diXa: a data infrastructure for chemical safety assessment

被引：18

作者：

Hendrickx, Diana M. ^{[1
]}

Aerts, Hugo J. W. L. ^{[2
]}

Caiment, Florian ^{[1
]}

Clark, Dominic ^{[3
]}

Ebbels, Timothy M. D. ^{[4
]}

Evelo, Chris T. ^{[5
]}

Gmuender, Hans ^{[6
]}

Hebels, Dennie G. A. J. ^{[1
]}

Herwig, Ralf ^{[7
]}

Hescheler, Juergen ^{[8
]}

Jennen, Danyel G. J. ^{[1
]}

Jetten, Marlon J. A. ^{[1
]}

Kanterakis, Stathis ^{[3
]}

Keun, Hector C. ^{[4
]}

Matser, Vera ^{[3
]}

Overington, John P. ^{[3
]}

Pilicheva, Ekaterina ^{[3
]}

Sarkans, Ugis ^{[3
]}

Segura-Lepe, Marcelo P. ^{[4
]}

Sotiriadou, Isaia ^{[8
]}

Wittenberger, Timo ^{[6
]}

Wittwehr, Clemens ^{[9
]}

Zanzi, Antonella ^{[9
]}

Kleinjans, Jos C. S. ^{[1
]}

机构：

[1] Maastricht Univ, Sch Oncol & Dev Biol GROW, Dept Toxicogen, NL-6200 MD Maastricht, Netherlands

[2] Harvard Univ, Brigham & Womens Hosp, Sch Med, Dana Farber Canc Inst, Boston, MA 02215 USA

[3] European Bioinformat Inst, European Mol Biol Lab, Hinxton CB10 1SD, Cambs, England

[4] Univ London Imperial Coll Sci Technol & Med, Dept Surg & Canc, Computat & Syst Med, London SW7 2AZ, England

[5] Maastricht Univ, Dept Bioinformat BiGCaT, NL-6200 MD Maastricht, Netherlands

[6] Genedata AG, CH-4053 Basel, Switzerland

[7] Max Planck Inst Mol Genet, Dept Vertebrate Genom, D-14195 Berlin, Germany

[8] Univ Cologne, Inst Neurophysiol, Ctr Physiol & Pathophysiol, D-50931 Cologne, Germany

[9] European Commiss, Joint Res Ctr, I-21027 Ispra, VA, Italy

来源：

BIOINFORMATICS | 2015年 / 31卷 / 09期

关键词：

D O I：

10.1093/bioinformatics/btu827

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Motivation: The field of toxicogenomics (the application of '-omics' technologies to risk assessment of compound toxicities) has expanded in the last decade, partly driven by new legislation, aimed at reducing animal testing in chemical risk assessment but mainly as a result of a paradigm change in toxicology towards the use and integration of genome wide data. Many research groups worldwide have generated large amounts of such toxicogenomics data. However, there is no centralized repository for archiving and making these data and associated tools for their analysis easily available. Results: The Data Infrastructure for Chemical Safety Assessment (diXa) is a robust and sustainable infrastructure storing toxicogenomics data. A central data warehouse is connected to a portal with links to chemical information and molecular and phenotype data. diXa is publicly available through a user-friendly web interface. New data can be readily deposited into diXa using guidelines and templates available online. Analysis descriptions and tools for interrogating the data are available via the diXa portal.

引用

页码：1505 / 1507

页数：3

共 11 条

[1] Assessing compound carcinogenicity in vitro using connectivity mapping [J].

Caiment, Florian ;

Tsamou, Maria ;

Jennen, Danyel ;

Kleinjans, Jos .

CARCINOGENESIS, 2014, 35 (01) :201-207

[2] Data integration in the era of omics: current and future challenges [J].

Gomez-Cabrero, David ;

Abugessaisa, Imad ;

Maier, Dieter ;

Teschendorff, Andrew ;

Merkenschlager, Matthias ;

Gisel, Andreas ;

Ballestar, Esteban ;

Bongcam-Rudloff, Erik ;

Conesa, Ana ;

Tegner, Jesper .

BMC SYSTEMS BIOLOGY, 2014, 8 :I1

[3] Toxicology for the twenty-first century [J].

Hartung, Thomas .

NATURE, 2009, 460 (7252) :208-212

[4]

Hebels DGA, 2014, BIOMARK MED, V8, P185, DOI 10.2217/bmm.13.154

[5]

Hoefkens J, 2014, CHIM OGGI, V32, P4

[6] Modeling sample variables with an Experimental Factor Ontology [J].

Malone, James ;

Holloway, Ele ;

Adamusiak, Tomasz ;

Kapushesky, Misha ;

Zheng, Jie ;

Kolesnikov, Nikolay ;

Zhukova, Anna ;

Brazma, Alvis ;

Parkinson, Helen .

BIOINFORMATICS, 2010, 26 (08) :1112-1118

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

Rocca-Serra, Philippe ;

Brandizi, Marco ;

Maguire, Eamonn ;

Sklyar, Nataliya ;

Taylor, Chris ;

Begley, Kimberly ;

Field, Dawn ;

Harris, Stephen ;

Hide, Winston ;

Hofmann, Oliver ;

Neumann, Steffen ;

Sterk, Peter ;

Tong, Weida ;

Sansone, Susanna-Assunta .

BIOINFORMATICS, 2010, 26 (18) :2354-2356

[8] A collaborative approach to develop a multi-omics data analytics platform for translational research [J].

Schumacher, Axel ;

Rujan, Tamas ;

Hoefkens, Jens .

APPLIED AND TRANSLATIONAL GENOMICS, 2014, 3 (04) :105-108

[9] Challenges for the implementation of integrated pest management of cucumber pests in protected crops - An Australian perspective [J].

Steiner, M. Y. ;

Goodwin, S. .

PROCEEDINGS OF THE IIIRD INTERNATIONAL SYMPOSIUM ON CUCURBITS, 2007, (731) :309-+

[10] Putting Chemicals on a Path To Better Risk Assessment [J].

Stokstad, Erik .

SCIENCE, 2009, 325 (5941) :694-695

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