CrossFire Beilstein database

The CrossFire Beilstein database is the world s largest compilation of chemical facts. This database indexes three primary data domains substances, reactions and literature. The substance domain stores structural information with aU associated facts and literature references, including chemical, physical and bioactivity data. The reaction domain details the preparation of substances, enabling scientists to investigate specific reaction pathways with reaction search queries. The literature domain includes citations, titles and abstracts, which are hyperhnked to the substance and reaction domain entries. It contains over 320 million experimental data, over 10 million reactions and data indexed from over 175 journals. 

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. 

Beilstein database The database covers the scientific literature from 1771 to the present and contains experimentally validated information on millions of chemical reactions and substances from original scientific publications. The electronic database was based on Beilstein s Handbook of Organic Chemistiy. In this database, each compound is given a unique Beilstein Registiy Number which helps in their easy identification. Each substance has up to 350 fields containing chemical and physical data. References to the literature in which the reaction or substance data appears are also given. The content is made available through the CrossFire Beilstein database. 

This tutorial, which is based on the Beilstein update BS0202PR (May, 2002) and on the retrieval program Cro.ssFire Commander V6,. shows. some typical advanced search examples in the Beilstein database. It is assumed that the user already knows some of the basic features of the retrieval program. Moreover, in this tutorial the CrossFire Structure Editor is used instead of the (SIS/Draw Structure Editor. The first example is a combined application of structure aiM fact retrieval, whereas the second example demonstrates reaction retrieval. 

Beilstein Database are described in The Beilstein System Strategies for Effective Searching, ed. S. R. Heller (Washington, DC American Chemical Society, 1997). In the 1990s, the Beilstein Institute together with MDL produced an Internet-based client-server system of the Beilstein Database, CrossFire Beilstein, which is now owned and updated by Elsevier Information Systems, Frankfurt. 

CrossFire Beilstein is available to subscribers as part of the CrossFire Database Suite. This package consists of CrossFire Beilstein, CrossFire Gmelin, and Patent Chemistry Database. Since January 2009, the contents of these three databases have been merged and are accessible through a new web-based interface, Reaxys (Table 1.4). 

Like CA, Beilstein is available on-line, with the useful search engine Crossfire Beilstein. The Beilstein database is one of the best databases for organic chemistry, particularly synthetic organic chemistry. It contains information on 9.4 million organic substances that have been fully characterized, as well as 9.8 million reactions. Information available includes ... 

While many technical reference libraries have Beilstein in print form, it is more convenient to search for information in the electronic form of the database, hi addition, the printed series is no longer being updated. The electronic database allows a variety of searches on compounds and properties. Access to the electronic database is offered through CrossFire Beilstein [see http //www.mdl.com] or through the STN database system of the Chemical Abstracts Service [http //www.cas.org/stn.html]. Some details given in the print version (such as experimental methods) were not carried over to the electronic version, so in some cases it may be necessary to consult the print version or the literature citation for further information. 

First, draw the structure of the compoimd in Crossfire s structure editor and search it against the Beilstein database. This brings up the record for the compound in question. A method of preparation using furfural and l-(3-nitrophenyl)ethanone is indicated under Reactions. If you follow the link to the Crossfire reaction record, you find two literature references D. L. Turner, /. Am. Chem. Soc. 71,1949, 612, and Li, Synth. Comm. 29,1999, 965. These articles describe methods of preparation from 2-furaldehyde and acetophenone. 

Beilstein and CrossFire and NetFire Database. The Beilstein Handbuch der Organischen Chemie contains evaluated numeric and factual data on millions of compounds. The complete Beilstein Online was available at the host STN in 1991. Also the host DIALOG offers the Beilstein database (see Factual Information Databases). 

CrossFire is the enhanced inhouse version of the Beilstein database. The database consists of about 30 million reports, of which five million are reactions. Hence this database is a reaction database. But apart from that, it covers structural, factual and bibliographic information. This means that CrossFire can also be classified as a structural and most of all as a numeric database. In a recently published article by Lawson, an example is shown, illustrating the use of substance-, reaction-, and document-based search techniques on the same problem. The special power of hyperlinks between reactions, substances, and documents is shown. 

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. 

Beilstein is a much more comprehensive database, marketed under the name of MDL Crossfire, and requires a subscription fee for access. It contains far more organic substances and lists many more properties. The search commands include ... 

Rouse, K. and Beckman, R. 1998. Beilstein s CrossFire a milestone in chemical information and interlibrary cooperation in academia, in The Beilstein System System Database and Software, S. Heller (Ed.), Washington, DC American Chemical Society, pp. 133-148. 

This statement is based on a search of the Beilstein Crossfire database. 

The Beilstein Crossfire database is available from Elsevier MDL, 2440 Camino Ramon, Suite 300, San Ramon, CA 94583, USA (http //www.mdl.com)... 

Beilstein Handbook of Organic Chemistry - The classic source of data on organic compounds, dating from the 18 century, Beilstein was converted to electronic form in the last decade of the 20" century. Over 8 million compounds and 5 million chemical reactions are now covered, with a broad range of physical properties as well as synthetic methods and ecolr cal data. The database is accessed by the CrossFire software... 

Although familiarity with the printed Beilstein Handbook is a useful skill for an organic chemist to have, in reality few chemists still use the printed version today. In the mid-1990s, the Beilstein Institute launched an online service that revolutionized the use of this extraordinary tool. The Crossfire system provides online access to the database of over eight million compounds, nine million reactions, and 36 million individual data points, through a dedicated client-server system that is accessed via the Internet. 

A new and valuable literature based database and search system, called NetFire, has recently been made available on the Internet by Beilstein Information Systems. It is the first attempt by Beilstein to provide chemical information outside the main area of extracted and evaluated data. The existing Beilstein system, provided via their CrossFire system, is an in-house system which has received wide acceptance since it was introduced in the mid 1990s. NetFire is a very new and different system, a valuable Internet resource. It is yet another example of the innovation of new and modem electronic products by Beilstein. NetFire provides free access to titles, abstracts, and authors from the organic chemical literature, from 1980 to the present. ... 

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. 

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). 

The Beilstein CrossFire Organic Chemistry Database provides worldwide coverage of the literature relating to the preparations and properties of organic compounds. Beilstein is searchable in multiple ways, including chemical structure, formula, and physical property parameters. Beilstein indexes periodicals, books, dissertations, and patents dated 1800 to the present. 

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... 

As a last comment on freely available data, it is probably fair to say that valuable and costly collections are rarely made available free of charge for an extended period of time. This comment is not intended to deprecate this source, merely to point out that large data sets are very expensive to gather and maintain, and simple economics suggests that they cannot be offered at below cost, or even free. As one measure of this, the comparison between the ChemFinder answer set to the class query MF=CioHi802 (as a fairly common MF) resulted in 20 hits in ChemFinder, but 4157 in CrossFire. Presumably these numbers are fairly typical, and therefore imply that the ChemFinder list is ca. 0.5% of the Beilstein coverage, despite the fact that the ChemFinder list incorporates several hundred databases. 

Figure 8 Reaction record from the CrossFire plus Reactions database (reprinted with permission of Beilstein Information Systems. Inc.)...

Many producers and public hosts offer reduced rates for academics or full academic programs , making expensive retrieval systems and databases affordable for academic institutions (e.g., MDL, retrieval system ISIS plus several databases Beilstein Information Systems, CrossFire FIZ Chemie, reduced rates for both Cheminform RX in house and at the host STN Springer/Infochem Synopsys). However, CASREACT is unfortunately not included at this time in the otherwise very useful CAS academic program. ... 

The situation is not nearly as favorable for exporting results. Accord by Synopsys, the new Beilstein CrossFire for Excel clients, and particularly ISIS, are much more flexible than others, enabling the user to extract almost any desired structure or data into a spreadsheet of her or his definition for postprocessing of results. One step further, condensing a number of similar structures into a common structure plus R groups, is already realized in ISIS structure-activity relationship (SAR) tables and Accord. Such a feature would be particularly useful for the large databases as they are the most in need of such tools, but they lack them at present. Apart from the standard display of reactions, the public database CASREACT (and STN Cheminform RX) permit only role-specific extraction with STN s powerful SmartSelect of compounds from reactions to collect, for example, reagents or solvents from a set of reactions. 

As quite a number of reactions are, like other chemical information, first, or only, published in patents, these are an important source of reaction information, even though one would normally assume that new synthetic methods would also be published in the journal literature. Since 1991, reactions taken from patents have been included in CASREACT patents comprise less than 10% of the CASREACT database in 1997, compared to about 16% of the CA database. CrossFire plus Reactions contains many reactions from patents registered before 1980, when Beilstein ceased to index patents. About 14% of the reactions in CRDS/JSM and 10% of those in ChemReact originate from patents CCR includes only US patents, which contribute about 10% of the reactions and Cheminform covers no patents at all. 

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