Is it correct to assume that genes that belong to a child category will automatically be a member of the parent term?
Yes, as every GO term must obey the true path rule: if the child term describes the gene product, then all its parent terms must also apply to that gene product (http://www.geneontology.org/GO.usage.shtml#truePathRule). The ontologies are structured as directed acyclic graphs, which are similar to hierarchies but differ in that a child, or more specialized, term can have many parents, or less specialized, terms. For example, the biological process term hexose biosynthesis has two parents, hexose metabolism and monosaccharide biosynthesis. This is because biosynthesis is a subtype of metabolism, and a hexose is a type of monosaccharide. When any gene involved in hexose biosynthesis is annotated to this term, it is automatically annotated to both hexose metabolism and monosaccharide biosynthesis (the above information originated from: http://www.geneontology.org/GO.doc.shtml#look) Please note however, that the true path rule is broken for those annotations which contain the ‘NOT’ qualifi
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