CELLTYPE
type: ObjectProperty
comment: A cell type, e.g. 'HeLa'. This should reference a term in a controlled vocabulary of cell types.
domain: bioSource
range: openControlledVocabulary

CELLULAR-LOCATION
type: ObjectProperty
comment: A cellular location, e.g. 'cytoplasm'. This should reference a term in the Gene Ontology Cellular Component ontology. The location referred to by this slot should be as specific as is known. If an interaction is known to occur in multiple locations, separate interactions (and physicalEntityParticipants) must be created for each different location. Note: If a location is unknown then the GO term for 'cellular component unknown' (GO:0008372) should be used in the LOCATION slot. Note: Cellular location describes a specific location of a physical entity as it would be used in e.g. a transport reaction. It does not describe all of the possible locations that the physical entity could be in the cell.
range: openControlledVocabulary
domain: physicalEntityParticipant

COFACTOR
type: ObjectProperty
comment: Any cofactor(s) or coenzyme(s) required for catalysis of the conversion by the enzyme.
sub property of: PARTICIPANTS
domain: catalysis
range: physicalEntityParticipant

COMPONENTS
type: ObjectProperty
comment: Defines the physicalEntity subunits of this complex.
domain: complex
range: physicalEntityParticipant

CONTROLLED
type: ObjectProperty
comment: The entity that is controlled, e.g., in a biochemical reaction, the reaction is controlled by an enzyme.
sub property of: PARTICIPANTS
domain: control
range: Class
  union of: entity
  union of: physicalEntityParticipant

CONTROLLER
type: ObjectProperty
comment: The controlling entity, e.g., in a biochemical reaction, an enzyme is the controlling entity of the reaction.
sub property of: PARTICIPANTS
domain: control
range: physicalEntityParticipant

DATA-SOURCE
type: ObjectProperty
comment: A free text description of the source of this data e.g. a database or person name.
range: dataSource
domain: entity

LEFT
type: ObjectProperty
comment: The participants on the left side of the conversion interaction. Since conversion interactions may proceed in either the left-to-right or right-to-left direction, occupants of the LEFT slot may be either reactants or products.
sub property of: PARTICIPANTS
domain: conversion
range: physicalEntityParticipant

NEXT-STEP
type: ObjectProperty
comment: The next step(s) of the pathway. Contains zero or more pathwayStep instances. If there is no next step, this slot is empty.
range: pathwayStep
domain: pathwayStep

ORGANISM
type: ObjectProperty
comment: An organism, e.g. 'Homo sapiens'.
range: bioSource
domain: Class
  union of: complex
  union of: pathway
  union of: protein
  union of: rna

PARTICIPANTS
type: ObjectProperty
comment: This slot lists the entities that participate in this interaction. For example, in a biochemical reaction, the participants are the union of the reactants and the products of the reaction.
domain: interaction
range: Class
  union of: entity
  union of: physicalEntityParticipant

PATHWAY-COMPONENTS
type: ObjectProperty
comment: A list of interactions and/or steps in this pathway/network. Note: Temporal ordering relationships among the interactions within a pathway are described using the pathwayStep instances. Each instance of the pathwayStep class defines the interactions that take place at a pathway step and an ordering relationship between pathway steps by pointing to the next pathwayStep in the pathway. This notion of ordering is not further formalized in the current BioPAX level to support other of types of ordering, like spatial ordering, or any detailed aspects of temporal ordering, like delay between events.
domain: pathway
range: Class
  union of: interaction
  union of: pathwayStep

PHYSICAL-ENTITY
type: ObjectProperty
comment: The physical entity annotated with stoichiometry and cellular location attributes from the physicalEntityParticipant instance.
range: physicalEntity
domain: physicalEntityParticipant

RIGHT
type: ObjectProperty
comment: The participants on the right side of the conversion interaction. Since conversion interactions may proceed in either the left-to-right or right-to-left direction, occupants of the RIGHT slot may be either reactants or products.
sub property of: PARTICIPANTS
domain: conversion
range: physicalEntityParticipant

STEP-INTERACTIONS
type: ObjectProperty
comment: The interactions that take place at this step of the pathway.
range: interaction
domain: pathwayStep

STRUCTURE
type: ObjectProperty
comment: Defines the chemical structure and other information about this molecule, using an instance of class chemicalStructure.
range: chemicalStructure
domain: smallMolecule

TAXON-XREF
type: ObjectProperty
comment: An xref to an organism taxonomy database, preferably NCBI taxon. This should be a unification xref, unless the organism is not in an existing database.
domain: bioSource
range: xref

TISSUE
type: ObjectProperty
comment: An external controlled vocabulary of tissue types.
domain: bioSource
range: openControlledVocabulary

XREF
type: ObjectProperty
comment: Values of this slot define external cross-references from this entity to entities in external databases.
range: xref
domain: Class
  union of: entity
  union of: openControlledVocabulary

AUTHORS
type: DatatypeProperty
comment: The authors of this publication, one per slot value.
domain: publicationXref
range: string

AVAILABILITY
type: DatatypeProperty
comment: Describes the availability of this data (e.g. a copyright statement).
domain: entity
range: string

CHEMICAL-FORMULA
type: DatatypeProperty
comment: The chemical formula of the small molecule. Note: chemical formula can also be stored in the STRUCTURE slot (in CML). In case of disagreement between the value of this slot and that in the CML file, the CML value takes precedence.
domain: smallMolecule
range: string

COMMENT
type: DatatypeProperty
comment: Comment on the data in the container class.
range: string
domain: Class
  union of: entity
  union of: utilityClass

CONTROL-TYPE
type: DatatypeProperty
comment: Defines the nature of the control relationship between the CONTROLLER and the CONTROLLED entities. The following terms are possible values: ACTIVATION: General activation The following term can not be used in the catalysis class: INHIBITION: General inhibition The following terms can only be used in the modulation class: INHIBITION-ALLOSTERIC Allosteric inhibitors decrease the specified enzyme activity by binding reversibly to the enzyme and inducing a conformational change that decreases the affinity of the enzyme to its substrates without affecting its VMAX. Allosteric inhibitors can be competitive or noncompetitive inhibitors, therefore, those inhibition categories can be used in conjunction with this category. INHIBITION-COMPETITIVE Competitive inhibitors are compounds that competitively inhibit the specified enzyme activity by binding reversibly to the enzyme and preventing the substrate from binding. Binding of the inhibitor and substrate are mutually exclusive because it is assumed that the inhibitor and substrate can both bind only to the free enzyme. A competitive inhibitor can either bind to the active site of the enzyme, directly excluding the substrate from binding there, or it can bind to another site on the enzyme, altering the conformation of the enzyme such that the substrate can not bind to the active site. INHIBITION-IRREVERSIBLE Irreversible inhibitors are compounds that irreversibly inhibit the specified enzyme activity by binding to the enzyme and dissociating so slowly that it is considered irreversible. For example, alkylating agents, such as iodoacetamide, irreversibly inhibit the catalytic activity of some enzymes by modifying cysteine side chains. INHIBITION-NONCOMPETITIVE Noncompetitive inhibitors are compounds that noncompetitively inhibit the specified enzyme by binding reversibly to both the free enzyme and to the enzyme-substrate complex. The inhibitor and substrate may be bound to the enzyme simultaneously and do not exclude each othe…
domain: control
range: Datatype
  one of: ACTIVATION
  one of: ACTIVATION-ALLOSTERIC
  one of: ACTIVATION-NONALLOSTERIC
  one of: ACTIVATION-UNKMECH
  one of: INHIBITION
  one of: INHIBITION-ALLOSTERIC
  one of: INHIBITION-COMPETITIVE
  one of: INHIBITION-IRREVERSIBLE
  one of: INHIBITION-NONCOMPETITIVE
  one of: INHIBITION-OTHER
  one of: INHIBITION-UNCOMPETITIVE
  one of: INHIBITION-UNKMECH

DB
type: DatatypeProperty
comment: The name of the external database to which this xref refers.
domain: xref
range: string

DB-VERSION
type: DatatypeProperty
comment: The version of the external database in which this xref was last known to be valid.
domain: xref
range: string

DELTA-G
type: DatatypeProperty
comment: 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'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 slot 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)
domain: biochemicalReaction
range: double

DELTA-H
type: DatatypeProperty
comment: 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'o. delta-G'o = delta-H'o - T delta-S'o (This definition from EcoCyc)
domain: biochemicalReaction
range: double

DELTA-S
type: DatatypeProperty
comment: 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'o. delta-G'o = delta-H'o - T delta-S'o (This definition from EcoCyc)
domain: biochemicalReaction
range: double

DIRECTION
type: DatatypeProperty
comment: Specifies the reaction direction of the interaction catalyzed by this instance of the catalysis class. Possible values of this slot are: REVERSIBLE: Interaction occurs in both directions in physiological settings. PHYSIOL-LEFT-TO-RIGHT PHYSIOL-RIGHT-TO-LEFT The interaction occurs in the specified direction in physiological settings, because of several possible factors including the energetics of the reaction, local concentrations of reactants and products, and the regulation of the enzyme or its expression. IRREVERSIBLE-LEFT-TO-RIGHT IRREVERSIBLE-RIGHT-TO-LEFT For all practical purposes, the interactions occurs only in the specified direction in physiological settings, because of chemical properties of the reaction. (This definition from EcoCyc)
domain: catalysis
range: Datatype
  one of: IRREVERSIBLE-LEFT-TO-RIGHT
  one of: IRREVERSIBLE-RIGHT-TO-LEFT
  one of: PHYSIOL-LEFT-TO-RIGHT
  one of: PHYSIOL-RIGHT-TO-LEFT
  one of: REVERSIBLE

EC-NUMBER
type: DatatypeProperty
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.
domain: biochemicalReaction
range: string

ID
type: DatatypeProperty
comment: The primary identifier in the external database of the object to which this xref refers.
domain: xref
range: string

ID-VERSION
type: DatatypeProperty
comment: The version number of the identifier (ID). E.g. The RefSeq accession number NM_005228.3 should be split into NM_005228 as the ID and 3 as the ID-VERSION.
domain: xref
range: string

KEQ
type: DatatypeProperty
comment: 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][Pi]/[ATP], The concentration of ATP refers to the total concentration of all of the following species: [ATP] = [ATP4-] + [HATP3-] + [H2ATP2-] + [MgATP2-] + [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, 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. (This definition from EcoCyc)
domain: biochemicalReaction
range: double

MOLECULAR-WEIGHT
type: DatatypeProperty
comment: Defines the molecular weight of the molecule, in daltons.
domain: smallMolecule
range: double

NAME
type: DatatypeProperty
comment: The preferred full name for this entity.
range: string
domain: Class
  union of: bioSource
  union of: dataSource
  union of: entity

RELATIONSHIP-TYPE
type: DatatypeProperty
comment: This slot names the type of relationship between the BioPAX object linked from, and the external object linked to, such as 'gene of this protein', or 'protein with similar sequence'.
domain: relationshipXref
range: string

SEQUENCE
type: DatatypeProperty
comment: Polymer sequence in uppercase letters.
range: string
domain: Class
  union of: protein
  union of: rna

SHORT-NAME
type: DatatypeProperty
comment: An abbreviated name for this entity. Preferably a name that is short enough to be used in a visualization application to label a graphical element that represents this entity. If no short name is available, an xref may be used for this purpose.
domain: entity
range: string

SOURCE
type: DatatypeProperty
comment: The source in which the reference was published, such as: a book title, or a journal title and volume and pages.
domain: publicationXref
range: string

SPONTANEOUS
type: DatatypeProperty
comment: 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.
domain: conversion
range: Datatype
  one of: L-R
  one of: R-L

STOICHIOMETRIC-COEFFICIENT
type: DatatypeProperty
comment: Each value of this slot represents the stoichiometric coefficient for one of the physical entities in an interaction or complex.
domain: physicalEntityParticipant
range: double

STRUCTURE-DATA
type: DatatypeProperty
comment: This slot holds a string of data defining chemical structure or other information, in either the CML or SMILES format, as specified in slot Structure-Format. If, for example, the CML format is used, then the value of this slot is a string containing the XML encoding of the CML data.
domain: chemicalStructure
range: string

STRUCTURE-FORMAT
type: DatatypeProperty
comment: This slot specifies which format is used to define chemical structure data.
domain: chemicalStructure
range: Datatype
  one of: CML
  one of: SMILES

SYNONYMS
type: DatatypeProperty
comment: One or more synonyms for the name of this entity.
domain: entity
range: string

TERM
type: DatatypeProperty
comment: The external controlled vocabulary term.
domain: openControlledVocabulary
range: string

TITLE
type: DatatypeProperty
comment: The title of the publication.
domain: publicationXref
range: string

URL
type: DatatypeProperty
comment: The URL at which the publication can be found, if it is available through the Web.
domain: publicationXref
range: string

YEAR
type: DatatypeProperty
comment: The year in which this publication was published.
domain: publicationXref
range: double

bioSource
type: Class
subclass of: utilityClass
subclass of: Restriction
  on property: NAME
  max cardinality: 1
subclass of: Restriction
  on property: CELLTYPE
  max cardinality: 1
subclass of: Restriction
  on property: TISSUE
  max cardinality: 1
subclass of: Restriction
  on property: TAXON-XREF
  cardinality: 1
disjoint with: chemicalStructure
disjoint with: dataSource
disjoint with: openControlledVocabulary
disjoint with: pathwayStep
disjoint with: physicalEntityParticipant
disjoint with: xref
comment: A utility class that defines the biological source of a protein or RNA. Other entities are either considered source-neutral (e.g. small molecules) or their biological source can be deduced from their constituents. Examples include human, mouse liver tissue, and HeLa cells. The optional NAME slot should be the full 'Genus species' name of the organism, with the genus capitalized and not abbreviated and the species not capitalized and not abbreviated.

biochemicalReaction
type: Class
subclass of: conversion
disjoint with: complexAssembly
comment: 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 what is typically done in biochemistry, and, in principle, all of the EC reactions should be biochemical reactions. Example: ATP + H2O = ADP + Pi. In this reaction, 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 important not to attach charges to the biochemical reactants and not 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. (This definition from EcoCyc) NOTE: 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.

catalysis
type: Class
subclass of: control
subclass of: Restriction
  on property: CONTROL-TYPE
  has value: ACTIVATION
subclass of: Restriction
  on property: DIRECTION
  max cardinality: 1
subclass of: Restriction
  on property: CONTROLLED
  all values from: conversion
subclass of: Restriction
  on property: CONTROLLER
  max cardinality: 1
disjoint with: modulation
comment: A control interaction in which a physical entity (a catalyst) increases the rate of a conversion interaction by lowering its activation energy. Instances of this class describe a pairing between a catalyzing entity and a catalyzed conversion. A separate catalysis instance should be created for each different conversion that a physical entity may catalyze and for each different physical entity that may catalyze a conversion. For example, a bifunctional enzyme that catalyzes two different biochemical reactions would be linked to each of those biochemical reactions by two separate instances of the catalysis class. Typically, each step in a metabolic pathway is either an instance of the catalysis class or a spontaneous conversion, which occurs under biological conditions without the aid of a catalyzing entity. Synonyms for this class include 'facilitation' and 'acceleration'. Examples of this class include the catalysis of a biochemical reaction by an enzyme, the enabling of a transport interaction by a membrane pore complex, and the facilitation of a complex assembly by a scaffold protein.

chemicalStructure
type: Class
subclass of: utilityClass
subclass of: Restriction
  on property: STRUCTURE-FORMAT
  cardinality: 1
subclass of: Restriction
  on property: STRUCTURE-DATA
  cardinality: 1
disjoint with: dataSource
disjoint with: openControlledVocabulary
disjoint with: pathwayStep
disjoint with: physicalEntityParticipant
disjoint with: xref
comment: A utility class that defines a small molecule structure. An instance of this class can also define additional information about a small molecule, such as its chemical formula, names, and synonyms. This information is stored in the slot STRUCTURE-DATA, in one of two formats: the CML format (see URL www.xml-cml.org) or the SMILES format (see URL www.daylight.com/dayhtml/smiles/). The STRUCTURE-FORMAT slot specifies which format used is used. An example is the following SMILES string, which describes the structure of glucose-6-phosphate: 'C(OP(=O)(O)O)[CH]1([CH](O)[CH](O)[CH](O)[CH](O)O1)'.

complex
type: Class
subclass of: physicalEntity
disjoint with: protein
disjoint with: rna
disjoint with: smallMolecule
comment: A physical entity whose structure is comprised of other physical entities bound to each other non-covalently, at least one of which is a macromolecule (protein or RNA). Complexes must be stable enough to function as a biological unit; in general, the temporary association of an enzyme with its substrate(s) should not be considered or represented as a complex. A complex is the physical product of an interaction (complex assembly), thus is not an interaction itself. Examples of this class include complexes of multiple protein monomers and complexes of proteins and small molecules. NOTE: Complexes can be defined recursively to describe smaller complexes within larger complexes, e.g., a participant in a complex can itself be a complex. NOTE: The boundaries on the size of complexes described by this class are not defined here, although elements of the cell as large and dynamic as, e.g., a mitochondrion would typically not be described using this class (later versions of this ontology may include a cellularComponent class to represent these). The strength of binding of the components is also not described.

complexAssembly
type: Class
subclass of: conversion
disjoint with: transport
comment: A conversion interaction in which a set of physical entities, at least one being a macromolecule (protein or RNA), aggregate via non-covalent interactions. One of the participants of a complexAssembly must be an instance of the class complex. Synonyms for this class include 'aggregation' and 'complexFormation'. Examples of this class include the assembling of the TFB2 and TFB3 proteins into the TFIIH complex, and the assembly of the ribosome through aggregation of its subunits. NOTE: This class is also used to represent complex disassembly. The direction in which the complexAssembly occurs (toward either assembly or disassembly) is specified via either the SPONTANEOUS slot or the DIRECTION slot (in the catalysis class), depending on whether the interaction occurs spontaneously or must be catalyzed in order to occur. NOTE: The following are not examples of complex assembly: Covalent phosphorylation of a protein (this is a biochemicalReaction), the TFIIH complex itself (this is an instance of the complex class, not the complexAssembly class).

control
type: Class
subclass of: interaction
subclass of: Restriction
  on property: CONTROL-TYPE
  max cardinality: 1
disjoint with: conversion
comment: An interaction in which one entity regulates, modifies, or otherwise influences another. Two types of control interactions are defined: activation and inhibition. Since this class is a superclass for specific types of control, instances of the control class should only be generated when none of its subclasses are applicable. One example of an instance of this class would be a small molecule that inhibits a pathway by an unknown mechanism. CLASS-NAME-SYNONYMS: regulation, mediation

conversion
type: Class
subclass of: interaction
subclass of: Restriction
  on property: SPONTANEOUS
  max cardinality: 1
subclass of: Restriction
  on property: PARTICIPANTS
  all values from: physicalEntityParticipant
comment: An interaction in which one or more entities is physically transformed into one or more other entities. This class is designed to represent a simple, single-step transformation. Multi-step transformations, such as the conversion of glucose to pyruvate in the glycolysis pathway, should be represented as pathways, if known. Since it is a highly abstract class in the ontology, instances of the conversion class should be created rarely, if ever.

dataSource
type: Class
subclass of: utilityClass
disjoint with: openControlledVocabulary
disjoint with: pathwayStep
disjoint with: physicalEntityParticipant
disjoint with: xref
comment: A description of the source of this data e.g. a database or person name. Currently, this class only contains a free text description, but may be made more structured in future levels.

entity
type: Class
subclass of: Thing
subclass of: Restriction
  on property: NAME
  max cardinality: 1
subclass of: Restriction
  on property: SHORT-NAME
  max cardinality: 1
disjoint with: utilityClass
comment: Any concept that we will refer to as a discrete biological unit when describing pathways. This is the root class for all biological concepts in the ontology, which include pathways, interactions and physical entities. Synonyms for this class include 'thing', 'object' and 'bioentity'. As the most abstract class in the ontology, instances of the entity class should be created rarely, if ever.

interaction
type: Class
subclass of: entity
subclass of: Restriction
  on property: PARTICIPANTS
  some values from: Class
    union of: entity
    union of: physicalEntityParticipant
disjoint with: pathway
disjoint with: physicalEntity
comment: An entity that defines a single biochemical interaction between two or more entities. An interaction cannot be defined without the entities it relates. Since it is a highly abstract class in the ontology, instances of the interaction class should be created rarely. CLASS-DESIGN-RATIONALE: Interaction was chosen as it is understood by biologists in a biological context and is compatible with PSI-MI (http://psidev.sf.net).

modulation
type: Class
subclass of: control
subclass of: Restriction
  on property: CONTROLLER
  max cardinality: 1
subclass of: Restriction
  on property: CONTROLLED
  all values from: catalysis
comment: A control interaction in which a physical entity modulates a catalysis interaction. Biologically, most modulation interactions describe an interaction in which a small molecule alters the ability of an enzyme to catalyze a specific reaction. Instances of this class describe a pairing between a modulating entity and a catalysis interaction. A separate modulation instance should be created for each different catalysis that a physical entity may modulate and for each different physical entity that may modulate a catalysis instance. A typical modulation instance has a small molecule as the controller entity and a catalysis instance as the controlled entity. Examples of instances of this class include allosteric activation and competitive inhibition of an enzyme's ability to catalyze a specific reaction.

openControlledVocabulary
type: Class
subclass of: utilityClass
disjoint with: pathwayStep
disjoint with: physicalEntityParticipant
disjoint with: xref
comment: A utility class used to import terms from external controlled vocabularies (CVs) into the ontology. To support consistency and compatibility, open, freely available CVs should be used whenever possible, such as the Gene Ontology (GO). A repository for open biological CVs has been created by the OBO project (http://obo.sourceforge.net/).

pathway
type: Class
subclass of: entity
subclass of: Restriction
  on property: ORGANISM
  max cardinality: 1
disjoint with: physicalEntity
comment: An entity that consists of a set of interactions. A pathway is a series of molecular interactions and reactions, often forming a network, that biologists have found useful to group together for organizational, historic, biophysical or other reasons. A synonym for this class is 'network'. NOTE: It is possible to define a pathway without specifying the interactions within the pathway. In this case, the pathway instance could consist simply of a name and could be treated as a black box.

pathwayStep
type: Class
subclass of: utilityClass
subclass of: Restriction
  on property: STEP-INTERACTIONS
  min cardinality: 1
disjoint with: physicalEntityParticipant
disjoint with: xref
comment: A utility class that describes the order in which interactions occur in a pathway. The interactions that take place at a pathway step are listed and an ordering relationship between pathway steps by pointing to the next pathwayStep(s) in the pathway is given. For example, a metabolic pathway may contain a pathway step composed of one biochemical reaction (BR1) and one catalysis (CAT1) instance, where CAT1 describes the catalysis of BR1.

physicalEntity
type: Class
subclass of: entity
comment: An entity that has a physical structure. This class serves as the super-class for all physical entities, although its current set of subclasses is limited to molecules. Physical entities are frequent building blocks of interactions. As a highly abstract class in the ontology, instances of the physicalEntity class should be created rarely, if ever. CLASS-DESIGN-RATIONALE: It's difficult to find a name that encompasses all of the subclasses of this class without being too general. E.g. PSI-MI uses interactor, BIND uses object, BioCyc uses chemicals. physicalEntity seems to be a good specialization of entity. CLASS-NAME-SYNONYMS: part, interactor, object

physicalEntityParticipant
type: Class
subclass of: utilityClass
subclass of: Restriction
  on property: STOICHIOMETRIC-COEFFICIENT
  max cardinality: 1
subclass of: Restriction
  on property: CELLULAR-LOCATION
  max cardinality: 1
subclass of: Restriction
  on property: PHYSICAL-ENTITY
  cardinality: 1
disjoint with: xref
comment: A utility class that describes any additional special characteristics of a physical entity required in order for it to participate in an interaction. In the current ontology, these include stoichiometric coefficient and cellular location. For example, in the interaction describing the transport of L-arginine into the cytoplasm in E. coli, the LEFT slot in the interaction would be filled with an instance of physicalEntityParticipant that specified the location of L-arginine as periplasm and the stoichiometric coefficient as one.

protein
type: Class
subclass of: physicalEntity
subclass of: Restriction
  on property: SEQUENCE
  max cardinality: 1
subclass of: Restriction
  on property: ORGANISM
  max cardinality: 1
disjoint with: rna
disjoint with: smallMolecule
comment: A physical entity consisting of a sequence of amino-acids; a protein monomer; a single polypeptide chain. An example is the EGFR protein.

publicationXref
type: Class
subclass of: xref
subclass of: Restriction
  on property: YEAR
  max cardinality: 1
subclass of: Restriction
  on property: TITLE
  max cardinality: 1
disjoint with: relationshipXref
disjoint with: unificationXref
comment: An xref that defines a reference to a publication such as a book, journal article, web page, or software manual. The reference may or may not be in a database, although references to PubMed are preferred when possible. The publication should make a direct reference to the instance it is attached to.

relationshipXref
type: Class
subclass of: xref
subclass of: Restriction
  on property: RELATIONSHIP-TYPE
  max cardinality: 1
subclass of: Restriction
  on property: ID
  cardinality: 1
subclass of: Restriction
  on property: DB
  cardinality: 1
disjoint with: unificationXref
comment: An xref that defines a reference to an entity in an external resource that does not have the same biological identity as the referring entity. For example, if one wished to define a link between a gene G in a BioPAX data collection, and the protein product P of that gene in an external database, one would use a relationship link, because G and P are different biological entities (one is a gene and one is a protein). Another example is a relationship xref for a protein that refers to the Gene Ontology biological process, e.g. 'immune response,' that the protein is involved in.

rna
type: Class
subclass of: physicalEntity
subclass of: Restriction
  on property: ORGANISM
  max cardinality: 1
subclass of: Restriction
  on property: SEQUENCE
  max cardinality: 1
disjoint with: smallMolecule
comment: A physical entity consisting of a sequence of ribonucleotide monophosphates; a ribonucleic acid (e.g. messengerRNA, microRNA, ribosomalRNA). A specific example is the let-7 microRNA.

smallMolecule
type: Class
subclass of: physicalEntity
subclass of: Restriction
  on property: MOLECULAR-WEIGHT
  max cardinality: 1
subclass of: Restriction
  on property: CHEMICAL-FORMULA
  max cardinality: 1
comment: Any bioactive molecule that is not a peptide, protein, or RNA. Generally these are non-polymeric, but complex carbohydrates and DNA are not explicitly modeled as classes in this version of the ontology, thus are forced into this class. Note that there is a known lack of adequate small molecule databases to cross-reference from this class.

transport
type: Class
subclass of: conversion
comment: A conversion interaction in which an entity (or set of entities) changes location within or with respect to the cell. A transport interaction does not include the transporter entity, even if one is required in order for the transport to occur. Instead, transporters are linked to transport interactions via the catalysis class. A synonym for the transport class is 'translocation'. One example of this class is the movement of Na+ into the cell through an open voltage-gated channel. NOTE: Transport interactions do not involve chemical changes of the participant(s). These cases are handled by the transportWithBiochemicalReaction class.

transportWithBiochemicalReaction
type: Class
subclass of: biochemicalReaction
subclass of: transport
comment: A conversion interaction that is both a biochemical reaction and a transport. In transportWithBiochemicalReaction interactions, one or more of the substrates change both their location and their physical structure. For example, in the PEP-dependent phosphotransferase system, transportation of sugar into an E. coli cell is accompanied by the sugar's phosphorylation as it crosses the plasma membrane. Also, active transporters that use ATP as an energy source fall under this category, even if the only covalent change is the hydrolysis of ATP to ADP.

unificationXref
type: Class
subclass of: xref
subclass of: Restriction
  on property: DB
  cardinality: 1
subclass of: Restriction
  on property: ID
  cardinality: 1
comment: A unification defines a reference to an entity in an external resource that has the same biological identity as the referring entity. For example, if one wished to link from a database record, C, describing a chemical compound in a BioPAX data collection to a record, C', describing the same chemical compound in an external database, one would use a unification xref since records C and C' describe the same biological identity. Generally, unification xrefs should be used whenever possible, although there are cases where they might not be useful, such as application to application data exchange. NOTE: Unification xrefs in physical entities are essential for data integration, but are less important in interactions. This is because unification xrefs on the physical entities in an interaction can be used to compute the equivalence of two interactions of the same type. NOTE: An xref in a protein pointing to a gene, e.g. in the LocusLink database, would not be a unification xref since the two entities do not have the same biological identity (one is a protein, the other is a gene). Instead, this link should be a captured as a relationship xref.

utilityClass
type: Class
comment: Utility classes are created when simple slots are insufficient to describe an aspect of an entity or to increase compatibility of this ontology with other standards. The utilityClass class is only present to organize the other helper classes under one class hierarchy; instances of utilityClass should never be created.

xref
type: Class
subclass of: utilityClass
subclass of: Restriction
  on property: ID
  max cardinality: 1
subclass of: Restriction
  on property: DB-VERSION
  max cardinality: 1
subclass of: Restriction
  on property: DB
  max cardinality: 1
subclass of: Restriction
  on property: ID-VERSION
  max cardinality: 1
comment: A utility class that defines a reference between an instance of a class in this ontology to an object in an external resource. As the most abstract xref class in the ontology, instances of the xref class should be created rarely, if ever.