE-TYPE :STRING)
(:DOMAIN |attributeListType|)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(SECONDARYREF NIL (
(:DOCUMENTATION "Secondary external cross-references")
(:VALUE-TYPE |dbReferenceType|)
(:MINIMUM-CARDINALITY 0)
(:DOMAIN |xrefType|)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(DB-VERSION NIL (
(:DOCUMENTATION "A database version")
(:VALUE-TYPE :STRING)
(:MAXIMUM-CARDINALITY 1)
(:MINIMUM-CARDINALITY 0)
(:DOMAIN |dbReferenceType|)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(SECONDARY NIL (
(:DOCUMENTATION "A secondary database identifier")
(:VALUE-TYPE :STRING)
(:MINIMUM-CARDINALITY 0)
(:MAXIMUM-CARDINALITY 1)
(:DOMAIN |dbReferenceType|)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(ID NIL (
(:DOCUMENTATION "A database identifier")
(:VALUE-TYPE :STRING)
(:CARDINALITY 1)
(:DOMAIN |dbReferenceType|)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(DB NIL (
(:DOCUMENTATION "A database name")
(:CARDINALITY 1)
(:VALUE-TYPE :STRING)
(:DOMAIN |dbReferenceType|)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(|dbReferenceType| T (
(COMMENT
 "A reference to a database. Refers to a unique object in an external database.")
(:CREATOR |Gary Bader|)
(:CREATION-DATE 3266870234)
(OCELOT::PARENTS |utilityClasses|) )
NIL)

(PRIMARYREF NIL (
(:DOCUMENTATION "Primary external cross-reference")
(:VALUE-TYPE |dbReferenceType|)
(:CARDINALITY 1)
(:DOMAIN |xrefType|)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(BIBREFCHOICE NIL (
(:DOCUMENTATION "A choice of bibliographic reference")
(:VALUE-TYPE (:ONE-OF |xrefType| |attributeListType|))
(:DOMAIN |bibrefType|)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(FULLNAME NIL (
(:DOCUMENTATION "A full name")
(:MAXIMUM-CARDINALITY 1)
(:MINIMUM-CARDINALITY 0)
(:VALUE-TYPE :STRING)
(:DOMAIN |namesType|)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(SHORTLABEL NIL (
(:DOCUMENTATION
 "A short label.  Short enough to be used in a visualization application to label a graphical element.")
(:CARDINALITY 1)
(:VALUE-TYPE :STRING)
(:DOMAIN |namesType|)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(|attributeListType| T (
(COMMENT "A list of user-defined attributes.")
(:CREATOR |Gary Bader|)
(:CREATION-DATE 3266865698)
(OCELOT::PARENTS |utilityClasses|) )
NIL)

(|xrefType| T (
(COMMENT "A cross-reference")
(:CREATOR |Gary Bader|)
(:CREATION-DATE 3266865689)
(OCELOT::PARENTS |utilityClasses|) )
NIL)

(|bibrefType| T (
(COMMENT
 "Bibliographic reference for the data source. Example: A paper which describes all interactions of the entry.")
(:CREATOR |Gary Bader|)
(:CREATION-DATE 3266865684)
(OCELOT::PARENTS |utilityClasses|) )
NIL)

(|namesType| T (
(COMMENT "A name")
(:CREATOR |Gary Bader|)
(:CREATION-DATE 3266865677)
(OCELOT::PARENTS |utilityClasses|) )
NIL)

(ATTRIBUTES NIL (
(:MAXIMUM-CARDINALITY 1)
(:MINIMUM-CARDINALITY 0)
(:VALUE-TYPE |attributeListType|)
(:DOCUMENTATION "A list of user-defined attributes")
(:DOMAIN |attributeListContainer|)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(|source| T (
(COMMENT "Desciption of the source of the information.")
(:CREATOR |Gary Bader|)
(:CREATION-DATE 3266857667)
(OCELOT::PARENTS |utilityClasses|) )
NIL)

(INTERACTIONS NIL (
(:DOCUMENTATION "A list of interactions in this pathway")
(:VALUE-TYPE |interaction|)
(:DOMAIN |pathway|)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(COMMENT NIL (
(:INHERITANCE-TYPE :UNIQUE)
(:VALUE-TYPE :STRING)
(:DOMAIN OCELOT::FRAMES)
(:DOCUMENTATION "Comment about the frame this slot is part of.")
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(GENES NIL (
(:DOCUMENTATION "A list of genes interacting")
(:VALUE-TYPE |dna|)
(:DOMAIN |genetic|)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(NAMES NIL (
(:DOCUMENTATION "Name(s)")
(:VALUE-TYPE |namesType|)
(:DOMAIN |entity| |bioSourceType| |experiment| |source|)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(CONFIDENCE NIL (
(:DOCUMENTATION "Statistical confidence")
(:VALUE-TYPE |confidenceContainer|)
(:MAXIMUM-CARDINALITY 1)
(:MINIMUM-CARDINALITY 0)
(:DOMAIN |interaction| |experiment|)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(INTERACTIONTYPE NIL (
(:DOCUMENTATION
 "The type of interaction (from a small controlled vocabulary of interaction types) e.g. phosphorylation.  This is meant to be used as a descriptive name for the interaction that would be useful for browsing or database searches.")
(:MAXIMUM-CARDINALITY 1)
(:MINIMUM-CARDINALITY 0)
(:VALUE-TYPE |cvType|)
(:DOMAIN |interaction|)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(PARTICIPANTLIST NIL (
(:DOCUMENTATION "The entities participating in this association")
(:VALUE-TYPE |entity|)
(:DOMAIN |molecularAssociation|)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(|interaction| T (
(CLASS-DESIGN-RATIONALE
 "One reason the name interaction was chosen is that PSI (http://psidev.sf.net) uses it and we would like to remain compatible with them.")
(COMMENT
 "One or two sets of entities and some relationship between them.  A relationship exists between two or more entities and is not defined without the entities. 
The relationship does not have to be a physical relationship.  It can be another type, such as logical, temporal, genetic, etc.")
(:CREATOR |Gary Bader|)
(:CREATION-DATE 3262707432)
(OCELOT::PARENTS |entity|) )
NIL)

(|control| T (
(CLASS-NAME-SYNONYMS "regulation" "modulation" "mediation")
(COMMENT
 "The control of a process (e.g. enzyme catalysis controls a biochemical reaction, 
gene regulation controls gene expression).
")
(:CREATOR |Gary Bader|)
(:CREATION-DATE 3262707444)
(OCELOT::PARENTS |interaction|) )
NIL)

(|conversion| T (
(COMMENT "A conversion process, which converts one set of entities to 
another set (e.g. a biochemical reaction converts substrates to products,
the process of complex assembly converts single molecules to a complex, 
transport converts entities in one compartment to the same entities in another 
compartment).
")
(:CREATOR |Gary Bader|)
(:CREATION-DATE 3262707449)
(OCELOT::PARENTS |interaction|) )
((RIGHT :FACET SLOT-NAME-SYNONYMS "products, output")
 (LEFT :FACET SLOT-NAME-SYNONYMS "reactants, input")))

(|genetic| T (
(COMMENT
 "A genetic interaction (e.g. a synthetic lethal interaction).  An interaction between 
elements of a genotype that results in a change in phenotype.
")
(:CREATOR |Gary Bader|)
(:CREATION-DATE 3262707457)
(OCELOT::PARENTS |interaction|) )
NIL)

(|equivalenceClass| T (
(THOUGHT
 "This class is considered useful, but its position in the ontology has not yet been decided.  It may be useful as part of the entity tree because it can then easily be used as part of an interaction.")
(COMMENT
 "A set of entities that can be considered equivalent in some context (e.g. a 
set of paralogs that can replace each other as enzymes in a biochemical 
reaction, a set of enzymes that may not be homologs, but are functionally 
identical e.g. glucose-6-phosphatase).
")
(:CREATOR |Gary Bader|)
(:CREATION-DATE 3262707502)
(OCELOT::PARENTS |interaction|) )
NIL)

(|molecularAssociation| T (
(THOUGHT
 "This class needs more conceptual work to clarify its use.  One issue to resolve is whether this class should be a physicalEntity.")
(COMMENT
 "An association between a set of molecules (e.g. Arp2-Arp3 protein-protein 
interaction; protein complex e.g. the result of a co-immunoprecipitation experiment; 
hexokinase-glucose).
")
(:CREATOR |Gary Bader|)
(:CREATION-DATE 3262707511)
(OCELOT::PARENTS |interaction|) )
NIL)

(|biochemicalReaction| T (
(COMMENT
 "A biochemical reaction is a reaction in which substrates are written in terms of sums of species.  This is what is
typically done in biochemistry, and, in principle, all of the EC reactions should be biochemical reactions.  Example:
     ATP + H<sub>2</sub>O = ADP + P<sub>i</sub>.
In this reaction, ATP is considered to be an equilibrium mixture of several species, namely ATP<sup>4-</sup>, HATP<sup>3-</sup>,
H<sub>2</sub>ATP<sup>2-</sup>, MgATP<sup>2-</sup>, MgHATP<sup>-</sup>, and Mg<sub>2</sub>ATP.
Additional species may also need to be considered if other ions (e.g. Ca<sup>2+</sup>) that bind ATP are present.
Similar considerations apply to ADP and to inorganic phosphate (P<sub>i</sub>).  
  When writing biochemical reactions, it is important not to attach charges to the biochemical reactants and 
not to include ions such as H<sup>+</sup> and Mg<sup>2+</sup> 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.
")
(:CREATOR |Gary Bader|)
(:CREATION-DATE 3262707528)
(OCELOT::PARENTS |conversion|) )
((KEQ :FACET :DOCUMENTATION
  "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<sub>i</sub>]/[ATP],

the concentration of ATP refers to the total concentration of all of the following species:

[ATP] = [ATP<sup>4-</sup>] + [HATP<sup>3-</sup>] + [H<sub>2</sub>ATP<sup>2-</sup>] + [MgATP<sup>2-</sup>] + [MgHATP<sup>-</sup>] + [Mg<sub>2</sub>ATP].

The apparent equilibrium constant is formally dimensionless, and can be kept so by inclusion of as many of the terms (1 mol/dm<sup>3</sup>) 
in the numerator or denominator as necessary.  It is a function of temperature (T), ionic strength (I), pH, and pMg (pMg = -log<sub>10</sub>[Mg<sup>2+</sup>]).
Therefore, these quantities must be specified, and values for KEQ for biochemical reactions are represented as 5-tuples of the form 
(K' T I pH pMg).  This slot may have multiple values, representing different measurements for K' obtained under the different experimental conditions 
listed in the 5-tuple.
")
 (DELTA-S :FACET :DOCUMENTATION
  "For biochemical reactions, this slot refers to the standard transformed entropy change for a reaction written in terms of 
biochemical reactants (sums of species), delta-S'<sup>o</sup>.

  delta-G'<sup>o</sup> = delta-H'<sup>o</sup> - T delta-S'<sup>o</sup>")
 (DELTA-H :FACET :DOCUMENTATION
  "For biochemical reactions, this slot refers to the standard transformed enthalpy change for a reaction written in terms of 
biochemical reactants (sums of species), delta-H'<sup>o</sup>.

  delta-G'<sup>o</sup> = delta-H'<sup>o</sup> - T delta-S'<sup>o</sup>")
 (DELTA-G :FACET :DOCUMENTATION
  "For biochemical reactions, this slot refers to the standard transformed Gibbs energy change for a reaction written in terms of 
biochemical reactants (sums of species), delta-G'<sup>o</sup>.

  delta-G'<sup>o</sup> = -RT lnK'
and
  delta-G'<sup>o</sup> = delta-H'<sup>o</sup> - T delta-S'<sup>o</sup>

delta-G'<sup>o</sup> has units of kJ/mol.  Like K', it is a function of temperature (T), ionic strength (I), pH, and pMg (pMg = -log<sub>10</sub>[Mg<sup>2+</sup>]).
Therefore, these quantities must be specified, and values for DELTA-G for biochemical reactions are represented as 5-tuples of the form 
(delta-G'<sup>o</sup> T I pH pMg).  This slot may have multiple values, representing different measurements for delta-G'<sup>o</sup> 
obtained under the different experimental conditions listed in the 5-tuple.
")))

(|enzymeCatalysis| T (
(COMMENT
 "Describes the catalysis by an enzyme of a particular reaction.  Instances of
this class describe properties of a pairing between an enzyme and a
reaction.  For example, a bifunctional enzyme that catalyzes two different
reactions would be linked to two instances of the enzymeCatalysis class
to describe the different properties of each function of that enzyme. Enzyme 
catalysis controls biochemicalReaction and together these classes can be used 
to describe typical metabolic pathways.")
(:CREATOR |Gary Bader|)
(:CREATION-DATE 3262707546)
(OCELOT::PARENTS |control|) )
NIL)

(|transportCatalysis| T (
(COMMENT
 "Control of the process of transportation.  An active or passive transporter can facilitate a translocation event.")
(:CREATOR |Gary Bader|)
(:CREATION-DATE 3262707575)
(OCELOT::PARENTS |control|) )
NIL)

(|transport| T (
(COMMENT
 "The process of transport from one spatial location to another, typically within or at "
 "least with respect to the cell.  This does not include a transporter molecule, which "
 "would be described in the transport control class.")
(:CREATOR |Gary Bader|)
(:CREATION-DATE 3262707588)
(OCELOT::PARENTS |conversion|) )
NIL)

(|geneRegulation| T (
(COMMENT
 "The process of gene regulation by a transcription factor. A transcription factor binds upstream "
 "of a gene to regulate it. This is the basis of genetic regulatory networks, where typically an "
 "arrow is drawn from the transcription factor to the regulated gene.")
(:CREATOR |Gary Bader|)
(:CREATION-DATE 3262707602)
(OCELOT::PARENTS |control|) )
NIL)

(|translation| T (
(COMMENT
 "Process of translation.  This is useful to describe translation when details are unknown.")
(THOUGHT
 "It is still an open issue whether to include production relationships of the central dogma, like transcription and translation.")
(:CREATOR |Gary Bader|)
(:CREATION-DATE 3262707611)
(OCELOT::PARENTS |conversion|) )
NIL)

(|transcription| T (
(THOUGHT
 "It is still an open issue whether to include production relationships of the central dogma, like transcription and translation.")
(COMMENT
 "The process of transcription.  This is useful to describe transcription when details are unknown.")
(:CREATOR |Gary Bader|)
(:CREATION-DATE 3262707618)
(OCELOT::PARENTS |conversion|) )
NIL)

(|synthetic| T (
(COMMENT
 "A synthetic genetic interaction.  Two genes have a synthetic phenotype if each gene 
separately mutated has no phenotype, but when both genes are mutated at the same 
time, the phenotype exists.")
(:CREATOR |Gary Bader|)
(:CREATION-DATE 3262707638)
(OCELOT::PARENTS |genetic|) )
NIL)

(|epistasis| T (
(COMMENT
 "An epistatic interaction occurs when an allele at one locus renders the genotype at a second locus irrelevant - the phenotype will be dictated by the genotype of the epistatic gene alone. (This definition from"
 "http://starklab.slu.edu/Coulter/genetics/handout3_2002.html)")
(:CREATOR |Gary Bader|)
(:CREATION-DATE 3262707644)
(OCELOT::PARENTS |genetic|) )
NIL)

(|suppression| T (
(COMMENT
 "A suppressor is generally defined as a mutation that completely or partially restores the mutant phenotype of another mutation. (This definition from"
 "http://dbb.urmc.rochester.edu/labs/Sherman_f/yeast/12.html#12.3)")
(:CREATOR |Gary Bader|)
(:CREATION-DATE 3262707660)
(OCELOT::PARENTS |genetic|) )
NIL)

(|co-occurrence| T (
(THOUGHT "This class needs more conceptual work to clarify its use.")
(COMMENT
 "The co-occurrence of entities in some context.  That context could be time, space, a sentence, sequence similarity space, etc. 
(e.g. colocalization of a few receptors e.g. in a GPI anchored lipid raft; co-migration of cells; genes expressed at the same time.)")
(:CREATOR |Gary Bader|)
(:CREATION-DATE 3262707827)
(OCELOT::PARENTS |interaction|) )
NIL)

(|co-localization| T (
(COMMENT "The co-occurrence of entities in space.")
(:CREATOR |Gary Bader|)
(:CREATION-DATE 3262707831)
(OCELOT::PARENTS |co-occurrence|) )
NIL)

(|complexAssembly| T (
(COMMENT
 "A step in the process of complex assembly.  This is not the same as a complex, which is a physical object, called molecular association in the interaction class hierarchy.")
(:CREATOR |Gary Bader|)
(:CREATION-DATE 3262707925)
(OCELOT::PARENTS |conversion|) )
NIL)

(|co-incidence| T (
(COMMENT "The co-occurrence of entities in time.")
(:CREATOR |Gary Bader|)
(:CREATION-DATE 3262707966)
(OCELOT::PARENTS |co-occurrence|) )
NIL)

(|physicalEntity| T (
(CLASS-DESIGN-RATIONALE
 "It's hard to find a name that encompasses all of the examples below without being too general.  PSI uses interactor here, so this may be an issue when discussing compatibility.")
(CLASS-NAME-SYNONYMS "part" "interactor")
(COMMENT
 "Describes all physical entities, from molecules to cells to organs.  A building block of simple interactions (simple interactions are those that do involve pathways or other interactions)")
(:CREATOR |Gary Bader|)
(:CREATION-DATE 3262708054)
(OCELOT::PARENTS |entity|) )
NIL)

(|pathway| T (
(COMMENT
 "A biological pathway.  A series of steps defined by biologists as a pathways.  A set of interactions (a pathway has interactions).")
(OCELOT::PARENTS |entity|)
(:CREATOR |Gary Bader|)
(:CREATION-DATE 3262708847) )
NIL)

(|entity| T (
(COMMENT
 "Any concept that we will refer to as a discrete unit when describing biological pathways.  e.g. a pathway, interaction or physical entity.")
(:CREATOR |Gary Bader|)
(:CREATION-DATE 3262708964)
(OCELOT::PARENTS OCELOT::FRAMES) )
NIL)

(|cell| T (
(THOUGHT
 "This class is needed to describe cell-cell interactions, but its use must be further defined. ")
(COMMENT
 "A specific type of cell. (e.g. cardiac myocyte, B lymphocyte)")
(:CREATOR |Gary Bader|)
(:CREATION-DATE 3262709402)
(OCELOT::PARENTS |physicalEntity|) )
NIL)

(|cellComponent| T (
(THOUGHT "This class needs to be further discussed.")
(COMMENT "A part of a cell (e.g. nucleus, mitochondrion). 
Use cellular components defined by Gene Ontology.")
(:CREATOR |Gary Bader|)
(:CREATION-DATE 3262709410)
(OCELOT::PARENTS |physicalEntity|) )
NIL)

(|dna| T (
(COMMENT
 "Deoxyribonucleic acid. (e.g. EGFR DNA sequence. See GenBank for more examples.)")
(:CREATOR |Gary Bader|)
(:CREATION-DATE 3262709422)
(OCELOT::PARENTS |physicalEntity|) )
NIL)

(|rna| T (
(COMMENT "Ribonucleic acid (e.g. messengerRNA, microRNA, ribosomalRNA)")
(:CREATOR |Gary Bader|)
(:CREATION-DATE 3262709456)
(OCELOT::PARENTS |physicalEntity|) )
NIL)

(|protein| T (
(COMMENT
 "A protein (e.g. The EGFR protein sequence.  See Swiss-Prot for more examples.)")
(:CREATOR |Gary Bader|)
(:CREATION-DATE 3262709464)
(OCELOT::PARENTS |physicalEntity|) )
NIL)

(|smallMolecule| T (
(THOUGHT "This should eventually be implemented as CML")
(COMMENT
 "A non-polymeric biomolecule.  Generally, any bioactive molecule that is not a 
peptide, protein, DNA, RNA or possibly not a complex carbohydrate (e.g. 
glucose, penicillin)
")
(:CREATOR |Gary Bader|)
(:CREATION-DATE 3262709627)
(OCELOT::PARENTS |physicalEntity|) )
NIL)

(|environment| T (
(THOUGHT "This class requires more conceptual work.")
(COMMENT "A physical or environmental effect.")
(:CREATOR |Gary Bader|)
(:CREATION-DATE 3262709649)
(OCELOT::PARENTS |physicalEntity|) )
NIL)

(|photon| T (
(THOUGHT
 "This class is unfinished.  Slots need to be added for wavelength and intensity.")
(CLASS-DESIGN-RATIONALE
 "Certain databases, such as BIND, contain this class of physical entities.  It is useful for describing many biological processes, such as radiation DNA damage and photosynthesis.")
(COMMENT
 "Light at either a specified or unspecified intensity and wavelength (e.g. UV light).")
(:CREATOR |Gary Bader|)
(:CREATION-DATE 3262709902)
(OCELOT::PARENTS |physicalEntity|) )
NIL)

(|entrySet| T (
(COMMENT "Root element of the Molecular interaction Format")
(:CREATOR |Gary Bader|)
(:CREATION-DATE 3266853832)
(OCELOT::PARENTS |utilityClasses|) )
NIL)

(|entry| T (
(COMMENT
 "Describes one or more interactions as a self-contained unit. Multiple entries from different files can be concatenated into a single entrySet.")
(:CREATOR |Gary Bader|)
(:CREATION-DATE 3266853864)
(OCELOT::PARENTS |utilityClasses|) )
NIL)

(LEVEL NIL (
(:DOCUMENTATION "The level of this ontology (e.g. Level 1, version 1)")
(:VALUE-TYPE :INTEGER)
(:DOMAIN |entrySet|)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(VERSION NIL (
(:DOCUMENTATION
 "The version of this ontology (e.g. Level 1, version 1)")
(:VALUE-TYPE :INTEGER)
(:DOMAIN |entrySet|)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(ENTRIES NIL (
(:DOCUMENTATION
 "A set of entries.  This is the top-level packaging class in the ontology.")
(:VALUE-TYPE |entry|)
(:MINIMUM-CARDINALITY 0)
(:DOMAIN |entrySet|)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(DELTA-G NIL (
(:VALUE-TYPE :LIST)
(:DOCUMENTATION
 "Standard Gibbs free energy change for a reaction (see notes in individual class definitions).")
(:DOMAIN |biochemicalReaction|)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(DELTA-H NIL (
(:DOCUMENTATION
 "Standard enthalpy change for a reaction (see notes in individual class definitions).")
(:VALUE-TYPE :NUMBER)
(:DOMAIN |biochemicalReaction|)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(DELTA-S NIL (
(:DOCUMENTATION
 "Standard entropy change for a reaction (see notes in individual class definitions).")
(:VALUE-TYPE :NUMBER)
(:DOMAIN |biochemicalReaction|)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(EC-NUMBER NIL (
(:DOCUMENTATION
 "The number assigned to a reaction by the Enzyme Commission.

Note that not all biochemical reactions currently have EC numbers assigned
to them.")
(:VALUE-TYPE :STRING)
(:DOMAIN |biochemicalReaction|)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(KEQ NIL (
(:DOCUMENTATION
 "The reaction equilibrium constant (see notes under individual reaction subclass definitions).")
(:VALUE-TYPE :NUMBER)
(:DOMAIN |biochemicalReaction|)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(SPONTANEOUS NIL (
(:DOCUMENTATION
 "Specifies whether a reaction occurs spontaneously (i.e. uncatalyzed, under biological conditions) left-to-right, right-to-left, or not at all.
An absence of a value for this slot implies that the reaction is not spontaneous, so the possible values need only distinguish between
the two possible directions.")
(:MAXIMUM-CARDINALITY 1)
(:VALUE-TYPE (:ONE-OF :L-R R-L))
(:DOMAIN |biochemicalReaction|)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(LEFT NIL (
(:DOCUMENTATION
 "The left hand value in the conversion process (e.g. the reactants in a biochemical reaction)")
(:VALUE-TYPE |entity|)
(:DOMAIN |conversion|)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(RIGHT NIL (
(:DOCUMENTATION
 "The right hand value in the conversion process (e.g. the products in a biochemical reaction)")
(:VALUE-TYPE |entity|)
(:DOMAIN |conversion|)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(ENTITIES NIL (
(:DOCUMENTATION "A list of entities")
(:VALUE-TYPE |entity|)
(:DOMAIN |co-occurrence| |equivalenceClass|)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(CONTROLLER NIL (
(:DOCUMENTATION
 "The controlling entity (e.g for a biochemical reaction, this would be an enzyme)")
(:VALUE-TYPE |entity|)
(:DOMAIN |control|)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(CONTROLLED NIL (
(:DOCUMENTATION
 "The entity that is controlled (e.g for a biochemical reaction, this would be a reaction).")
(:VALUE-TYPE |entity|)
(:DOMAIN |control|)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(THOUGHT NIL (
(:INHERITANCE-TYPE :UNIQUE)
(:VALUE-TYPE :STRING)
(:DOMAIN OCELOT::FRAMES)
(:DOCUMENTATION
 "Comment about how much thought has been invested in the design of this slot or frame.")
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(CLASS-NAME-SYNONYMS NIL (
(:INHERITANCE-TYPE :UNIQUE)
(:VALUE-TYPE :STRING)
(:DOMAIN OCELOT::FRAMES)
(:DOCUMENTATION "Synonym for the name of the frame or slot.")
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)

(SLOT-NAME-SYNONYMS NIL (
(:DOMAIN NIL)
(OCELOT::PARENTS OCELOT::DOMAIN-SLOTS) )
NIL)