Beilstein file, data structure

The projected, numerical factual database BEILSTEIN-ONLINE represents a natural extension of the Beilstein Handbook of Organic Chemistry which has been published for more than 100 years in more than 300 volumes. The Handbook together with the structure file cards of the literature period 1960-1980 (E-V Period) contain factual and structural information on more than 4 million compounds. The computer representation of organic chemical structures therefore constitutes the centre part of the database design. The chemical structure is described in a post-topological format. Not only constitutional information is included but also a complete stereochemical representation. Bond orders are replaced by electronic information. This allows a much more global and unique representation of tautomers. This paper gives an overview not only of the data structure of chemical compounds but also of its associated physical numerical data and keywords. 

While the Beilstein file contains a good deal of data in this area, there are also excellent compilations dedicated to thermodynamic quantities. DETHERM is produced by Dechema, and contains thermophysical properties for ca. 17000 compounds and mixtures (see Chemical Engineering Databases). The subject matter is taken from phase equilibria, PVT behavior, thermodynamic quantities, transport phenomena, surface properties, and electrolyte properties. Attention must also be drawn to the compilations of the US National Institute of Standards and Technology (NIST). The NIST Chemistry WebBook contains thermodynamic data for over 5000 compounds and ion energetics data for over 10000 compounds. The user may search on specific compounds based on name, chemical formula, or CAS Registry Number. Structures are given for all species, as well as common and commercial names. 

Factual databases are generally described in terms of the standardization of the data structure and the data content. In the case of the Beilstein file and CrossFire the following distinction is important to note, and will apply also to other major sources of factual data (e.g., Gmelin). 

This description sees the elements of the database as structures linked to properties linked to references, and a chemical reactions database is included . This reflects exactly the historical development of the Beilstein Handbook, and later the Beilstein file on STN and DIALOG these collections are lists of compounds, with subsections on property type, linked to sub-subsections of reference lists. But the CrossFire implementation is much more than this. It has a different data orientation, and can justly be regarded as a new implementation, in fact a... 

The top level of architecture (Table 4) of this very large data collection is fundamentally different in its data structure from the Beilstein Handbook, or the Beilstein file at STN or DIALOG, which have never claimed to be reaction- or document-oriented, and are simple linear lists. It is ultimately responsible for the unifying hyperlink philosophy in CrossFire, which contains upwards of 50 million hyperlinks (see below). 

All fields may be displayed individually. Figure 157 shows the hierarchic structure of the Beilstein file, through the example of Preparation. When displaying format CHE, Chemical Data, the field Preparation is also displayed. 

A number of systems now offer graphics-based substructure search capabilities for online access to a variety of chemical structure data bases. From December 1988 the first subset of the Beilstein Online data bank (organic heterocyclic compounds reported in the literature prior to 1960) goes online on STN International. Other hosts, which at present offer only name-based structure and substructure search capabilities are also likely to provide online access to the Beilstein files in the near future these include Dialog, Pergamon Orbit Infoline and Datastar. 

Bradshaw et al. have disclosed a rapid and facile method for the dereplication of a purified natural product library [58]. The method integrates the molecular weight from low resolution MS data with the exact count of the number of methyl, methylene and methine groups obtained from ]H-13C NMR correlation data. Those structure properties were converted into a searchable text file that could be downloaded into a customized software program with chemical structure information in a specific format - SMILES. In the program, more than 120,000 unique structures were derived from commercial databases, such as Dictionary of Natural Products and Beilstein. 

Scientific Technical Network (STN) (http //stnweb.cas.org/) is probably the most useful and extensive structure-searchable resource for chemistry worldwide. More than 200 scientific databases are available via STN (this service is not free). Several related databases can be searched simultaneously ( cluster search ). Cluster presearch is free and very useful, as the number of relevant hits per database can be visualized in this way. The most important files on STN are the CA Registry, CA Plus, Beilstein and the INPADOC (patent data) file. 

This section will describe examples of a variety of different types of 2D and 3D chemical structure databases and data collections. These range from comprehensive collections of small organic molecules (CAS registry file and Beilstein), to specialized collections of analytically derived 3D structures (CSD and PDB), to commercial reagent catalogs (ACD), to prospective and actual pharmaceutical entities (MDDR, NCI, and the typical corporate pharmaceutical database). Access to all but proprietary collections is available for a fee. For additional information, see also Online Databases in Chemistry. 

Fact files mostly include a great number of single fields which are non-text fields but often containing numeric, such as physical and thermodynamic data of compounds. Fact files are for instance Registry File, Beilstein and Gmelin as well as Specinfo. Some numeric databases - special kind of fact files - even allow calculations to be made, e.g. in Inorganic Crystal Structure Data. 

---