Community standards for open cell migration data

  1. Alejandra N Gonzalez-Beltran
  2. Paola Masuzzo
  3. Christophe Ampe
  4. Gert-Jan Bakker
  5. Sébastien Besson
  6. Robert H Eibl
  7. Peter Friedl
  8. Matthias Gunzer
  9. Mark Kittisopikul
  10. Sylvia E Le Dévédec
  11. Simone Leo
  12. Josh Moore
  13. Yael Paran
  14. Jaime Prilusky
  15. Philippe Rocca-Serra
  16. Philippe Roudot
  17. Marc Schuster
  18. Gwendolien Sergeant
  19. Staffan Strömblad
  20. Jason R Swedlow
  21. Merijn van Erp
  22. Marleen Van Troys
  23. Assaf Zaritsky
  24. Susanna-Assunta Sansone
  25. Lennart Martens

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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.

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  1. GigaScience

    Now published in GigaScience doi: 10.1093/gigascience/giaa041

    Alejandra N. Gonzalez-Beltran 1Oxford e-Research Centre, Department of Engineering Science, University of Oxford, Oxford, UK2Scientific Computing Department, Rutherford Appleton Laboratory, Science and Technology Facilities Council, Didcot, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Alejandra N. Gonzalez-BeltranPaola Masuzzo 3VIB-UGent Center for Medical Biotechnology, Ghent, Belgium4Department of Biomolecular Medicine, Ghent University, Ghent, Belgium5Institute for Globally Distributed Open Research and Education (IGDORE), Ghent, BelgiumFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Paola MasuzzoChristophe Ampe 4Department of Biomolecular Medicine, Ghent University, Ghent, BelgiumFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Christophe AmpeGert-Jan Bakker 6Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Nijmegen, The NetherlandsFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Gert-Jan BakkerSébastien Besson 7Centre for Gene Regulation & Expression & Division of Computational Biology, University of Dundee, Dundee, Scotland, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Sébastien BessonRobert H. Eibl 8German Cancer Research Center, DKFZ Alumni Association, Heidelberg, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Robert H. EiblPeter Friedl 6Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands9David H. Koch Center for Applied Genitourinary Medicine, UT MD Anderson Cancer Center, Houston, TX, USA10Cancer Genomics Center, Utrecht, The NetherlandsFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Peter FriedlMatthias Gunzer 11Institute for Experimental Immunology and Imaging, University Hospital, University Duisburg-Essen, Essen, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Matthias GunzerMark Kittisopikul 12Department of Biophysics, UT Southwestern Medical Center, Dallas, TX, USA13Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Mark KittisopikulSylvia E. Le Dévédec 14Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, the NetherlandsFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Sylvia E. Le DévédecSimone Leo 7Centre for Gene Regulation & Expression & Division of Computational Biology, University of Dundee, Dundee, Scotland, UK15Center for Advanced Studies, Research, and Development in Sardinia (CRS4), Pula(CA), ItalyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Simone LeoJosh Moore 7Centre for Gene Regulation & Expression & Division of Computational Biology, University of Dundee, Dundee, Scotland, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Josh MooreYael Paran 16IDEA Bio-Medical Ltd, Rehovot, IsraelFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Yael ParanJaime Prilusky 17Life Science Core Facilities, Weizmann Institute of Science, Rehovot, IsraelFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Jaime PriluskyPhilippe Rocca-Serra 1Oxford e-Research Centre, Department of Engineering Science, University of Oxford, Oxford, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Philippe Rocca-SerraPhilippe Roudot 18Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Philippe RoudotMarc Schuster 11Institute for Experimental Immunology and Imaging, University Hospital, University Duisburg-Essen, Essen, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Marc SchusterGwendolien Sergeant 4Department of Biomolecular Medicine, Ghent University, Ghent, BelgiumFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Gwendolien SergeantStaffan Strömblad 19Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, SwedenFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Staffan StrömbladJason R. Swedlow 7Centre for Gene Regulation & Expression & Division of Computational Biology, University of Dundee, Dundee, Scotland, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Jason R. SwedlowMerijn van Erp 6Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Nijmegen, The NetherlandsFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Merijn van ErpMarleen Van Troys 4Department of Biomolecular Medicine, Ghent University, Ghent, BelgiumFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Marleen Van TroysAssaf Zaritsky 20Department of Software and Information Systems Engineering, Ben-Gurion University of the Negev, Beer-Sheva, IsraelFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Assaf ZaritskySusanna-Assunta Sansone 1Oxford e-Research Centre, Department of Engineering Science, University of Oxford, Oxford, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Susanna-Assunta SansoneFor correspondence: susanna-assunta.sansone@oerc.ox.ac.uk lennart.martens@vib-ugent.beLennart Martens 3VIB-UGent Center for Medical Biotechnology, Ghent, Belgium4Department of Biomolecular Medicine, Ghent University, Ghent, BelgiumFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Lennart MartensFor correspondence: susanna-assunta.sansone@oerc.ox.ac.uk lennart.martens@vib-ugent.be

    A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa041 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.

    These peer reviews were as follows:

    Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102224 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102225

  2. GigaScience

    Now published in GigaScience doi: 10.1093/gigascience/giaa041

    Alejandra N. Gonzalez-Beltran 1Oxford e-Research Centre, Department of Engineering Science, University of Oxford, Oxford, UK2Scientific Computing Department, Rutherford Appleton Laboratory, Science and Technology Facilities Council, Didcot, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Alejandra N. Gonzalez-BeltranPaola Masuzzo 3VIB-UGent Center for Medical Biotechnology, Ghent, Belgium4Department of Biomolecular Medicine, Ghent University, Ghent, Belgium5Institute for Globally Distributed Open Research and Education (IGDORE), Ghent, BelgiumFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Paola MasuzzoChristophe Ampe 4Department of Biomolecular Medicine, Ghent University, Ghent, BelgiumFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Christophe AmpeGert-Jan Bakker 6Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Nijmegen, The NetherlandsFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Gert-Jan BakkerSébastien Besson 7Centre for Gene Regulation & Expression & Division of Computational Biology, University of Dundee, Dundee, Scotland, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Sébastien BessonRobert H. Eibl 8German Cancer Research Center, DKFZ Alumni Association, Heidelberg, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Robert H. EiblPeter Friedl 6Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands9David H. Koch Center for Applied Genitourinary Medicine, UT MD Anderson Cancer Center, Houston, TX, USA10Cancer Genomics Center, Utrecht, The NetherlandsFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Peter FriedlMatthias Gunzer 11Institute for Experimental Immunology and Imaging, University Hospital, University Duisburg-Essen, Essen, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Matthias GunzerMark Kittisopikul 12Department of Biophysics, UT Southwestern Medical Center, Dallas, TX, USA13Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Mark KittisopikulSylvia E. Le Dévédec 14Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, the NetherlandsFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Sylvia E. Le DévédecJosh Moore 7Centre for Gene Regulation & Expression & Division of Computational Biology, University of Dundee, Dundee, Scotland, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Josh MooreYael Paran 16IDEA Bio-Medical Ltd, Rehovot, IsraelFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Yael ParanJaime Prilusky 17Life Science Core Facilities, Weizmann Institute of Science, Rehovot, IsraelFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Jaime PriluskyPhilippe Rocca-Serra 1Oxford e-Research Centre, Department of Engineering Science, University of Oxford, Oxford, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Philippe Rocca-SerraPhilippe Roudot 18Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Philippe RoudotMarc Schuster 11Institute for Experimental Immunology and Imaging, University Hospital, University Duisburg-Essen, Essen, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Marc SchusterGwendolien Sergeant 4Department of Biomolecular Medicine, Ghent University, Ghent, BelgiumFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Gwendolien SergeantStaffan Strömblad 19Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, SwedenFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Staffan StrömbladJason R. Swedlow 7Centre for Gene Regulation & Expression & Division of Computational Biology, University of Dundee, Dundee, Scotland, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Jason R. SwedlowMerijn van Erp 6Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Nijmegen, The NetherlandsFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Merijn van ErpMarleen Van Troys 4Department of Biomolecular Medicine, Ghent University, Ghent, BelgiumFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Marleen Van TroysAssaf Zaritsky 20Department of Software and Information Systems Engineering, Ben-Gurion University of the Negev, Beer-Sheva, IsraelFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Assaf ZaritskySusanna-Assunta Sansone 1Oxford e-Research Centre, Department of Engineering Science, University of Oxford, Oxford, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Susanna-Assunta SansoneFor correspondence: susanna-assunta.sansone@oerc.ox.ac.uk lennart.martens@vib-ugent.beLennart Martens 3VIB-UGent Center for Medical Biotechnology, Ghent, Belgium4Department of Biomolecular Medicine, Ghent University, Ghent, BelgiumFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Lennart MartensFor correspondence: susanna-assunta.sansone@oerc.ox.ac.uk lennart.martens@vib-ugent.be

    A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa041 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.

    These peer reviews were as follows:

    Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102224 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102225

  3. Version published to 10.1093/gigascience/giaa041
  4. Version published to 10.1101/803064v1 on bioRxiv