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Applying linked data approaches to pharmacology: Architectural decisions and implementation

Alasdair J.G. Gray, Paul Groth, Antonis Loizou, Sune Askjaer, Christian Brenninkmeijer, Kees Burger, Christine Chichester, Chris T. Evelo, Carole Goble, Lee Harland, Steve Pettifer, Mark Thompson (+2 others)
2014 Semantic Web Journal  
In this application report, we describe a linked data platform for integrating multiple pharmacology datasets that form the basis for several drug discovery applications.  ...  The discovery of new medicines requires pharmacologists to interact with a number of information sources ranging from tabular data to scientific papers, and other specialized formats.  ...  of financial contribution from the European Union's Seventh Framework Programme (FP7/2007-2013) and EFPIA companies' in kind contribution.  ... 
doi:10.3233/sw-2012-0088 fatcat:l5vohyessjejbbbrvb62vcoyzu

Agent-Based Modeling in Systems Pharmacology

J Cosgrove, J Butler, K Alden, M Read, V Kumar, L Cucurull-Sanchez, J Timmis, M Coles
2015 CPT: Pharmacometrics & Systems Pharmacology  
Modeling and simulation (M&S) techniques provide a platform for knowledge integration and hypothesis testing to gain insights into biological systems that would not be possible a priori.  ...  This tutorial introduces ABM to systems pharmacologists, using relevant case studies to highlight how ABM-specific strengths have yielded success in the area of preclinical mechanistic modeling.  ...  The first two authors contributed equally to this work. Partly funded by the Wellcome Trust  ... 
doi:10.1002/psp4.12018 pmid:26783498 pmcid:PMC4716580 fatcat:kf7lhaq7hbcb3li5queac5yjam

Genomic architecture of pharmacological efficacy and adverse events

Aparna Chhibber, Deanna L Kroetz, Kelan G Tantisira, Michael McGeachie, Cheng Cheng, Robert Plenge, Eli Stahl, Wolfgang Sadee, Marylyn D Ritchie, Sarah A Pendergrass
2014 Pharmacogenomics (London)  
Pharmacogenomics-based tests are already being applied in clinical decision making.  ...  The pharmacokinetic and pharmacodynamic disciplines address pharmacological traits, including efficacy and adverse events.  ...  Acknowledgments The authors thank the Pharmacogenomics Research Network (PGRN) and its trans-network project on 'Polygenic  ... 
doi:10.2217/pgs.14.144 pmid:25521360 pmcid:PMC4308414 fatcat:harmjdduwzfzhjli4kb3fvnfsm

Implementation of Quantitative and Systems Pharmacology in Large Pharma

S A G Visser, D P de Alwis, T Kerbusch, J A Stone, S R B Allerheiligen
2014 CPT: Pharmacometrics & Systems Pharmacology  
and experimental methods to elucidate, validate, and apply new pharmacological concepts to the development and use of small molecule and biologic drugs. 8 A unique feature of quantitative and systems  ...  A focus on the development of system-level (mathematical) models through the integration of experimental data and knowledge has led to an improved understanding of human biology, pharmacology, and safety  ...  The authors thank all our colleagues from Merck and our external collaborators, who have contributed to the countless study and modeling activities, to the implementation and to its associated impact as  ... 
doi:10.1038/psp.2014.40 pmid:25338195 pmcid:PMC4474169 fatcat:4ll7iteqvnes5kjenlxhcd5434

Harnessing Big Data for Systems Pharmacology [article]

Lei Xie, Eli Draizen, Philip Bourne
2016 bioRxiv   pre-print
Here, we discuss several upcoming issues in systems pharmacology and potential solutions to them using big data technology.  ...  Data-driven modeling plays a central role in systems pharmacology, and has already enabled biologists to generate novel hypotheses. However, more is needed.  ...  (A) Architecture of model management systems. Models are linked with associated data sets, metadata and software that is wrapped within a container and accessed through a model commons.  ... 
doi:10.1101/077115 fatcat:owkyissq65agrdovh2vdgux24m

Toward an integrated software platform for systems pharmacology

Samik Ghosh, Yukiko Matsuoka, Yoshiyuki Asai, Kun-Yi Hsin, Hiroaki Kitano
2013 Biopharmaceutics & drug disposition  
This is particularly true for systems pharmacology, which aims to understand the action of drugs and their interactions in a systems context.  ...  Software platforms play a dominant role in creativity and productivity support and have transformed many industries, techniques that can be applied to biology as well.  ...  pharmacology (QSP), defined as '.. as an approach to translational medicine that combines computational and experimental methods to elucidate, validate and apply new pharmacological concepts to the development  ... 
doi:10.1002/bdd.1875 pmid:24150748 pmcid:PMC4253131 fatcat:l4dvxrd4qzeqro75ysop35j4b4

Global mapping of pharmacological space

Gaia V Paolini, Richard H B Shapland, Willem P van Hoorn, Jonathan S Mason, Andrew L Hopkins
2006 Nature Biotechnology  
Using the data matrix, we are able to catalog the links between proteins in chemical space as a polypharmacology interaction network.  ...  The relationships between proteins, chemical structures and drug-like properties provide a framework for developing a probabilistic approach to drug discovery that can be exploited to increase research  ...  Thus, both chemoinformatics and bioinformatics techniques can be applied directly to the data-mining of the integrated data set.  ... 
doi:10.1038/nbt1228 pmid:16841068 fatcat:axmif2jgqvhp7lgn27khjslw4i

Harnessing Big Data for Systems Pharmacology

Lei Xie, Eli J. Draizen, Philip E. Bourne
2017 Annual Review of Pharmacology and Toxicology  
Beyond the data challenge, models are strongly coupled with algorithms underlying the model, software that implements the algorithm to execute the model, and tools that process inputs and outputs.  ...  Here, we discuss several upcoming issues in systems pharmacology and potential solutions to them using big data technology.  ...  (A) Architecture of model management systems. Models are linked with associated data sets, metadata and software that is wrapped within a container and accessed through a model commons.  ... 
doi:10.1146/annurev-pharmtox-010716-104659 pmid:27814027 pmcid:PMC5626567 fatcat:oajwecyapvbghjgft2wizxoeze

Electronic Medical Records as a Tool in Clinical Pharmacology: Opportunities and Challenges

D M Roden, H Xu, J C Denny, R A Wilke
2012 Clinical Pharmacology and Therapeutics  
in the fields of basic, translational, and implementation sciences.  ...  more sophisticated, and links being established with DNA repositories.  ...  Emr-basEd disCovEry in CliniCal pharmaCology approach to Emr-based phenotyping A common experimental design starts with construction of a cohort of cases and controls for a specific phenotype (e.g., a  ... 
doi:10.1038/clpt.2012.42 pmid:22534870 pmcid:PMC3819803 fatcat:wa366oirjrdltdpzrdp5gblhtm

Enabling personalized cancer medicine decisions: The challenging pharmacological approach of PBPK models for nanomedicine and pharmacogenomics (Review)

2016 Oncology Reports  
Development of PBPK models and advanced ex vivo pharmacological assays to support PTx and implement clinical pharmacology guidelines 4.  ...  The economic burden and cost-effectiveness of PGx to enable personalized cancer medicine decisions 3.  ...  ADME) and v) innovative approaches and tools on patient electronic data Enabling personalized cancer medicine decisions: The challenging pharmacological approach of PBPK models for nanomedicine and pharmacogenomics  ... 
doi:10.3892/or.2016.4575 pmid:26781205 fatcat:vrkndmrwb5biboijnaqw4p5jwe

Poster Session (abstracts)

1992 Fundamental & Clinical Pharmacology  
Additional tools and modules allow the user to assess risk and implement necessary control methods prior to bringing the material on site, thus allowing for educated decision making with respect to nanomaterial  ...  The Service-Oriented, federated approaches developed for the DoD can also be adopted and applied to nanoinformatics supporting the nanotechnology domain.  ... 
doi:10.1111/j.1472-8206.1992.tb00143.x fatcat:zcx4fjes2bdy7doigfmdonkgea

Predicting protein-ligand interactions based on bow-pharmacological space and Bayesian additive regression trees

Li Li, Ching Chiek Koh, Daniel Reker, J. B. Brown, Haishuai Wang, Nicholas Keone Lee, Hien-haw Liow, Hao Dai, Huai-Meng Fan, Luonan Chen, Dong-Qing Wei
2019 Scientific Reports  
The algorithm applies Bayesian Additive Regression Trees (BART) on a newly proposed proteochemical space, termed the bow-pharmacological space.  ...  For the rapid identification of protein-ligand interactions, we here present a novel chemogenomics algorithm for the prediction of protein-ligand interactions using a new machine learning approach and  ...  We thank Etienne Caron and Lorenz Blum for reading the manuscript drafts and providing comments.  ... 
doi:10.1038/s41598-019-43125-6 pmid:31118426 pmcid:PMC6531441 fatcat:5ivfmrrq55bklnmtfok2rjrc64

History and Future Perspectives on the Discipline of Quantitative Systems Pharmacology Modeling and Its Applications

Karim Azer, Chanchala D. Kaddi, Jeffrey S. Barrett, Jane P. F. Bai, Sean T. McQuade, Nathaniel J. Merrill, Benedetto Piccoli, Susana Neves-Zaph, Luca Marchetti, Rosario Lombardo, Silvia Parolo, Selva Rupa Christinal Immanuel (+1 others)
2021 Frontiers in Physiology  
With an increased focus on the pharmacology application of system models and the advances in data science spanning mechanistic and empirical approaches, there is a significant opportunity and promise to  ...  In this paper, we will review milestones in the evolution of mathematical biology and pharmacology models, highlight some of the gaps and challenges in developing and applying systems pharmacology models  ...  When a decision is made to invest in building a QSP model, several approaches can be implemented, depending on the modeling scope and the available data.  ... 
doi:10.3389/fphys.2021.637999 pmid:33841175 pmcid:PMC8027332 fatcat:bfy3cijfqjceth3zk276bqtwem

Pharmacologic Management of Aneurysms

Jan H. Lindeman, Jon S. Matsumura
2019 Circulation Research  
Preclinical studies in the context of abdominal aortic aneurysm identified hundreds of candidate strategies for stabilization, and data from preoperative clinical intervention studies show that interventions  ...  Preclinical models more reflective of human pathophysiology, identification of biomarkers to predict severity of disease progression, and improved design of clinical trials may more rapidly advance the  ...  Research grant funding to University of Wisconsin (Dr Matsumura): Abbott, Gore, Endologix, Cook, Medtronic, and NIH.  ... 
doi:10.1161/circresaha.118.312439 pmid:30763216 pmcid:PMC6386187 fatcat:obojnm5vdzckrlr4jg7lkwq3pm

Prerequisites to Implementing a Pharmacogenomics Program in a Large Health-Care System

K D Levy, B S Decker, J S Carpenter, D A Flockhart, P R Dexter, Z Desta, T C Skaar
2014 Clinical Pharmacology and Therapeutics  
A multifaceted approach was applied. We invited nationally known experts to take part in a symposium to address clinical implementation challenges.  ...  CPIC guidelines on gene/drug pairs were used to help select targeted medications and the micro-array architecture. Decisions were based on the clinical evidence associated with each reportable SNP.  ... 
doi:10.1038/clpt.2014.101 pmid:24807457 pmcid:PMC4441093 fatcat:ui5qvfibanenncfg22jygw6sbm
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