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What Database Management System(s) Should Be Employed in Bioinformatics Applications?

1. No DBMS: Although most computer scientists would dismiss this alternative as ridiculous, I would wager that a significant number of the hundreds of molecular biology DBs that now exist are not constructed using any DBMS. This should make us all stop and think. Either the biologists who are constructing these DBs know something that computer scientists don’t know, or they don’t know something that computer scientists do know. I believe the latter is the case—I believe that the vast majority of biologists have not received even the most elementary education in DBs, and have little idea of how DBMSs can help them, nor of how to go about using a DBMS. Note that the situation today is far improved over that of ten years ago. Today most large DB projects do employ a DBMS, whereas 10 years ago virtually none did so. Bioinformatics is still suffering from those mistakes. 2. Open-source DBMSs: Many of the molecular-biology DB projects that are employing DBMSs are employing open-source DBMSs to save money and because they believe that access to the source code will be useful in fixing any DBMS bugs that are discovered, or in extending the DBMS. My limited understanding of these DBMSs is that they have significant technical limitations compared to commercial DBMS product, yet little hard information about this issue is circulating in the bioinformatics community. We should obtain and circulate such information, whether from the literature or by empirical study. I also believe that the DBMSs are sufficiently complex that access to their source code is essentially useless to any but the most experienced DBMS hacker (and perhaps not even to them), and that this point must be articulated to the community. 3. Commercial DBMSs: Many projects use commercial relational DBMSs, specifically, Oracle. Virtually no projects use commercial object-oriented DBMSs (OO DBMSs). Why? OO DBMSs were developed to overcome limitations of relational DBMSs, and have now existed for about a decade. Little hard information about this issue is circulating in the bioinformatics community. We should obtain and circu-