InChl

The lUPAC International Chemical Identifier (InChl ) is a nonproprietary identifier for chemical substances that can be used in printed and electronic data sources thus enabling easier linking of diverse data compilations. It was... 

Table 1 shows an example of markup, generated using the OSCAR 3 system. The abstract of a polymer research paper has been parsed by OSCAR and the resulting markup for the first sentence of the abstract is shown in-line with the text (Table IB). The first chemical entity encountered in the sentence is oleic acid , which has been marked up as type = CM (Chemical Moiety) and a number of other annotations, such as in-line representations of chemical structure (InChl, SMILES) have been attached. 

Note1. t psi(pounds/square inchl = 0.0069 megapascal (MPa). Designation of Magnesium Alloys lan. 1.17 M system now accepted by the Ss f.). A four-pan system is used-. 

Elements can specify data or information in two ways. First, data can be contained between the start and end of any particular element,such as and numeric data, as in the example above, which uses both the CAS Registry Number, a unique identifier assigned to chemical structures by CAS (see Appendix 12-3), and a unique canonical molecule identifier known as InChl (International Chemical Identifier) (for more on InChl, see Appendix 8-1). 

Whereas the theory needed for conversion of a structure to a unique string of characters has been known for a long time, when work on InChl began there were no freely available unique representations for compound identification, nor... 

An example of an InChl representation is given in Figure 8A-1. The acronym InChl and version number are regarded as part of the InChl string (InChI=l in this case). It is important to recognize, however, that InChl strings are intended for use by computers, and end users need not understand any of their details. In fact, the open nature of InChl and its flexibility of representation, after implementation into software systems, may allow chemists to be even less concerned with the details of structure representation by computers. Source code and an executable version of the structure-to-InChl conversion algorithm are freely available from the IUPAC InChl Web site at http //www.iupac.org/inchi. 

Figure 8A-1. InChl for guanine (A) input structure (B) mobile H canonical numbering, with the attachment points of four mobile H and changeable bonds indicated in bold and (C) with fixed H canonical numbering.

Project Prospect endeavors to use and build acceptance of standards for chemical information by using the International Chemical Identifiers (InChls) created by the International Union of Pure and Applied Chemistry (IUPAC) as a way to provide a nonproprietary way to make chemical information more machine-readable. To illustrate the potential of this in the simplest way, an InChl for benzene (i.e., InChI=l/ C6H6/cl-2-4-6-5-3-l/hl-6H) was pasted into a Google search bar (www.google. com), this resulted in 37 hits in the fall of 2007 and over 1,000 hits 6 months later in the spring of 2008. The top hits were directed at the IUPAC Gold Book as shown in Figure 1.1. 

Integration of select Internet resources, such as the public chemical databases mentioned above, provides a very practical approach to structure searching the Internet and internal resources (Dong et al. 2007). Chapter 8 elaborates on this concept. As summarized in Chapter 2, another facet of chemical structure mining involves finding information within full text documents that do not traditionally contain identifiers like InChl or SMILE strings. Chapter 5 contains an in-depth discussion of these identifiers. 

Google searches on the InChl chemical identifiers for benzene (left) and aspirin (right) demonstrate the potential of structure searching... 

The most commonly used identifiers today include line notation identifiers (e.g., Simplified Molecular Input Line Entry System [SMILES] and International Chemical Identifier [InChls]), tabular identifiers (e.g., Molfile and Structure Definition [SD] file types), and portable mark-up language identifiers (e.g., Chemical Markup Language [CML] and FlexMol). Each identifier has its strengths and weaknesses as detailed in Chapter 5. Chapters 5 and 6 provide enough information to guide researchers in choosing the most appropriate formats for their individual use. 

Wikipedia Discussions Forum. 2007. Embedded InChls in images http //en.wikipedia. org/wiki/Wikipedia talk WikiProject Chemistry/Structure drawing workgroup/ Archive Jun 2007 ACD ChemSketch - the company is willing to make a Wikipedia Template on their Freeware. 

Even though InChl (discussed in the next section) is quickly gaining support as the linear format of choice, the fact that SMILES can be read and written by humans... 

Another important feature of InChl is its layered structure. Unlike in SMILES, where all data related to one atom are stored in one place, in InChl different properties of the structure are encoded in different parts of the identifier. This organization of the data has one very important advantage molecules with the same basic structure that differ only in some minor property, such as in stereochemistry or isotopic composition, have the same InChl, with only the exception of the corresponding layer. This makes it possible not only to compare two InChls to find if they represent exactly the same structure, but to use a more intelligent comparison of two InChl strings to reveal molecules with the same basic structure that differ only in some detail. It is then up to the user to decide which deviations in the InChl are significant for his or her purpose and which are not. 

The layer structure of InChl is demonstrated in Figure 5.3, and Figure 5.4 shows several similar structures and the influence different changes in the structure have on the resulting InChl. 

The following list briefly mentions all possible InChl layers and discusses some important facts that arise from properties of each layer ... 

Component charge Net charge of the molecule (or charges of individual components) no information about position of charge is stored in InChl. It is important to be aware of this the same InChl will be generated for two structures that differ only in the position of charge. 

FIGURE 5.4 Influence of chemical structure on individual InChl layers. 

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