The CAS ONLINE search system. 1. General system design and selection, generation, and use of search screens

J. Chem. Inf. Comput. Sci.

and

Downs

1998

1,648

1,643

This paper reviews the use of similarity searching in chemical databases. It begins by introducing the concept of similarity searching, differentiating it from the more common substructure searching, and then discusses the current generation of fragment-based measures that are used for searching chemical structure databases. The next sections focus upon two of the principal characteristics of a similarity measure: the coefficient that is used to quantify the degree of structural resemblance between pairs of molecules and the structural representations that are used to characterize molecules that are being compared in a similarity calculation. New types of similarity measure are then compared with current approaches, and examples are given of several applications that are related to similarity searching.

Section: Fragment-based Similarity Searchingmentioning

confidence: 99%

Section: Structural Representations For Similarity Searchingmentioning

confidence: 99%

Chemical Similarity Searching

J. Chem. Inf. Comput. Sci.

and

Downs

1998

1,648

1,643

“…The first approach would be by reference to the major operational systems (which are, of course, based on the techniques considered here). Examples of such milestones include the appearance of: the batch [67] and then online [68,69] …”

Section: Selection Of Key Papersmentioning

confidence: 99%

From chemical documentation to chemoinformatics: 50 years of chemical information science

Journal of Information Science

2008

This paper summarises the historical development of the discipline that is now called 'chemoinformatics'. It shows how this has evolved, principally as a result of technological developments in chemistry and biology during the past decade, from long-established techniques for the modelling and searching of chemical molecules. A total of 30 papers, the earliest dating back to 1957, are briefly summarised to highlight some of the key publications and to show the development of the discipline.Keywords: Chemical documentation; Chemical structures; Chemoinformatics; Drug discovery; History; Informatics; Molecules; Pharmaceutical research IntroductionChemistry is, and has been for many years, one of the most information-rich academic disciplines. The very first journal devoted to chemistry was Chemisches Journal, which was published 1778-1784 and then, under the name of Chemische Annalen, till 1803 [1]. The growth in the chemical literature during the 19 th century led to a recognition of the need for comprehensive abstracting and indexing services for the chemical sciences. The principal such service is Chemical Abstracts Service (CAS), which was established in 1907 and which acts as the central repository for the world's published chemical (and, increasingly, life-sciences) information. The size of this repository is impressive: at the end of its first year of operations, the CAS database contained ca. 12K abstracts; by the end of 2006, this had grown to ca. 25M abstracts with ca. 1M being added each year. Most chemical publications will refer to one or more chemical substances. The structures of these substances form a vitally important part of the chemical literature, and one that distinguishes chemistry from many other disciplines. The CAS Registry System was started in 1965 to provide access to substance information, initially registering just small organic and inorganic molecules but now also registering biological sequences [2]. At the end of 1965 there 1 Correspondence to: Prof. Peter Willett, Department of Information Studies, University of Sheffield, 211 Portobello Street, Sheffield S1 4DP, UK; p.willett@sheffield.ac.uk. Journal of Information Science, XX (X) 2007, pp. 1-24 © CILIP, DOI: 10.1177/0165551506nnnnnn 1 Peter Willettwere ca. 222K substances in the System; by the end of 2006 this had grown to ca. 89M substances, of which ca. one-third were small molecules and the remainder biological sequences, with ca. 1.5M being added each year. There are also many additional molecular structures in public databases such as the Beilstein Database [3], and corporate files, in particular those of the major pharmaceutical, agrochemical and biotechnology companies.The presence of chemical structures requires very different computational techniques from those used for processing conventional textual information. These specialised techniques -now referred to by the name of chemoinformatics as discussed further below -have developed steadily over the fifty years that have passed since the founding of the I...

“…This is of considerable interest owing to the novel computer configuration which has been developed to allow for interactive searching of the circa eight million substances currently in the Registry file. 39 The system involves a network of DEC minicomputers, pairs of which each serially scan a small subset of the database, with one carrying out the screen search and then passing potential matches to the second for the atom-by-atom search. The file is partitioned to avoid the huge overheads associated with the maintenance of an inverted file, while achieving a sufficiently rapid response for interactive retrieval.…”

Section: Operational Chemical Information Systemsmentioning

confidence: 99%

A review of chemical structure retrieval systems

Journal of Chemometrics

1987

SUMMARYThis paper describes the development and current state-of-the-art in computerized systems for the storage and retrieval of chemical structure information. The main types of machine-readable structure representation -fragmentation codes, linear notations and connection tables -are described, together .with the retrieval algorithms which are used to provide structure and substructure search facilities. Current research work in chemical structure retrieval includes the development of techniques for the representation and searching of the generic structures which occur in chemical patents, for searching files of threedimensional structures, for ranking searches designed to identify compounds structurally similar to a given query compound, and the use of parallel computers to increase the efficiency of substructure searching. Chemical structure handling techniques are also applicable in a range of application areas, including chemical reaction indexing, computer-aided synthesis design and structure elucidation, and substructural analysis methods for the study of quantitative structure-activity relationships. KEY WORDSChemical information systems Machine-readable structure representation Registration search Structure search Substructure search