BIOPAX Ontology

Contents:

Class definitions
Slot definitions

Class Definitions

This section of the HTML version of the ontology contains the class definitions of the ontology. Each class defines a type of entity. A class is defined to have a set of slots, where each slot defines attributes and properties that may be used by an instance of that class.

Slots are inherited by a class from its parent classes. Usually this HTML form of the ontology shows only the names of the slots at each class, with links provided to the full definition of the slot in the slot section of the ontology. However, when the definition of a slot is changed within a class with respect to its parent, the full definition of the slot is shown.

Class: entity

Any concept that we will refer to as a discrete unit when describing biological pathways. e.g. a pathway, interaction or physical entity.

Subclasses: interaction, physicalEntity, pathway

Slots:

ATTRIBUTELIST
AVAILABILITY
CLASS-DESIGN-RATIONALE
CLASS-NAME-SYNONYMS
COMMENT
NAMES
THOUGHT

Class: interaction

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.

Supperclasses: entity

Subclasses: control, conversion, genetic, equivalenceClass, molecularAssociation, co-occurrence

Slots:

ATTRIBUTELIST
AVAILABILITY
CLASS-DESIGN-RATIONALE
CLASS-NAME-SYNONYMS
COMMENT
CONFIDENCE
EXPERIMENTLIST
INTERACTIONTYPE
NAMES
THOUGHT

Class: control

The control of a process (e.g. enzyme catalysis controls a biochemical reaction, gene regulation controls gene expression).

Supperclasses: interaction

Subclasses: enzymeCatalysis, transportCatalysis, geneRegulation

Slots:

ATTRIBUTELIST
AVAILABILITY
CLASS-DESIGN-RATIONALE
CLASS-NAME-SYNONYMS
COMMENT
CONFIDENCE
CONTROLLED
CONTROLLER
EXPERIMENTLIST
INTERACTIONTYPE
NAMES
THOUGHT

Class: enzymeCatalysis

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.

Supperclasses: control

Slots:

ATTRIBUTELIST
AVAILABILITY
CLASS-DESIGN-RATIONALE
CLASS-NAME-SYNONYMS
COMMENT
CONFIDENCE
CONTROLLED
CONTROLLER
EXPERIMENTLIST
INTERACTIONTYPE
NAMES
THOUGHT

Class: transportCatalysis

Control of the process of transportation. An active or passive transporter can facilitate a translocation event.

Supperclasses: control

Slots:

ATTRIBUTELIST
AVAILABILITY
CLASS-DESIGN-RATIONALE
CLASS-NAME-SYNONYMS
COMMENT
CONFIDENCE
CONTROLLED
CONTROLLER
EXPERIMENTLIST
INTERACTIONTYPE
NAMES
THOUGHT

Class: geneRegulation

The process of gene regulation by a transcription factor. A transcription factor binds upstream

Supperclasses: control

Slots:

ATTRIBUTELIST
AVAILABILITY
CLASS-DESIGN-RATIONALE
CLASS-NAME-SYNONYMS
COMMENT
CONFIDENCE
CONTROLLED
CONTROLLER
EXPERIMENTLIST
INTERACTIONTYPE
NAMES
THOUGHT

Class: conversion

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).

Supperclasses: interaction

Subclasses: biochemicalReaction, transport, translation, transcription, complexAssembly

Slots:

ATTRIBUTELIST
AVAILABILITY
CLASS-DESIGN-RATIONALE
CLASS-NAME-SYNONYMS
COMMENT
CONFIDENCE
EXPERIMENTLIST
INTERACTIONTYPE
LEFT:

VALUE-TYPE: entity
SLOT-NAME-SYNONYMS: reactants, input
NAMES
REVERSIBILITY
RIGHT:

VALUE-TYPE: entity
SLOT-NAME-SYNONYMS: products, output
THOUGHT

Class: biochemicalReaction

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 + H₂O = ADP + P_i. In this reaction, ATP is considered to be an equilibrium mixture of several species, namely ATP^4-, HATP^3-, H₂ATP^2-, MgATP^2-, 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 (P_i). 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.

Supperclasses: conversion

Slots:

ATTRIBUTELIST
AVAILABILITY
CLASS-DESIGN-RATIONALE
CLASS-NAME-SYNONYMS
COMMENT
CONFIDENCE

DELTA-G:

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.

VALUE-TYPE: LIST

DELTA-H:

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

VALUE-TYPE: NUMBER

DELTA-S:

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

VALUE-TYPE: NUMBER

EC-NUMBER
EXPERIMENTLIST
INTERACTIONTYPE

KEQ:

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, 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.

VALUE-TYPE: NUMBER

LEFT
NAMES
REVERSIBILITY
RIGHT
SPONTANEOUS
THOUGHT

Class: transport

The process of transport from one spatial location to another, typically within or at

Supperclasses: conversion

Slots:

ATTRIBUTELIST
AVAILABILITY
CLASS-DESIGN-RATIONALE
CLASS-NAME-SYNONYMS
COMMENT
CONFIDENCE
EXPERIMENTLIST
INTERACTIONTYPE
LEFT
NAMES
REVERSIBILITY
RIGHT
THOUGHT

Class: translation

Process of translation. This is useful to describe translation when details are unknown.

Supperclasses: conversion

Slots:

ATTRIBUTELIST
AVAILABILITY
CLASS-DESIGN-RATIONALE
CLASS-NAME-SYNONYMS
COMMENT
CONFIDENCE
EXPERIMENTLIST
INTERACTIONTYPE
LEFT
NAMES
REVERSIBILITY
RIGHT
THOUGHT

Class: transcription

The process of transcription. This is useful to describe transcription when details are unknown.

Supperclasses: conversion

Slots:

ATTRIBUTELIST
AVAILABILITY
CLASS-DESIGN-RATIONALE
CLASS-NAME-SYNONYMS
COMMENT
CONFIDENCE
EXPERIMENTLIST
INTERACTIONTYPE
LEFT
NAMES
REVERSIBILITY
RIGHT
THOUGHT

Class: complexAssembly

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.

Supperclasses: conversion

Slots:

ATTRIBUTELIST
AVAILABILITY
CLASS-DESIGN-RATIONALE
CLASS-NAME-SYNONYMS
COMMENT
CONFIDENCE
EXPERIMENTLIST
INTERACTIONTYPE
LEFT
NAMES
REVERSIBILITY
RIGHT
THOUGHT

Class: genetic

A genetic interaction (e.g. a synthetic lethal interaction). An interaction between elements of a genotype that results in a change in phenotype.

Supperclasses: interaction

Subclasses: synthetic, epistasis, suppression

Slots:

ATTRIBUTELIST
AVAILABILITY
CLASS-DESIGN-RATIONALE
CLASS-NAME-SYNONYMS
COMMENT
CONFIDENCE
EXPERIMENTLIST
GENES
INTERACTIONTYPE
NAMES
THOUGHT

Class: synthetic

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.

Supperclasses: genetic

Slots:

ATTRIBUTELIST
AVAILABILITY
CLASS-DESIGN-RATIONALE
CLASS-NAME-SYNONYMS
COMMENT
CONFIDENCE
EXPERIMENTLIST
GENES
INTERACTIONTYPE
NAMES
THOUGHT

Class: epistasis

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

Supperclasses: genetic

Slots:

ATTRIBUTELIST
AVAILABILITY
CLASS-DESIGN-RATIONALE
CLASS-NAME-SYNONYMS
COMMENT
CONFIDENCE
EXPERIMENTLIST
GENES
INTERACTIONTYPE
NAMES
THOUGHT

Class: suppression

A suppressor is generally defined as a mutation that completely or partially restores the mutant phenotype of another mutation. (This definition from

Supperclasses: genetic

Slots:

ATTRIBUTELIST
AVAILABILITY
CLASS-DESIGN-RATIONALE
CLASS-NAME-SYNONYMS
COMMENT
CONFIDENCE
EXPERIMENTLIST
GENES
INTERACTIONTYPE
NAMES
THOUGHT

Class: equivalenceClass

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).

Supperclasses: interaction

Slots:

ATTRIBUTELIST
AVAILABILITY
CLASS-DESIGN-RATIONALE
CLASS-NAME-SYNONYMS
COMMENT
CONFIDENCE
ENTITIES
EXPERIMENTLIST
INTERACTIONTYPE
NAMES
THOUGHT

Class: molecularAssociation

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).

Supperclasses: interaction

Slots:

ATTRIBUTELIST
AVAILABILITY
CLASS-DESIGN-RATIONALE
CLASS-NAME-SYNONYMS
COMMENT
CONFIDENCE
EXPERIMENTLIST
INTERACTIONTYPE
NAMES
PARTICIPANTLIST
THOUGHT

Class: co-occurrence

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.)

Supperclasses: interaction

Subclasses: co-localization, co-incidence

Slots:

ATTRIBUTELIST
AVAILABILITY
CLASS-DESIGN-RATIONALE
CLASS-NAME-SYNONYMS
COMMENT
CONFIDENCE
ENTITIES
EXPERIMENTLIST
INTERACTIONTYPE
NAMES
THOUGHT

Class: co-localization

The co-occurrence of entities in space.

Supperclasses: co-occurrence

Slots:

ATTRIBUTELIST
AVAILABILITY
CLASS-DESIGN-RATIONALE
CLASS-NAME-SYNONYMS
COMMENT
CONFIDENCE
ENTITIES
EXPERIMENTLIST
INTERACTIONTYPE
NAMES
THOUGHT

Class: co-incidence

The co-occurrence of entities in time.

Supperclasses: co-occurrence

Slots:

ATTRIBUTELIST
AVAILABILITY
CLASS-DESIGN-RATIONALE
CLASS-NAME-SYNONYMS
COMMENT
CONFIDENCE
ENTITIES
EXPERIMENTLIST
INTERACTIONTYPE
NAMES
THOUGHT

Class: physicalEntity

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)

Supperclasses: entity

Subclasses: cell, cellComponent, dna, rna, protein, smallMolecule, environment, photon

Slots:

ATTRIBUTELIST
AVAILABILITY
CLASS-DESIGN-RATIONALE
CLASS-NAME-SYNONYMS
COMMENT
NAMES
THOUGHT

Class: cell

A specific type of cell. (e.g. cardiac myocyte, B lymphocyte)

Supperclasses: physicalEntity

Slots:

ATTRIBUTELIST
AVAILABILITY
CLASS-DESIGN-RATIONALE
CLASS-NAME-SYNONYMS
COMMENT
NAMES
THOUGHT

Class: cellComponent

A part of a cell (e.g. nucleus, mitochondrion). Use cellular components defined by Gene Ontology.

Supperclasses: physicalEntity

Slots:

ATTRIBUTELIST
AVAILABILITY
CLASS-DESIGN-RATIONALE
CLASS-NAME-SYNONYMS
COMMENT
NAMES
THOUGHT

Class: dna

Deoxyribonucleic acid. (e.g. EGFR DNA sequence. See GenBank for more examples.)

Supperclasses: physicalEntity

Slots:

ATTRIBUTELIST
AVAILABILITY
CLASS-DESIGN-RATIONALE
CLASS-NAME-SYNONYMS
COMMENT
NAMES
ORGANISM
SEQUENCE
THOUGHT

Class: rna

Ribonucleic acid (e.g. messengerRNA, microRNA, ribosomalRNA)

Supperclasses: physicalEntity

Slots:

ATTRIBUTELIST
AVAILABILITY
CLASS-DESIGN-RATIONALE
CLASS-NAME-SYNONYMS
COMMENT
NAMES
ORGANISM
SEQUENCE
THOUGHT

Class: protein

A protein (e.g. The EGFR protein sequence. See Swiss-Prot for more examples.)

Supperclasses: physicalEntity

Slots:

ATTRIBUTELIST
AVAILABILITY
CLASS-DESIGN-RATIONALE
CLASS-NAME-SYNONYMS
COMMENT
NAMES
ORGANISM
SEQUENCE
THOUGHT

Class: smallMolecule

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)

Supperclasses: physicalEntity

Slots:

ATTRIBUTELIST
AVAILABILITY
CLASS-DESIGN-RATIONALE
CLASS-NAME-SYNONYMS
COMMENT
NAMES
THOUGHT

Class: environment

A physical or environmental effect.

Supperclasses: physicalEntity

Slots:

ATTRIBUTELIST
AVAILABILITY
CLASS-DESIGN-RATIONALE
CLASS-NAME-SYNONYMS
COMMENT
NAMES
THOUGHT

Class: photon

Light at either a specified or unspecified intensity and wavelength (e.g. UV light).

Supperclasses: physicalEntity

Slots:

ATTRIBUTELIST
AVAILABILITY
CLASS-DESIGN-RATIONALE
CLASS-NAME-SYNONYMS
COMMENT
NAMES
THOUGHT

Class: pathway

A biological pathway. A series of steps defined by biologists as a pathways. A set of interactions (a pathway has interactions).

Supperclasses: entity

Slots:

ATTRIBUTELIST
AVAILABILITY
CLASS-DESIGN-RATIONALE
CLASS-NAME-SYNONYMS
COMMENT
INTERACTIONS
NAMES
THOUGHT

Class: utilityClasses

These classes are taken directly from PSI-MI and are named as closely as possible to the PSI naming scheme.

Subclasses: baseLocationType.BeginEnd, intervalType, positionType, baseLocationType, feature, confidenceContainer, cvType, openCvType, bioSourceType, experiment, attributeListContainer, dbReferenceType, attributeListType, xrefType, bibrefType, namesType, source, entrySet, entry

Slots:

Class: baseLocationType.BeginEnd

Supperclasses: utilityClasses

Slots:

Class: intervalType

A sequence interval

Supperclasses: utilityClasses

Slots:

Class: positionType

Supperclasses: utilityClasses

Slots:

This section of the HTML version of the ontology contains the slot definitions of the ontology. Each slot itself has several properties such as documentation about that slot, a cardinality (specifying the number of values that the slot may have), a value type (specifying the data type of slot values), and a domain (specifying the class(es) in which the slot is used).

Slot Name Documentation Properties

ATTRIBUTE A user-defined attribute CARDINALITY: 1
VALUE-TYPE: STRING
DOMAIN: attributeListType

ATTRIBUTELIST A list of user defined attributes for experiment MINIMUM-CARDINALITY: 0
MAXIMUM-CARDINALITY: 1
VALUE-TYPE: attributeListContainer
DOMAIN: entity, entry, openCvType, experiment, source

ATTRIBUTES A list of user-defined attributes MINIMUM-CARDINALITY: 0
MAXIMUM-CARDINALITY: 1
VALUE-TYPE: attributeListType
DOMAIN: attributeListContainer

AVAILABILITY Describes the availability of this data (e.g. a copyright statement) MINIMUM-CARDINALITY: 0
VALUE-TYPE: STRING
DOMAIN: entity, entry

BASELOCATIONCHOICE A choice of sequence location VALUE-TYPE: (ONE-OF positionType intervalType baseLocationType.BeginEnd)
DOMAIN: baseLocationType

BEGIN The start of a sequence interval. CARDINALITY: 1
VALUE-TYPE: INTEGER
DOMAIN: intervalType

BIBREF A bibliographic reference MINIMUM-CARDINALITY: 0
MAXIMUM-CARDINALITY: 1
VALUE-TYPE: bibrefType
DOMAIN: experiment, source

BIBREFCHOICE A choice of bibliographic reference VALUE-TYPE: (ONE-OF xrefType attributeListType)
DOMAIN: bibrefType

CELLTYPE A cell type MINIMUM-CARDINALITY: 0
MAXIMUM-CARDINALITY: 1
VALUE-TYPE: openCvType
DOMAIN: bioSourceType

CHOICE.1 A choice of sequence location VALUE-TYPE: (ONE-OF positionType intervalType)
DOMAIN: baseLocationType.BeginEnd

CHOICE.2 A choice of sequence location VALUE-TYPE: (ONE-OF positionType intervalType)
DOMAIN: baseLocationType.BeginEnd

CLASS-DESIGN-RATIONALE Describes the design rationale for this frame or slot. INHERITANCE-TYPE: UNIQUE
VALUE-TYPE: STRING
DOMAIN: THING

CLASS-NAME-SYNONYMS Synonym for the name of the frame or slot. INHERITANCE-TYPE: UNIQUE
VALUE-TYPE: STRING
DOMAIN: THING

COMMENT Comment about the frame this slot is part of. INHERITANCE-TYPE: UNIQUE
VALUE-TYPE: STRING
DOMAIN: THING

COMPARTMENT A cellular compartment. The Gene Ontology cellular component controlled vocabulary should be used here. MINIMUM-CARDINALITY: 0
MAXIMUM-CARDINALITY: 1
VALUE-TYPE: openCvType
DOMAIN: bioSourceType

CONFIDENCE Statistical confidence MINIMUM-CARDINALITY: 0
MAXIMUM-CARDINALITY: 1
VALUE-TYPE: confidenceContainer
DOMAIN: interaction, experiment

CONTROLLED The entity that is controlled (e.g for a biochemical reaction, this would be a reaction). VALUE-TYPE: entity
DOMAIN: control

CONTROLLER The controlling entity (e.g for a biochemical reaction, this would be an enzyme) VALUE-TYPE: entity
DOMAIN: control

DB A database name CARDINALITY: 1
VALUE-TYPE: STRING
DOMAIN: dbReferenceType

DB-VERSION A database version MINIMUM-CARDINALITY: 0
MAXIMUM-CARDINALITY: 1
VALUE-TYPE: STRING
DOMAIN: dbReferenceType

DELTA-G Standard Gibbs free energy change for a reaction (see notes in individual class definitions). VALUE-TYPE: LIST
DOMAIN: biochemicalReaction

DELTA-H Standard enthalpy change for a reaction (see notes in individual class definitions). VALUE-TYPE: NUMBER
DOMAIN: biochemicalReaction

DELTA-S Standard entropy change for a reaction (see notes in individual class definitions). VALUE-TYPE: NUMBER
DOMAIN: biochemicalReaction

EC-NUMBER 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

END The end of a sequence interval. CARDINALITY: 1
VALUE-TYPE: INTEGER
DOMAIN: intervalType

ENTITIES A list of entities VALUE-TYPE: entity
DOMAIN: co-occurrence, equivalenceClass

ENTRIES A set of entries. This is the top-level packaging class in the ontology. MINIMUM-CARDINALITY: 0
VALUE-TYPE: entry
DOMAIN: entrySet

EXPERIMENTLIST A list of supporting experiments MINIMUM-CARDINALITY: 1
VALUE-TYPE: experiment
DOMAIN: interaction

FEATUREDESCRIPTION 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) MINIMUM-CARDINALITY: 0
MAXIMUM-CARDINALITY: 1
VALUE-TYPE: cvType
DOMAIN: feature

FEATUREDETECTION Experimental method used to detect this feature MINIMUM-CARDINALITY: 0
MAXIMUM-CARDINALITY: 1
VALUE-TYPE: cvType
DOMAIN: feature, experiment

FULLNAME A full name MINIMUM-CARDINALITY: 0
MAXIMUM-CARDINALITY: 1
VALUE-TYPE: STRING
DOMAIN: namesType

GENES A list of genes interacting VALUE-TYPE: dna
DOMAIN: genetic

HOSTORGANISM The host organism this experiment was performed in MINIMUM-CARDINALITY: 0
MAXIMUM-CARDINALITY: 1
VALUE-TYPE: bioSourceType
DOMAIN: experiment

ID A database identifier CARDINALITY: 1
VALUE-TYPE: STRING
DOMAIN: dbReferenceType

INTERACTIONDETECTION The experimental method used to detect this interaction CARDINALITY: 1
VALUE-TYPE: cvType
DOMAIN: experiment

INTERACTIONLIST A list of interactions MINIMUM-CARDINALITY: 1
VALUE-TYPE: interaction
DOMAIN: entry

INTERACTIONS A list of interactions in this pathway VALUE-TYPE: interaction
DOMAIN: pathway

INTERACTIONTYPE 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. MINIMUM-CARDINALITY: 0
MAXIMUM-CARDINALITY: 1
VALUE-TYPE: cvType
DOMAIN: interaction

KEQ The reaction equilibrium constant (see notes under individual reaction subclass definitions). VALUE-TYPE: NUMBER
DOMAIN: biochemicalReaction

LEFT The left hand value in the conversion process (e.g. the reactants in a biochemical reaction) VALUE-TYPE: entity
DOMAIN: conversion

LEVEL The level of this ontology (e.g. Level 1, version 1) VALUE-TYPE: INTEGER
DOMAIN: entrySet

NAME The name of this attribute CARDINALITY: 1
VALUE-TYPE: STRING
DOMAIN: attributeListType

NAMES Name(s) VALUE-TYPE: namesType
DOMAIN: entity, bioSourceType, experiment, source

NAMES.REQ Name(s) CARDINALITY: 1
VALUE-TYPE: namesType
DOMAIN: openCvType, cvType

NCBITAXID The NCBI taxonomy ID for this organism CARDINALITY: 1
VALUE-TYPE: INTEGER
DOMAIN: bioSourceType

ORGANISM The organismal source MINIMUM-CARDINALITY: 0
MAXIMUM-CARDINALITY: 1
VALUE-TYPE: bioSourceType
DOMAIN: dna, rna, protein

PARTICIPANTDETECTION Experimental method used to detect the participant in the interaction MINIMUM-CARDINALITY: 0
MAXIMUM-CARDINALITY: 1
VALUE-TYPE: cvType
DOMAIN: experiment

PARTICIPANTLIST The entities participating in this association VALUE-TYPE: entity
DOMAIN: molecularAssociation

POSITION The position on a sequence (e.g. amino acid position 76) CARDINALITY: 1
VALUE-TYPE: INTEGER
DOMAIN: positionType

PRIMARYREF Primary external cross-reference CARDINALITY: 1
VALUE-TYPE: dbReferenceType
DOMAIN: xrefType

REVERSIBILITY 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

RIGHT The right hand value in the conversion process (e.g. the products in a biochemical reaction) VALUE-TYPE: entity
DOMAIN: conversion

SECONDARY A secondary database identifier MINIMUM-CARDINALITY: 0
MAXIMUM-CARDINALITY: 1
VALUE-TYPE: STRING
DOMAIN: dbReferenceType

SECONDARYREF Secondary external cross-references MINIMUM-CARDINALITY: 0
VALUE-TYPE: dbReferenceType
DOMAIN: xrefType

SEQUENCE Amino acid or nucleotide sequence in uppercase MINIMUM-CARDINALITY: 0
MAXIMUM-CARDINALITY: 1
VALUE-TYPE: STRING
DOMAIN: dna, rna, protein

SHORTLABEL A short label. Short enough to be used in a visualization application to label a graphical element. CARDINALITY: 1
VALUE-TYPE: STRING
DOMAIN: namesType

SLOT-NAME-SYNONYMS
DOMAIN: NIL

SOURCE The source of this data MINIMUM-CARDINALITY: 0
MAXIMUM-CARDINALITY: 1
VALUE-TYPE: source
DOMAIN: entry

SPONTANEOUS 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

THOUGHT Comment about how much thought has been invested in the design of this slot or frame. INHERITANCE-TYPE: UNIQUE
VALUE-TYPE: STRING
DOMAIN: THING

TISSUE An external controlled vocabulary of tissue types MINIMUM-CARDINALITY: 0
MAXIMUM-CARDINALITY: 1
VALUE-TYPE: openCvType
DOMAIN: bioSourceType

UNIT Unit of confidence CARDINALITY: 1
VALUE-TYPE: STRING
DOMAIN: confidenceContainer

VALUE Value of confidence CARDINALITY: 1
VALUE-TYPE: STRING
DOMAIN: confidenceContainer

VERSION The version of this ontology (e.g. Level 1, version 1) VALUE-TYPE: INTEGER
DOMAIN: entrySet

XREF.REQ An external cross-reference CARDINALITY: 1
VALUE-TYPE: xrefType
DOMAIN: cvType

Slot Name	Documentation	Properties
ATTRIBUTE	A user-defined attribute	CARDINALITY: 1 VALUE-TYPE: STRING DOMAIN: attributeListType
ATTRIBUTELIST	A list of user defined attributes for experiment	MINIMUM-CARDINALITY: 0 MAXIMUM-CARDINALITY: 1 VALUE-TYPE: attributeListContainer DOMAIN: entity, entry, openCvType, experiment, source
ATTRIBUTES	A list of user-defined attributes	MINIMUM-CARDINALITY: 0 MAXIMUM-CARDINALITY: 1 VALUE-TYPE: attributeListType DOMAIN: attributeListContainer
AVAILABILITY	Describes the availability of this data (e.g. a copyright statement)	MINIMUM-CARDINALITY: 0 VALUE-TYPE: STRING DOMAIN: entity, entry
BASELOCATIONCHOICE	A choice of sequence location	VALUE-TYPE: (ONE-OF positionType intervalType baseLocationType.BeginEnd) DOMAIN: baseLocationType
BEGIN	The start of a sequence interval.	CARDINALITY: 1 VALUE-TYPE: INTEGER DOMAIN: intervalType
BIBREF	A bibliographic reference	MINIMUM-CARDINALITY: 0 MAXIMUM-CARDINALITY: 1 VALUE-TYPE: bibrefType DOMAIN: experiment, source
BIBREFCHOICE	A choice of bibliographic reference	VALUE-TYPE: (ONE-OF xrefType attributeListType) DOMAIN: bibrefType
CELLTYPE	A cell type	MINIMUM-CARDINALITY: 0 MAXIMUM-CARDINALITY: 1 VALUE-TYPE: openCvType DOMAIN: bioSourceType
CHOICE.1	A choice of sequence location	VALUE-TYPE: (ONE-OF positionType intervalType) DOMAIN: baseLocationType.BeginEnd
CHOICE.2	A choice of sequence location	VALUE-TYPE: (ONE-OF positionType intervalType) DOMAIN: baseLocationType.BeginEnd
CLASS-DESIGN-RATIONALE	Describes the design rationale for this frame or slot.	INHERITANCE-TYPE: UNIQUE VALUE-TYPE: STRING DOMAIN: THING
CLASS-NAME-SYNONYMS	Synonym for the name of the frame or slot.	INHERITANCE-TYPE: UNIQUE VALUE-TYPE: STRING DOMAIN: THING
COMMENT	Comment about the frame this slot is part of.	INHERITANCE-TYPE: UNIQUE VALUE-TYPE: STRING DOMAIN: THING
COMPARTMENT	A cellular compartment. The Gene Ontology cellular component controlled vocabulary should be used here.	MINIMUM-CARDINALITY: 0 MAXIMUM-CARDINALITY: 1 VALUE-TYPE: openCvType DOMAIN: bioSourceType
CONFIDENCE	Statistical confidence	MINIMUM-CARDINALITY: 0 MAXIMUM-CARDINALITY: 1 VALUE-TYPE: confidenceContainer DOMAIN: interaction, experiment
CONTROLLED	The entity that is controlled (e.g for a biochemical reaction, this would be a reaction).	VALUE-TYPE: entity DOMAIN: control
CONTROLLER	The controlling entity (e.g for a biochemical reaction, this would be an enzyme)	VALUE-TYPE: entity DOMAIN: control
DB	A database name	CARDINALITY: 1 VALUE-TYPE: STRING DOMAIN: dbReferenceType
DB-VERSION	A database version	MINIMUM-CARDINALITY: 0 MAXIMUM-CARDINALITY: 1 VALUE-TYPE: STRING DOMAIN: dbReferenceType
DELTA-G	Standard Gibbs free energy change for a reaction (see notes in individual class definitions).	VALUE-TYPE: LIST DOMAIN: biochemicalReaction
DELTA-H	Standard enthalpy change for a reaction (see notes in individual class definitions).	VALUE-TYPE: NUMBER DOMAIN: biochemicalReaction
DELTA-S	Standard entropy change for a reaction (see notes in individual class definitions).	VALUE-TYPE: NUMBER DOMAIN: biochemicalReaction
EC-NUMBER	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
END	The end of a sequence interval.	CARDINALITY: 1 VALUE-TYPE: INTEGER DOMAIN: intervalType
ENTITIES	A list of entities	VALUE-TYPE: entity DOMAIN: co-occurrence, equivalenceClass
ENTRIES	A set of entries. This is the top-level packaging class in the ontology.	MINIMUM-CARDINALITY: 0 VALUE-TYPE: entry DOMAIN: entrySet
EXPERIMENTLIST	A list of supporting experiments	MINIMUM-CARDINALITY: 1 VALUE-TYPE: experiment DOMAIN: interaction
FEATUREDESCRIPTION	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)	MINIMUM-CARDINALITY: 0 MAXIMUM-CARDINALITY: 1 VALUE-TYPE: cvType DOMAIN: feature
FEATUREDETECTION	Experimental method used to detect this feature	MINIMUM-CARDINALITY: 0 MAXIMUM-CARDINALITY: 1 VALUE-TYPE: cvType DOMAIN: feature, experiment
FULLNAME	A full name	MINIMUM-CARDINALITY: 0 MAXIMUM-CARDINALITY: 1 VALUE-TYPE: STRING DOMAIN: namesType
GENES	A list of genes interacting	VALUE-TYPE: dna DOMAIN: genetic
HOSTORGANISM	The host organism this experiment was performed in	MINIMUM-CARDINALITY: 0 MAXIMUM-CARDINALITY: 1 VALUE-TYPE: bioSourceType DOMAIN: experiment
ID	A database identifier	CARDINALITY: 1 VALUE-TYPE: STRING DOMAIN: dbReferenceType
INTERACTIONDETECTION	The experimental method used to detect this interaction	CARDINALITY: 1 VALUE-TYPE: cvType DOMAIN: experiment
INTERACTIONLIST	A list of interactions	MINIMUM-CARDINALITY: 1 VALUE-TYPE: interaction DOMAIN: entry
INTERACTIONS	A list of interactions in this pathway	VALUE-TYPE: interaction DOMAIN: pathway
INTERACTIONTYPE	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.	MINIMUM-CARDINALITY: 0 MAXIMUM-CARDINALITY: 1 VALUE-TYPE: cvType DOMAIN: interaction
KEQ	The reaction equilibrium constant (see notes under individual reaction subclass definitions).	VALUE-TYPE: NUMBER DOMAIN: biochemicalReaction
LEFT	The left hand value in the conversion process (e.g. the reactants in a biochemical reaction)	VALUE-TYPE: entity DOMAIN: conversion
LEVEL	The level of this ontology (e.g. Level 1, version 1)	VALUE-TYPE: INTEGER DOMAIN: entrySet
NAME	The name of this attribute	CARDINALITY: 1 VALUE-TYPE: STRING DOMAIN: attributeListType
NAMES	Name(s)	VALUE-TYPE: namesType DOMAIN: entity, bioSourceType, experiment, source
NAMES.REQ	Name(s)	CARDINALITY: 1 VALUE-TYPE: namesType DOMAIN: openCvType, cvType
NCBITAXID	The NCBI taxonomy ID for this organism	CARDINALITY: 1 VALUE-TYPE: INTEGER DOMAIN: bioSourceType
ORGANISM	The organismal source	MINIMUM-CARDINALITY: 0 MAXIMUM-CARDINALITY: 1 VALUE-TYPE: bioSourceType DOMAIN: dna, rna, protein
PARTICIPANTDETECTION	Experimental method used to detect the participant in the interaction	MINIMUM-CARDINALITY: 0 MAXIMUM-CARDINALITY: 1 VALUE-TYPE: cvType DOMAIN: experiment
PARTICIPANTLIST	The entities participating in this association	VALUE-TYPE: entity DOMAIN: molecularAssociation
POSITION	The position on a sequence (e.g. amino acid position 76)	CARDINALITY: 1 VALUE-TYPE: INTEGER DOMAIN: positionType
PRIMARYREF	Primary external cross-reference	CARDINALITY: 1 VALUE-TYPE: dbReferenceType DOMAIN: xrefType
REVERSIBILITY	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
RIGHT	The right hand value in the conversion process (e.g. the products in a biochemical reaction)	VALUE-TYPE: entity DOMAIN: conversion
SECONDARY	A secondary database identifier	MINIMUM-CARDINALITY: 0 MAXIMUM-CARDINALITY: 1 VALUE-TYPE: STRING DOMAIN: dbReferenceType
SECONDARYREF	Secondary external cross-references	MINIMUM-CARDINALITY: 0 VALUE-TYPE: dbReferenceType DOMAIN: xrefType
SEQUENCE	Amino acid or nucleotide sequence in uppercase	MINIMUM-CARDINALITY: 0 MAXIMUM-CARDINALITY: 1 VALUE-TYPE: STRING DOMAIN: dna, rna, protein
SHORTLABEL	A short label. Short enough to be used in a visualization application to label a graphical element.	CARDINALITY: 1 VALUE-TYPE: STRING DOMAIN: namesType
SLOT-NAME-SYNONYMS		DOMAIN: NIL
SOURCE	The source of this data	MINIMUM-CARDINALITY: 0 MAXIMUM-CARDINALITY: 1 VALUE-TYPE: source DOMAIN: entry
SPONTANEOUS	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
THOUGHT	Comment about how much thought has been invested in the design of this slot or frame.	INHERITANCE-TYPE: UNIQUE VALUE-TYPE: STRING DOMAIN: THING
TISSUE	An external controlled vocabulary of tissue types	MINIMUM-CARDINALITY: 0 MAXIMUM-CARDINALITY: 1 VALUE-TYPE: openCvType DOMAIN: bioSourceType
UNIT	Unit of confidence	CARDINALITY: 1 VALUE-TYPE: STRING DOMAIN: confidenceContainer
VALUE	Value of confidence	CARDINALITY: 1 VALUE-TYPE: STRING DOMAIN: confidenceContainer
VERSION	The version of this ontology (e.g. Level 1, version 1)	VALUE-TYPE: INTEGER DOMAIN: entrySet
XREF.REQ	An external cross-reference	CARDINALITY: 1 VALUE-TYPE: xrefType DOMAIN: cvType