openFDA

Using openFDA can be a breeze, if you know how to construct good queries. This short guide will get you started with openFDA, and show you how to put together more complicated queries.

library(openFDA)

set_api_key("tvzdUXoC3Yi21hhxtKKochJlQgm6y1Lr7uhmjcpT")

The openFDA API

The openFDA API makes public FDA data available from a simple, public API. Users of this API have access to FDA data on food, human and veterinary drugs, devices, and more. You can read all about it at their website.

A simple openFDA query

The simplest way to query the openFDA API is to identify the endpoint you want to use and provide other search terms. For example, this snippet retrieves 1 record about adverse events in the drugs endpoint. The empty search string ("") means the results will be non-specific.

search <- openFDA(search = "", endpoint = "drug-event", limit = 1)
search
#> <httr2_response>
#> GET https://api.fda.gov/drug/event.json?api_key=[API_KEY]&search=&limit=1
#> Status: 200 OK
#> Content-Type: application/json
#> Body: In memory (1819 bytes)

openFDA results

The function returns an httr2 response object, with attached JSON data. We use httr2::resp_body_json() to extract the underlying data.

json <- httr2::resp_body_json(search)

If you don’t specify a field to count on, the JSON data has two sections - meta and results.

Results

For non-count queries, this will be a set of records which were found in the endpoint and match your search term.

json$results
#> [[1]]
#> [[1]]$safetyreportid
#> [1] "5801206-7"
#> 
#> [[1]]$transmissiondateformat
#> [1] "102"
#> 
#> [[1]]$transmissiondate
#> [1] "20090109"
#> 
....

Results when `count`-ing

If you set the count query, then the openFDA API will not return full records. Instead, it will count the number of records for each member in the openFDA field you specified for count. For example, let’s look at drug manufacturers in the Drugs@FDA endpoint for "paracetamol". We’ll use the limit parameter to limit our results to the first 3 drug manufacturers found.

count <- openFDA(search = "",
                 endpoint = "drug-drugsfda",
                 limit = 3,
                 count = "openfda.manufacturer_name.exact") |>
  httr2::resp_body_json()
count$results
#> [[1]]
#> [[1]]$term
#> [1] "Aurobindo Pharma Limited"
#> 
#> [[1]]$count
#> [1] 417
#> 
#> 
#> [[2]]
#> [[2]]$term
#> [1] "Hikma Pharmaceuticals USA Inc."
#> 
#> [[2]]$count
#> [1] 323
#> 
#> 
#> [[3]]
#> [[3]]$term
#> [1] "Fresenius Kabi USA, LLC"
#> 
#> [[3]]$count
#> [1] 289

You can count on fields with a date to create a time series, as demonstrated on the openFDA website.

Using search terms

We can increase the complexity of our query using the search parameter, which lets us search against specific openFDA API fields. These fields are harmonised to different degrees in each API, which you will need to check online.

Searching on one field

You can provide search strategies to openFDA() as single strings. They are constructed as [FIELD_NAME]:[STRING], where FIELD_NAME is the openFDA field you want to search on. If your STRING contains spaces, you must surround it with double quotes, or openFDA will search against each word in the string. So, for example, a search for drugs with the class "thiazide diuretic” should be formatted as "openfda.pharm_class_epc:\"thiazide diuretic\"", or the API will collect all drugs which have the words "thiazide" or "diuretic" in their established pharmacological class (EPC). Let’s do an unrefined search first:

search_unrefined <- openFDA(
  search = "openfda.pharm_class_epc:thiazide diuretic",
  endpoint = "drug-drugsfda",
  limit = 1
)
httr2::resp_body_json(search_unrefined)$meta$results$total
#> [1] 224

Let’s compare this to our refined search, where we add double-quotes around the search term:

search_refined <- openFDA(
  search = "openfda.pharm_class_epc:\"thiazide diuretic\"",
  endpoint = "drug-drugsfda",
  limit = 1
)
httr2::resp_body_json(search_refined)$meta$results$total
#> [1] 124

As you can see, the unrefined search picked up 100 more results, most of which would have probably been non-thiazide diuretics.

Searching on multiple fields

The openFDA API lets you search on various fields at once. Simple methods for doing this are implemented in openFDA.

Write your own search term

Using the guides on the openFDA website, you can put together your own query. For example, the following query looks for up to 5 records which were submitted by Walmart and are taken orally. We can use purrr functions to extract a brand name for each record. Note that though a single record can have multiple brand names, we are choosing to only extract the first one.

search_term <- "openfda.manufacturer_name:Walmart+AND+openfda.route=oral"
search <- openFDA(search = search_term,
                  limit = 5,
                  endpoint = "drug-drugsfda")
json <- httr2::resp_body_json(search)
purrr::map(json$results, .f = \(x) {
  purrr::pluck(x, "openfda", "brand_name", 1)
})
#> [[1]]
#> [1] "CHILDREN ALLERGY"
#> 
#> [[2]]
#> [1] "AMAZON BASIC CARE ACETAMINOPHEN"
#> 
#> [[3]]
#> [1] "ALLERGY RELIEF"
#> 
#> [[4]]
#> [1] "NAPROXEN"
#> 
#> [[5]]
#> [1] "OMEPRAZOLE"

Let `openFDA()` construct the search term

You can let the package do the heavy lifting for you with openFDA(), by providing a named character vector with many field/search term pairs to the search parameter. The function will automatically add double quotes ("") around your search terms, if you’re providing field/value pairs like this.

search <- openFDA(search = c("openfda.generic_name" = "amoxicillin"),
                  endpoint = "drug-drugsfda")
httr2::resp_body_json(search)$meta$results$total
#> [1] 60

You can include as many fields as you like, as long as you only provide each field once. By default, the terms are combined with an OR operator in openFDA(). The below search strategy will therefore pick up all entries in Drugs@FDA which are taken by mouth.

search <- openFDA(search = c("openfda.generic_name" = "amoxicillin",
                             "openfda.route" = "oral"),
                  endpoint = "drug-drugsfda", limit = 1)
httr2::resp_body_json(search)$meta$results$total
#> [1] 7019

Pre-construct a search term

To apply multiple search terms with AND operators, use format_search_term() with mode = "and":

search_term <- format_search_term(c("openfda.generic_name" = "amoxicillin",
                                    "openfda.route" = "oral"),
                                  mode = "and")
search <- openFDA(search = search_term,
                  endpoint = "drug-drugsfda", limit = 1)
httr2::resp_body_json(search)$meta$results$total
#> [1] 57

Wildcards

You can use the wildcard character "*" to match zero or more characters. For example, we could take the prototypical ending to a common drug class - e.g. the sartans, which are angiotensin-II receptor blockers - and see which manufacturers are most represented in Drugs@FDA for this class. When using wildcards, either pre-format the string yourself without double-quotes or use format_search_term() with exact = FALSE. If you try to search with both double-quotes and the wildcard character, you will get a 404 error from openFDA.

search_term <- format_search_term(c("openfda.generic_name" = "*sartan"),
                                  exact = FALSE)
search <- openFDA(search = search_term,
                  count = "openfda.manufacturer_name.exact",
                  endpoint = "drug-drugsfda",
                  limit = 5)
terms <- purrr::map(
  .x = httr2::resp_body_json(search)$results,
  .f = purrr::pluck("term")
)
counts <- purrr::map(
  .x = httr2::resp_body_json(search)$results,
  .f = purrr::pluck("count")
)

setNames(counts, terms)
#> $`Alembic Pharmaceuticals Limited`
#> [1] 15
#> 
#> $`Alembic Pharmaceuticals Inc.`
#> [1] 14
#> 
#> $`Macleods Pharmaceuticals Limited`
#> [1] 14
#> 
#> $`Aurobindo Pharma Limited`
#> [1] 13
#> 
#> $`Lupin Pharmaceuticals, Inc.`
#> [1] 10

It looks like "Alembic Pharmaceuticals" is very active in this space - interesting!

Other openFDA API features

This short guide does not cover all aspects of openFDA. It is recommended that you go to the openFDA API website and check out the resources there to see information on: