Discovering drug–drug interactions: a text-mining and reasoning approach based on properties of drug metabolism

Motivation: Identifying drug–drug interactions (DDIs) is a critical process in drug administration and drug development. Clinical support tools often provide comprehensive lists of DDIs, but they usually lack the supporting scientific evidences and different tools can return inconsistent results. In this article, we propose a novel approach that integrates text mining and automated reasoning to derive DDIs. Through the extraction of various facts of drug metabolism, not only the DDIs that are explicitly mentioned in text can be extracted but also the potential interactions that can be inferred by reasoning. Results: Our approach was able to find several potential DDIs that are not present in DrugBank. We manually evaluated these interactions based on their supporting evidences, and our analysis revealed that 81.3% of these interactions are determined to be correct. This suggests that our approach can uncover potential DDIs with scientific evidences explaining the mechanism of the interactions. Contact: luis.tari@roche.com

• Publication year

  2010

• Venue

  Bioinform.

• Publication date

  2010-09-01

• Fields of study

  Chemistry, Medicine, Computer Science

• Identifiers
  DOI 10.1093/bioinformatics/btq382PMID 20823320PMCID 2935409
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Pharmspresso: a text mining tool for extraction of pharmacogenomic concepts and relationships from full text

  2009influential reference
• Constraint Answer Set Solving

  2009cited by this paper
• Drug interactions

  2009cited by this paper
• Clinically Significant Drug–Drug Interactions Between Oral Anticancer Agents and Nonanticancer Agents: Profiling and Comparison of Two Drug Compendia

  2008cited by this paper
• Inter-species normalization of gene mentions with GNAT

  2008cited by this paper
• Network analysis of adverse drug interactions.

  2008cited by this paper
• BANNER: An Executable Survey of Advances in Biomedical Named Entity Recognition

  2007cited by this paper
• Knowledge-based framework for hypothesis formation in biochemical networks

  2005cited by this paper
• DrugBank: a comprehensive resource for in silico drug discovery and exploration

  2005cited by this paper
• Knowledge Representation, Reasoning and Declarative Problem Solving

  2003cited by this paper
• Effective mapping of biomedical text to the UMLS Metathesaurus: the MetaMap program

  2001cited by this paper
• EDGAR: extraction of drugs, genes and relations from the biomedical literature.

  1999cited by this paper
• Stable Model Semantics of Logic Programs

  1997cited by this paper
• Parsing English with a Link Grammar

  1995cited by this paper
• Classical negation in logic programs and disjunctive databases

  1991cited by this paper
• Computer‐aided synthesis of biochemical pathways

  1990cited by this paper
• The Stable Model Semantics for Logic Programming

  1988cited by this paper
• Pacific Symposium on Biocomputing 15:465-476(2010) SYNTHESIS OF PHARMACOKINETIC PATHWAYS THROUGH KNOWLEDGE ACQUISITION AND AUTOMATED REASONING

  year unknowncited by this paper
• Pacific Symposium on Biocomputing 15:305-314(2010) IMPROVING THE PREDICTION OF PHARMACOGENES USING TEXT-DERIVED DRUG-GENE RELATIONSHIPS

  year unknowncited by this paper

• Contrastive learning-based multi-mechanism disentangled assessment for drug-drug interaction

  2025cites this paper
• SVDTI: Stacked variational autoencoder with SMILES-based drug representations for identifying drug-target interaction

  2025cites this paper
• PharmaMap-LLM: Fine-Tuning Large Language Models for Drug-Drug Interaction (DDI) Analysis

  2025cites this paper
• Drug–Drug Interaction Prediction: Paradigm Shifts, Key Bottlenecks, and Future Directions

  2025cites this paper
• Identification of Potential Drug-Drug Interactions Using EMR Text-Mining on Atherosclerotic Heart Disease Patients

  2024cites this paper
• DDI-KGAT: A Graph Attention Network on Biomedical Knowledge Graph for the Prediction of Drug-Drug Interactions

  2024cites this paper
• PTB-DDI: An Accurate and Simple Framework for Drug–Drug Interaction Prediction Based on Pre-Trained Tokenizer and BiLSTM Model

  2024cites this paper
• An accurate prediction of drug-drug interactions and side effects by using integrated convolutional and BiLSTM networks

  2024cites this paper
• A review of deep learning algorithms for modeling drug interactions

  2024cites this paper
• DDI‐Transform: A neural network for predicting drug‐drug interaction events

  2024cites this paper
• A comprehensive survey explores Drug-Drug interaction prediction using Machine-Learning techniques

  2024cites this paper
• DAS-DDI: A dual-view framework with drug association and drug structure for drug-drug interaction prediction

  2024cites this paper
• Application of Artificial Intelligence in Drug-Drug Interactions Prediction: A Review.

  2023cites this paper
• DPSP: a multimodal deep learning framework for polypharmacy side effects prediction

  2023cites this paper
• Comprehensive Review of Drug-Drug Interaction Prediction Based on Machine Learning: Current Status, Challenges, and Opportunities

  2023cites this paper
• Leveraging BERT-GRU Model for Drugs Interaction Relationship Extraction

  2023cites this paper
• A Study of Knowledge Discovery and Pattern Recognition Based on Large-Scale Sentiment Data in Online Education for College Students

  2023cites this paper
• Machine learning to predict metabolic drug interactions related to cytochrome P450 isozymes

  2022cites this paper
• DDREL: From drug-drug relationships to drug repurposing

  2022cites this paper
• CNN-DDI: a learning-based method for predicting drug–drug interactions using convolution neural networks

  2022cites this paper
• Attention Retrieval Model for Entity Relation Extraction From Biological Literature

  2022cites this paper
• A Review of Approaches for Predicting Drug–Drug Interactions Based on Machine Learning

  2022cites this paper
• DAEM: Deep attributed embedding based multi-task learning for predicting adverse drug-drug interaction

  2022cites this paper
• Environmental Variables and their Relation with the SARS-COV-2 Transmission: A Data Mining Approach

  2022cites this paper
• Comparing neural models for nested and overlapping biomedical event detection

  2022cites this paper
• LPInsider: a webserver for lncRNA–protein interaction extraction from the literature

  2022cites this paper
• Stress Test Evaluation of Biomedical Word Embeddings

  2021cites this paper
• Search and visualization of gene-drug-disease interactions for pharmacogenomics and precision medicine research using GeneDive

  2021cites this paper
• Signal Detection in Pharmacovigilance: A Review of Informatics-driven Approaches for the Discovery of Drug-Drug Interaction Signals in Different Data Sources

  2021cites this paper
• Drug-drug interaction extraction from biomedical texts based on multi-attention mechanism

  2021cites this paper
• An Efficient Pattern Recognition Based Method for Drug-Drug Interaction Diagnosis

  2021cites this paper
• Prediction of Drug–Drug Interactions by Using Profile Fingerprint Vectors and Protein Similarities

  2020cites this paper
• D4: Deep Drug-drug interaction Discovery and Demystification

  2020cites this paper
• Feature-Based Learning in Drug Prescription System for Medical Clinics

  2020cites this paper
• Predicting Drug-Drug Interactions Based on Integrated Similarity and Semi-Supervised Learning

  2020cites this paper
• On Adversarial Examples for Biomedical NLP Tasks

  2020cites this paper
• CNN-DDI: A novel deep learning method for predicting drug-drug interactions

  2020cites this paper
• A computational approach to predict multi-pathway drug-drug interactions: A case study of irinotecan, a colon cancer medication

  2020influential citation
• ADDI: Recommending alternatives for drug-drug interactions with negative health effects

  2020cites this paper
• SFLLN: A sparse feature learning ensemble method with linear neighborhood regularization for predicting drug-drug interactions

  2019cites this paper
• Computational Advances in Drug Safety: Systematic and Mapping Review of Knowledge Engineering Based Approaches

  2019influential citation
• DDIGIP: predicting drug-drug interactions based on Gaussian interaction profile kernels

  2019cites this paper
• Translational Knowledge Discovery Between Drug Interactions and Pharmacogenetics

  2019cites this paper
• Drug-Drug Interaction Prediction Based on Knowledge Graph Embeddings and Convolutional-LSTM Network

  2019cites this paper
• SUPP.AI: finding evidence for supplement-drug interactions

  2019cites this paper
• Machine learning algorithms to infer trait‐matching and predict species interactions in ecological networks

  2019cites this paper
• CuDDI: A CUDA-Based Application for Extracting Drug-Drug Interaction Related Substance Terms from PubMed Literature

  2019cites this paper
• Extracting evidence of supplement-drug interactions from literature

  2019cites this paper
• An Informatics-based Approach to Identify Key Pharmacological Components in Drug-Drug Interactions.

  2019cites this paper
• Navigating the disease landscape: knowledge representations for contextualizing molecular signatures

  2018cites this paper
• Translational Biomedical Informatics and Pharmacometrics Approaches in the Drug Interactions Research

  2018cites this paper
• Automatic recognition of argumentation structure in short monological texts

  2018cites this paper
• Mapping FHIR Resources to Ontology for DDI reasoning

  2018cites this paper
• In silico methods for drug repositioning and drug-drug interaction prediction

  2018cites this paper
• Exploring the Use of a Network Model in Drug Prescription Support for Dental Clinics

  2018influential citation
• Deep learning improves prediction of drug–drug and drug–food interactions

  2018cites this paper
• Detection of drug‐drug interactions through data mining studies using clinical sources, scientific literature and social media

  2018cites this paper
• GeneDive: A gene interaction search and visualization tool to facilitate precision medicine

  2018cites this paper
• Predicting potential drug-drug interactions on topological and semantic similarity features using statistical learning

  2018cites this paper
• Answer Set Programming in Linguistics

  2018cites this paper
• A meta-learning framework using representation learning to predict drug-drug interaction

  2018cites this paper
• Drug prescription support in dental clinics through drug corpus mining

  2018cites this paper
• Drug-Drug Interactions Prediction Based on Similarity Calculation and Pharmacokinetics Mechanism

  2018cites this paper
• Drug-Drug Interaction Extraction via Recurrent Neural Network with Multiple Attention Layers

  2017cites this paper
• Text Mining in Biomedical Domain with Emphasis on Document Clustering

  2017cites this paper
• Computational prediction of drug-drug interactions based on drugs functional similarities

  2017cites this paper
• Distant Supervision with Transductive Learning for Adverse Drug Reaction Identification from Electronic Medical Records

  2017cites this paper
• Dynamic sorted convolutional neural networks for drug-drug interaction extraction

  2017cites this paper
• A semantic-based workflow for biomedical literature annotation

  2017cites this paper
• Automated nanopublications generation from biomedical literature

  2017cites this paper
• Identifying articles relevant to drug-drug interaction: Addressing class imbalance

  2017cites this paper
• Characterization of the mechanism of drug-drug interactions from PubMed using MeSH terms

  2017cites this paper
• A Short Survey of Biomedical Relation Extraction Techniques

  2017cites this paper
• Drug-drug interaction discovery and demystification using Semantic Web technologies

  2017cites this paper
• Mining Drug Properties for Decision Support in Dental Clinics

  2017cites this paper
• DRUG-DRUG INTERACTION; FACTS AND COMPARISONS WITH NATIONAL AND INTERNATIONAL BENTCH MARKS. A THREAT MORE THAN A CHALLENGE FOR PATIENT SAFETY IN CLINICAL AND ECONOMIC SCENARIO

  2017cites this paper
• A Survey of Current Work in Medical Text Mining---Data Source Perspective

  2017cites this paper
• LimTox: a web tool for applied text mining of adverse event and toxicity associations of compounds, drugs and genes

  2017cites this paper
• Information Retrieval and Text Mining Technologies for Chemistry.

  2017cites this paper
• Gestion de l'incertitude et de l'imprécision dans un processus d'extraction de connaissances à partir des textes. (Uncertainty and imprecision management in a knowledge extraction process from unstructured texts)

  2017influential citation
• Use Text Mining and Complex Networks to Analyze TCM Syndromes

  2017cites this paper
• Positive-Unlabeled Learning for inferring drug interactions based on heterogeneous attributes

  2017cites this paper
• PubMedPortable: A Framework for Supporting the Development of Text Mining Applications

  2016cites this paper
• Generalized enrichment analysis improves the detection of adverse drug events from the biomedical literature

  2016cites this paper
• Extracting drug-enzyme relation from literature as evidence for drug drug interaction

  2016cites this paper
• Overview on the current status of virtual high-throughput screening and combinatorial chemistry approaches in multi-target anticancer drug discovery; Part I.

  2016cites this paper
• @MInter: automated text-mining of microbial interactions

  2016cites this paper
• Rare diseases and big data : biocomputing solutions towards knowledge-guided analyses : applications to ciliopathies

  2016cites this paper
• Modelling of compound combination effects and applications to efficacy and toxicity: state-of-the-art, challenges and perspectives.

  2016cites this paper
• QSAR Modeling and Prediction of Drug-Drug Interactions.

  2016cites this paper
• Leveraging syntactic and semantic graph kernels to extract pharmacokinetic drug drug interactions from biomedical literature

  2016cites this paper
• DINTO: Using OWL Ontologies and SWRL Rules to Infer Drug-Drug Interactions and Their Mechanisms

  2015cites this paper
• Recognizing Social Constructs from Textual Conversation

  2015cites this paper
• Drug interaction and its implication in clinical practice and personalized medicine

  2015influential citation
• The D3 Pharmacovigilance System: Characterization of Drug-Drug Interactions by Statistical Inference Based on Big Data Mining and Semantic Web Technologies

  2015influential citation
• Research status and trend analysis of global biomedical text mining studies in recent 10 years

  2015cites this paper
• Improving Detection of Arrhythmia Drug-Drug Interactions in Pharmacovigilance Data through the Implementation of Similarity-Based Modeling

  2015cites this paper
• Event Extraction from Biomedical Literature

  2015cites this paper
• Supersemantics for Knowledge Extraction

  2015cites this paper
• Pattern-based system to detect the adverse drug effect sentences in medical case reports

  2015cites this paper