tliu526/icd9

Python library for hierarchy of ICD9 Codes

Python library for ICD9 Codes

My edits

A fork of sirrice's ICD9 repository. The target website in the original repo has inconsistent structure and as a result the ICD9 data pulled is incomplete. Here I put together a simple scraper using requests and BeautifulSoup that targets the icd9data.com website to generate the code.json used by the ICD9 class. The structure is consistent and complete for the 2015 ICD9-CM Volume 1 diagnosis codes.

Description

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.

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

description

  # get the text description of the node
  tree.find('001.0').description

Scraper

icd9_data_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.