Volume 7, Issue 2; August 2003
Editor: Jonathan M Goodman
- ChemBank was mentioned in (Chem. Inf. Lett. 2002, 5, #3, 1). It now has a website, explaining that it is a freely available collection of data about small molecules and resources for studying their properties, especially relating chemistry to biology, and a suite of informatics tools and databases aimed at promoting the development and use of chemical genetics by scientists worldwide. It was described in Science, 2003, 300, 294-5. Chembank currently has a database of about 2000 compounds, with SMILES strings, chemical structures and biological activity. Soon other files will be downloadable.
Clustering Search Results
- If a web-search produces a large number of hits, it is useful to be able to cluster them into groups. A new service that does this is Vivisimo. It produces a textual analysis, which might be compared to Kartoo's visualisations.
RefViz is a text analysis and visualization package designed to analyze, organize, and facilitate the comprehension of data, which is being used by
Thomson, the publishers of the ISI Web of Knowledge to analyse literature.
- The Royal Society of Chemistry is digitising all its journals from 1841 to 1996. These will be available for outright purchase or for annual lease. The ACS is also digitising its journals although its earliest publications were more recent (1879) and are only available by annual lease. Elsevier has a similar programme going back to 1939, which are available for a one-off fee.
Digital Libraries Initiative, phase 2
- The Digital Libraries Initiative, phase 2 has produced a report on Revolutionizing Science and Engineering through Cyberinfrastructure. The National Digital Library is one of the NSF's projects in this area (Chem. Inf. Lett. 2003, 6, #1, 12). A part of this is iLumina, a digital library of sharable undergraduate teaching materials for chemistry, biology, physics, mathematics, and computer science.
- Haystack is a tool developed at MIT to manage information in the way that makes the most sense to each user - a platform for authoring end-user semantic web applications. A preliminary release of the software is available, free of charge, but there is no user manual yet.
- MERLOT (Multimedia Educational Resource for Learning and Online Teaching) is a free and open resource with links to online learning materials, for many subjects, including over two hundred for chemistry. It is also a variety of grape.
Macromolecular Structure Database Server
- The EBI's Macromolecular Structure Database (MSD) has announced new services, including MSDchem, a consistent and enriched library of ligands, small molecules and monomers that are referred to as residues and hetgroups in a PDB entry.
- This web site appears to be an index of molecular modelling and drug design resources and 'softwares'.
- NetEquation is a part of ThinkQuest's educational library, and claims to be 'a complete on-line chemistry resource'. It is a well set out introduction to chemistry.
- This site, part of the World Wide Web virtual library, provides an index to chemistry programs available for the Linux operating system. It continues to be updated, and more than twenty links to programs have been added this year.
- CLiDE is a chemical literature data extraction tool from SymBioSys Inc, a company which started from Professor Peter Johnson's group at Leeds University. It recognises scans of chemical structures and changes them in to structures with chemical sense. The program has been available for some time.
- ChemIndex is the professional's version of Cambridgesoft's ChemFinder - it searches the same database, but provides more facilities for a subscription fee.
© 2003 J M Goodman, Cambridge