Joshua Carl Smith
August 23, 2019
Posted in

DEB2 is a medication indication and adverse effect knowledgebase derived from five publicly available sources: the VA’s National Drug File-Reference Terminology, MEDLINE, the US Food and Drug Administration’s drug product labels (via the SIDER2 database), the MedlinePlus consumer health information website, and DrugBank, a manually-curated drug target database. All medications, indications, and adverse effects in DEB2 are represented using the RxNorm and SNOMED-CT terminologies.

Indications and adverse effects in DEB2 were extracted from the constituent sources using natural language processing and other ontology methods. The DEB2 knowledgebase requires indications and adverse effects to be corroborated by two or more of its constituent drug information sources, resulting in improved accuracy and precision over the original DEB1, and other popular medication databases.

The DEB2 Dataset contains 6431 indications and 11,539 adverse effects. It includes 1163 distinct drugs and 1601 distinct clinical features (symptoms, findings, diseases, etc.). Based on physician review, DEB2 has an estimated precision of 86% (+/- 3.1%) overall, with indications being slightly more accurate and adverse effects slightly less. Indications and adverse effects for the most commonly-prescribed medications were shown to have a precision of 94% (+/- 3.5%). Drug relationships found in more sources were generally found more likely to be correct.

The DEB2 Full Data Superset is also available for download. It includes all drug-indication and drug-adverse effect pairs found in any of the five sources (including those found in only 1 source and therefore not corroborated elsewhere). The DEB2 Full Data Superset includes over 131,000 pairs (consisting of 31,203 indications and 98,745 adverse effects). While it was not reviewed separately, we suspect the superset should have a higher recall and lower precision than the primary DEB2 Dataset.

DEB2 is available for free download. It is intended for research and is not a substitute for professional clinical advice. We believe this resource can be useful for research in the areas of pharmacovigilance, clinical data mining, clinical phenotyping, and clinical decision support systems, among others. It can be used unaltered, or as a valuable starting point for developing manually-curated indication and adverse effect datasets.

Please cite the reference below when using this resource. Contact joshua.smith@vumc.org with any questions.

*The DEB2 manuscript has been submitted for publication. If this website has not been updated with the correct reference, please contact me for instructions on how to cite DEB2 in your work.

Browse DEB2 online [coming soon]

 

Download links:

 

DEB2.txt - The DEB2 knowledgebase, containing medication indications and adverse effects found in at least two sources. Tab-Separated text file; first line contains column names; double-quotes around any field values with commas.

DEB2.xlsx - The DEB2 knowledegbase in Microsoft Excel format. Color-coded for human readability.

DEB2_full_data_superset.txt - The raw data superset from which DEB2 was constructed, containing medication indications and adverse effects found in any of the sources. The vast majority of drug-CF pairs in this file are from only one source. Tab-Separated text file; first line contains column names; double-quotes around any field values with commas.

README.txt - description of data elements in the above files.

 


Creative Commons License
DEB2 by Dr. Joshua C. Smith, et al., is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.

 

 

Reference:

 

Smith JC, Chen Q, Denny JC, Roden DM, Johnson KB, Miller RA. DEB2: An Improved Drug Evidence Base for Biomedical Research. Manuscript submitted for publication. Currently under review.