8
votes
Disease and Symptoms Hierarchy
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 ...
- 181
8
votes
List of United States cities
The US Census Bureau also has a national gazeteer file with state and city info, including incorporation information.
For metadata/excel file column please have a look at HERE.
- 201
7
votes
Accepted
Searching by disease through openFDA API
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 ...
- 406
6
votes
Accepted
List of United States cities
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.
http://www.opengeocode.org/download.php#statecity
In case you must ...
- 8,637
5
votes
OpenFDA: Why is the database updated infrequently, given that recall notices are pretty time sensitive . . . and when is it likely to get improved?
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 ...
- 5,174
5
votes
List of United States cities
You might try using data from the Geonames.org database. You can download gazateer data by country from this list.
Another potential source is the the MaxMind GeoLite2 dataset.
- 169
4
votes
Comparing FDA drug data with other countries
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/
...
- 41
4
votes
Accepted
OpenFDA report_date for Food/Enforcement doesn't seem to work after 9/23/2015
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 ...
- 619
4
votes
Accepted
I get 'certificate verify failed' URLError when trying to download data from openFDA
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:
import requests
url = 'https://...
- 17.5k
3
votes
Disease and Symptoms Hierarchy
Check Bioportal for an ontology suiting your needs. There are various disease, anatomy and symptom related ontologies out there, which might help you there.
Use the European Bioinformatics Institute ...
- 488
3
votes
Disease and Symptoms Hierarchy
Have a look at the supplementary material of Learning disease relationships from clinical drug trials. disease_mappings10.txt file in the supplementary contains the info you need.
For instance, if ...
- 141
3
votes
Disease and Symptoms Hierarchy
I am not exactly sure that this is what you are referring to, but the MEDDRA database costs money in most cases, but I believe there are some research licenses. It is a hierarchy of indications.
...
- 619
3
votes
OpenFDA Data: Labels with Boxed Warnings
You are pretty close, you just have a syntax error on the query that is getting interpreted as a search string: it should be +AND+set_id: not +AND+set_id=
Also, that particular set_id does not have a ...
- 619
3
votes
Can someone explain "openfda data is not for clinical use"?
openFDA is not for clinical use since it is a research project still in beta. Additional details can be found on the about page:
https://open.fda.gov/about/
If you need labeling information for ...
- 184
3
votes
Can someone explain "openfda data is not for clinical use"?
Basically, the data can't be considered "complete" and thus trustworthy.
Most of the information contained there comes from sources that need to handle their data really carefully. Consider drug ...
- 191
3
votes
API for getting data from a disease name?
Have you tried a Wolfram Alpha search. There is a lot of information there.
Wolfram|Alpha: lung adenocarcinoma
You can get this information in Mathematica as well for analysis by using the ...
- 387
3
votes
Accepted
Synchronize with the openFDA S3 bucket
It took quite a while to figure this out myself, so I thought I'd share!
The openFDA bucket is Requestor Pays, so you have to enable yourself -- in your amazon account -- to pay for requests to that ...
- 146
3
votes
Accepted
Adverse Events Reported Term + MEDDRA coding dataset
I'm one the many folks working on Open FDA. We've searched across FDA data sets open to the public and, unfortunately, did not identify one that would meet your requirement at this time.
- 891
3
votes
Accepted
Endpoint not returning expected data based on NDC package code
openFDA has only the NDC codes that are in the National Drug Code Directory. This particular one -- "10135-150-01" -- isn't there, which is why you are getting no results back.
- 891
3
votes
Open FDA - Medical device search -> summary pdf
Most 510K records have the value "Summary" stored in the Summary field.
There is no such thing as the "Summary" field.
A statement or summary can be provided per 21 CFR 807.3(n) and (o). A
510(k)...
- 2,955
3
votes
Accepted
why doesn't FDA drug list include all meds?
The FDA CDER database, which you linked to, covers small molecule drugs.
Monovisc is a medical device, so you'll need to search the medical device database: https://www.accessdata.fda.gov/scripts/...
3
votes
OpenFDA API Suspension effective 12/20/2019?
I'm Jack with the openFDA Team. The temporary suspension of updates to the openFDA datasets has ended. We're in the process of updating all datasets. Please stay tuned in to the API Status page for ...
- 406
3
votes
Unzipping the openfda data in R
Just use for:
# unzipping the files
temp<-tempfile()
for (f in files) {
download.file(f,temp)
unzip(temp)
}
- 2,955
3
votes
New Indications via OpenFDA API
openFDA builds its Drugs@FDA dataset from the downloadable data files at the FDA. Unfortunately, the information you are looking for is currently absent from these files: if you scroll down to the ER ...
- 891
2
votes
How can I access FDA drug and medical device recall data from 1970 to 2014?
The process isn't as nice as the API at openFDA, but you can always file a Freedom of Information Act request: http://www.fda.gov/RegulatoryInformation/FOI/HowtoMakeaFOIARequest/
- 213
2
votes
OpenFDA: Why is the database updated infrequently, given that recall notices are pretty time sensitive . . . and when is it likely to get improved?
From the commentators here and further research, it appears that the OpenFDA API allows access to the FDA's repository for enforcement reports, which they don't want apps to use for recall alert data....
2
votes
Accepted
Get All medicine names
If, for some reason, you must use openFDA for this use case, you could go ahead and page through the following API call:
https://api.fda.gov/drug/label.json?count=openfda.brand_name.exact&limit=...
- 5,174
2
votes
Return an Enforcement record for search=recall_number
@Mark - I think you are trying to do something like this:
https://api.fda.gov/device/enforcement.json?search=recall_number.exact:Z-2338-2012
but are instead doing the following which, indeed, does ...
- 5,174
2
votes
OpenFDA API: Including the skip parameter limit
Thanks for your note. The skip limit was, until recently, unbounded. Unfortunately, we found that queries with large skip values were overloading the servers. To ensure the service remained ...
- 141
2
votes
Option 2: Structured Product Labeling & Language - Which data to pick up?
J- Yes, that's right. Two different data elements: "boxed_warning" for Level 1, and "warnings" for Level 2.
Jess
- 21
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