O'Really?

January 5, 2007

NAR Database Issue 2007: Not Waving But Drowning?

The 14th annual Nucleic Acids Research (NAR) database issue 2007 has just been published, open-access. This year is the largest yet (again) with 968 molecular biology databases listed, 110 more than the previous one (see figure below). In the world of biological databases, are we waving or drowning?

NAR Database Growth 2007

Nine hundred and sixty eight is a lot of databases, and even that mind-boggling number is not an exhaustive or comprehensive tally. But is counting all these databases waving or drowning [1]? Will we ever stop stamp-collecting the databases and tools we have in molecular biology? What prompted this is, an employee of the The Boeing Company once told me they have given up counting their databases because there were just too many. Just think of all the databases of design and technical documentation that accompanies the myriad of different aircraft that Boeing manufacture, like the iconic 747 jumbo jet. Now, combine that with all the supply chain, customer and employee information and you can begin to imagine the data deluge that a large multi-national corporation has to handle.

Like Boeing, in Biology we’ve clearly got more data than we know what to do with [2,3]. It won’t be news to bioinformaticians and its been said many times before but its worth repeating again here:

  • We know how many databases we have but we don’t know what a lot of the data in these databases means, think of all those mystery proteins of unknown function. It will obviously take time until we understand it all…
  • Most of the data only begins to make sense when it is integrated or mashed-up with other data. However, we still don’t know how to integrate all these databases, or as Lincoln Stein puts it “so far their integration has proved problematic” [4], a bit of an understatement. Many grandiose schemes for the “integration” of biological databases have been proposed over the years, but unfortunately none have been practical to the point of implementation [5]


IMGP4592
Despite this, it is still useful to know how many molecular biology databases there are. At least we know how many databases we are drowning in. Thankfully, unlike Boeing, most biological data, algorithms and tools are open-source and more literature is becoming open access which will hopefully make progress more rapid. But biology is more complicated than a Boeing 747, so we’ve got a long-haul flight ahead of us. OK, I’ve managed to completely overstretch that aerospace analogy now so I’ll stop there.

Whatever databases you’ll be using in 2007, have a Happy New Year mining, exploring and understanding the data they contain, not drowning in it.

References

  1. Stevie Smith (1957) Not waving but drowning
  2. Michael Galperin (2007) The Molecular Biology Database Collection: 2007 update Nucleic Acids Research, Vol. 35, Database issue. DOI:10.1093/nar/gkl1008
  3. Alex Bateman (2007) Editorial: What makes a good database? Nucleic Acids Research, Vol. 35, Database issue. DOI:10.1093/nar/gkl1051
  4. Lincoln Stein (2003) Biological Database Integration Nature Reviews Genetics. 4 (5), 337-45. DOI:10.1038/nrg1065
  5. Michael Ashburner (2006) Keynote at the Pacific Symposium on Biocomputing (PSB2006) in Hawaii seeAlso Aloha: Biocomputing in Hawaii
  6. This post originally published on nodalpoint with comments

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1 Comment »

  1. […] did fine suitable graphs on two pages (See 1 and 2), however these are a number of years out of date (2 and 6, respectively) and sadly don’t […]

    Pingback by Michael Bell » The growth of biological databases — March 28, 2013 @ 1:44 pm | Reply


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