Philosophy and Definition for a Universal Genetic Sequence Database

Modern sequence databases have many problems because they are not carefully defined. For example, when one searches for homology with a given sequence, many duplicate sequences are found in each database and similar but not identical results are obtained from other databases. The extra copies of inconsistent information are slowing down research. This situation could easily be avoided by removing redundancy in the databases, but this goal is not a fundamental component of the database design and has been neglected. A clear statement of goals for storing genetic sequence information is required. To this end, five documents, in decreasing order of importance, are proposed: (1) The Philosophy document defines guiding principles for the design and use of the database. (2) The Definition document identifies what is to be stored in the database, following the guidance of the philosophy. It is machine and computer-language independent. (3) The Implementation document translates the definition into computer code which can be run on machines. (4) Examples of all database objects allow users to test their database analysis programs. (5) A Tutorial explains how the database is organized. A philosophy and the beginnings of a definition are given in this paper. Individual researchers can help by: 1. providing correct and complete sequence data; 2. annotating their sequences with experimentally deduced features; 3. providing standard genetic names for all features; 4. updating the annotation as new knowledge is obtained; 5. periodically verifying the accuracy of the data and annotation in the public ∗National Institutes of Health National Cancer Institute at Frederick, Gene Regulation and Chromosome Biology Laboratory, P. O. Box B, Frederick, MD 21702-1201. (301) 846-5581, email: [email protected] http://alum.mit.edu/www/toms/