Drug–drug Interaction Extraction

The DDIExtraction 2013 task relies on the DDI corpus which contains MedLine abstracts on drug-drug interactions as well as documents describing drug-drug interactions from the DrugBank database. Source: DDIExtraction 2013 Image Source: https://www.aclweb.org/anthology/S13-2056.pdf

This dataset consists of 1634 biomedical abstracts, expert-annotated for the purpose of extracting information about the efficacy of drug combinations from the scientific literature. Beyond its practical utility, the dataset also presents a unique NLP challenge, as the first relation extraction dataset consisting of variable-length relations. Furthermore, the relations in this dataset predominantly require language understanding beyond the sentence level, adding to the challenge of this task. We provide a promising baseline model (see the paper/repo) and identify clear areas for further improvement. We ask that new methods on this dataset are posted to our public leaderboard to improve visibility: https://leaderboard.allenai.org/drug_combo/submissions/public

Abstract: First released in 2006, DrugBank (https://go.drugbank.com) has grown to become the 'gold standard' knowledge resource for drug, drug-target and related pharmaceutical information. DrugBank is widely used across many diverse biomedical research and clinical applications, and averages more than 30 million views/year. Since its last update in 2018, we have been actively enhancing the quantity and quality of the drug data in this knowledgebase. In this latest release (DrugBank 6.0), the number of FDA approved drugs has grown from 2646 to 4563 (a 72% increase), the number of investigational drugs has grown from 3394 to 6231 (a 38% increase), the number of drug-drug interactions increased from 365 984 to 1 413 413 (a 300% increase), and the number of drug-food interactions expanded from 1195 to 2475 (a 200% increase). In addition to this notable expansion in database size, we have added thousands of new, colorful, richly annotated pathways depicting drug mechanisms and drug metabolism. Likewise, existing datasets have been significantly improved and expanded, by adding more information on drug indications, drug-drug interactions, drug-food interactions and many other relevant data types for 11 891 drugs. We have also added experimental and predicted MS/MS spectra, 1D/2D-NMR spectra, CCS (collision cross section), RT (retention time) and RI (retention index) data for 9464 of DrugBank's 11 710 small molecule drugs. These and other improvements should make DrugBank 6.0 even more useful to a much wider research audience ranging from medicinal chemists to metabolomics specialists to pharmacologists. #### More Information: - Paper: DrugBank 6.0: the DrugBank Knowledgebase for 2024 - PMID: 37953279 - PMCID: PMC10767804 - DOI: 10.1093/nar/gkad976 Knox, C., Wilson, M., Klinger, C. M., Franklin, M., Oler, E., Wilson, A., Pon, A., Cox, J., Chin, N. E. L., Strawbridge, S. A., Garcia-Patino, M., Kruger, R., Sivakumaran, A., Sanford, S., Doshi, R., Khetarpal, N., Fatokun, O., Doucet, D., Zubkowski, A., Rayat, D. Y., … Wishart, D. S. (2024). DrugBank 6.0: the DrugBank Knowledgebase for 2024. Nucleic acids research, 52(D1), D1265–D1275. https://doi.org/10.1093/nar/gkad976