Literature DB >> 21963522

Empowering industrial research with shared biomedical vocabularies.

Lee Harland1, Christopher Larminie, Susanna-Assunta Sansone, Sorana Popa, M Scott Marshall, Michael Braxenthaler, Michael Cantor, Wendy Filsell, Mark J Forster, Enoch Huang, Andreas Matern, Mark Musen, Jasmin Saric, Ted Slater, Jabe Wilson, Nick Lynch, John Wise, Ian Dix.   

Abstract

The life science industries (including pharmaceuticals, agrochemicals and consumer goods) are exploring new business models for research and development that focus on external partnerships. In parallel, there is a desire to make better use of data obtained from sources such as human clinical samples to inform and support early research programmes. Success in both areas depends upon the successful integration of heterogeneous data from multiple providers and scientific domains, something that is already a major challenge within the industry. This issue is exacerbated by the absence of agreed standards that unambiguously identify the entities, processes and observations within experimental results. In this article we highlight the risks to future productivity that are associated with incomplete biological and chemical vocabularies and suggest a new model to address this long-standing issue. Copyright Â
© 2011 Elsevier Ltd. All rights reserved.

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Year:  2011        PMID: 21963522      PMCID: PMC7098809          DOI: 10.1016/j.drudis.2011.09.013

Source DB:  PubMed          Journal:  Drug Discov Today        ISSN: 1359-6446            Impact factor:   7.851


  32 in total

1.  Vocabularies and retrieval tools in biomedicine: disentangling the terminological knot.

Authors:  Klaar Vanopstal; Robert Vander Stichele; Godelieve Laureys; Joost Buysschaert
Journal:  J Med Syst       Date:  2009-11-12       Impact factor: 4.460

Review 2.  Arguments against precompetitive collaboration.

Authors:  G Vargas; B Boutouyrie; S Ostrowitzki; L Santarelli
Journal:  Clin Pharmacol Ther       Date:  2010-05       Impact factor: 6.875

3.  Putting data to work.

Authors: 
Journal:  Nat Chem Biol       Date:  2010-11       Impact factor: 15.040

4.  Identifying disease-causal genes using Semantic Web-based representation of integrated genomic and phenomic knowledge.

Authors:  Ranga Chandra Gudivada; Xiaoyan A Qu; Jing Chen; Anil G Jegga; Eric K Neumann; Bruce J Aronow
Journal:  J Biomed Inform       Date:  2008-08-23       Impact factor: 6.317

Review 5.  Visualizing the drug target landscape.

Authors:  Stephen J Campbell; Anna Gaulton; Jason Marshall; Dmitri Bichko; Sid Martin; Cory Brouwer; Lee Harland
Journal:  Drug Discov Today       Date:  2009-10-17       Impact factor: 7.851

6.  An ontology for carcinoma classification for clinical bioinformatics.

Authors:  Anand Kumar; Yum Lina Yip; Barry Smith; Dirk Marwede; Daniel Novotny
Journal:  Stud Health Technol Inform       Date:  2005

7.  ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level.

Authors:  Philippe Rocca-Serra; Marco Brandizi; Eamonn Maguire; Nataliya Sklyar; Chris Taylor; Kimberly Begley; Dawn Field; Stephen Harris; Winston Hide; Oliver Hofmann; Steffen Neumann; Peter Sterk; Weida Tong; Susanna-Assunta Sansone
Journal:  Bioinformatics       Date:  2010-08-02       Impact factor: 6.937

8.  Collaborative development of predictive toxicology applications.

Authors:  Barry Hardy; Nicki Douglas; Christoph Helma; Micha Rautenberg; Nina Jeliazkova; Vedrin Jeliazkov; Ivelina Nikolova; Romualdo Benigni; Olga Tcheremenskaia; Stefan Kramer; Tobias Girschick; Fabian Buchwald; Joerg Wicker; Andreas Karwath; Martin Gütlein; Andreas Maunz; Haralambos Sarimveis; Georgia Melagraki; Antreas Afantitis; Pantelis Sopasakis; David Gallagher; Vladimir Poroikov; Dmitry Filimonov; Alexey Zakharov; Alexey Lagunin; Tatyana Gloriozova; Sergey Novikov; Natalia Skvortsova; Dmitry Druzhilovsky; Sunil Chawla; Indira Ghosh; Surajit Ray; Hitesh Patel; Sylvia Escher
Journal:  J Cheminform       Date:  2010-08-31       Impact factor: 5.514

9.  Megascience. 'Omics data sharing.

Authors:  Dawn Field; Susanna-Assunta Sansone; Amanda Collis; Tim Booth; Peter Dukes; Susan K Gregurick; Karen Kennedy; Patrik Kolar; Eugene Kolker; Mary Maxon; Siân Millard; Alexis-Michel Mugabushaka; Nicola Perrin; Jacques E Remacle; Karin Remington; Philippe Rocca-Serra; Chris F Taylor; Mark Thorley; Bela Tiwari; John Wilbanks
Journal:  Science       Date:  2009-10-09       Impact factor: 47.728

Review 10.  Can literature analysis identify innovation drivers in drug discovery?

Authors:  Pankaj Agarwal; David B Searls
Journal:  Nat Rev Drug Discov       Date:  2009-11       Impact factor: 84.694

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  8 in total

1.  Metadata Standard and Data Exchange Specifications to Describe, Model, and Integrate Complex and Diverse High-Throughput Screening Data from the Library of Integrated Network-based Cellular Signatures (LINCS).

Authors:  Uma D Vempati; Caty Chung; Chris Mader; Amar Koleti; Nakul Datar; Dušica Vidović; David Wrobel; Sean Erickson; Jeremy L Muhlich; Gabriel Berriz; Cyril H Benes; Aravind Subramanian; Ajay Pillai; Caroline E Shamu; Stephan C Schürer
Journal:  J Biomol Screen       Date:  2014-02-11

2.  Toward interoperable bioscience data.

Authors:  Susanna-Assunta Sansone; Philippe Rocca-Serra; Dawn Field; Eamonn Maguire; Chris Taylor; Oliver Hofmann; Hong Fang; Steffen Neumann; Weida Tong; Linda Amaral-Zettler; Kimberly Begley; Tim Booth; Lydie Bougueleret; Gully Burns; Brad Chapman; Tim Clark; Lee-Ann Coleman; Jay Copeland; Sudeshna Das; Antoine de Daruvar; Paula de Matos; Ian Dix; Scott Edmunds; Chris T Evelo; Mark J Forster; Pascale Gaudet; Jack Gilbert; Carole Goble; Julian L Griffin; Daniel Jacob; Jos Kleinjans; Lee Harland; Kenneth Haug; Henning Hermjakob; Shannan J Ho Sui; Alain Laederach; Shaoguang Liang; Stephen Marshall; Annette McGrath; Emily Merrill; Dorothy Reilly; Magali Roux; Caroline E Shamu; Catherine A Shang; Christoph Steinbeck; Anne Trefethen; Bryn Williams-Jones; Katherine Wolstencroft; Ioannis Xenarios; Winston Hide
Journal:  Nat Genet       Date:  2012-01-27       Impact factor: 38.330

3.  On the evolving portfolio of community-standards and data sharing policies: turning challenges into new opportunities.

Authors:  Susanna-Assunta Sansone; Philippe Rocca-Serra
Journal:  Gigascience       Date:  2012-07-12       Impact factor: 6.524

4.  The eTOX data-sharing project to advance in silico drug-induced toxicity prediction.

Authors:  Montserrat Cases; Katharine Briggs; Thomas Steger-Hartmann; François Pognan; Philippe Marc; Thomas Kleinöder; Christof H Schwab; Manuel Pastor; Jörg Wichard; Ferran Sanz
Journal:  Int J Mol Sci       Date:  2014-11-14       Impact factor: 5.923

5.  Structure-based classification and ontology in chemistry.

Authors:  Janna Hastings; Despoina Magka; Colin Batchelor; Lian Duan; Robert Stevens; Marcus Ennis; Christoph Steinbeck
Journal:  J Cheminform       Date:  2012-04-05       Impact factor: 5.514

6.  SARConnect: A Tool to Interrogate the Connectivity Between Proteins, Chemical Structures and Activity Data.

Authors:  Mats Eriksson; Ingemar Nilsson; Thierry Kogej; Christopher Southan; Martin Johansson; Christian Tyrchan; Sorel Muresan; Niklas Blomberg; Marcus Bjäreland
Journal:  Mol Inform       Date:  2012-08-07       Impact factor: 3.353

7.  Effects of guideline-based training on the quality of formal ontologies: a randomized controlled trial.

Authors:  Martin Boeker; Ludger Jansen; Niels Grewe; Johannes Röhl; Daniel Schober; Djamila Seddig-Raufie; Stefan Schulz
Journal:  PLoS One       Date:  2013-05-07       Impact factor: 3.240

Review 8.  Metabolomics and systems pharmacology: why and how to model the human metabolic network for drug discovery.

Authors:  Douglas B Kell; Royston Goodacre
Journal:  Drug Discov Today       Date:  2013-07-26       Impact factor: 7.851

  8 in total

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