Molecules InChl identifiers

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). 

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. 

Semantic Eye (Casher and Rzepa 2006) is a test-of-principle scheme for the semantic enrichment of journal articles. Rather unusually, it treats the PDF as the locus of semantic enrichment. The identifiers are mapped onto RDF triples that are then serialized as XML using Adobe s Extensible Metadata Platform (XMP) schema within the PDF. It uses InChls as identifiers for molecules and DOIs for the articles themselves. The idea is that the identifiers derived from the PDFs can be stored locally on a user s machine inside the PDFs, which are then mined by desktop indexing services, creating a sort of semantic intranet or semantic desktop. Exactly how the identifiers are assigned to the papers in the first place is left open to the user. 

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