8

I am interested in sample data of real patient medical records (anonymized or demographics removed completely) for the purpose of running through NLP system - specifically diagnoses, admissions and progress notes - anything where medical terminology is used. I have no interest in linking data to specific patient types or categories - I just want the text of the notes

Ideally I would like a data such as:

10/4/2011 - 59 year old male admitted with right sided chest pain, reduced air entry and fever for 7 days. X-ray showed occlusion of right lower lobe consistent with community-acquired bacterial pneumonia.Non-smoker.

13/4/2011 - Reviewed by MO. Left leg swelling noted with some tenderness on extension - DVT suspected. No fever, SOB. BP 120/90. Ix to follow. U/S ordered. Heparin commenced.

Are there any free data sets with this sort of data? I have looked at various public data repositories such as http://www.healthdata.gov/ and https://www.nlm.nih.gov/hsrinfo/datasites.html without much luck.

  • MIMIC III Dataset has the clinical text as per tomp's response. The specific file is called NOTEEVENTS_DATA_TABLE.csv – DataMania Dec 16 '15 at 2:57
  • i need these data. can you give me access to these dataset. – Sameer Kumar Pandey Jun 24 at 21:28
  • @John Snow Can you please share the analytics ready (CSV/JSON) version of this dataset mtsamples data set? – John Smith Aug 6 at 21:41
4

The MIMIC-III dataset would be well suited to the kind of natural language processing (NLP) study that you are interested in doing. MIMIC-III includes deidentified nursing progress notes, imaging reports, and discharge summaries for tens of thousands of patients who were admitted to intensive care units in the US.

You can read about several NLP studies that have used the MIMIC dataset on PubMed (note that most use MIMIC-II, an earlier version of MIMIC). For example, the following study explored text classification methods for use in risk adjustment: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4147615/

While MIMIC-III is a freely available dataset, the information that it contains is sensitive and so there is a formal process for requesting access. For details, see: http://mimic.physionet.org/gettingstarted/access/

  • I had to do an online course on patient privacy and then applied to get access. They asked some questions to try and make sure I was legitimate. took about a day. The MIMIC database consists of 26 CSV files and does contain the data I am looking for. Also comes with specs on loading it all into PostgresSQL. – DataMania Dec 10 '15 at 23:37
3

Another good-size data set of natural language patient notes is available here: http://www.mtsamples.com/

It covers notes across multiple specialities and conditions.

We can also provide an analytics-ready (CSV/JSON) version of this dataset. Please contact me if that's of interest.

Good luck!

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.