Beilstein Structures File

The system has been designed for both an optimised vectorial coprocessing unit connected to a mainframe to free the main CPU from the very special burden of substructure search, and a stand alone microprocessor-based substructure search system for selected parts of the Beilstein structure file (Beilstein Selects). 

The SDF structure file is used for delivery to hosts and in-house customers of the Beilstein structure file. Other delivery formats produced by the registry software include Tel6systemes-DARC and MDL MOLfile formats. Large DARC and MOLfile structure files have been created at the Beilstein Institute for the purpose of benchmarking the DARC-SMS and MDL MACCS-II substructure search systems against the S4 substructure search system developed jointly by the Beilstein Institute and the software house Softron GmbH . 

The S4 search system itself embodies several novel and interesting concepts. The search file is built from the Beilstein structure file by encoding every atom of every molecule in terms of its extended connectivity encompassing every atom in the molecule. These compact atom codes are sorted into a file and further compressed. From this large file of atom codes a search tree is generated consisting of the first ten spheres around each atom. This tree forms the index through which the atom code file is accessed. 

The ROSDAL syntax is also currently being extended to accommodate inorganic substances. Details of these developments and other aspects relating to structure representation in the Beilstein structure file can be obtained from the authors. 

ROSDAL. Linear notation scheme devised by the Beilstein Institute. It can contain just connection table information, or it may also contain atom coordinates. Several chemical information systems can convert ROSDAL strings to other structure file formats. 

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. 

H atoms In the SD file exported by Beilstein structures are coded without H atoms. H atoms are, however, requited for calculating some indices and for calculating 3D molecular models. H atoms were thus added according to the valences of all non-H atoms. (The MDL SD file format is a popular exchange format for molecular structures, see [53]. 

Databases include the Beilstein File, the Gmeliu File, the Registry File, the Description. Acquisition. Retrieval, and Correlation File, and Ihc Structure and Nomenclature Search System. 

CAS/STN International. CAS/STN offers structure searchable files such as Registry, Beilstein, MARPAT, CASREACT, and Gmelin a variety of learning files, eg, LRegistry, LBeilstein, LMARPAT, and LCASREACT and software products such as STN Express for on-line structure and substructure searching. Chemical Abstracts Service, a division of the American Chemical Society, has published Chemical Abstracts since 1907 and joindy operates STN International with FIZ Kadsruhe and the Japan Information Center of Science and Technology. 

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. 

In-silico screening is one way to expand the chemical space beyond what has been reported after some 200 years of chemistry. While Chemical Abstracts and Beilstein might contain millions of chemical structures, there is another real chemical world that has yet to be mined and that is lost chemistry, the chemistry that was done but never reported. Current estimates are that on the order of 80% of the chemistry performed over the past years has not been published. It is to be found in files and lab books around the world, on dusty shelves, or destroyed long ago and lost forever. How some of the lost chemistry can be retrieved and evaluated is not our subject here. The visible chemistry that is real, the actual compounds in vials, is the center of the current focus. 

Preparation of structure queries, transfer of queries for on-line database searches, and capture of hits. Imports structures from ChemDraw, Alchemy III, and ISIS/Draw. Structures can be used to search BEILSTEIN, GMELIN, MARPAT (the CAS Markush patent file), REGISTRY, SPECINFO, CASREACT, and ChemInformRX databases. SciFinder for graphical user interface to STN databases. Internet address stnc.cas.org (134.243.5.32). 12th Collectii/e Index of Chemical Abstracts on CD-ROM. CASurveyor with recent CAS abstracts on CD-ROM. PCs (DOS and Windows) and Macintosh. 

Third, the tautomer information from the normalised BRCT is utilised in the tautomer search option of the Softron S4 search system. Although this is not yet fully implemented, S4 uses the tautomer information to control the mapping of the query structure onto all valid tautomeric forms of candidates in the Beilstein file. 

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). 

Structure Distribution File, File and Record Formats , Version 2.03, December 1991, Technical Documentadon, Beilstein Institute, Frankfurt/Main, 1991. 

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