Tuesday, March 10, 2009

Economic crisis & public data deposition in GEO

Does stunning global economic crisis starting from the late 2007 influence each gorvernment to cut down the budget for scientific research? If you're an independent researcher, you've already experienced how serious it is. If you are not, you don't know the actual influence of it on science research.

Starting with just interest, I tried to answer to above question by analyze the trend of data deposition to the largest public gene expression database, GEO. Since the number of gene expression data deposition has been increasing from the creation of GEO, I hypothesize that the data deposition might be not continuously increasing in year 2008 if the global economic crisis was really a matter for cutting down the budget for the science research.

Look at the table above! The number of data deposition to GEO in 2008 is slightly decreased as I expected. The number of data deposition has continuously increased from 2001 through 2007 but this trend stop in the year 2008.

This trend is repeately found for the top 5 countries of budget for science. By the way, USA is really a huge player in the basic science. Look at the size of data! US itself deposited several fold more data than the sum of all the data the other four countries deposited. Anyhow, back to the main point, I think this trend represent the effect of economic crisis on shirinking science budget in each gorvernment.

Except the USA from the chart, another interesting point shows up. That's UK. Deposition of data from UK was decreased from 2007 not 2008. Their contribution to public data was peak in 2006 but the number is less than a half in 2007. What happened in UK at that time? I don't have any evidence on this matter. Just I expect that UK changed their research plan for biology using microarray since microarray generally lack reproducibility and consistency. Or there might be some big scientific project to producing microarray data in 2006 only.

Among the 5 countries I mentioned here, Germany showed least decreasing nubmer of deposited
data. They deposited only 21 data set less compared to previous year ( 14% ) while the other four countries decreased that number around 50%.

The small contributing countries with less than 50 deposition in each year, some countries seem that they are not affected by economic crisis. South Korea is one of the exam. Their deposition increased from 16 in 2007 to 19 in 2008. As I'm researching in Korea, I think it's not because Korean gorvernment did not cut budget for science but most of researchers who producing microarray data don't know GEO at all or don't consider to deposit their data. Why? most of them are just wet-lab biologist. So they usually don't use public data for their own resarch. Even when they want to contribute, depositing data to GEO needs some computational skills for easy or automatic depositing. Without any programming skill, the process to deposit the data is very tedious and boring. So three more data sets of deposited data does not show the actual trend of Korean science budget related to economic crisis. I think the minor contributing countries might have similar situation.

That's all I want to say today! In one sentence, global economic crisis seems actually to force each gorvenment to cut their science budget.