A biochemical reaction is a reaction in which substrates are written in terms of sums of species. This is further defined in Peter Karp's interactions ontology hppt://www.ai.sri.com/~pkarp/misc/interactions1.html. Note: This class does not contain any reference to enzyme kinetics. Examples: ATP +H2O -> ADP + P_i; all EC reactions A container for the list of attributes. The control of a process. Examples: Enzyme catalysis controls a biochemical reaction, gene regulation controls gene expression A step in the processes of comoplex assembly. This is not the same as a complex, which is a physical object, called molecular association in the interaction class hierarchy. A set of entities that can be considered equivalent in some context. Examples: 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-phosphate. This class is considered useful, but its position in the ontology has not yet been decided. It may be useful as part of the entity tree because it can then easily be used as part of an interaction. A genetic interaction. An interaction between elements of a genotype that results in a change in phenotype. Examples: Synthetic lethal interaction Desciption of the source of the information. These classes are taken directly from PSI-MI and are named as closely as possible to the PSI naming scheme. The co-occurrence of entities in time. Examples: co-migration of cells; genes expressed at the same time Describes one or more interactions as a self-contained unit. Multiple entries from different files can be concatenated into a single entrySet. Bibliographic reference for the data source. Example: A paper which describes all interactions of the entry. Ribonucleic acid (e.g. messengerRNA, microRNA, ribosomalRNA). A reference to a database. Refers to a unique object in an external database. The process of enzyme catalysis. An enzyme interacts with a biochemical reaction. This class contains information about the enzyme catalyzing the reaction and enzyme kinetics. Enzyme catalysis controls biochemical reactions and together these classes can be used to describe typical metabolic pathways. Examples: Hexokinase -> (The "Glucose + ATP -> Glucose-6-phosphate + ADP" reaction) A set or sets of entities and some relationship between them. An interaction is an entity. A building block of simple interactions (simple interactions are those that involve pathways or other interactions). Examples: protein, small molecule, RNA, DNA, photon, etc. Deoxyribonucleic acid. (e.g. EGFR DNA sequence. See GenBank for more examples.) 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. Examples: Gene A and gene B are syntentic lethal if a double of gene A and gene B mutant results in death, but neither mutation is leathal independently. Root Class of ontology. Any concept that we will refer to as a discrete unti when describing biological pathways. e.g. a pathway, an interaction, a part. Light at either a specified or unspecified intensity and wavelength (e.g. UV light). This class is unfinished. Slots need to be added for wavelength and intensity. The process of gene regulation by a transcription factor. A transcription factor binds upstream of a gne to regulate it. This is th basis of genetic regulatory networks, where typically an arrow is drawn from the transcription factor to the regulated gene. Examples: Transcription factor -> Regulated gene A name. A controlled vocabulary that is external to the ontology. A protein (e.g. The EGFR protein sequence. See Swiss-Prot for more examples.) The process of transport from one spatial location to another, typically within or at least with respect to the cell. This does not include a transporter molecule, wich would be described in the transport control class. This class requires more conceptual work. A physical or environmental effect. A list of user-defined attributes. The process of translation. This is useful to generally describe translation. It is still an open issue whether to include production relationships of the central dogma, like transcription and translation. The co-occurrence of entities in space. Examples: Colocalization of a few receptors e.g. in a GPI anchored lipid raft Root element of the Molecular interaction Format. A controlled vocabulary that is included in the ontology. A sequence interval. Currently the feature description system is only implemented for sequences. A feature is some part of a physicalEntity (e.g. a domain on a protein, a functional group on a small molecule). A statistical confidence value. The process of transcription. This is useful to generally describe transcription. It is still an open issue whether to include production relationships of the central dogma, like transcription and translation. The co-occurrence of entities in some context. The context could be time, space, a sentence, sequence similarity space, etc. Examples: Colocalization of a few receptors in a GPI anchored lipid raft; co-migration of cells; genes expressed at the same time. This class needs more conceptual work to clarify its use. An ordered set of interactions (a pathway has interactions). A pathway is an enity. Example: apoptosis, glycolysis. The pathway may have subclasses (e.g. all of the elements in GO Processes). A biological source. An epistatic interaction occurs when an allele at one locus renders the genotype at a second locs irrelevant - the phenotype will be dictated by the genotype of the epistatic gene alone. (Definition from http://starklab.slu.edu/Coulter/genetics/handout3_2002.html) Examples: Gene A -> Gene B (Gene A is epistatic to Gene B) A supressor is generally defined as a mutation that completely or partially restores the mutant phenotype of another mutation. (Defintion from hppt://urmc.rochester.edu/labs/Sherman_f/12.html#12.3) Examples: Gene A -> Gene B (Gene A supresses Gene B) This class is directly copied from the PSI-MI definition. Because of this, only describes experiments related to proteins and protein interactions. This class is directly copied from the PSI-MI definition. A cross-reference. An association between a set of molecules/ Examples: Arp2-Arp3 protein-protein interaction; protein complex, i.e. the result of a co-immunoprecipitation experiment; hexokinase-glucose This class needs more conceptual work to clarify its use. One issue to resolve is whether this class should be a physicalEntity. Control of the process of transportation. An active transporter can facilitate a translocation event. Examples: nuclear pore complex -> (The "Protein A (cytoplasm) -> Protein A (nucleus)" translocation) A part of a cell (e.g. nucleus, mitochondrion). Use cellular components defined by Gene Ontology. This class needs to be further discussed. 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). This should eventually be implemented as CML. This class is needed to describe cell-cell interactions, but its use must be further defined. A specific type of cell. (e.g. cardiac myocyte, B lymphocyte). A conversion process, which converts one set of entities to another set. Examples: A biochemical reaction converts substrates into products, the proces of complex assembly converts single molecules to a complex, transport converts entities in one compartment to the same entities in another compartment The entity that is controlled (e.g. for a biochemical reaction catalyzed by an enzyme, this would be the reaction). Name(s) 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). A list of interactions in this pathway. A choice of bibliographic reference. A list of interactions A list of genes interacting A bibliographic reference. A set of entries. This is the top-level packaging class in the ontology. A choice of sequence location. A cell type. The right hand value in the conversion process (e.g. the products in a biochemical reaction). A list of entities A choice of sequence location. The type of interaction (from a small controlled vocabulary of interaction types) e.g. phosphorylation. This is meant to be a descriptive name for the interaction that would be useful for browsing or database searching. Describes the temporal characteristics of this state (e.g. a certain phase of the cell cycle). The entities participating in this association. An external controlled vocabulary of tissue types. A list of supporting experiments. The left hand value in the conversion process (e.g. the reactants in a biochemical reaction). The controlling entity (e.g. for a biochemical reaction, this would be an enzyme). Name(s) Experimental method used to detect this feature. Secondary external cross-reference. A database version This is a comment about how much thought has been invested in the design of this class. This slot describes the design rationale for this class. Standard enthalpy change for a reaction, in kJ/mol. A full name. The start of a sequence interval. The number assigned to a reaction by the Enzyme Commission. The end of a sequence interval The NCBI taxonomy ID for this organism (e.g. "9606"). A database identifier The reaction equilibrium constant. The level of this ontology (e.g.Level 1 version 1). The version number of this ontology (e.g. Level 1 version 1). Standard Gibbs free energy change for a reaction, in kJ/mol. Unit of confidence. Standard entropy change for a reaction, in kJ/mol. Synonym(s) for the name of this class. A short label - short enough to be used in a vizualization application to label a graphical element. An external cross reference. A cellular compartment. The Gene Ontology cellular component controlled vocabulary should be used here. A secondary database identifier Statistical confidence. This slot describes the reversibility and directionality of the conversion. 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. The organismal source. 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 value for this slot implies that the reaction is not spontaneous. A user-defined attribute. Amino acid or nucleotide sequence in uppercase. The position on a sequence (e.g. amino acid position 76.) A database name The source of this data An external cross-reference. A choice of sequence location. Value of confidence. A list of user-defined attributes. Primary external cross-reference. The name of this attribute. A list of user defined attributes for experiment.