Wednesday, February 13, 2008

Ruby, Perl and Python medical autocoders

In the past two days on this blog, I've provided very short, fast, and accurate medical autocoders in Ruby and Perl. I thought I might as well offer the equivalent Python script. The Python script runs about twice as fast as either the Ruby or the Perl script.

The Ruby, Perl and Python scripts and their equivalent output are provided at:

They are distributed under a GNU license.

All three scripts use a public domain file of 20,000 PubMed Citations, available at:

They all use an external tumor nomenclature contained within the Neoplasm Classification and available as a gzipped XML file distributed under a GNU license at:

- Jules Berman
Science is not a collection of facts. Science is what facts teach us; what we can learn about our universe, and ourselves, by deductive thinking. From observations of the night sky, made without the aid of telescopes, we can deduce that the universe is expanding, that the universe is not infinitely old, and why black holes exist. Without resorting to experimentation or mathematical analysis, we can deduce that gravity is a curvature in space-time, that the particles that compose light have no mass, that there is a theoretical limit to the number of different elements in the universe, and that the earth is billions of years old. Likewise, simple observations on animals tell us much about the migration of continents, the evolutionary relationships among classes of animals, why the nuclei of cells contain our genetic material, why certain animals are long-lived, why the gestation period of humans is 9 months, and why some diseases are rare and other diseases are common. In “Armchair Science”, the reader is confronted with 129 scientific mysteries, in cosmology, particle physics, chemistry, biology, and medicine. Beginning with simple observations, step-by-step analyses guide the reader toward solutions that are sometimes startling, and always entertaining. “Armchair Science” is written for general readers who are curious about science, and who want to sharpen their deductive skills.