There are a number of ways to display phenotype/genotype data to the public -- our group makes frequent use of some excellent mouse gene expression datasets available at (in no particular order) MGI, LAMHDI, Allen Brain, GENSAT, and BGEM, for example. These data are then compared to results from our own in-house experiments, and we use a number of further tools -- some home-grown, some available through the web -- to address various hypotheses. But all of these analysis pipelines usually begin with mining a fair amount of publicly available data from somewhere.
What are users' experiences about the best ways to display datasets so that bioinformaticians can use them? What publicly available databases have the best user interfaces? Why? What features are essential to you as a bioinformatician when you need to get specific data, get the data quickly, and in a format you can use?
Some examples of features: How often do you need to (or wish you could) batch queries? Do you prefer a web-based utility that allows you to directly query the database backend? How often do you wish for the ability to download a local copy of data? What about the way the data is presented on the web -- the usual table format -- or graphics? Or both? What file format do you prefer to use to export your data?
Do you prefer a web-based dataset to be standalone -- and you build a local analysis pipeline yourself -- or do you prefer the web-based dataset to be already part of an analysis pipeline that gives the data to other open-access sites for you? (There may be a flexibility trade-off here...pipelines that are locally built can be changed to meet local needs...but what of the time saved and reproducibility of using an open-access established pipe? Where is the balance in your opinion?)
What works for you? Looking forward to hearing your thoughts!