Fragmentation code systems

A different consideration arises when one employs indicator variables to represent structural fragments. There are many kinds of fragment code systems in use, most of which were designed to assist in classification of large collection of... 

The problem of poor retrieval precision, and the development of search systems based on unambiguous (complete) representations of the structure has led to the general demise of fragment codes as a primary representation of chemical structures, at least for specific compounds. However, hidden from the user they remain an important component of structure search systems, and a few user-visible fragment-code systems continue to be used in the handling of Markush structures from chenaical patents these are discussed in more detail in Markush Structure Searching in Patents. 

The representation is unambiguous since it corresponds to one and only one substance, but it is not unique because alternative numberings of the connection table would result in different representations for the same chemical substance (the connection table representation is discussed in more detail below). In addition to being categorized according to their uniqueness and ambiguity, chemical substance representations commonly used within computer-based systems can be further classified as systematic nomenclature, fragment codes, linear notations, connection tables, and coordinate representations. 

With the variety of chemical substance representations, i.e., fragment codes, systematic nomenclature, linear notations, and connection tables, a diversity of approaches and techniques are used for substructure searching. Whereas unique, unambiguous representations are essential for some registration processes, it is important to note that this often cannot be used to advantage in substructure searching. With connection tables, there is no assurance that the atoms cited in the substructure will be cited in the same order as the corresponding atoms in the structure. With nomenclature or notation representation systems, a substructural unit may be described by different terms or... 

Plants will have a specific DNA bar code, which will be a useful forensic tool. The DNA bar code is made up of a standard short region (or regions) of DNA selected from one or more of the genomes. It can be applied universally across land plants but is also variable enough to provide individual identification at species level. The bar code system can be applied to access a database for identification of known plants. It can be used to identify unknown samples from fragments of plant material by comparing them to the known standards and has applications for verification of material in natural products like herbal medicines and foodstuffs. 

As with the numeric data, the content of stmctural information in the secondary literature is fimited, and we therefore have a situation in which many specicdised systems have been developed to deal with stractural data. Files of chemical stractures, and means of accessing them, have been with us for a number of years, certainly from before computers. Traditionally, these have used notations, fragment codes, etc., as the means of recording structural information, and have allowed searches to be made for complete compounds or for all compounds containing certain specified substractures. More recently, topographical systems have been developed. In these the complete stractures are recorded in the form of "connection tables", which store full details of all the atoms and bonds in a molecule, and the precise arrangement in which they are connected. 

Traditional substructure search systems work in two stages the first stage is a preliminary filter using fragment codes the second stage applies atom-by-atom search to check the isomorphism of the subgraphs. 

Whatever the search software offered, however, the database was of utmost importance. The DARC system not only offered a means to search generic structures in the short term, it also offered a way to record all of the information about structures found in patents, through a new and flexible input system. This capability was of incredible import to Derwent we could build a database that would not only serve the users today, but in future could be of more utility as search software was further developed. As opposed to the fragmentation code, there should never be a question of time-ranging. Moreover, though we assume that Markush DARC is a system not only of today but of tomorrow, we are building a database that can be converted and adapted to other search systems that may be offered by other organisations. 

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