Image Data Resource: a bioimage data integration and publication platform

Eleanor Williams 1, 2, 3 Josh Moore 1, 2 Simon Li 1, 2 Gabriella Rustici 1, 2 Aleksandra Tarkowska 1, 2 Anatole Chessel 4, 5, 6, 7 Simone Leo 1, 2, 8 Bálint Antal 4, 5, 6 Richard Ferguson 1, 2 Ugis Sarkans 3 Alvis Brazma 3 Rafael Carazo Salas 4, 5, 6, 9 Jason Swedlow 1, 2
1 Centre for Gene Regulation and Expression, School of Life Sciences Dundee
2 Division of Computational Biology
3 European Molecular Biology Laboratory [Hinxton]
4 Department of Pharmacology - University of Cambridge
5 Department of Genetics University of Cambridge
6 CSBC - Cambridge Systems Biology Centre & Department of Biochemistry
7 LOB - Laboratoire d'Optique et Biosciences
8 CRS4 - Center for Advanced Studies, Research and Development in Sardinia
9 School of Cellular and Molecular Medicine
Abstract : Access to primary research data is vital for the advancement of science. To extend the data types supported by community repositories, we built a prototype Image Data Resource (IDR). IDR links data from several imaging modalities, including high-content screening, multi-dimensional microscopy and digital pathology, with public genetic or chemical databases and cell and tissue phenotypes expressed using controlled ontologies. Using this integration, IDR facilitates the analysis of gene networks and reveals functional interactions that are inaccessible to individual studies. To enable reanalysis, we also established a computational resource based on Jupyter notebooks that allows remote access to the entire IDR. IDR is also an open-source platform for publishing imaging data. Thus IDR provides an online resource and a software infrastructure that promotes and extends publication and reanalysis of scientific image data.
Keywords : Data integration Protein databases
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Journal articles
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https://hal-polytechnique.archives-ouvertes.fr/hal-01760728
Contributor : Aurélien Arnoux <>
Submitted on : Friday, April 6, 2018 - 3:52:48 PM
Last modification on : Saturday, June 8, 2019 - 2:20:23 PM

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Eleanor Williams, Josh Moore, Simon Li, Gabriella Rustici, Aleksandra Tarkowska, et al.. Image Data Resource: a bioimage data integration and publication platform. Nature Methods, Nature Publishing Group, 2017, 14 (8), pp.775 - 781. ⟨10.1038/nmeth.4326⟩. ⟨hal-01760728⟩

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