Connection Table Representation

A connection table has been the predominant form of chemical structure representation in computer systems since the early 1980s and it is an alternative way of representing a molecular graph. Graph theory methods can equally well be applied to connection table representations of a molecule. 

Conversion in both directions needs heuristic information about conjugation. It would therefore be more sensible to input molecules directly into the RAMSES notation. Ultimately, we hope that the chemist s perception of bonding will abandon the connection table representation of a single VB structure and switch to one accounting for the problems addressed in this section in a manner such as that laid down in the RAMSES model. 

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. 

Given an arbitrarily numbered connection table representation of a structure with n non-hydrogen atoms, the unique numbering is obtained as follows ... 

The conversion of chemical names and identihers into appropriate chemical structure representations offers the ideal path for chemists and organizations to mine chemical information. Because chemical names are not unique and a multitude of labels can map to a single chemical entity, the facile conversion of alphanumeric text identihers to a connection table representation enables superior data capture, representation, indexing, and mining. The industry s need to mine more information from both the historical corpus as well as new sources is obvious, and a number of researchers have initiated research into the domain of chemical identiher text mining and conversion. Multiple efforts have been made in the held of bioinformatics research,8 and, while interesting as a parallel, in this chapter we will focus the efforts to extract and convert identihers related to chemical entities rather than, for example, genes, enzymes, or proteins. 

Barnard, J. M., M. F. Lynch, and S. M. Welford. 1982. Computer storage and retrieval of generic structures in chemical patents. 4. An extended connection table representation for generic structures. J. Chem. Inf. Comput. Sci. 22(3) 160-164. 

One of the first approaches for substructure search was published by Feldmann et al. [7]. They used connection table representations of 2D chemical structures to search for particular substructures within these larger structures. The resulting system — the National Institutes of Health-Environmental Protection Agency (NIH-EPA) Chemical Information System — started in 1973 as a joint project in mass spectrometry and structure searching between the NIH and the EPA [8]. 

Extended Connection Table Representation molecular graph... 

Connection Tables In practice, the node-oriented connection table is applied. This table can be derived from the connection matrix of atoms (cf. Table 7.6) and contains only the numbered chemical elements, the bonds connected to the atoms, and the type of the actual bond. In Table 7.7, the connection table for the phosgene molecule is written down. A less redundant connection table representation is given in Table 7.8. 

Barnard, J.M. Lynch, M.F. Welford, S.M. Computer Storage and Retrieval of Generic Chemical Structures in Patents, Part 4, An Extended Connection Table Representation for Generic Structures. J. Chem. Inf. Comput. Sci. 1982, 22, 160-164. 

The internal representation of GENSAL is called ECTR (Extended Connection Table Representation). It was described first by Barnard, Welford and Lynch in... 

Extended Connection Table Representation (ECTR) Example ... 

Several methods for structure representation have been developed. Each representation derives from the two-dimensional structural diagram and is sufficient to provide a simple characterization of that structure. This characterization is ambiguous if it represents more than a single structure, as in the case of fragmentation codes, or unambiguous if it represents a single structure only, as in the case of nomenclature, linear notation, and connection table representations. 

In this article, we assume that the reader is familiar with standard connection table representations of chemical molecules. This section recapitulates the main features of connection tables by means of an example. 

Suppose 23 was the input structure, say, from a drawing program. The 2D display coordinates do not differentiate between different molecules. Therefore, they are not included in the connection table representation. 

One purpose of canonical numbering is the construction of a unique name of a compound. The canonically numbered connection table representation is uniquely defined. However, it usually contains a lot of redundancy and perceived information. The final unique name is normally a compressed form of the connection table which contains just enough information to reconstruct the connection table in its canonical form. Examples of such codes are the SEMA (stereochemically extended Morgan algorithm) name and canonical SMILES. 

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