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Large quantities of ecological and environmental data are increasingly available thanks to initiatives sponsoring the collection of large-scale data and efforts to increase the publication of already collected datasets. As a result, progress in ecology is increasingly limited by the speed at which we can organize and analyze data. To help improve ecologists' ability to quickly access and analyze data we have been developing software that designs database structures for ecological datasets and then downloads the data, pre-processes it, and installs it into major database management systems (at the moment we support MySQL, PostreSQL, and SQLite, but we are planning to eventually add support for MS Access).

Once the Database Toolkit has loaded the data into the database it is easy to connect to the database using standard tools (e.g., MS Access, Filemaker, etc.).These Database Toolkits can download and install small datasets in seconds and large datasets in minutes. The programs also cleanup known issues with the datasets and automatically restructure them into a format appropriate for standard database management systems. The automation of this process reduces the time for a user to get most large datasets up and running by hours, and in some cases days.

Download the full Database Toolkit package (Windows)

Access the current source code (at the moment this is the actively under development code in our SVN repository and is not guaranteed to work at any moment in time; accessing the repository is also currently very annoying in Chrome)

Read the API documentation

Comments

Submitted by Allen Hurlbert on Tue, 2010-10-05 06:41

I'm unclear on what I should be specifying for Connection Info. I specified MS Access early on, so here it appears to be wanting an Access database file. This window could use a sentence of explanation. I get an error just using the default filename : "There was an error with your databae connection .... Not a valid filename."

Submitted by Allen Hurlbert on Tue, 2010-11-16 15:39

Ok, so I take pride in being your quintessential idiot end user. For idiots like me, I would have to say that it is still unclear how exactly the Toolkit is supposed to work. It is providing me with a way to connect to the datasets that you are hosting? It is a way of downloading and pre-processing the data and storing a copy on my own machine? I guess it's unclear to me what I'm supposed to have done prior to running dbtk.exe. I created a blank Access database. Does it matter what the "Data file directory" is? This is just where raw data files are going to get stored right? Is there some specific directory structure I'm supposed to be using here? I tried leaving it as the default, as well as creating some new folder. At any rate, after specifying the directory and connection info, clicking on any of the datasets results in a "There was an error with your database connection."

Submitted by Ethan White on Fri, 2010-11-19 06:39

Thanks for the feedback Allen (FYI I still don't have notifications set up for this part of the site so you might want to ping me via email if you'd like a quick response). I think Ben just rolled out an update that at least instructs the user to create the MS Access file before proceeding, but we've clearly got a long way to go in this area.

To answer your questions briefly:

  1. The idea of the system is that it is storing a copy of all of the data one your machine. This circumvents all of the complexities related to hosting other people's data.
  2. You are right about the "Data file directory" and the default should work, but I'm wondering if this is something that should be removed or at least hidden in an advanced tab to avoid confusion since most users won't care.

You shouldn't be getting an error if you created a blank Access database and then selected that file when asked for your connection information. Can you give us a detailed run down of the steps you took so that we can track down the problem. Thanks.