RxNorm

RxNorm

The RxNormLookup class can be used for database lookups, an example is shown below. Similar code is also appended to the end of rxnorm.py and executed if you simply run the file in the Shell. You might want to insert RxNorm.check_databases() before this code so you will get an exception if the databases haven't been set up.

look = RxNormLookup()
rxcui = '328406'
meaning = look.lookup_code_meaning(rxcui, preferred=False)
related = look.lookup_related(rxcui)
print('RxCUI          "{0}":  {1}'.format(rxcui, meaning))
for rrxcui, rrela in sorted(related, key=lambda x: x[1]):
	rname, rtty, a, b = look.lookup_rxcui(rrxcui)
	print('  {}:  {} {}  {}'.format(rrela, rrxcui, rtty, rname))

---

RxCUI          "328406":  Methotrexate 25 MG/ML [SCDC]
Relationships  "328406":
            constitutes:  1655956   SCD  40 ML Methotrexate 25 MG/ML Injection
            constitutes:  1655960   SCD  2 ML Methotrexate 25 MG/ML Injection
            constitutes:  1655967   SCD  4 ML Methotrexate 25 MG/ML Injection
            constitutes:  1655968   SCD  8 ML Methotrexate 25 MG/ML Injection
            constitutes:  1441402   SCD  0.4 ML Methotrexate 25 MG/ML Auto-Injector
            constitutes:  1441409   SBD  Methotrexate 25 MG/ML Auto-Injector [Otrexup]
            constitutes:  1655957   SCD  Methotrexate 25 MG/ML Injection
            constitutes:  1441407   SBD  0.4 ML Methotrexate 25 MG/ML Auto-Injector [Otrexup]
            constitutes:  1441408   SCD  Methotrexate 25 MG/ML Auto-Injector
            constitutes:  1655959   SCD  10 ML Methotrexate 25 MG/ML Injection
         has_ingredient:     6851    BN  Methotrexate
          has_tradename:  1441404  SBDC  Methotrexate 25 MG/ML [Otrexup]

Database

The RxNormLookup class depends on a local SQLite database to query data and relationships. It is created with the databases/rxnorm.sh script, which will tell you what to do. It will need the path to the directory containing your unzipped RxNorm download containing the RRF-files, from which it will import all the data. To download these files you need a UMLS username.

databases/rxnorm.sh ~/Downloads/RxNorm_full_04042016

NDC Normalizer

Normalizes an NDC (National Drug Code) number. It's built after the pseudo-code published by NIH, first identifies the format (e.g. "6-3-2") and then normalizes based on that finding. The pseudocode always normalizes the NDC to 5-4-2, padded with leading zeroes and removing all dashes afterwards. This implementation achieves the same normalization.

It also handles NDC codes that come in the "6-4" format, which usually is a 6-4-2 format with omitted package code. Those codes first get normalized to 6-4-2 by appending "-00", then go through the standard normalization.

RxNorm.ndc_normalize('000074-1486-14')  # '00074148614'
RxNorm.ndc_normalize('012579-*056')     # '12579005600'
RxNorm.ndc_normalize('057982-987-9')    # '57982098709'
...

rxnorm_link.py

This script precomputes ingredients, generics, treatment intents, drug classes and mechanisms of action per RxNorm concept (of specific TTYs). The script will run for a couple of minutes but NOT STORE ANYTHING as-is. You can uncomment a line that prints the generated document or do your own things, or even better: use the script rxnorm_link_run.sh after you've set up your MongoDB credentials and the script will store one JSON document per RXCUI and TTY combination into a NoSQL database. Look into rxnorm_link_run.py (note the file ending) where the server connections are set up and insertion happens; a Couchbase implementation is missing.

rxnorm_graph.py

Create a graphical representation (PDF) of relationships for a given RXCUI. You need to have dot installed (part of the GraphViz package). Run the script from command line and provide a RXCUI as the first argument. The script will then traverse the relationship graph of that concept to a specific depth (8 by default) and plot the relationships into a dot file and a PDF.

python rxnorm_graph.py 328406