Erratum to: Image Data Resource: a bioimage data integration and publication platform (Nature Methods, (2017), 14, 8, (775-781), 10.1038/nmeth.4326);Image Data Resource: A bioimage data integration and publication platform

Nature Methods

Volumn 14, Issue 8, 2017, Pages 775-781

  Williams, Eleanor ^a   Moore, Josh ^a   Li, Simon W ^b   Rustici, Gabriella ^c   Tarkowska, Aleksandra ^c   Chessel, Anatole ^d   Leo, Simone ^e   Antal, Bálint ^f   Ferguson, Richard K ^g   Sarkans, Ugis ^a   Brazma, Alvis ^c   Carazo Salas, Rafael E ^d   Swedlow, Jason R ^a  

^a UNIVERSITY OF DUNDEE   (United Kingdom)

^b EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

^c UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^d UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^e UNIVERSITÉ PARIS SACLAY   (France)

^f CENTER FOR ADVANCED STUDIES   (Italy)

^g UNIVERSITY OF BRISTOL   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHEMICAL DATABASE; GENE; GENETICS; IMAGING; METADATA; MICROSCOPY; MULTIDIMENSIONAL MICROSCOPY; ONTOLOGY; PHENOTYPE; PRIORITY JOURNAL; PUBLICATION; PUBLISHING; SCREENING; SOFTWARE; ALGORITHM; COMPUTER ASSISTED DIAGNOSIS; COMPUTER INTERFACE; DATABASE MANAGEMENT SYSTEM; FACTUAL DATABASE; INFORMATION DISSEMINATION; PROCEDURES; SYSTEM ANALYSIS;

ALGORITHMS; DATABASE MANAGEMENT SYSTEMS; DATABASES, FACTUAL; IMAGE INTERPRETATION, COMPUTER-ASSISTED; INFORMATION DISSEMINATION; PUBLISHING; SOFTWARE; SYSTEMS INTEGRATION; USER-COMPUTER INTERFACE;

EID: 85026475117     PISSN: 15487091     EISSN: 15487105     Source Type: Journal    
DOI: 10.1038/s41592-018-0169-x     Document Type: Erratum

References (56)

1. Uhl?n, M. et al. Proteomics. Tissue-based map of the human proteome. Science 347, 1260419 (2015).
2. Hawrylycz, M.J. et al. An anatomically comprehensive atlas of the adult human brain transcriptome. Nature 489, 391-399 (2012).
3. Armit, C. et al. eMouseAtlas, EMAGE, and the spatial dimension of the transcriptome. Mamm. Genome 23, 514-524 (2012).
4. Neumann, B. et al. Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes. Nature 464, 721-727 (2010).
5. Graml, V. et al. A genomic Multiprocess survey of machineries that control and link cell shape, microtubule organization, and cell-cycle progression. Dev. Cell 31, 227-239 (2014).
6. Koh, J.L. et al. CYCLoPs: a comprehensive database constructed from automated analysis of protein abundance and subcellular localization patterns in Saccharomyces cerevisiae. G3 (Bethesda) 5, 1223-1232 (2015).
7. G?nczy, P. et al. Functional genomic analysis of cell division in C. elegans using RNAi of genes on chromosome III. Nature 408, 331-336 (2000).
8. Fowlkes, C.C. et al. A quantitative spatiotemporal atlas of gene expression in the Drosophila blastoderm. Cell 133, 364-374 (2008).
9. Lawson, C.L. et al. EMDataBank.org: unified data resource for CryoEM. Nucleic Acids Res. 39, D456-D464 (2011).
10. Orloff, D.N., Iwasa, J.H., Martone, M.E., Ellisman, M.H. & Kane, C.M. The cell: an image library-CCDB: a curated repository of microscopy data. Nucleic Acids Res. 41, D1241-D1250 (2013).
11. Iudin, A., Korir, P.K., Salavert-Torres, J., Kleywegt, G.J. & Patwardhan, A. EMPIAR: a public archive for raw electron microscopy image data. Nat. Methods 13, 387-388 (2016).
12. McEntyre, J., Sarkans, U. & Brazma, A. The BioStudies database. Mol. Syst. Biol. 11, 847 (2015).
13. Petryszak, R. et al. Expression Atlas update-An integrated database of gene and protein expression in humans, animals and plants. Nucleic Acids Res. 44, D746-D752 (2016).
14. UniProt Consortium. UniProt: a hub for protein information. Nucleic Acids Res. 43, D204-D212 (2015).
15. Yates, A. et al. Ensembl 2016. Nucleic Acids Res. 44, D710-D716 (2016).
16. Jupp, S. et al. The cellular microscopy phenotype ontology. J. Biomed. Semantics 7, 28 (2016).
17. Allan, C. et al. OMERO: flexible, model-driven data management for experimental biology. Nat. Methods 9, 245-253 (2012).
18. Gorgolewski, K.J. et al. NeuroVault.org: a web-based repository for collecting and sharing unthresholded statistical maps of the human brain. Front. Neuroinform. 9, 8 (2015).
19. Masuzzo, P. et al. An open data ecosystem for cell migration research. Trends Cell Biol. 25, 55-58 (2015).
20. Brazma, A., Krestyaninova, M. & Sarkans, U. Standards for systems biology. Nat. Rev. Genet. 7, 593-605 (2006).
21. Sansone, S.A. et al. Toward interoperable bioscience data. Nat. Genet. 44, 121-126 (2012).
22. Rayner, T.F. et al. A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. BMC Bioinformatics 7, 489 (2006).
23. Li, S. et al. Metadata management for high content screening in OMERO. Methods 96, 27-32 (2016).
24. Linkert, M. et al. Metadata matters: access to image data in the real world. J. Cell Biol. 189, 777-782 (2010).
25. Goldberg, I.G. et al. The Open Microscopy Environment (OME) Data Model and XML file: open tools for informatics and quantitative analysis in biological imaging. Genome Biol. 6, R47 (2005).
26. H?rich?, J.K. et al. Integration of biological data by kernels on graph nodes allows prediction of new genes involved in mitotic chromosome condensation. Mol. Biol. Cell 25, 2522-2536 (2014).
27. Simpson, J.C. et al. Genome-wide RNAi screening identifies human proteins with a regulatory function in the early secretory pathway. Nat. Cell Biol. 14, 764-774 (2012).
28. Shah, G.N. et al. Carbonic anhydrase IV and XIV knockout mice: roles of the respective carbonic anhydrases in buffering the extracellular space in brain. Proc. Natl. Acad. Sci. USA 102, 16771-16776 (2005).
29. Scheibe, R.J. et al. Carbonic anhydrases IV and IX: subcellular localization and functional role in mouse skeletal muscle. Am. J. Physiol. Cell Physiol. 294, C402-C412 (2008).
30. Wandernoth, P.M. et al. Role of carbonic anhydrase IV in the bicarbonate-mediated activation of murine and human sperm. PLoS One 5, e15061 (2010).
31. Rebello, G. et al. Apoptosis-inducing signal sequence mutation in carbonic anhydrase IV identified in patients with the RP17 form of retinitis pigmentosa. Proc. Natl. Acad. Sci. USA 101, 6617-6622 (2004).
32. Yang, Z. et al. Mutant carbonic anhydrase 4 impairs pH regulation and causes retinal photoreceptor degeneration. Hum. Mol. Genet. 14, 255-265 (2005).
33. Szklarczyk, D. et al. STRING v10: protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res. 43, D447-D452 (2015).
34. Cline, M.S. et al. Integration of biological networks and gene expression data using Cytoscape. Nat. Protoc. 2, 2366-2382 (2007).
35. Antal, B., Chessel, A. & Carazo Salas, R.E. Mineotaur: a tool for high-content microscopy screen sharing and visual analytics. Genome Biol. 16, 283 (2015).
36. Adebayo, S. et al. PhenoImageShare: an image annotation and query infrastructure. J. Biomed. Semantics 7, 35 (2016).
37. Orlov, N. et al. WND-CHARM: Multi-purpose image classification using compound image transforms. Pattern Recognit. Lett. 29, 1684-1693 (2008).
38. Boulton, G., Rawlins, M., Vallance, P. & Walport, M. Science as a public enterprise: the case for open data. Lancet 377, 1633-1635 (2011).
39. Fuchs, F. et al. Clustering phenotype populations by genome-wide RNAi and multiparametric imaging. Mol. Syst. Biol. 6, 370 (2010).
40. Rohn, J.L. et al. Comparative RNAi screening identifies a conserved core metazoan actinome by phenotype. J. Cell Biol. 194, 789-805 (2011).
41. Breker, M., Gymrek, M. & Schuldiner, M. A novel single-cell screening platform reveals proteome plasticity during yeast stress responses. J. Cell Biol. 200, 839-850 (2013).
42. Thorpe, P.H., Alvaro, D., Lisby, M. & Rothstein, R. Bringing Rad52 foci into focus. J. Cell Biol. 194, 665-667 (2011).
43. Toret, C.P., D?Ambrosio, M.V., Vale, R.D., Simon, M.A. & Nelson, W.J. A genome-wide screen identifies conserved protein hubs required for cadherin-mediated cell-cell adhesion. J. Cell Biol. 204, 265-279 (2014).
44. Fong, K.W. et al. Whole-genome screening identifies proteins localized to distinct nuclear bodies. J. Cell Biol. 203, 149-164 (2013).
45. Srikumar, T. et al. Global analysis of SUMO chain function reveals multiple roles in chromatin regulation. J. Cell Biol. 201, 145-163 (2013).
46. Doil, C. et al. RNF168 binds and amplifies ubiquitin conjugates on damaged chromosomes to allow accumulation of repair proteins. Cell 136, 435-446 (2009).
47. Karsenti, E. et al. A holistic approach to marine eco-systems biology. PLoS Biol. 9, e1001177 (2011).
48. Wawer, M.J. et al. Toward performance-diverse small-molecule libraries for cell-based phenotypic screening using multiplexed high-dimensional profiling. Proc. Natl. Acad. Sci. USA 111, 10911-10916 (2014).
49. Breinig, M., Klein, F.A., Huber, W. & Boutros, M. A chemical-genetic interaction map of small molecules using high-throughput imaging in cancer cells. Mol. Syst. Biol. 11, 846 (2015).
50. Sero, J.E. et al. Cell shape and the microenvironment regulate nuclear translocation of NF-B in breast epithelial and tumor cells. Mol. Syst. Biol. 11, 790 (2015).
51. Barr, A.R. & Bakal, C. A sensitised RNAi screen reveals a ch-TOG genetic interaction network required for spindle assembly. Sci. Rep. 5, 10564 (2015).
52. Lawo, S., Hasegan, M., Gupta, G.D. & Pelletier, L. Subdiffraction imaging of centrosomes reveals higher-order organizational features of pericentriolar material. Nat. Cell Biol. 14, 1148-1158 (2012).
53. Szymborska, A. et al. Nuclear pore scaffold structure analyzed by super-resolution microscopy and particle averaging. Science 341, 655-658 (2013).
54. Dickerson, D. et al. High resolution imaging reveals heterogeneity in chromatin states between cells that is not inherited through cell division. BMC Cell Biol. 17, 33 (2016).
55. Pascual-Vargas, P. et al. RNAi screens for Rho GTPase regulators of cell shape and YAP/TAZ localisation in triple negative breast cancer. Sci. Data 4, 170018 (2017).
56. Yang, W. et al. Regulation of meristem morphogenesis by cell wall synthases in Arabidopsis. Curr. Biol. 26, 1404-1415 (2016).