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Flexible Science Databases with OWW

I recently came across the desire/need for a flexible database system in my research (bioinformatics). For example, I want to know about phage gene expression. Not knowing enough biology to perform an efficient literature search (coming from a physics background), I have made a little database that allows me to input author name, citation info, abstract, and some relevancy measure while I search in the literature. (For the specific implementation, please visit PubMed Searches for Phage Gene Expression.)

The point that this little example illustrates is the creative use of small, easily customizable databases in scientific investigations. Accumulation of litearature search results is one example (you can see that common citation managers like EndNote are just specific, albeit not very flexible views of a literature database), but you can imagine many more, from entering specific observations from experiments, to bioinformatic data collection, ... The goal is some flexible framework where it is easy to create and modify databases on the fly, with nice user interfaces for database entry.

Which is why I bring this discussion to OWW. There are a couple of ways to do this. The easiest method (almost available) comes from Wufoo (used in the example above). I have been using this recently with a beta-key and it has many nice features, but I think something could be made that is more geared towards scientists (and when released, Wufoo will require a monthly fee). I am wondering if this could be done in the framework of a wiki such as OWW. I imagine a scenario where through template features, users could easily define fields in a database in wikimarkup. Once this is done, pages would be generated to allow data input, as well as retrieval (dumps in CSV format, or even automatically formatting a wiki table ...)

This idea is more along the lines of the Science 2.0 article, but I think it would be very useful, could be integrated into many aspects of scientific investigation, and could be implemented in something like OWW.

--Lucks 17:45, 24 March 2006 (EST)

If I understand you right - you are trying to implement database functionality in OWW - this is the direction I always thought and hoped projects like OWW will move into, eventually - after all, almost everything in science has to do with huge amounts of data... Flexible online databases, customizable and maintained by a big group people with little computer knowledge - but expert knowledge on the subject covered by the database - would add an enormous value to OWW, for sure. One can also envision some sort of peer evaluation for the validity of the entries (i.e. something along the lines of what they use for stories and comments, over at digg.com). That's a huge project, though... Smeister 07:58, 25 March 2006 (EST)

While a big project, with some discussion, it could be possible to come up with a few hacks that would be relatively easy to implement so that the idea could at least be tested. I have some experience with running a mediawiki, but I have never looked into the code. Alternatively, some software could be developed external to OWW, but linked so that new database entreis are automatically inselted into pages in OWW - a lot of alternatives here. I have put together a database web interface before with Perl-CGI (using CGI::Builder), which works great (see the Pica Literature Database), but requires the user to make an HTML form with limited, but ugly Perl HTML:Template variable references - basically not very user friendly at the initial setup. I am now learning a little bit about Ruby on Rails, which is fantastically flexible for this sort of thing. (I am pretty sure this is the framework that Wufoo uses.) I can imagine a wiki design page that allows someone to make a form design via wiki-markup, which then gets fed to a rails program that creates the database, and then passes entries back to the wiki.

--lux 10:57, 25 March 2006 (EST)

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