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

Abstract

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...

Chemoinformatics at the University of Sheffield 2002–2014

“…However, we have also made other contributions, e.g., in the application of chemoinformatics techniques to the representation and searching of biological macromolecules such as protein and RNA structures, [71][72][73][74][75] in the analysis of matched molecular pairs [76] and in charting the historical development of chemoinformatics and of its associated literature. [77][78][79][80] We have also sought to influence the development of the field by means of conferences and educational programmes. Thus, in 1998 we were invited by the Chemical Structure Association Trust This paper has focused on research in Sheffield, but we have also been active in teaching the subject; indeed, arguably the very first textbook in the field was based on material taught in a one-semester module that Lynch developed shortly after coming to Sheffield.…”

Academic librarians at play in the field of cheminformatics: building the case for chemistry research data management

“…The relative sizes of the texts reflect the relative frequencies of different types of data and methods presented in the publications and their formats as well as locations. As shown in the figure for this lab, the types of data reported most often were substance structures, reaction schemes, 1 H-NMR, 13 C-NMR, yields, diastereomeric ratios, mass spectrum etc. The majority of the data were only available in PDF format with only one occurrence out of 52 being a reusable format-CIF (crystallographic data).…”

“…Librarians are applying expertise in curation, management, and preservation of documentation to data and gradually taking substantial roles in research data services [11,12]. In the course of this work, chemistry librarians are becoming more involved with organizing, manipulating, and even mining chemical data, traditionally considered cheminformatics activities [13,14].…”

A possible extension to the RInChI as a means of providing machine readable process data

“…Connection tables store information on the atoms, bonds and, optionally, the atoms’ coordinates for a given molecule, making it a graph representation of a molecule [17, 18]. Connection tables can be canonicalised to provide one unique table per molecule, for example, using the Morgan algorithm, first proposed in 1965 and still in use with some modifications [19, 20].…”

“…One of the earliest mentions of connection tables was in 1957 [21]. Subsequently, the tables found wide adoption and are used by the CAS database as well as other data formats, such as the Chemical Mark-up Language (CML) and as a basis to generate InChIs [17, 22–24]. A consequence of the way bonds are represented in traditional connection tables is that they struggle to represent delocalised bonds, inorganics and reaction intermediates, which is something that has seen some attempts at being addressed [16, 25].…”