Can I ask a dumb question as a completely database-naive person? I'm an occasional scientist, and I have a fair bit of experimental data lying around, stored as files. I've had it suggested to me before that I clearly need to get the data into a database (and that our center in fact should force people to store their raw data this way). At the same time, my daily workflow revolves around files. I use software that opens and deals with files. Some of the software expects to find the files organized in directories in particular ways. So my question is simply this: how do I put my data into a database but have it still work with the many software packages that have been written to do this kind of work? I can't rewrite the software. Do database systems let you expose the contents as though they were in directories, while somehow maintaining the organizing facility of the database? I know this is a dumb question, but having never used databases, I don't know what I would tell, for example, a medical image viewer when it opens up a file dialog and asks me which brain image I want to look at.
I'm also an occasional software developer. Maybe that's claiming too much, but I do write software for doing this kind of research. My software opens, reads, and writes files. I'm not anxious to rewrite it to access databases, and of course I can't know in advance what kind of database system end users will have set up (the software is not just used locally). So at some level, I need to know the answer to this question from the other end as well. However, the users of our software also use dozens of other packages that will never be rewritten, I suspect there's no point to modifying my code to deal with data stored in database systems.
I should mention that when I've thought about this before, it's occurred to me that possibly it's only being suggested that the raw data be organized in databases, and that processed data can be stored as files. But this is obviously irrelevant, since it's both (but especially the processed and intermediate data) that need to be organized in labs with a lot of data.
In any case, please help us database-naive scientists understand. Thanks.