A few thoughts:
For a simple and down to the point description, Brian's suggestion of MedlinePlus' Web Services is a good start however if you do a search such as http://wsearch.nlm.nih.gov/ws/query?db=healthTopics&term=Levodopa you'll notice that it returns generic information about Parkinkson's disease and not this more appropriate page at http://www....
The NIH has published the UMLS database, which consists of more than 7 million concepts, diseases and symptoms. It's a very wealthy resource. The license is pretty permissive if you are working in the United States. Check it out on the UMLS website. It's completely free and curated by the National Library of Medicine.
I'm Jack Finch with the openFDA team. Looking at what you're trying to do, I'll suggest a couple queries that should satisfy your needs and link you to the appropriate sections of documentation which explains how it works.
If you just want a list of drugs which are related to a specific disease (or any other text string, for that matter), you can search for ...
You're looking for the limit URL parameter which maxes out at a value of 100.
For example: https://api.fda.gov/drug/event.json?search=receivedate:[2012-08-09+TO+3000-01-01]&limit=100
This is explained at the "Query parameters" section of the API documentation at https://open.fda.gov/api/reference/#query-parameters
Here are two ways to do your query:
Using the OpenFDA API directly by specifying a brand_name and reactionmedrapt value: https://api.fda.gov/drug/event.json?search=patient.drug.openfda.brand_name:(tysabri)+AND+patient.reaction.reactionmeddrapt:(death)&limit=50&skip=0
Using a tool I helped build which is a searchable web interface to the OpenFDA data ...
The current OpenFDA Adverse Event dataset isn't really well suited for a query like that. An API for the drug SPLs (Structured Product Labels) is coming soon according to https://open.fda.gov/about/ though.
For now, check out the following resources for the data you're looking for:
NLM Pillbox API (http://pillbox.nlm.nih.gov) - recommended - most developer ...
I have a CSV file you can download that lists all US cities by state. The data was compiled from the US Census 2013 Gazetteer.
In case you must have the data from that domain, each state's information is listed on the states index pagef, and follows similar naming conventions. For example, here's Virginia'...
If you take a look at our API documentation (http://open.fda.gov/drug/event/reference/), you'll see a complete reference for every field we return and the range of possible values. We follow the E2b specification for adverse drug reporting (http://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Surveillance/AdverseDrugEffects/UCM350390....
You might want to try hurl.it for testing your calls: https://www.hurl.it/ it's really useful.
I looked at the API reference:
which has directions, but all of the info there is geared towards drugs, not food.
This URL has food recall info:
The examples are pretty good. Does that ...
Emily you could check out the MedlinePlus Web Services - http://www.nlm.nih.gov/medlineplus/webservices.html
We used a simple search of Medline from the presentation of the adverse events drug name's in ResearchAE but the webservice might provide a bit more detail.
Another option could be to check out NLM DailyMed - http://dailymed.nlm.nih.gov/dailymed/...
What about MeSH?
The MeSH Browser is an online vocabulary look-up aid available for use
with MeSH® (Medical Subject Headings). It is designed to help quickly
locate descriptors of possible interest and to show the hierarchy in
which descriptors of interest appear. Virtually complete MeSH records
are available, including the scope notes, ...
I don't disagree that the openFDA APIs should be updated more often however the site does specifically mention: (emphasis mine)
This API should not be used as a method to collect data to issue alerts to the public. FDA seeks publicity about a recall only when it believes the public needs to be alerted to a serious hazard. FDA works with industry and our ...
I'm one of the core team members for openFDA. Really sorry to hear that you find the documentation cryptic - one big goal that we have is to make the API as easy to understand as possible!
The main documentation for drugs has a number of sample queries: http://open.fda.gov/drug/event/
You can hit "Run Query" next to any of those and it will show the ...
Joe is correct here. We don't currently offer data on patient claim of false advertising. In our scope for the future, we plan to offer data on product recalls and product labels. We're definitely listening to the community, though, and will add patient claims of false advertising to our list of potential datasets for the future!
Sean Herron, openFDA Team ...
As of right now, SPL (structured product labels) are not part of the openFDA list of APIs for drugs (https://open.fda.gov/drug/event/ - note how "product labels" is greyed out). You can learn more about the SPL standard, guidance, etc. directly from the FDA at http://www.fda.gov/ForIndustry/DataStandards/StructuredProductLabeling/default.htm.
While you wait ...
Thanks for the complement on our ResearchAE.com project. Glad you found it useful and as an example of what people can do with the openFDA data.
To answer your question, I believe the query you mean to be doing is this:
Clickable link for that openFDA query: https:...
You cannot do a two-way table where you get a list of adverse events by drug using the current openFDA API.
What you can do is find most of* this information in a two step process which can of course be automated:
Get a list of drugs by generic name: https://api.fda.gov/drug/event.json?search=&count=patient.drug.openfda.generic_name.exact&limit=...
and also please add up total reports=male(total) + female(total) + unknown(total) + missing(total). If you do it you might get the right answer.
This is perhaps a bit late, but I'm interested in this as well and have made some progress.
With respect to drugs, the WHO has a lookup service for ATC codes: http://www.whocc.no/atc_ddd_index/
They also have a listing of International Non-proprietary Names:
Various countries call these different things, but ...
Thanks for catching this one. It is true for all of the enforcement endpoints (food, drug and device).
The link on the FDA that we are crawling is dead (it hangs). There is a bug in pipeline code that shows the enforcement step as complete even though the download of the XML file is timing out. I will get that fixed right now. I will also contact the FDA ...
I'm not sure what underlying HTTP packages pandas uses, but I found that the default settings of the requests package in python does not work with SSL and this site:
url = 'https://api.fda.gov/drug/event.json?'
gives an error like:
requests.exceptions.SSLError: [Errno 1] _ssl.c:504: error:14090086:SSL routines:...
Joe, we don't support CSV downloads for the time being. Drug adverse event data is highly relational, a format that does not easily lend itself to being represented in a format like CSV. For instance, a given record may have 5-10 different drugs associated with it and an additional 5-10 different reactions, each of which all have their own additional ...
This is not open data but from my experience looking for data like this for quite a while even on a site with a lot of terms and conditions, the following is a relatively robust source:
http://www.drugs.com/stats/top100/units has sales and unit figures for the top 100 drugs of each quarter going back to 2011 and then top 200 from 2003 through 2010. The ...
They way openFDA stands, it is an API which returns JSON for a search. I too have asked for bulk downloads.
The information you seem to be looking for is available by modifying the following API call:
If you are ...
The problem was a minor one with query syntax: You're using equals signs = when you should be using colons :.
For example, adverse_event_flag=Y should be adverse_event_flag:Y.
The new query returns only 23 results instead of about 1300.
The openFDA API basics page has information about the correct syntax for these queries.
There is no way to make the connection you seek using the data in the openFDA drug adverse events API. Reports include all suspected adverse reactions, and all known drugs the patient was taking. While the classification of drugs as suspect or concomitant may be helpful, it is not always present, and it is often impossible to know which drug caused a ...