gommap: Golang tools for working with MetaMap

gommap is a set of tools for interacting with the National Library of Medicine's MetaMap concept identification and extraction tool. While a lovely piece of software, MetaMap as shipped operates in two different modes, neither of which work for all situations:

1. Batch-processing, e.g. of a directory full of files
2. An "interactive" mode via a REPL-style shell.

While both have their uses, I wanted to use MetaMap as a component in a larger application in a more dynamic way. Really, what I wanted was a REST-ish API for MetaMap; the NLM does provide a web service, but it's not really intended for one-off and realtime queries. So I did what any self-respecting hacker would do- I rolled my own!

Go happens to be a lovely language for this sort of thing. The mm_server executable manages a pool of MetaMap instances as well as I/O channels to each, and multiplexes HTTP requests to an instance. It also includes a trivial example of a web-based UI.

TODO

• gommap relies on a couple of hard-coded paths; that obviously needs to change
• More configurability
• More documentation
• Currently, the MMOs struct in mmo_struct.go doesn't capture all of the data in MetaMap's output.
• Refactoring- mm_server should only handle network-related stuff, the actual MetaMap I/O should be handled elsewhere.