Sometimes solving little problems can be fun. You stare at the project requirements, then stare at the available tools and figure out how to bridge the gap from the tools to the problem solution. However, sometimes I get frustrated when I’m treading new ground, because the task needs to be done yesterday. So I’m always on the lookout for little snippets I can reuse for solving a particular style of problem. With this in mind, I’d like to share with you some snippets I hope you can reuse, since I spent a bit of time inventing them in the first place.
Sometimes solving little problems can be fun. You stare at the project requirements, then stare at the available tools and figure out how to bridge the gap from the tools to the problem solution. However, sometimes I get frustrated when I’m treading new ground, because the task needs to be done yesterday. So I’m always on the lookout for little snippets I can reuse for solving a particular style of problem. With this in mind, I’d like to share with you some snippets I hope you can reuse, since I spent a bit of time inventing them in the first place.
In one of my many roles, I’m working with Lincoln Stein (best known as the creator of CGI.pm) to create and modify software to support data exchange for genetics research, including the famous Human Genome project. The Gene-Ontology database (http://www.geneontology.org) provides a “dictionary” so all the researchers can use the same terminology when talking about similar discoveries. My job was to provide an “explorer-style” interface to browse and search this database. What I had available was an interface through the Ace Perl modules (maintained by Lincoln) to the database, and I had to respond to browsers using an Apache::Registry-compatible CGI script.
Each entry in the database is a term with four “aspects.” The details of the aspects are not important, except that each is linked to zero or more other terms. Each term also has a unique, unchanging ID. The database needed to be “connected,”…
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