Ndc Map

Mapping U.S. FDA National Drug Codes (NDC) to Drug Classes and Codes

Project README

Mapping U.S. Food and Drug Administration (FDA) National Drug Codes (NDC) to Drug Classes and Codes

codename: ndc_map

Mapping NDCs to Anatomical Therapeutic Chemical (ATC) Level 5, Veterans' Affairs Drug Classes, MESH Pharmacological Actions, SNOMED Clinical Terms, and other Drug Classification Systems and Terminologies

This script provides the drug class (or classes) from a given drug classification system (e.g. ATC) of each FDA National Drug Code (NDC), if any is available. It does that by querying the online RxNorm API at https://rxnav.nlm.nih.gov/. This script is just a helper to query the API in bulk and write the resposes to a convenient CSV file -- the mappings themselves are maintained and provided for free by RxNorm. The program can read the input NDCs from a flat list (text file, one NDC per line) or from one column in a CSV file.

It is also possible to request:

  • the generic active ingredients of the NDC, which are independent of drug classification systems,
  • whether the NDC is a brand name or a generic,
  • the strength of the drug product (as an unstructured text string),
  • the SNOMED CT (Clinical Terms) code corresponding to the NDC,
  • the MESH Pharmacological Actions code corresponding to the NDC,
  • the Veterans' Affairs Drug Class code corresponding to the NDC,
  • if ATC level 5 is requested, the script will additionally scrape each code's Administration Route, Defined Daily Dose (DDD), and Note (if any) from the website of the official ATC index at https://whocc.no/atc_ddd_index/.

This work is an update from what was presented as a poster at the 2017 Annual Symposium of the American Medical Informatics Association (AMIA). If you are going to use this script or its NDC <-> drug class maps, please take time to understand the numbers contained in the poster (PDFs are in this repository), because they CAN affect data analyses. At the very minimum, you need to understand the issues regarding coverage (missing codes) and ambiguity (duplication of codes). I have also published a deeper analysis and comparison of drug classification systems in a paper (https://mor.nlm.nih.gov/pubs/pdf/2016-dmmi-fk.pdf). TL;DR: unless your use case is particularly specific, ATC is the best drug classification for most cases of large dataset analyses. The Veterans' Affairs Drug Classes attain the same high level of coverage of NDCs as ATC, but they don't provide a comprehensive and accessible hierarchy like ATC.

How to run

This script should work out of the box if you follow the instructions in the .R file under the heading "How to execute this script."

Contributing to this script

There are extra features that could be implemented. See the TODOs in the .R file.

About performance

The RxNav API Terms of Service requires users to make no more than 20 requests per second per IP address (https://rxnav.nlm.nih.gov/TermOfService.html). This script will respect this limit. It will also cache its internet calls, so it works faster towards the end because more NDCs map to RxCUIs that have already appeared before (which means just 1 API call is needed, instead of 2). From my experience on a laptop over reliable wi-fi, I have seen 12 to 18 hours of execution time per 100,000 unique NDCs, i.e. about 1.5-2.3 unique NDCs per second. If execution is interrupted (intentionally or not), next time it will start from zero, but the queries will be cached (stored in RDS files), so it will progress very fast in the beginning, until it reaches NDCs needing novel online queries at the exact point it was interrupted.

This script allows you to query for multiple coding systems in the same run (e.g. ATC codes and VA Drug Classes). However, because of the caching, and the limit of queries per second, I do not advise you use that feature because it is unlikely to be faster than doing separate full runs. In fact, it could even be slower, because rows will get duplicated whenever one NDC maps to multiple codes, and the duplications of one coding system will multiply those from other coding systems. For example, if one NDC maps to 3 ATC codes and 2 VA Drug Class codes, there will be 2 * 3 = 6 rows in the results corresponding to all combinations of these codes.

License

All contents of this repository are under an Attribution-ShareAlike-NonCommercial 4.0 International license. Please see details at http://creativecommons.org/licenses/by-nc-sa/4.0/.

Pre-made NDC-to-drug class maps

If you do not know the R programming language or can't run the code yourself for any reason, but need an NDC-to-drug class map for your project, see the folder "FDA NDC Database File with ATC4." The CSV files in there contain all NDCs from the FDA database (https://www.fda.gov/drugs/drug-approvals-and-databases/national-drug-code-directory) with their classes as indicated by the folder and file names. Notice, however, that this file does not contain all NDCs you may find in a given dataset. If that doesn't work, and you can send me your list of NDCs, I can easily run the script for you.

Contact the author

Please feel free to contact me about this work! Reading and reusing code can become so much easier after a quick talk with the original author.
Contact me at [email protected]. --Fabrício Kury

Search tags: thesaurus drug class map equivalence correspondence classification

Do I need the year and month the NDC was used?

You do not. The script does not consider dates, only NDCs. Although one same NDC can have been recycled, i.e. represented different drugs at different points in time (https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfcfr/CFRSearch.cfm?fr=207.35, paragraph 4.ii; regulation changed in 2017: https://www.fda.gov/Drugs/GuidanceComplianceRegulatoryInformation/DrugRegistrationandListing/ucm2007058.htm), as far as I have witnessed such situation is exceedingly rare, to the point of being negligible even in nation-wide datasets with over one billion records spanning 10 years of filled prescriptions in U.S. pharmacies.

Do I need to convert the codes between NDC-10, NDC-11, XXXXX-XXX-XX (5-3-2), XXXX-XXXX-XX (4-4-2), XXXXX-XXXX-X (5-4-1)?

This is not necessary because RxNorm natively supports any valid NDC format. If for some other reason you need to convert NDC formats yourself, here is a guide to the equivalencies: https://phpa.health.maryland.gov/OIDEOR/IMMUN/Shared%20Documents/Handout%203%20-%20NDC%20conversion%20to%2011%20digits.pdf

Open Source Agenda is not affiliated with "Ndc Map" Project. README Source: fabkury/ndc_map
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