Contents:
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.
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:
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:
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:
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:
Control of the process of transportation. An active or passive transporter can facilitate a translocation event.
Supperclasses: control
Slots:
The process of gene regulation by a transcription factor. A transcription factor binds upstream
Supperclasses: control
Slots:
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:
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VALUE-TYPE: entity |
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VALUE-TYPE: entity |
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 + 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.
Supperclasses: conversion
Slots:
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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 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 |
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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 |
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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 |
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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. |
VALUE-TYPE: NUMBER |
The process of transport from one spatial location to another, typically within or at
Supperclasses: conversion
Slots:
Process of translation. This is useful to describe translation when details are unknown.
Supperclasses: conversion
Slots:
The process of transcription. This is useful to describe transcription when details are unknown.
Supperclasses: conversion
Slots:
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:
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:
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:
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:
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:
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:
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:
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:
The co-occurrence of entities in space.
Supperclasses: co-occurrence
Slots:
The co-occurrence of entities in time.
Supperclasses: co-occurrence
Slots:
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:
A specific type of cell. (e.g. cardiac myocyte, B lymphocyte)
Supperclasses: physicalEntity
Slots:
A part of a cell (e.g. nucleus, mitochondrion). Use cellular components defined by Gene Ontology.
Supperclasses: physicalEntity
Slots:
Deoxyribonucleic acid. (e.g. EGFR DNA sequence. See GenBank for more examples.)
Supperclasses: physicalEntity
Slots:
Ribonucleic acid (e.g. messengerRNA, microRNA,
ribosomalRNA)
Supperclasses: physicalEntity
Slots:
A protein (e.g. The EGFR protein sequence. See Swiss-Prot for more examples.)
Supperclasses: physicalEntity
Slots:
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:
A physical or environmental effect.
Supperclasses: physicalEntity
Slots:
Light at either a specified or unspecified intensity and wavelength (e.g. UV light).
Supperclasses: physicalEntity
Slots:
A biological pathway. A series of steps defined by biologists as a pathways. A set of interactions (a pathway has interactions).
Supperclasses: entity
Slots:
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:
Supperclasses: utilityClasses
Slots:
A sequence interval
Supperclasses: utilityClasses
Slots:
Supperclasses: utilityClasses
Slots:
Supperclasses: utilityClasses
Slots:
A feature is some part of a physicalEntity (e.g. a domain on a protein, a functional group on a small molecule)
Supperclasses: utilityClasses
Slots:
A statistical confidence value.
Supperclasses: utilityClasses
Slots:
A controlled vocabulary that is included in the ontology.
Supperclasses: utilityClasses
Slots:
A controlled vocabulary that is external to the ontology.
Supperclasses: utilityClasses
Slots:
A biological source
Supperclasses: utilityClasses
Slots:
Describes an experiment.
Supperclasses: utilityClasses
Slots:
A container for the list of attributes.
Supperclasses: utilityClasses
Slots:
A reference to a database. Refers to a unique object in an external database.
Supperclasses: utilityClasses
Slots:
A list of user-defined attributes.
Supperclasses: utilityClasses
Slots:
A cross-reference
Supperclasses: utilityClasses
Slots:
Bibliographic reference for the data source. Example: A paper which describes all interactions of the entry.
Supperclasses: utilityClasses
Slots:
A name
Supperclasses: utilityClasses
Slots:
Desciption of the source of the information.
Supperclasses: utilityClasses
Slots:
Root element of the Molecular interaction Format
Supperclasses: utilityClasses
Slots:
Describes one or more interactions as a self-contained unit. Multiple entries from different files can be concatenated into a single entrySet.
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).
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Slot Name |
Documentation |
Properties |
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A user-defined attribute |
CARDINALITY: 1 |
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A list of user defined attributes for experiment |
MINIMUM-CARDINALITY: 0 |
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A list of user-defined attributes |
MINIMUM-CARDINALITY: 0 |
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Describes the availability of this data (e.g. a copyright statement) |
MINIMUM-CARDINALITY: 0 |
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A choice of sequence location |
VALUE-TYPE: (ONE-OF positionType
intervalType baseLocationType.BeginEnd) |
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The start of a sequence interval. |
CARDINALITY: 1 |
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A bibliographic reference |
MINIMUM-CARDINALITY: 0 |
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A choice of bibliographic reference |
VALUE-TYPE: (ONE-OF xrefType attributeListType) |
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A cell type |
MINIMUM-CARDINALITY: 0 |
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A choice of sequence location |
VALUE-TYPE: (ONE-OF positionType
intervalType) |
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A choice of sequence location |
VALUE-TYPE: (ONE-OF positionType
intervalType) |
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Describes the design rationale for this frame or slot. |
INHERITANCE-TYPE: UNIQUE |
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Synonym for the name of the frame or slot. |
INHERITANCE-TYPE: UNIQUE |
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Comment about the frame this slot is part of. |
INHERITANCE-TYPE: UNIQUE |
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A cellular compartment. The Gene Ontology cellular component controlled vocabulary should be used here. |
MINIMUM-CARDINALITY: 0 |
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Statistical confidence |
MINIMUM-CARDINALITY: 0 |
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The entity that is controlled (e.g for a biochemical reaction, this would be a reaction). |
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The controlling entity (e.g for a biochemical reaction, this would be an enzyme) |
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A database name |
CARDINALITY: 1 |
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A database version |
MINIMUM-CARDINALITY: 0 |
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Standard Gibbs free energy change for a reaction (see notes in individual class definitions). |
VALUE-TYPE: LIST |
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Standard enthalpy change for a reaction (see notes in individual class definitions). |
VALUE-TYPE: NUMBER |
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Standard entropy change for a reaction (see notes in individual class definitions). |
VALUE-TYPE: NUMBER |
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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 |
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The end of a sequence interval. |
CARDINALITY: 1 |
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A list of entities |
VALUE-TYPE: entity |
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A set of entries. This is the top-level packaging class in the ontology. |
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A list of supporting experiments |
MINIMUM-CARDINALITY: 1 |
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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 |
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Experimental method used to detect this feature |
MINIMUM-CARDINALITY: 0 |
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A full name |
MINIMUM-CARDINALITY: 0 |
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A list of genes interacting |
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The host organism this experiment was performed in |
MINIMUM-CARDINALITY: 0 |
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A database identifier |
CARDINALITY: 1 |
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The experimental method used to detect this interaction |
CARDINALITY: 1 |
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A list of interactions |
MINIMUM-CARDINALITY: 1 |
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A list of interactions in this pathway |
VALUE-TYPE: interaction |
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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 |
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The reaction equilibrium constant (see notes under individual reaction subclass definitions). |
VALUE-TYPE: NUMBER |
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The left hand value in the conversion process (e.g. the reactants in a biochemical reaction) |
VALUE-TYPE: entity |
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The level of this ontology (e.g. Level 1, version 1) |
VALUE-TYPE: INTEGER |
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The name of this attribute |
CARDINALITY: 1 |
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Name(s) |
VALUE-TYPE: namesType |
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Name(s) |
CARDINALITY: 1 |
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The NCBI taxonomy ID for this organism |
CARDINALITY: 1 |
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The organismal source |
MINIMUM-CARDINALITY: 0 |
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Experimental method used to detect the participant in the interaction |
MINIMUM-CARDINALITY: 0 |
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The entities participating in this association |
VALUE-TYPE: entity |
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The position on a sequence (e.g. amino acid position 76) |
CARDINALITY: 1 |
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Primary external cross-reference |
CARDINALITY: 1 |
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This slot describes the reversibility and directionality of the reaction. Possible values are: :REVERSIBLE -- The reaction can proceed in either
direction. |
MAXIMUM-CARDINALITY: 1 |
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The right hand value in the conversion process (e.g. the products in a biochemical reaction) |
VALUE-TYPE: entity |
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A secondary database identifier |
MINIMUM-CARDINALITY: 0 |
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Secondary external cross-references |
MINIMUM-CARDINALITY: 0 |
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Amino acid or nucleotide sequence in uppercase |
MINIMUM-CARDINALITY: 0 |
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A short label. Short enough to be used in a visualization application to label a graphical element. |
CARDINALITY: 1 |
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DOMAIN: NIL |
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SOURCE |
The source of this data |
MINIMUM-CARDINALITY: 0 |
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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 |
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Comment about how much thought has been invested in the design of this slot or frame. |
INHERITANCE-TYPE: UNIQUE |
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An external controlled vocabulary of tissue types |
MINIMUM-CARDINALITY: 0 |
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Unit of confidence |
CARDINALITY: 1 |
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Value of confidence |
CARDINALITY: 1 |
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The version of this ontology (e.g. Level 1, version 1) |
VALUE-TYPE: INTEGER |
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An external cross-reference |