Beilstein Data File

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. 

Beilstein File. Beilstein first went on-line on STN International in December 1988 with information on 350,000 compounds, and several months later it was also on Dialog. Beilstein Online now comprises data on five million compounds. The organic substance records contain the critically reviewed and evaluated documents from the beilstein Handbook of Organic Chemist main volume and supplements 1—5, which cover the chemical Hterature from 1779 through 1979. These evaluated data are indicated as Handbook Data in the notes of Hterature references. The Beilstein Eile also contains organic substance records for unreviewed excerpts from the primary Hterature from 1980 to 1991. 

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. 

When the comparison is with the real chemical world, novelty concerns much smaller numbers. In March 2002, the Chemical Abstracts Registry file contained more than 37 million chemical substance registrations, which contained almost 19.5 million organic and inorganic substances. The CrossFire Beilstein database contained data on over 8 million organic compounds on the same search date. It is a tedious exercise, but very much worth the effort, to take databases such as these based on Beilstein and remove trivial small molecules ( non-druglike ) and see how many compounds remain. The result is less than half a million. 

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. 

In respect of the different sources of available information, the database can be divided into a Short File and a Full File, The Full File will consist of all the data which have been published in the Handbook series and which have been checked for errors and redundancies by Beilstein information specialists. The Short File is built directly from the abstracts of the primary literature without any further checking. Factual data of the current, primary literature will be added to the Short File on a regular basis. The Full File will be continuously extended by processing the raw material of the Short File via an error checking and removal of redundancies. 

The Beilstein and Gmelin files (now contained in the Reaxys system) include spectral data for organic and inorganic compounds respectively, excerpted from the journal literature. Reaxys does not contain graphical spectra diagrams, and may only provide the pertinent literature reference. 

Many chemists therefore take the view that the Beilstein and Gmelin files may be regarded as factual files, while the CAS and Derwent files are not. In the sense of the approach of the present article, this is certainly unfair to the latter pair, It is certainly true that in particular cases the generalized description of a property described in a generalized way in the abstract of a document may lead to valuable results which would be difficult or impossible to obtain without this form of soft data retrieval. For this very reason, Beilstein s CrossFire system has now started to include more and more soft data in the form of abstracts, titles, and other qualitative free text in its databases. 

Traditionally certain numeric experimental data are required in publications of results, to permit validation by subsequent workers or for qualitative analysis purposes. Apart from elemental analysis, these include notably the melting point for solids, the boiling point and refractive index for liquids, and optical rotation data for optically active materials. Also, the same sort of data on certain derivatives of substances are used for the same purpose (e.g., the melting points of 2,4-dinitrophenylhydrazones, carbazides, etc., for carbonyl compounds). The largest single repository of such data is the Beilstein file, described in detail in Section 6. 

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). 

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. 

Four years later the first version of the system was complete. It was immediately integrated into the production scheme of the Beilstein Handbook and the Beilstein database. The Beilstein database was extended names generated by the system became a normal searchable data field in the Beilstein file offered by both DIALOG and STN information networks. Later, they also became fully searchable in the CD-ROM Current Facts information service, as well as in the biggest in-house chemical database system, CrossFire, which has been offered by Beilstein since 1994. 

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. 

LC STN Files ANABSTR. BEILSTEIN. BIOBUSINESS, BIOSIS, CA, CAOLD, CAPREVIEWS, CASREACT, CHEMINFORMRX, CHEMLIST, CBNB, CIN, CJACS, CSCHEM, DETHERM, EMBASE, GMELIN, HODOC, IFICDB, IFIPAT, IFIUDB, MEDLINE, NAPRALERT, PNI, RTECS, SPECINFO ( File contains numerically searchable property data)... 

A first difference to Chemical Abstracts has already been mentioned. There is another one. Beilstein facts are critically evaluated, i.e. all the contents of the Beilstein Handbook are counterchecked by chemists working in the Beilstein Institute. This is so at least for all data recorded up to 1959. The Supplement Series V, 1960-1979, is part of the file but indicated as Unchecked Data. 

Numerical properties may all be searched for using numerical operators (<, <=, >, >=, =). Every field has a singular unit, retrievable in the manual The Beilstein File - Database Description. As a supplement to the field Property Hierarchy (PH), the subfield Keywords (XYZ.KW) is usable. It gives out descriptions of given numeric data. The following keywords are used ... 

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. 

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