The Molecular Biology Database Collection: an online compilation of relevant database resources

With systematic sequencing efforts on the human and other model organisms in full swing, a tremendous flood of sequence data is being produced at breakneck speed. Considering the Human Genome Project alone, it is currently estimated that over 2 million bases are deposited into GenBank each day. This growth will only accelerate in the future, given the new goal of having a working draft covering 90% of the genome by the spring of 2000 and the complete sequence in-hand in 2002 (1). When considering all organismal sequencing efforts together, it immediately becomes obvious that there must be concrete and coherent plans in place to both warehouse and access these data, data which will become more and more important as we enter into an era of sequence-based biology. The most recent five-year plan for the Human Genome Project (1) recognizes the importance of the connection between the in silico world and the bench, and has put forth recommendations regarding bioinformatics and computational biology, particularly with respect to databases and the development of analytical tools. Databases that grow out of the human and other systematic sequencing efforts should not be just storehouses for thousands of bases or amino acids; rather, they need to make logical connections to other types of information that are available, such as phenotypic or expression data, as these types of connections serve to increase the intrinsic value of the raw sequence data, allowing for biological discovery. Of particular importance will be the curation and annotation of specialized databases, which will help to ensure data quality as well as foster the ability to access and analyze sequence data. Many such specialized databases have emerged over the years, and this journal has devoted its first issue over the last several years to documenting the availability and features of these databases. With the current issue, Nucleic Acids Research will be facilitating access to these databases online through a new entity called the Molecular Biology Database Collection. By doing so, it is hoped that individual investigators will be able to more easily find and use specialized databases that are appropriate to their scientific needs. The initial set of databases included in the online compilation, available at http://www.oup.co.uk/nar/Volume_28/Issue_01/html/gkd115_gml.html, is shown in Table ​Table1.1. The list includes databases for which there are full-length descriptions in the current issue, as well as other databases which represent a valuable resource to the biological community. Also included are databases collected by Christian Burks as part of the 1999 Database Issue (2). Efforts have been made to reduce redundancy in the list with respect to content wherever possible. An emphasis has also been placed on including databases where new value is added to the underlying data by virtue of curation, new data connections, or other innovative approaches. While Table ​Table11 attempts to classify these databases by type, it is often true that these databases are more global in nature, providing multiple types of information. Links to these databases will be updated regularly. Suggestions for the inclusion of additional database resources in this online compendium are encouraged and may be directed to the author (andy@nhgri.nih.gov). Table 1. Molecular Biology Database Collection