Skip to content

HTTPS clone URL

Subversion checkout URL

You can clone with HTTPS or Subversion.

Download ZIP
branch: master

Fetching latest commit…

Cannot retrieve the latest commit at this time

..
Failed to load latest commit information.
README.md
cache
codes.json
icd9.py
scraper.py

README.md

Python library for ICD9 Codes

The library encodes ICD9 codes in their natural hierarchy. For example, Cholera due to vibrio cholerae has the ICD9 code 0010, and are categorized as as type of Cholera, which in turn is a type of Intestinal Infectious Disease. Specifically, 001.0 has the following hierarchy:

001-139 Infectious and Parasitic Diseases 001-009 Intestinal Infectious Diseases 001 Cholera 001.0 Cholera due to vibrio cholerae

This library encodes all ICD9 codes into a tree that captures this relationship. This tree only contains codes, and not the description text.

Using the library

Include icd9.py in your python path. The following is an example:

from icd9 import ICD9

tree = ICD9('codes.json')

# list of top level codes (e.g., '001-139', ...) toplevelnodes = tree.children toplevelcodes = [node.code for node in toplevelnodes] print '\t'.join(toplevelcodes)

The hierarchy is encoded in a tree of Node objects. Node has the following methods:

search(code)

# find all sub-nodes whose codes contain '001' tree.search('001')

find(code)

# find sub-node with code '001.0'. Returns None if code is not found tree.find('001.0')

And the following properties:

children

# get node's children tree.children

# search for '001.0' in root's first child tree.children[0].search('001.0')

parent

# get 001.0 node's parent. None if node is a root tree.find('001.0').parent

parents

# get 001.0 node's parent path from the root. Root node is the first element tree.find('001.0').parents

leaves

# get all leaf nodes under root's first child tree.children[0].leaves

siblings

# get all of 001.0 node's siblings that share the same parent tree.find('001.0').siblings

ICD9 Descriptions

descriptions.txt contains a fixed width file of all ICD9 codes and their short and long descriptions. This file can be used in conjuction with this library to look up descriptions of each code.

NOTE: The hierarchy uses codes that contain a period (.). This description file doesn't include the periods. This must be taken into account when using this file as a lookup table.

Alternatively, you can use drobhbins's csv file of ICD9 descriptions.

Scraper

The scraper/ directory includes the scraper code used to generate the dataset. scraper/scraper.py creates a json file codes.json of each ICD9 code's parent codes:

[None, "001-139", "001-009", "001", "001.0"]

The last element is the actual code, the preceeding elements are coarser groupings of codes

Something went wrong with that request. Please try again.