Reaction ontology

Sankar P, Aghila G (2006) Design and development of chemical ontologies for reaction representation. J Chem Inf Model 46 2355-2368... 

Sankar P, Aghila G (2007) Ontology aided modeling of organic reaction mechanisms with flexible and fragment based XML markup procedures. J Chem Inf Model 47 1747-1762... 

Finally, there are computable properties tliat do not correspond to physical observables. One may legitimately ask about tlie utility of such ontologically indefensible constructs However, one should note that unmeasurable properties long predate computational chemistry - some examples include bond order, aromaticity, reaction concertedness, and isoelec-tronic, -steric, and -lobal behavior. These properties involve conceptual models that have proven sufficiently useful in furthering chemical understanding that they have overcome objections to their not being uniquely defined. 

The chemistry community, understandably, failed to respond at all, even though Bohmian mechanics probably holds the key to the development of a theory of chemistry, soundly based on quantum theory and relativity. The problem with molecular structure is resolved by the ontological interpretation of quantum-mechanical orbital angular momentum and the key to chemical reactivity and reaction mechanism is provided by the quantum potential function. 

In this work a prototypical reaction prediction system which makes use of known reaction informatiorr, the molecular stractrrre of reactants and structural and environmental irtformation, like the backbone of the molecule and the reaction pH, is presented. First the POPE ontology, which includes descriptions of the material, chemical reaction and structru e descriptors, is briefly presented. The next section is dedicated to the description of the prototype reaction prediction system, followed by application examples. The last section discusses other potential applications of the ontological approach and future work. 

The Purdue Ontology for Pharmaceutical Engineering (POPE) was developed with its component ontologies for descriptions of materials, chemical stractures, reactions, material properties and experiments. Based on POPE an excipient interaction prediction/diagnosis apphcation which made use of stmctural and environmental information was presented. There are several challenges in the horizon, which include the consideration of rates of reaction to determine relevance and evaluation of multiple measures of molecular similarity. 

A many number of modelling and simulation systems have been developed to aid in process and product engineering. In this paper the knowledge based process plant simulation model was developed. On the model development side, the issues of knowledge representation in the form of systematic component composition, ontology, and interconnections were illustrated. As a case study a plant for starch sweet syrup production was used. The system approach permits the evaluation of feasibility and global plant integration, and a predicted behavior of the reaction systems. The obtained results of the this paper have shown the variety quality of syrups simulation for different products. 

It is tempting to suppose that the whole of this elaborate graphical and spatially expressed calculus is a merely formal accounting scheme with no direct ontological content. It is a successful scheme in aceounting for most of the features of molecular structures and many of the features of ehemical reactions. It has often been used in making predictions and deductions about such of these features as are directly measurable for comparison. But for all of its empirical success, it may be only a formal scheme. 

From the scientific perspective, some materials with covalent bonding will exist in the form of molecules, but others may have extensive covalently bound lattices. Metals, and salts, are bonded, but do not consist of molecules. Yet research suggests that learners do not readily appreciate such structural diversity just as they tend to assume elements in reactions are present as separate atoms (see an atomic ontology , above), many also tend to conceptualise bonded materials as always being in the form of molecules. 

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/... 

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