$Id: motifml.daml,v 1.1 2001/11/17 21:28:19 kenb Exp $ Genetic Regulatory Motif Ontology A named genetic entity. A genetic structure that can be regulated. A DNA sequence that codes for a protein. A genetic sequence specified probabilistically. A genetic sequence within a genome located upstream from a gene. A chemical consisting of a linear chain of amino acids. A part of a protein that plays a special metabolic role. The most elementary classification of living organisms. An instance of a genetic regulatory motif that is involved in the regulation of a specific gene. A regulation relationship between regulatory entities. It can be activated in many ways, such as by a single protein (monomer), by two copies of the same protein (dimer) or by two different proteins at the same time (heterodimer). A point location on a genome. A probabilistically specified DNA nucleotide. An algorithm for finding genetic regulatory motifs. A unit for specifying a point position on a genome. The centiMorgan genomic position unit. The base pair genomic position unit. The type of regulation in a regulatory relationship. Regulation that increases the activity of some other regulatory unit. Regulation that decreases the activity of some other regulatory unit. The direction in which a regulatory entity is to be read. The direction can be expressed either absolutely or relatively. The direction on a chromosome toward the 3-prime end. The direction on a chromosome toward the 5-prime end. The forward direction toward a gene. The reverse direction away from a gene. The DNA nucleotides. Adenine Cytosine Guanine Thymine The amino acids. The primary name used for identifying an entity. Alternative name used for describing an entity. The species to which a gene belongs. The general location of a point in a genome. GenBank identifier. A precise location of a point in a genome. The unit used for specifying a position in a genome. The starting location of a gene in a genome. A regulation relationship that is determined by a regulatory region. The protein that activates a regulation relationship. The protein that contains a domain. The transcription or recognition direction of a genomic entity. The transcription or recognition length of a genomic entity. The position of a protein domain in its protein. The length of a protein domain. The multiplicity of protein subunits required for a regulatory function. The type of regulation in a regulatory relationship. The strength of regulation in a regulatory relationship. The regulatory entity regulated by a regulatory relationship. A motif to which a regulatory region belongs. The starting position of a regulatory region relative to the gene it regulates. The ending position of a regulatory region relative to the gene it regulates. The complementary DNA nucleotide. The nucleotide of a probabilistically specified nucleotide. The probability of a probabilistically specified nucleotide. The posterior probability that a regulatory region has been properly identified as belonging to a motif The sequence of a genomic or proteomic structure. The algorithm that identified a genetic regulatory motif.