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Toward a complete dataset of drug–drug interaction information from publicly available sources

Serkan Ayvaz, John Horn, Oktie Hassanzadeh, Qian Zhu, Johann Stan, Nicholas P. Tatonetti, Santiago Vilar, Mathias Brochhausen, Matthias Samwald, Majid Rastegar-Mojarad, Michel Dumontier, Richard D. Boyce
2015 Journal of Biomedical Informatics  
Although potential drug-drug interactions (PDDIs) are a significant source of preventable drug-related harm, there is currently no single complete source of PDDI information.  ...  In the current study, all publically available sources of PDDI information that could be identified using a comprehensive and broad search were combined into a single dataset.  ...  A special note of thanks to Lisa Hines, PharmD, Center for Health Outcomes & PharmacoEconomic Research, University of Arizona, for providing the initial list of individual drugs associated with the drug  ... 
doi:10.1016/j.jbi.2015.04.006 pmid:25917055 pmcid:PMC4464899 fatcat:ynz7dtb3ajccdne7pdj44oib2m

Information Extraction From FDA Drug Labeling to Enhance Product-Specific Guidance Assessment Using Natural Language Processing

Yiwen Shi, Ping Ren, Yi Zhang, Xiajing Gong, Meng Hu, Hualou Liang
2021 Frontiers in Research Metrics and Analytics  
To meet the needs, we developed a Natural Language Processing (NLP) pipeline by integrating multiple disparate publicly available data resources to extract drug product information with minimal human intervention  ...  To generate a PSG, the assessor needs to retrieve supportive information about the drug product of interest, including from the drug labeling, which contain comprehensive information about drug products  ...  METHODS We collected drug product information from multiple publicly available data sources, including Orange Book, Drugs@FDA, DailyMed, and DrugBank.  ... 
doi:10.3389/frma.2021.670006 pmid:34179681 pmcid:PMC8222600 fatcat:utwqlbvuubemvjmvrhfc2aoc3q

A review of computational drug repositioning: strategies, approaches, opportunities, challenges, and directions

Tamer N. Jarada, Jon G. Rokne, Reda Alhajj
2020 Journal of Cheminformatics  
Since drug repositioning relies on data for existing drugs and diseases the enormous growth of publicly available large-scale biological, biomedical, and electronic health-related data along with the high-performance  ...  Fourth, we address prospective opportunities, including a few target areas.  ...  The authors used text mining to obtain data from publicly available sources that then used to produce a set of logical facts.  ... 
doi:10.1186/s13321-020-00450-7 pmid:33431024 fatcat:yymhfsis4vgibo4surxzcrvp5m

Extracting drug-drug interaction articles from MEDLINE to improve the content of drug databases

Stephany Duda, Constantin Aliferis, Randolph Miller, Alexander Statnikov, Kevin Johnson
2005 AMIA Annual Symposium Proceedings  
MEDLINE represents a respected source of peer-reviewed biomedical citations that potentially might serve as a valuable source of drug-drug interaction information, if relevant articles could be pinpointed  ...  We used a corpus of "positive" and"negative" drug interaction citations to generate datasets composed of MeSH terms, CUI-tagged title and abstract text, and stemmed text words.  ...  Acknowledgements This research was supported by a Training Grant from the National Library of Medicine (T15 LM 007450-03).  ... 
pmid:16779033 pmcid:PMC1560879 fatcat:wakqb6hnx5ebrbg5wqbml3tlpq

Data science in unveiling COVID-19 pathogenesis and diagnosis: evolutionary origin to drug repurposing

Jayanta Kumar Das, Giuseppe Tradigo, Pierangelo Veltri, Pietro H Guzzi, Swarup Roy
2021 Briefings in Bioinformatics  
The availability of large multiomics, radiological, bio-molecular and medical datasets requires the development of novel exploratory and predictive models, or the customisation of existing ones in order  ...  The current study should give a detailed sketch of the road map towards handling COVID-19 like situations by leveraging data science experts in choosing the right tools.  ...  Major phases of data science pipeline towards decision making and analysis. Data initially collected and integrated from many sources.  ... 
doi:10.1093/bib/bbaa420 pmid:33592108 pmcid:PMC7929414 fatcat:2vdkzlrrcfhvncx4d2jfepx4la

When to include clinical study reports and regulatory documents in systematic reviews

Tom Jefferson, Peter Doshi, Isabelle Boutron, Su Golder, Carl Heneghan, Alex Hodkinson, Mark Jones, Carol Lefebvre, Lesley A Stewart
2018 BMJ evidence-based medicine  
Organisations and other stakeholders such as Cochrane should encourage the use of data from clinical study reports as an important source of data in reviews of pharmaceutical interventions particularly  ...  Reporting bias is a major threat to the validity and credibility of systematic reviews.  ...  She previously received a research grant from YODA for her research team to independently analyse individual participant data and data from CSRs supplied by Medtronic. Patient consent Not required.  ... 
doi:10.1136/bmjebm-2018-110963 pmid:30309870 fatcat:x5kftcund5bprcbqecdmrvwg2m

Semantic Medical Prescriptions -- Towards Intelligent and Interoperable Medical Prescriptions

Ali Khalili, Bita Sedaghati
2013 2013 IEEE Seventh International Conference on Semantic Computing  
However, dealing with the heterogeneity of available information sources is still one of the main challenges of e-prescription systems.  ...  There already exists different sources of information addressing different aspects of pharmaceutical research (e.g. chemical, pharmacological and pharmaceutical drug data, clinical trials, approved prescription  ...  This work was supported by a grant from the European Union's 7th Framework Programme provided for the project LOD2 (GA no. 257943) and by a grant from the German Academic Exchange Service (DAAD).  ... 
doi:10.1109/icsc.2013.66 dblp:conf/semco/KhaliliS13 fatcat:mgivw725sbdfbnp5s4wpuw22iy

(Q)SAR Models of HIV-1 Protein Inhibition by Drug-Like Compounds

Leonid A. Stolbov, Dmitry S. Druzhilovskiy, Dmitry A. Filimonov, Marc C. Nicklaus, Vladimir V. Poroikov
2019 Molecules  
Despite the achievements of antiretroviral therapy, discovery of new anti-HIV medicines remains an essential task because the existing drugs do not provide a complete cure for the infected patients, exhibit  ...  To predict the interaction of drug-like compounds with multiple targets for HIV treatment, ligand-based drug design approach is widely applied.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/molecules25010087 pmid:31881687 pmcid:PMC6983201 fatcat:2b2oih7subc3jfipkfparl6bca

Biomedical Semantic Resources for Drug Discovery Platforms [chapter]

Ali Hasnain, Dietrich Rebholz-Schuhmann
2017 Lecture Notes in Computer Science  
Since the data sources are publicly available, the amount of content can be measured giving an overview on the accessible content but also on the state of the data representation in comparison to the existing  ...  As a result, any approach for drug discovery would profit from the data on molecular entities, but would lack content from data resources that represent disease pathomechanisms.  ...  This paper also highlights biomedical services that provide ontologies and databases resources relevant for drug discovery.  ... 
doi:10.1007/978-3-319-70407-4_34 fatcat:2bzddzat5zdcrinfwd6m4xqlai

Developing User Personas to Aid in the Design of a User-Centered Natural Product-Drug Interaction Information Resource for Researchers

Richard D Boyce, Isabelle Ragueneau-Majlessi, Jingjing Yu, Jessica Tay-Sontheimer, Chris Kinsella, Eric Chou, Mathias Brochhausen, John Judkins, Brandon T Gufford, Bruce E Pinkleton, Rebecca Cooney, Mary F Paine (+1 others)
2018 AMIA Annual Symposium Proceedings  
The researchers suggested a number of specific requirements for a natural product-drug interaction information resource, including specific information about a given interaction, the potential to cause  ...  As part of a user-centered design process, three types of intended researchers were surveyed: drug-drug interaction scientists, clinical pharmacists, and drug compendium editors.  ...  Prior experience with an existing proprietary repository of human in vitro and clinical drug-drug interaction (DDI) data 6 informed the initial design of a new publicly accessible database for NPDI studies  ... 
pmid:30815066 pmcid:PMC6371317 fatcat:lb2viqocpjawfpfssw4epguwjm

Strengths and Weaknesses of Existing Data Sources to Support Research to Address the Opioids Crisis

Rosanna Smart, Courtney A. Kase, Erin A. Taylor, Bradley D. Stein
2019 Preventive medicine reports  
Multiple secondary data sources exist that can be used to examine the impact of public health approaches to addressing the opioid crisis.  ...  lags and difficulties matching individual-level data over time or across datasets.  ...  NAVIPPRO collects and compiles information on product-specific opioid use, initiation, route of administration, and source of opioids from two proprietary systems and several publicly available data sources  ... 
doi:10.1016/j.pmedr.2019.101015 pmid:31993300 pmcid:PMC6971390 fatcat:wpepab3vfrg2dbegytchcx2snu

Large-scale regulatory and signaling network assembly through linked open data

M Lefebvre, A Gaignard, M Folschette, J Bourdon, C Guziolowski
2021 Database: The Journal of Biological Databases and Curation  
The proposed tool is pyBRAvo (python Biological netwoRk Assembly), and here we have applied it to a dataset of 910 gene expression measurements issued from liver cancer patients.  ...  The tool is publicly available at https://github.com/pyBRAvo/pyBRAvo.  ...  It also benefited from the support of the French government via the National Research Agency in the context of the investment expenditure program IDEALG ANR-10-BTBR-02-04-11. Conflicts of interest.  ... 
doi:10.1093/database/baaa113 pmid:33459761 pmcid:PMC7812716 fatcat:qtxpgtgljvb4hdmck6i3w4yzwy

Scientific competency questions as the basis for semantically enriched open pharmacological space development

Kamal Azzaoui, Edgar Jacoby, Stefan Senger, Emiliano Cuadrado Rodríguez, Mabel Loza, Barbara Zdrazil, Marta Pinto, Antony J. Williams, Victor de la Torre, Jordi Mestres, Manuel Pastor, Olivier Taboureau (+7 others)
2013 Drug Discovery Today  
Publicly available data sources used to target these questions as well as the need for and potential of semantic web-based technology will be presented. Reviews INFORMATICS  ...  The focus of this work is the integration of compound-target-pathway-disease/phenotype data for public and industrial drug discovery research.  ...  from the European Union's Seventh Framework Programme (FP7/2007-2013) and inkind contribution of EFPIA companies.  ... 
doi:10.1016/j.drudis.2013.05.008 pmid:23702085 fatcat:cdg6j3hxhrce5jwruwtgvigcky

Drug Target Commons 2.0: a community platform for systematic analysis of drug–target interaction profiles

ZiaurRehman Tanoli, Zaid Alam, Markus Vähä-Koskela, Balaguru Ravikumar, Alina Malyutina, Alok Jaiswal, Jing Tang, Krister Wennerberg, Tero Aittokallio
2018 Database: The Journal of Biological Databases and Curation  
Drug Target Commons 2.0: a community platform for systematic analysis of drug-target interaction profiles.  ...  Abstract Drug Target Commons (DTC) is a web platform (database with user interface) for community-driven bioactivity data integration and standardization for comprehensive mapping, reuse and analysis of  ...  Acknowledgements We thank the teams from ChEMBL, UniChem, UniProt, DisGeNET, Cancer Genome Interpreter, BindingDB, GtopDB and ClinicalTrials for making their data publicly available.  ... 
doi:10.1093/database/bay083 pmid:30219839 pmcid:PMC6146131 fatcat:d572uzhyr5h7rnvxlxv7obzew4

From Bytes to Bedside: Data Integration and Computational Biology for Translational Cancer Research

Jomol P. Mathew, Barry S. Taylor, Gary D. Bader, Saiju Pyarajan, Marco Antoniotti, Arul M. Chinnaiyan, Chris Sander, Steven J. Burakoff, Bud Mishra
2007 PLoS Computational Biology  
The unprecedented completeness, accuracy, and volume of genomic and molecular data necessitate a new kind of computational biology for translational research.  ...  Key challenges are standardization of data capture and communication, organization of easily accessible repositories, and algorithms for integrated analysis based on heterogeneous sources of information  ...  Acknowledgments We apologize to those whose publications we were not able to refer to in this review because of space limitations. Author Contributions.  ... 
doi:10.1371/journal.pcbi.0030012 pmid:17319736 pmcid:PMC1808026 fatcat:oabzbjv4o5cmzmgvtkxhel6vwq
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