Getting the Immunization Coding System for Indivo X v1.0 or above

HL7_V3_VACCINES.py

# NCBO BioPortal API Key
api_key = '[API Key]'

# UMLS Terminology Services (UTS) Username and Password
username = '[Username]'
password = '[Password]'

# lxml for Parsing HL7 Ontology from NCBO BioPortal: http://lxml.de/
from lxml.etree import iterparse
from urllib2 import urlopen
from StringIO import StringIO

# SUDS for consuming Web Services: https://fedorahosted.org/suds/
from suds.client import Client
from suds.xsd.doctor import Import, ImportDoctor

# Logging for Debugging
import logging
logging.basicConfig(format = '%(levelname)s:%(message)s', level = logging.INFO)

# LexGrid Namespaces
namespaces = {'lgCon': 'http://LexGrid.org/schema/2009/01/LexGrid/concepts',
              'lgCommon': 'http://LexGrid.org/schema/2009/01/LexGrid/commonTypes'}

# URLs for UTS Web Services
cas_wsdl = 'https://uts-ws.nlm.nih.gov/authorization/services/AuthorizationPort?WSDL'
umlsks_wsdl = 'https://uts-ws.nlm.nih.gov/UMLSKS/services/UMLSKSService?wsdl'
umlsks_url = 'http://umlsks.nlm.nih.gov'

# Instantiating Client Class for Consuming Web Services
schema_import = Import('http://schemas.xmlsoap.org/soap/encoding/')
schema_doctor = ImportDoctor(schema_import)
cas_client = Client(cas_wsdl, doctor = schema_doctor)
umlsks_client = Client(umlsks_wsdl, autoblend = True)

# Obtaining a Proxy Granting Ticket
pgt = cas_client.service.getProxyGrantTicket(username, password)
logging.info("UMLS Terminology Services Authenticated with User '%s'" % username)

# Getting the Current UMLS Release
proxy_ticket = cas_client.service.getProxyTicket(pgt, umlsks_url)
request = umlsks_client.factory.create('{http://query.kss.nlm.nih.gov}CurrentUMLSRequest')
request.casTicket = proxy_ticket
umls_release = umlsks_client.service.getCurrentUMLSVersion(request)
logging.info("Current UMLS Release: %s" % umls_release)

# Downloading HL7 Ontology from NCBO BioPortal
ontology = urlopen('http://rest.bioontology.org/bioportal/virtual/download/1343?apikey=%s' % api_key).read()
logging.info("HL7 Ontology Downloaded (%d bytes)" % len(ontology))

# Instantiating iterparse Class with HL7 Ontology
context = iterparse(StringIO(ontology), tag = '{%s}entity' % namespaces['lgCon'], huge_tree = True)

# Preparing a Request Message for ConceptIdExactRequest
request = umlsks_client.factory.create('{http://meta.query.kss.nlm.nih.gov}ConceptIdExactRequest')
request.release = umls_release
request.SABs = ['HL7V3.0']
request.CVF = 0x00000000L
request.includeSuppressibles = False

# Iterating the Entire Tree
count = 0
for event, element in context:
  sources = element.xpath("./lgCon:presentation[@propertyId='T0']/lgCommon:source", namespaces = namespaces)
  if sources and (sources[0].text == 'VaccineType'):
    value1 = element.xpath("./lgCon:presentation[@propertyId='T0']/lgCommon:propertyQualifier[@propertyQualifierName='source-code']/lgCommon:value", namespaces = namespaces)[0].text
    value2 = element.xpath("./lgCommon:entityDescription", namespaces = namespaces)[0].text
    value3 = element.xpath("./lgCon:definition[@propertyId='D0']/lgCommon:value", namespaces = namespaces)[0].text

    # Removing Some Multiple Spaces
    value2 = ' '.join(value2.split())
    value3 = ' '.join(value3.split())

    # Finding UMLS CUI by Exact Match
    proxy_ticket = cas_client.service.getProxyTicket(pgt, umlsks_url)
    request.casTicket = proxy_ticket
    request.searchString = value2
    response = umlsks_client.service.findCUIByExact(request)
    value4 = response.contents[0].CUI

    # Printing out a Line
    print '%s|%s|%s|%s' % (value1, value2, value3, value4)

    count += 1
    logging.info("%d - %s" % (count, value2))

Best script ever! Thanks so much.

The script cann't apply to the last edition of HL7 ontology on BioPortal. The namespaces are changed.

We can modify the URL to get the old edition of HL7 ontology :
ontology = urlopen('http://rest.bioontology.org/bioportal/ontologies/download/46442?apikey=%s' % api_key).read()