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Protein Ontology Concept Hierarchy
Various Concepts of Protein Ontology (PO) are in the hierarchy below. You can click on each concept to find more information about it. More details about these can be found at Documentation Page.
- ProteinOntology
The Root Concept in PO is ProteinOntology. For each instance of protein that is entered into PO, the submission information is entered for ProteinOntology Concept.
Data about binding atoms in Chemical Bonds like Hydrogen Bond, Residue Links, and Salt Bridges is entered into PO as AtomicBind Concept. Records in Protein databases identify and describe each of the hydrogen bonds, residue links and salt bridges found in protein and polypeptide structures by identifying the two atoms involved in the bonds.
Atom records in protein databases present the atomic coordinates for standard residues. They also present the occupancy and temperature factor for each atom.
Data about each of the both the binding residues in Chemical Bonds like Disulphide Bonds and CIS Peptides is entered into PO as Bind Concept. Records in Protein databases identify and describe each of the disulfide bonds, prolines and other peptides found to be in the cis conformation in protein and polypeptide structures by identifying the two residues involved in the bonds.
Chains in Protein Ontology describe the amino acid or nucleic acid sequence of residues in each chain of the macromolecule that was studied. In Protein Data Sources they are simply represented by sequence of residues like SEQRES in PDB format.
A protein family is a group of evolutionarily related proteins. Superfamily is a group of protein families. More details about the classification of proteins into families and superfamilies can be found in SCOP.
A protein complex is a group of two or more associated proteins. Protein complexes are a form of quaternary structure. Understanding the sequence, structure and functional interactions of proteins is an important research focus in biochemistry, often referred to as proteomics. The Main Concept for definition of Protein Complexes in the Protein Ontology is ProteinComplex.
ChemicalBonds concept in PO allows specifying the existence and location of disulfide bonds and other linkages and describes various chemical bonds used to bind various substructures in protein structure. Chemical Bonds are defined by their respective sub concepts are: DisulphideBond, CISPeptide, HydrogenBond, ResidueLink, and SaltBridge. They are defined using generic concepts of Bind and Atomic Bind. Chemical Bonds that have Binding Residues (DisulphideBond, CISPeptide) reuse the generic concept of Bind. Similarly the Chemical Bonds that have Binding Atoms (HydrogenBond, ResidueLink, and SaltBridge) reuse the generic concept of AtomicBind.
CIS Peptide linkages present in the protein structure are described using sub concept of CISPeptide.
Disulphide Bonds present in the protein structure are described using sub concept of DisulphideBond.
Hydrogen Bonds present in the protein structure are described using sub concept of HydrogenBond.
Residue Links present in the protein structure are described using sub concept of ResidueLink.
Salt Bridges present in the protein structure are described using sub concept of SaltBridge.
Various constraints that affect final protein structural conformation are defined using Constraints concept of PO. The constraints described in PO at the moment are: Monogenetic and Polygenetic defects present in genes that are present in molecules making proteins described using GeneDefects sub concept, Hydrophobic properties of proteins described using Hydrophobicity sub concept, and Modification in Residue Sequences due to changes in chemical environment and mutations are described using in ModifiedResidue sub concept.
Monogenetic and Polygenetic defects present in the underlying genes that generated the protein are described using GeneticDefects concept.
Hydrophobicity sub concept defines water solubility of the protein.
ModifiedResidue sub concept describes any residue modifications that occurred in the protein and resulted in change of residue structure and properties.
Entry describes the experiment and the biological macromolecules present in the protein. Protein Complex Entry and the Molecules contained in Protein Complex are described using sub concepts of Entry: Description, Molecule and Reference.
Data and Information about protein entry and the experiments that identify protein is described using Description sub concept.
Molecule Concept specifies the biological and/or chemical source of each biological molecule in the entry. Sources are described by both the common name and the scientific name, e.g., genus and species. Strain and/or cell-line for immortalized cells are given when they help to uniquely identify the biological entity studied.
Reference sub concept describes the Literature references for the protein entry.
PO has the first Functional Domain Classification Model for proteins defined using the derived concept of FunctionalDomains. Family and Super Family of the organism in which protein is present are represented in FunctionalDomains by reference to generic concept of Family. FunctionalDomains describes Cellular and Organism Source of Protein using SourceCell sub concept, Biological Functionality of Protein using BiologicalFunction sub concept, and describes Active Binding Sites in Protein using ActiveBindingSites sub concept. Active Binding Sites are represented in PO as a collection of various Site Groups, defined using SiteGroup generic concept.
Active Binding Sites in a protein are described using the sub concept of ActiveBindingSites and represented as collection of generic concept of SiteGroup.
BiologicalFunction Concept describes biological functions of the Protein categorized further as Physiological and Pathological Functions represented using sub concepts of PhysiologicalFunctions and PathologicalFunctions.
Modification of Protein Structure based on significant biochemical and structural changes are described here. This kind of information is normally entered in Protein Ontology through Knowledge Bases and Scientific Literature.
Features of Protein Structure describing significant biochemical and structural homology in them to improve the understanding of Physiological Functions are defined here. This kind of information is normally entered in Protein Ontology through Knowledge Bases and Scientific Literature.
The Organism and Cellular Source where the protein resides is described by SourceCell Concept.
Structural Folds and Domains defining Secondary Structures of Proteins are defined in StructuralDomains Class. The subclasses of StructuralDomains are Helices, Sheets, and OtherFolds.
Helix, which is a sub concept of Helices, identifies a helix. Helix has a sub concept HelixStructure that gives the detailed composition of the helix. In this way PO distinguishes concepts for identification and structure of secondary structures in a protein.
HelixStructure is a sub concept of Helix, and it describes detailed composition of the helix in terms of Chains and Residues.
Sheets have a sub concept Sheet that identifies a sheet. Sheet has a sub concept Strands that describes detailed structure of a sheet.
Strands is a sub concept of Sheet, and it describes detailed composition of the sheet in terms of Chains and Residues.
Similarly turns in protein structure are repented in PO using OtherFolds Concept. Turn is a sub concept of OtherFolds that identifies a turn and TurnStructure describes its structure. Turns in protein structure are categorized as OtherFolds in Protein Ontology as there are less frequent than Helices and Sheets in Protein Structure.
Loose and flexible structural patterns of turns or loops just describing the Chain and Residue to point the position of turn or loop are defined here.
Protein Structure Contains the collection of atomic coordinates and describes the geometry of the crystallographic experiment and the coordinate system transformations. Structure Concept has sub concepts ATOMSequence and UnitCell. They represent protein sequence, protein structure and crystallographic data.
ATOMSequence is an example of reuse of concepts in PO; it is constructed using generic concepts of Chains, Residues, and Atoms. The reasoning is already there in the underlying Protein Data, as each Chain in a Protein represents a sequence of Residues, and each Residue is defined by a number of three-dimensional atoms in the Protein Structure.
Protein Crystallographic Data is described using parameters, space group, and Z value. If the structure was not determined by crystallographic means, data simply defines a unit cube.
Residue refers to a portion of a larger molecule; for example in biochemistry and molecular biology, a residue refers to a specific monomer of a polysaccharide, protein or nucleic acid. In context of Protein Ontology residue represents one of the 20 amino acids that build protein sequence represented by a three-alphabet code like: CYS.
Identification of groups comprising important sites in the macromolecule is done using Site parameter, represented as string in protein databases. They specify residues comprising catalytic, cofactor, anticodon, regulatory, or other important sites.