Chemical Informatics Letters

Volume 6, Issue 2; February 2003

Editor: Jonathan M Goodman

Electronic journals and retracted articles
Elsevier has removed some articles from the on-line versions of their journals. Some people are outraged (Elsevier's vanishing act), but removal seems a reasonable response. Unlike traditional printed journals it is possible to remove articles which are retracted. Retractions and corrections may easily be missed if only print versions are accessible. Electronic archives can easily replace retracted papers with notices explaining why they were retracted, although it might be useful to keep access to the paper, if it is clearly marked as having been retracted.

Chemical Informatics
What is the difference between Chemical Informatics, Chemoinformatics, Chemiinformatics, or Cheminformatics?

Definitions may be built on 'Chemometrics' which is usually defined as 'statistics on chemical data' (D.L. Massart, B.G.M. Vandeginste, S.N. Deming, Y. Michotte, and L. Kaufmann, Chemometrics: a textbook Elsevier, Amsterdam, 1988).

Chemoinformatics is often defined by citing an article by Frank K Brown ( 'Chemoinformatics: what is it and how does it impact drug discovery.' Ann. Rep. Med. Chem. 1998, 33, 375-384), in which it is defined as ' the mixing of those information resources [information technology and information management] to transform data into information and information into knowledge for the intended purpose of making better decisions faster in the arena of drug lead identification and optimization.' There is a strong link with drug discovery, restricting the subject to this area. Brown says that chemoinformatics includes chemometrics. There seems to be no clear distinction between chemoinformatics, chemiinformatics and cheminformatics. Use of the terms in the chemical literature appears to begin in the late 1990s, and often cites this paper.

'Chemical Informatics', however, is the oldest term, appearing in the literature in the early 1980s. It includes those chemistry-related areas of information handling which are not drug-related, and so chemoinformatics is a subset of chemical informatics. A useful definition is:

Chemical Informatics:
'Computer-assisted storage, retrieval and analysis of chemical information, from data to chemical knowledge'.

This definition is consistent with Gary Wiggins' essay (Indiana University) which addresses the question: What is Chemical Informatics?. The 'analysis' of chemical information may include molecular modelling and other computational methods of using the chemical information contained in Schrodinger's equation to explain and predict other chemical data.

Tetrahedron Info
A new website providing easy access to all resources and information relating to the family of Tetrahedron journals

The ACS has just released a new web-based system providing a personalized web page for authors and reviewers.

Institute of Physics full text search
The Institute of Physics has made full text searching available in their Electronic Journals. The facility is free to use and searches the entire archive back to 1874. Access to full text of articles requires a subscription, except for papers published in the last month.

Research Instrumentation and Informatics Department
The University of Miskolc Institute of Applied Chemistry (ME AKKI) has a Research Instrumentation and Informatic Department. This investigates problems in process control and industrial information systems development.

In the department of Applied Physics and Physico-Informatics at Keio University, Physico-Informatics emphasizes the importance of the advanced mathematical analysis of information governed by the laws of physics. Professor Masanori Matoba's research interests include 'Spectroscopy and quantum physico-informatics of strongly correlated materials'

Department of Informatics, Torun University
The department of informatics (computer science) at Torun, Poland, has a number of chemistry-related projects, including quantum chemistry and molecular dynamics.

JMol reads many molecular data formats, and animates and displays three-dimensional molecules. It is an open-source program, like JChemPaint which is also at sourceforge. JChemPaint draws two-dimensional structures. Its development is now being transferred to its successor: JCPCDK, and its underlying library the Chemical Development Kit

Chemistry Development Kit (CDK)
CDK classes are Java utitility classes for ChemoInformatics and Computational chemistry, written in Java, developed from JChemPaint, a Java Editor for 2D chemical structures, and JMDraw. The project involves Chris Steinbeck (University of Cologne's Bioinformatics Centre), Egon Willighagen (University of Nijmegen) and Dan Gezelter (Notre Dame, Indiana). "The Chemistry Development Kit (CDK): An Open-Source Java Library for Chemo- and Bioinformatics" Christoph Steinbeck, Yongquan Han, Stefan Kuhn, Oliver Horlacher, Edgar Luttmann, and Egon Willighagen J. Chem. Inf. Comp. Sci. Web Release Date: 11-Feb-2003; (Article) DOI: 10.1021/ci025584y

The European Molecular Biology Laboratory is based on five sites in four countries, with over seventy research groups.

JOELib's web page describes it as a platform independent open source computational chemistry package written in Java. It is able to build and edit structures in a variety of formats, calculate some atom property descriptors and create pictures. Its computational chemsitry capabilities seem very limited, so far, and its main strengths are in chemical informatics.

© 2003 J M Goodman, Cambridge
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