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Linked open drug data for pharmaceutical research and development

Matthias Samwald, Anja Jentzsch, Christopher Bouton, Claus Kallesøe, Egon Willighagen, Janos Hajagos, M Marshall, Eric Prud'hommeaux, Oktie Hassenzadeh, Elgar Pichler, Susie Stephens
2011 Journal of Cheminformatics  
In this paper, we present past and ongoing work of LODD and discuss the growing importance of Linked Data as a foundation for pharmaceutical R&D data sharing.  ...  Linking Open Drug Data (LODD) is a task force within the World Wide Web Consortium's (W3C) Health Care and Life Sciences Interest Group (HCLS IG).  ...  The article has been independently prepared by the authors and been subject to the journal's standard peer review process.  ... 
doi:10.1186/1758-2946-3-19 pmid:21575203 pmcid:PMC3121711 fatcat:3wlztkqvsraotenaqkstjo2xr4

Open Systems Pharmacology community – an open access, open source, open science approach to modeling and simulation in pharmaceutical sciences

Jörg Lippert, Rolf Burghaus, Andrea Edginton, Sebastian Frechen, Mats Karlsson, Andreas Kovar, Thorsten Lehr, Peter Milligan, Valerie Nock, Sergej Ramusovic, Matthew Riggs, Stephan Schaller (+7 others)
2019 CPT: Pharmacometrics & Systems Pharmacology  
In recent years, systems pharmacology and its applications in pharmaceutical development have gained significant visibility and attention as an important pillar of model-informed drug (discovery and) development  ...  OSP offers professional open access and open source software tools (PK-Sim/MoBi) and models via a platform for collaborative development and qualification.  ...  All authors use Open Systems Pharmacology software, tools, or models in their professional roles.  ... 
doi:10.1002/psp4.12473 pmid:31671256 pmcid:PMC6930856 fatcat:b3k2mlruyjayfcs7qarwgh7wlm

Open Data for Research and Strategic Monitoring in the Pharmaceutical and Biotech Industry

Baldissera Giovani
2017 Data Science Journal  
The companies interviewed use open data to complement proprietary data for research purposes, to implement licensing-in/licensing-out strategies, to map partnerships and connections among players or to  ...  of companies exploiting open data (aggregators, developers, enrichers and enablers) participated.  ...  Open research data to complement proprietary data The use of open research data to complement proprietary data is linked to the use the companies make of the data as suppliers, aggregators, developers,  ... 
doi:10.5334/dsj-2017-018 fatcat:7dmb47xqibg57i6ac5obiwrczy

Semantic Medical Prescriptions -- Towards Intelligent and Interoperable Medical Prescriptions

Ali Khalili, Bita Sedaghati
2013 2013 IEEE Seventh International Conference on Semantic Computing  
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  ...  Pharmer employs datasets such as DBpedia, DrugBank, DailyMed and RxNorm to automatically detect the drugs in the prescriptions and to collect multidimensional data on them.  ...  ACKNOWLEDGEMENT We would to thank the AKSW research group members especially Prof. Sören Auer for their support during the development of Pharmer.  ... 
doi:10.1109/icsc.2013.66 dblp:conf/semco/KhaliliS13 fatcat:mgivw725sbdfbnp5s4wpuw22iy

Design of the Internet plus Drug Circulation Business Model Based on Value Chain

Linmeng Liang, Yang Gao
2021 Journal of Healthcare Engineering  
With the continuous development of computers and the Internet, all industries in China have brought new opportunities for change, and pharmaceutical e-commerce has also shown great potential for development  ...  This thesis can enrich the application of value chain and business model theories in the field of "Internet + drug distribution," and it is hoped that the model experience developed in this thesis can  ...  between internal ERP data and pharmaceutical B2B e-commerce mall and paves the way for the transformation and upgrading of commercial companies and leapfrog development [14] .  ... 
doi:10.1155/2021/6673649 pmid:33953898 pmcid:PMC8057869 fatcat:jyetzewsgzbnvfggwnezg4ec3a

CDEK: Clinical Drug Experience Knowledgebase

2019 Database: The Journal of Biological Databases and Curation  
and development.  ...  The Clinical Drug Experience Knowledgebase (CDEK) is a database and web platform of active pharmaceutical ingredients with evidence of clinical testing as well as the organizations involved in their research  ...  Research reported in this publication was supported by the Washington University Institute of Clinical and Translational Sciences grant UL1TR002345, sub-award TL1TR002344, from the NCATS of the NIH.  ... 
doi:10.1093/database/baz087 pmid:31411687 pmcid:PMC6693031 fatcat:f3y2z5jvgvcjvkzrlnuq6sx6fq

Pharmacoinformatics Infrastructure for Genome-based Personalized Medicine

Tsuguchika Kaminuma, Kotoko Nakata, Tatsuya Nakano, Takako Takai-Igarashi
2001 Chem-Bio Informatics Journal  
The infrastructure would also be useful in pharmaceutical research for finding leads and analyzing detailed mechanisms of drug actions.  ...  As the only national institution for pharmaceutical research in Japan, we have started to implement some components of the infrastructure and put their prototypes on the Web.  ...  Acknowledgements The future goals in this vision paper came into the authors minds through discussions with many researchers including Prof.  ... 
doi:10.1273/cbij.1.1 fatcat:seyallemenc6jhwp3m3lu6suse

Open-source approaches for the repurposing of existing or failed candidate drugs: learning from and applying the lessons across diseases

Minna Allarakhia
2013 Drug Design, Development and Therapy  
The open-source model permits for the sharing of data, resources, compounds, clinical molecules, small libraries, and screening platforms to cost-effectively advance old drugs and/or candidates into clinical  ...  Open-source models can support human-capital development through collaborative data generation, open compound access, open and collaborative screening, preclinical and possibly clinical studies.  ...  the pools, and the royalty-free, open licensing for drug development targeting NTDs.  ... 
doi:10.2147/dddt.s46289 pmid:23966771 pmcid:PMC3743608 fatcat:uf7u6doa2zgyjiwwxbaei4tceu

Open Drug Discovery Teams: A Chemistry Mobile App for Collaboration

Sean Ekins, Alex M. Clark, Antony J. Williams
2012 Molecular Informatics  
The photo for Sanfillipo Syndrome in the ODDT app is courtesy of Jill Wood  ...  the open data and the researchers.  ...  With investment resources we intend to adapt the product for licensing to pharmaceutical research institutions for internal use and make it a closed app.  ... 
doi:10.1002/minf.201200034 pmid:23198003 pmcid:PMC3503260 fatcat:vvh4o6lsfje2hfhqe7wo6wtdti

Annual Meeting Symposia

2015 Journal of Pharmacological Sciences  
However, in Drug-Development Process, analysis data of pharmacological effects, which are directly linked to the clinical endpoint, are needed for the evaluation of candidate products based on evidence-based  ...  It is widely recognized that the promotion of open innovation for drug innovation provides a platform for idea-sharing and lowers the barrier for collaborations among researchers in basic and clinical  ... 
doi:10.1016/j.jphs.2015.07.024 fatcat:xisgnsq2vnfvlgu45jc2axyefi

Open PHACTS: A Semantic Knowledge Infrastructure for Public and Commercial Drug Discovery Research [chapter]

Lee Harland
2012 Lecture Notes in Computer Science  
The Open PHACTS project consortium consists of leading experts in semantics, pharmacology and informatics including academic institutions, pharmaceutical companies and scientific software companies.  ...  Finally, I would like to thank Niklas Blomberg, Carole Goble, Alasdair Gray, Paul Groth, Antonis Loizou and Antony Williams for valuable input and feedback on the article.  ...  Increasingly, pharmaceutical companies are outsourcing elements of drug discovery and development to contract research organisations and academic collaboration.  ... 
doi:10.1007/978-3-642-33876-2_1 fatcat:q2via6rvgnaufln43kgj3pi4yu

Data Linkages to Study Pharmaceutical Health Services Delivery: Three Applied Examples

Karin Johnson, Lanlan Xu, Zippora Kiptanui, Christine Gill, Corey Triebwasser, Danielle Emery, Evan Perlman, Ilene Harris
2018 International Journal of Population Data Science  
Conclusion/ImplicationsMany data sources are available for pharmaceutical health services research studies and linkage can be made at the patient, region, or payer level to support program monitoring and  ...  Targeted beneficiaries are determined using Medicare administrative data and delivery of services is assessed based on a custom-developed encounter data set, linked by beneficiary.  ...  Conclusion/Implications Many data sources are available for pharmaceutical health services research studies and linkage can be made at the patient, region, or payer level to support program monitoring  ... 
doi:10.23889/ijpds.v3i4.747 fatcat:imxzgcj3pbgbzmzown3l4ltdke

CSTNPD: a database for cancer specific toxic natural products

Mohammad Ajmal Ali, Mohammad Tabrez Quasim, Mohammad Abul Farah, Fahad Mohammad Al-Hemaid, Joongku Lee, Khalid Mashay Al-Anazi, Soo Yong Kim, Tapan Pan
2019 Indian Journal of Science and Technology  
All those novel natural product molecules failed to proceed towards further detailed research or to reach into clinical trial and pharmaceutical drug development and drug approval.  ...  Result: The compound database provides opportunities for researchers to obtain various information required for the successful identification of pharmaceutically relevant substances.  ...  The authors extend their appreciation to the Deanship of Scientific Research at King Saud University for funding the work through the research group project No RGPxxxxx.  ... 
doi:10.17485/ijst/2019/v12i10/141396 fatcat:dqirm6ahcrfdzd3qh5sbfy4gwa

Open PHACTS: semantic interoperability for drug discovery

Antony J. Williams, Lee Harland, Paul Groth, Stephen Pettifer, Christine Chichester, Egon L. Willighagen, Chris T. Evelo, Niklas Blomberg, Gerhard Ecker, Carole Goble, Barend Mons
2012 Drug Discovery Today  
OPS is intended to facilitate improvements in drug discovery in academia and industry and to support open innovation and in-house non-public drug discovery research.  ...  Open PHACTS is a public-private partnership between academia, publishers, small and medium sized enterprises and pharmaceutical companies.  ...  We acknowledge all of the collaborators for their contributions to Open PHACTS.  ... 
doi:10.1016/j.drudis.2012.05.016 pmid:22683805 fatcat:qnqlnrdv3zbijesyhdat2knoeu


Elisabetta Vaudano
2013 Computational and Structural Biotechnology Journal  
Acknowledgements I gratefully acknowledge Catherine Brett, Alessandra Paccamiccio, Hugh Laverty and Michel Goldman for critically reading the manuscript. Disclaimer The  ...  organisation created to support open innovation and pre-competitive research in the pharmaceutical sector [16] .  ...  Introduction Investment in pharmaceutical research and development (R&D) has increased substantially in the last decades.  ... 
doi:10.5936/csbj.201303017 pmid:24688725 pmcid:PMC3962198 fatcat:o7kmqbclmvfdtosul73gws6cey
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