BioUpdateS biotechnology links

Netsurfer Science Home Page

ScienceDaily Magazine

Drug and Market Development

J. Biol. Chem. Papers in Press

HighWire Press

Bugs in the News!

FDA/CFSAN Bad Bug Book

Microbiology Jumpstation

pharmaceutical structures

Klotho: the Biochemical Compounds Declarative Database

proteases and protease inhibitors

enzyme nomenclature

Online Mendelian Inheritance in Man

GeneCards

Frontiers in Science Virtual Library

Dictionary of Cell Biology

The National Center for Biotechnology Information

RSCB PD protein structures

ExPASy secondary databases

The Kyoto Encyclopedia of Genes and Genomes

BioUpdateS Bioinformatics guided tour

Glossary

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Biological information sources on the internet

The internet gives access to an ever- increasing range of information sources. From general news services to specialised genome databases.

In this section we introduce you to a selection of sites which may be useful.

News services

There are many regularly updated science news services which run items on current developments in science, from research findings, through commercial applications to political aspects. These include a significant amount of biology and biotechnology-related material. Some of the main ones are listed below:

General science news

Netsurfer Science Home Page and ScienceDaily Magazine are both examples of sites with news items on a range of science subjects. They are updated very frequently. Items are usually brief, and with little depth, but may contain useful links.

Biology and biotechnology

Drug and Market Development is a more focused site with useful material. Also the shopwindow for comprehensive industry reports. Biospace.com carries news and features on Biotech, Biotechnology and Pharmaceutics. Also jobs, companies, stocks. BIONEWS is a similar site targetted at the biotech industry.

BioMedNet is a special case. The site includes biology newspaper ("Beagle") with many useful links to items and websites of current interest. It also runs reviews and discussions of topical fields, has a database section with search facilities for journal articles, books and equipment. It is well worth registering (free) with this site and visiting it regularly.

Scientific Journals

Many scientific journals now have websites. Some of these simply offer contents pages and abstracts from the journal, with an option to subscribe for downloadable full-text papers. Others offer a more comprehensive service with some freely viewable material. Nature and New Scientist offer good quality topical material, although at different levels.

Some scientific journal publishers are now realising that publication on the internet is cheaper than hard copy and offer free access to full-text versions of their content. This ususally only extends to articles more than 6 or 12 months old, but is nevertheless a welcome concession for those without access to a library. The Journal of Biological Chemistry has now started a Papers in Press service which gives free full-text access to papers which are still awaiting publication.

The HighWire Press at Stanford University is a gateway to a long list of scientific publishers who offer full-text access to their journals.

Finally, some publishers run short-term offers of free access to full-text material. The BioMedNet site often alerts visitors to these offers.

Specialist sites

There are countless sites which offer useful information in specialist areas. Many are run by university or college lecturers in their own time, or by government organisations.

There are a number of microbiology information sources, from Bugs in the News! ; through the FDA/CFSAN Bad Bug Book to the "Microbiology Jumpstation"

As well as the macromolecular structure databases listed below, there is a very useful database of pharmaceutical structures, and Klotho: the Biochemical Compounds Declarative Database. Information on proteases and protease inhibitors can be found at the Universite de Tours site. And finally, a searchable list of enzyme nomenclature is available.

Human genetics and its clinical implications are well covered, as might be expected. There are two main information sources in this area; both searchable by disease or gene name. They are Online Mendelian Inheritance in Man (OMIM) and GeneCards. Both carry extensive links to other useful sites.

More generally there is the Frontiers in Science Virtual Library and the Dictionary of Cell Biology.

Molecular databases and bioinformatics
The new "discipline" of bioinformatics has developed over the past ten years with the aim of making sense of the enormous amount of data being produced by the various genome sequencing projects and other related studies. Databases of properties and sequences of proteins and nucleic acids are central to bioinformatics (and to the development of applications and understanding in biology as a whole).

Database types
1. Sequence databases
The data used in bioinformatics are centred around DNA nucleotide or protein amino acid sequences. There are two types of database; those used for storage of nucleic acid or protein sequences. Since each of these carry "raw" information obtained from sequencing experiments (together with a certain amount of interpretation), they are called primary databases. e.g.GenBank and SwissProt accessible through Entrez search at The National Center for Biotechnology Information

2. Protein structure database
The 3D structure of proteins is essential to their biological function. This means that further protein databases are necessary to store information on the tertiary and quaternary structure of proteins, where this is known. This is also a primary database. e.g. The RSCB PDB site which carries the full list of protein structure files.

3. Secondary databases
To simplify the analysis that individual users need to do, and increase the effectiveness of searches, the sequences contained in primary databases may be processed to detect features of interest and reclassified. These form the basis for new, secondary databases. Secondary databases are therefore about patterns. e.g. ProSite and other faciliities at ExPASy.

4. Data integration projects
Finally, there are a number of projects which are attempting to integrate information from the genome sequencing projects and that from biochemistry, molecular biology and genetics to produce biochemical models for the operation of an organism. These sites usually have data warehouse and various other search facilities. e.g. The Kyoto Encyclopedia of Genes and Genomes (KEGG).

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last updated 01/01