]> OBO Essentials -- a selected subset of important classes from various OBO ontologies. TODO: capitalize class labels Anatomical structure / organism Material anatomical entity that has inherent 3D shape and is generated by coordinated expression of the organism's own genome. Multi-cellular organism Anatomical structure that is an individual member of a species and consists of more than one cell. Cell Anatomical structure that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. Cell component Anatomical structure that is a direct part of the cell. Simple organ Multi-tissue structure that is not part of a compound organ. Portion of tissue Anatomical structure, that consists of similar cells and intercellular matrix, aggregated according to genetically determined spatial relationships. Molecular entity Molecular structure Group (part of molecular entity) Ion Nucleic acid (RNA, DNA) Protein Peptide amidation (process) The posttranslational conversion of C-terminal glycine-extended peptides to C-terminal alpha-amidated peptides. Occurs to over half of all peptide hormones to give bioactive peptides. This is a two step process catalyzed by a peptidyl-glycine alpha-hydroxylating monooxygenase and a peptidyl-alpha-hydroxyglycine alpha-amidating lyase. In some organisms, this process is catalyzed by two separate enzymes, whereas in higher organisms, one polypeptide catalyzes both reactions. Catalytic activity (disposition) Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. Binding (disposition) The selective, often stoichiometric interaction of a molecule with one or more specific sites on another molecule. Protein amino acid acetylation (process) The addition of an acetyl group to a protein amino acid. An acetyl group is CH3CO-, derived from acetic [ethanoic] acid. Transport The directed movement of substances (such as macromolecules, small molecules, ions) into, out of, within or between cells. Metabolic process Processes that cause many of the chemical changes in living organisms, including anabolism and catabolism. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. Protein amino acid biotinylation (process) The addition of biotin (vitamin B7 / vitamin H) to a protein amino acid. Phosphorylation (process) The process of introducing a phosphoric group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide. Protein ubiquitination (process) The process by which one or more ubiquitin moieties are added to a protein. Protein sumoylation (process) The process by which a SUMO protein (small ubiquitin-related modifier) is conjugated to a target protein via an isopeptide bond between the carboxyl terminus of SUMO with an epsilon-amino group of a lysine residue of the target protein. Protein amino acid nitrosylation (process) The addition of a nitrosyl group to a protein amino acid. Protein amino acid bromination (process) Protein amino acid hydroxylation (process) The addition of a hydroxy group to a protein amino acid. Protein amino acid carboxylation (process) The addition of a carboxy group to a protein amino acid. Protein amino acid formylation (process) The addition of a formyl group to a protein amino acid. Protein farnesylation (process) The enzymatic addition of a farnesyl moiety to a protein as a posttranslational modification. Protein palmitoylation (process) The covalent or non-covalent attachment of a palmitoyl moiety to a protein. Protein myristoylation (process) The covalent or non-covalent attachment of a myristoyl moiety to a protein. Methylation (process) The process by which a methyl group is covalently attached to a molecule. Macromolecular complex disassembly (process) The disaggregation of a macromolecular complex into its constituent components. Regulation of gene expression, epigenetic (process) Any process that modulates the frequency, rate or extent of gene expression; the process is mitotically or meiotically heritable, or is stably self-propagated in the cytoplasm of a resting cell, and does not entail a change in DNA sequence. Protein amino acid acylation (process) The addition of an acyl group, any group or radical of the form RCO- where R is an organic group, to a protein amino acid. Negative regulation of gene expression, epigenetic (process) Any epigenetic process that stops, prevents or reduces the rate of gene expression. Positive regulation of gene expression, epigenetic (process) Any epigenetic process that activates or increases the rate of gene expression. Protein dimerization activity (disposition) The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits. Positive regulation of biological process (process) Negative regulation of biological process (process) Any process that stops, prevents or reduces the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. Macromolecular complex assembly (process) The aggregation and bonding together of a set of macromolecules to form a complex. Biological regulation (process) Any process that modulates the frequency, rate or extent of any biological process, quality or function. Mass Classic metabolic pathway The various, enzyme controlled, series of reactions allowing for the conversion of materials, energy availability and biodegradation of xenobiotics. Signaling pathway The pathways where a signal - hormone, neurotransmitter, growth factor, peptide, any molecule - triggers one or multiple cascades of events. This involves a number of molecules, including receptors, proteins, ligands, messengers, any participating molecule. A signaling pathway may be upstream or downstream of other signaling pathways. Signaling pathways control a very broad spectrum of processes as well as pathways. Regulatory pathway The pathways that control the processes by which a cell or organism develops, adjusts, behaves, responds to conditions or changes in these conditions, or in any manner helps promote and maintain its efficient functioning. Binding (process) Protein dimerization (process) The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits. Ki value Pathway