Protein structure ontologies

An ontology structures concepts (e.g., a gene, a physiological process, physical interaction vs. indirect interactions between proteins) in a cyclical graph or network structure. A concept can be related to another concept via a relationship ontology. The is-a relation is used to indicate is-a-child, is-a-parent, and is-a-synonym. The part-of can relate tissues and organs in the body. Cardiac tissue is part-of the... 

V) c u S u C BIND BindingDB BRENDA DIP IntAct project InterDom MINT Biomolecular interaction network database Collection on experimental data on the noncovalent association of molecules in solution Enzyme Information System Sequence, structure, specificity, stability, reaction parameters, isolation data, and molecular functions ontology Database of interacting proteins Public repository for annotated protein-protein interaction data Putative interacting protein domain database derived from multiple sources A molecular interaction database http //www. bind.ca http //www. bindingdb.oig http //www. brenda. uni-koeln.de http //dip.doe-mbi.ucla.edu http //www.ebi.ac.uk/intact http //interdom.lit.org.sg http //mint.bio.uniroma2.it/ mint/... 

Second, I suggest that the notion of structural representation can properly be addressed only within the context of a class. The reasons have to do with the following hypothesized ontology of objects. As we know, objects in nature do not pop up out of nowhere but always take time to appear, and in each case the way an object appears is similar to the way some other, similar , objects appear, i.e. an object always appears as an element of some class of closely related objects, be it an atom, a stone, a protein, or a stop sign. Moreover, an object co-evolves also together with its class there is an invisible permanent bond between an object and its class. 

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