Chemical names conversion into structures

Thus, the conversion of chemical names into structures consists of parsing the name into longest text fragments. These fragments are submitted to lexical analysis and the derived lexical units are compared with a collection of predefined units in a dictionary. 

Nowadays, thanks to the availability, cost, and ease-of use of chemical structure databases, many of these text databases have been converted into a structure format, and most chemical databases are now structure searchable. A simple search of the Internet will show that many databases still lack chemical structures and therefore are not searchable by structure in the original format, for example, an online HTML page. These pages, however, can contain valuable information and, with the application of the appropriate name-to-structure (N2S) conversion tools can be made searchable. 

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. 

The first publication about the computer translation of chemical names was published by Garfield in 1961. In that article, he described the conversion of names into chemical formulas and initiated the path toward N2S algorithm development.45 Developments in 1967 at CAS provided internal procedures for the automatic conversion of CAS names into chemical diagrams.46 47 The first commercially available software program was CambridgeSoft s Name=Struct released in 1999,48 now patented,49 which was followed shortly by ACD/Labs ACD/Name to Structure product released in 2000.50 Two more commercial products are available Chemlnnovation s NameExpert51 and... 

The conversion of chemical names into chemical structures can be represented as two intersecting schemes utilizing a lookup dictionary and using syntax analysis. A combination of these two approaches is definitely needed for the analysis of chemical names in the real world. 

For the conversion of systematic names, a more powerful and flexible approach must be based on the parsing of the chemical names and the application of syntax analysis. Figure 3.4 illustrates the principle steps of this procedure. The first step in the process, lexical analysis, splits the whole chemical name into a series of name fragments, known as lexemes, that have structural or grammatical meaning. Also... 

Development of computer methods for the interconversion of chemical nomenclatures to and from molecular formulae, connection tables, and structural diagrams followed and seems to continue to follow two separate paths. On the one hand there are a great many reports, mainly from university sources, dealing with translation of systematic names into structural diagrams, and on the other hand there is relatively limited literature on translation of structural diagrams directly into systematic chemical names. Although these are two opposite directions of the same conversion, they have in practice very little in common as far as algorithms and applicable methods are concerned. 

Conversion of Structural Diagrams into Chemical Names... 

Two-Dimensional Representation of Chemical Structures. The lUPAC standardization of organic nomenclature allows automatic translation of a chemical s name into its chemical stmcture, or, conversely, the naming of a compound based on its stmcture. The chemical formula for a compound can be translated into its stmcture once a set of semantic rules for representation are estabUshed (26). The semantic rules and their appHcation have been described (27,28). The inverse problem, generating correct names from chemical stmctures, has been addressed (28) and explored for the specific case of naming condensed benzenoid hydrocarbons (29,30). 

The opening window of Chem3D consists of the workspace (display window where 3D structures are displayed with rotation bar, slider knob, and action buttons), the menu bar (File, Edit, View, Tools, Object, Analyze, MM2, Gaussian, MOPAC, and Window menus), tool pallette (action icons for the cursor), and replacement text box (element, label, or structure name typed in this box is converted to chemical structure). Structure hie in. mol,. pdb, or. sml can be opened and saved from the File menu. Note PDB hies saved from Chem3D do not contain residue IDs.) The accompanying program, ChemDraw, draws 2D structures (.cdx) that are converted into 3D models (.c3d) by Chem3D. The molecular sketches from ISIS Draw (. skc) have to be converted to. cdx with ChemDraw for the 3D conversion. 

Our intention in this chapter is to examine the challenges of extracting identihers from chemistry-related documents and the conversion of those identihers into chemical structures. The authors of this work each have well over a decade of experience in chemical structure representation and systematic nomenclature. We have been deeply involved in the development of software algorithms and software for the generation of systematic names and the conversion of chemical identihers into chemical structures.9 Although we have our own biases concerning approaches to the problem of N2S conversion, we have done our utmost to be objective in our review of the subject and comparison of approaches and performance. 

It is not quite clear how growth hormone exerts its effect at the cellular level. One hypothesis proposes that the major function of the hormone is to stimulate protein synthesis and that this is achieved by the release of insulin-like substances namely, somatomedin A and B. These substances are found in plasma, but their chemical structure is still unknown. Two somato-medins have been found in plasma a large (mol wt 44,000) and a small one (mol wt 22,000). Although there is no evidence of conversion of the large into the small somatomedin, it has been proposed that the high is a precursor of the low molecular weight component [166]. 

The isothermal conversion of chemical energy into mechanical work is the base of motility of all living organisms, and it is manifested of all levels of structural organisation, namely 1) molecular motility, which is based on the conformational changes of the proteins macromolecules 2) intracelular movements (flagellar or ciliar), contraction of muscular fibres, heart beats, plants movement and 3) movement of pluricellular organisms (locomotion). 

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