Community standards for open cell migration data.

Yael Paran, Lennart Martens, Susanna-Assunta Sansone, Assaf Zaritsky, Marleen Van Troys, Merijn van Erp, Jason R Swedlow, Staffan Strömblad, Gwendolien Sergeant, Marc Schuster, Philippe Roudot, Philippe Rocca-Serra, Jaime Prilusky, Alejandra N Gonzalez-Beltran, Josh Moore, Simone Leo, Sylvia E Le Dévédec, Mark Kittisopikul, Matthias Gunzer, Peter Friedl, Robert H Eibl, Sébastien Besson, Gert-Jan Bakker, Christophe Ampe, Paola Masuzzo

Journal: GigaScience 2021;9(5):giaa041

PMID: 32396199

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Abstract

Cell migration research has become a high-content field. However, the quantitative information encapsulated in these complex and high-dimensional datasets is not fully exploited owing to the diversity of experimental protocols and non-standardized output formats. In addition, typically the datasets are not open for reuse. Making the data open and Findable, Accessible, Interoperable, and Reusable (FAIR) will enable meta-analysis, data integration, and data mining. Standardized data formats and controlled vocabularies are essential for building a suitable infrastructure for that purpose but are not available in the cell migration domain. We here present standardization efforts by the Cell Migration Standardisation Organisation (CMSO), an open community-driven organization to facilitate the development of standards for cell migration data. This work will foster the development of improved algorithms and tools and enable secondary analysis of public datasets, ultimately unlocking new knowledge of the complex biological process of cell migration.

Address: Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, Oxford OX1 3QG, Oxford, UK.; VIB-UGent Center for Medical Biotechnology, VIB, A. Baertsoenkaai 3, B-9000, Ghent, Belgium.; Department of Biomolecular Medicine, Ghent University, A. Baertsoenkaai 3, B-9000, Ghent, Belgium.; Institute for Globally Distributed Open Research and Education (IGDORE), Kabupaten Gianyar, Bali 80571, Indonesia.; Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Geert Grooteplein 28 6525 GA Nijmegen, The Netherlands.; Centre for Gene Regulation & Expression & Division of Computational Biology, University of Dundee, School of Life Sciences, Dow St Dundee DD1 5EH, Scotland, UK.; German Cancer Research Center, DKFZ Alumni Association, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.; David H. Koch Center for Applied Genitourinary Medicine, UT MD Anderson Cancer Center, 6767 Bertner Ave, Mitchell Basic Science Research Building, 77030 Houston, TX, USA.; Cancer Genomics Center, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands.; Institute for Experimental Immunology and Imaging, University Hospital, University Duisburg-Essen, Universitätsstr. 2, 45141 Essen, Germany.; Leibniz Institute for Analytical Sciences, ISAS, Bunsen-Kirchhoff-Straße 11, 44139 Dortmund, Germany.; Department of Biophysics, UT Southwestern Medical Center, 5323 Harry Hines Blvd. Dallas, TX 75390, USA.; Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, 303 E. Chicago Ave, Chicago, IL 60611, USA.; Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, PO box 9502 2300 RA Leiden, The Netherlands.; Center for Advanced Studies, Research, and Development in Sardinia (CRS4), Loc. Piscina Manna, Edificio 1, 09050 Pula (CA) , Italy.; IDEA Bio-Medical Ltd, 2 Prof. Bergman St., Rehovot 76705, Israel.; Life Science Core Facilities, Weizmann Institute of Science, P.O. Box 26 Rehovot 76100, Israel.; Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, 5323 Harry Hines Blvd. Dallas, TX 75390, USA.; Department of Biosciences and Nutrition, Karolinska Institutet, Neo, SE-141 83 Huddinge, Sweden.; Department of Software and Information Systems Engineering, Ben-Gurion University of the Negev, P.O.B. 653, 8410501 Beer-Sheva, Israel.

DOI: 10.1093/gigascience/giaa041

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MeSH Terms: Biomarkers, Cell Movement, Computational Biology, Data Analysis, Databases, Factual, Metadata, Research