CRS4

Image Data Resource: a bioimage data integration and publication platform

Eleanor Williams, Josh Moore, Simon W. Li, Gabriella Rustici, Aleksandra Tarkowska, Anatole Chessel, Simone Leo, Bálint Antal, Richard K. Ferguson, Ugis Sarkans, Alvis Brazma, Rafael E. Carazo Salas, Jason R. Swedlow
Nature Methods, Volume 14, page 775--781 - june 2017
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.

BibTex references

@Article{WMLRTCLAFSBCS17,
  author       = {Williams, E. and Moore, J. and Li, S. and Rustici, G. and Tarkowska, A. and Chessel, A. and Leo, S. and Antal, B. and Ferguson, R. and Sarkans, U. and Brazma, A. and Carazo Salas, R. and Swedlow, J.},
  title        = {Image Data Resource: a bioimage data integration and publication platform},
  journal      = {Nature Methods},
  volume       = {14},
  pages        = {775--781},
  month        = {june},
  year         = {2017},
  publisher    = {Nature Publishing Group},
  keywords     = {data integration,protein databases,image data},
  doi          = {10.1038/nmeth.4326},
  url          = {http://publications.crs4.it/pubdocs/2017/WMLRTCLAFSBCS17},
}

Other publications in the database

» Josh Moore
» Aleksandra Tarkowska
» Simone Leo
» Jason R. Swedlow