Ontology, chemical

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

Feldman HJ, Dumontier M, Lng S et al. (2005) CO a chemical ontology for identification of functional groups and semantic comparison of small molecules. FEES Lett 579 4685-4691... 

Most chemists immediately utilized the compositional relationships derived from the atomic hypothesis, but for most of the century they continued to dispute the ontological reality of the atoms that rationalized their useful consequences. Even those most doubtful of the reality of the atom found its operational utility indispensible. Humphry Davy was expressing composition by the relative numbers of proportions by i8io, and William Wollaston attempted a calculus of chemical equivalents in 1814. Jons Jakob Berzelius undertook a systematic determination of the most accurate values to assign each of the atomic weights, publishing his first list in 1813. 

Although Le Poidevin is trying to establish the ontological dependence of the chemical upon the physical, he is attempting to do this without appeal to... 

Le Poidevin writes that because the thesis of ontological reduction is about properties, we do have to have a clear conception of what is to count as a chemical property. He then takes the identity of an element, as defined by its position in a periodic ordering, and its associated macroscopic properties to be paradigmatically chemical properties. About these properties we can be unapologetic realists. He also claims that a periodic ordering is a classification rather than a theory, so this conception of chemical properties is as theory-neutral as it can be.v He believes that the question of the ontological reduction of chemistry is the question of whether these paradigmatically chemical properties reduce to more fundamental properties. He then adds,... 

Finally there is a somewhat general objection to the use of combinatorialism in order to ground the ontological reduction of chemistry. Surely the assumption of that fundamental entities combine together to form macroscopic chemical entities ensures from the start that the hoped for asymmetry is present. But it seems to do so in a circular manner. If one assumes that macroscopic chemical entities like elements are comprised of sub-atomic particles then of course it follows that the reverse is not true. The hoped for asymmetry appears to have been written directly into the account, or so it would seem. 

Dybkaer, R. (2004), An ontology on property for physical, chemical, and biological systems. APMIS, 112 Blackwell Munksgaard 2004 (University of Copenhagen). 

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. 

In this paper we discuss a number of issues which manifest the theoretical particularity of quantum chemistry and which are usually not discussed in an explicit manner either in the historical or in the philosophical studies related to quantum chemistry. We shall focus on five issues the re-thinking of the problem of reductionism, the discourse of quantum chemistry as a confluence of the traditions of physics, chemistry, and mathematics, the role of textbooks in consolidating this discourse, the ontological status of resonance, and the more general problem of the status of the chemical bond. Finally, we shall briefly discuss the impact of large scale computing. 

Textbooks in general are - necessarily - a-historical and only in a very few instances do we find a mention and, in even fewer cases, a discussion of some of the disputes in a discipline s early history. Interestingly, the early textbooks of quantum chemistry could also be read as polemic or partisan texts by proposing and arguing in favor of particular (ontological) hypotheses and approximation methods, each one of them adopts a particular viewpoint on how to answer the question of whether quantum chemistry is an application or use of quantum mechanics for chemical problems. 

The two foundational relationships between entries in an ontology are is a and part of. The is a relationship is a taxonomic one thus, a dog is a animal, a spaniel is a dog, and so forth. Likewise, the part of relationship specifies that a hinge is part of a door, a door is part of a room, and so on. However, there is a subtlety. Not all parts can be described with the part of relationship, because if you say that type A part of type B, that means that all instances of A are necessarily part of some instance of B. So hydrogen is not part of methane. There are very few genuine cases of a part of relationship that describes chemical compounds. It is better to use a reciprocal relationship, has part, in which all type A has part some type B, or all methane molecules have some hydrogen atoms as parts. 

In this section we will describe the three general identifier strategies for objects of chemical discourse InChls (already introduced in Chapter 3), ontology IDs, and BioRDF. 

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