The NCBI Handbook

Bioinformatics consists of a computational approach to biomedical information management and analysis. It is being used increasingly as a component of research within both academic and industrial settings and is becoming integrated into both undergraduate and postgraduate curricula. The new generation of biology graduates is emerging with experience in using bioinformatics resources and, in some cases, programming skills.

The National Center for Biotechnology Information (NCBI) is one of the world's premier Web sites for biomedical and bioinformatics research. Based within the National Library of Medicine at the National Institutes of Health, USA, the NCBI hosts many databases used by biomedical and research professionals. The services include PubMed, the bibliographic database; GenBank, the nucleotide sequence database; and the BLAST algorithm for sequence comparison, among many others.

Although each NCBI resource has online help documentation associated with it, there is no cohesive approach to describing the databases and search engines, nor any significant information on how the databases work or how they can be leveraged, for bioinformatics research on a larger scale. The NCBI Handbook is designed to address this information gap.

All of our users know how to execute a straightforward PubMed or BLAST search. However, feedback from help desk personnel and booth staff at scientific meetings suggests that people often want to know how to use our resources in a more sophisticated manner and are frequently unaware of less well-known databases that might be helpful to them. The intended audience for The NCBI Handbook is, therefore, the growing number of scientists and students who would like a more in-depth guide to NCBI resources—powerusers and aspiring powerusers.

The NCBI Handbook is focused on the relatively stable information about each resource; it is not a point-and-click user guide (this type of information can be found in the online help documents, referred to frequently but not repeated, in the Handbook). Each chapter is devoted to one service; after a brief overview on using the resource, there is an account of how the resource works, including topics such as how data are included in a database, database design, query processing, and how the different resources relate to each other. For example, the BLAST chapter briefly describes what to use BLAST for, the various varieties of the BLAST algorithm, and BLAST statistics, before discussing output formats, query processing, and tips for setting up a BLAST database. A certain amount of biological knowledge is assumed.

The online content will be updated when necessary, although major changes are not expected to occur more than once every few years. (For example, PubMed query processing does not change dramatically year after year.) We hope that The NCBI Handbook will provide a valuable reference for anyone who wants to use our resources more effectively.