Community standards for open cell migration data

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

doi:10.1093/gigascience/giaa041

Community standards for open cell migration data

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

Department of Software and Information Systems Engineering

Research output: Contribution to journal › Review article › peer-review

14 Scopus citations

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.

Original language	English
Article number	giaa041
Journal	GigaScience
Volume	9
Issue number	5
DOIs	https://doi.org/10.1093/gigascience/giaa041
State	Published - 20 May 2020

Keywords

CMSO
FAIR data
MIACME
biotracks
cell migration
data standards
frictionless data package
metadata

ASJC Scopus subject areas

Health Informatics
Computer Science Applications

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10.1093/gigascience/giaa041

Cite this

Gonzalez-Beltran, A. N., Masuzzo, P., Ampe, C., Bakker, G. J., Besson, S., Eibl, R. H., Friedl, P., Gunzer, M., Kittisopikul, M., Dévédec, S. E. L., Leo, S., Moore, J., Paran, Y., Prilusky, J., Rocca-Serra, P., Roudot, P., Schuster, M., Sergeant, G., Strömblad, S., ... Martens, L. (2020). Community standards for open cell migration data. GigaScience, 9(5), Article giaa041. https://doi.org/10.1093/gigascience/giaa041

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title = "Community standards for open cell migration data",

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.",

keywords = "CMSO, FAIR data, MIACME, biotracks, cell migration, data standards, frictionless data package, metadata",

author = "Gonzalez-Beltran, {Alejandra N.} and Paola Masuzzo and Christophe Ampe and Bakker, {Gert Jan} and S{\'e}bastien Besson and Eibl, {Robert H.} and Peter Friedl and Matthias Gunzer and Mark Kittisopikul and D{\'e}v{\'e}dec, {Sylvia E.Le} and Simone Leo and Josh Moore and Yael Paran and Jaime Prilusky and Philippe Rocca-Serra and Philippe Roudot and Marc Schuster and Gwendolien Sergeant and Staffan Str{\"o}mblad and Swedlow, {Jason R.} and {Van Erp}, Merijn and {Van Troys}, Marleen and Assaf Zaritsky and Sansone, {Susanna Assunta} and Lennart Martens",

note = "Publisher Copyright: {\textcopyright} 2020 The Author(s) 2020. Published by Oxford University Press.",

year = "2020",

month = may,

day = "20",

doi = "10.1093/gigascience/giaa041",

language = "English",

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Gonzalez-Beltran, AN, Masuzzo, P, Ampe, C, Bakker, GJ, Besson, S, Eibl, RH, Friedl, P, Gunzer, M, Kittisopikul, M, Dévédec, SEL, Leo, S, Moore, J, Paran, Y, Prilusky, J, Rocca-Serra, P, Roudot, P, Schuster, M, Sergeant, G, Strömblad, S, Swedlow, JR, Van Erp, M, Van Troys, M, Zaritsky, A, Sansone, SA & Martens, L 2020, 'Community standards for open cell migration data', GigaScience, vol. 9, no. 5, giaa041. https://doi.org/10.1093/gigascience/giaa041

TY - JOUR

T1 - Community standards for open cell migration data

AU - Gonzalez-Beltran, Alejandra N.

AU - Masuzzo, Paola

AU - Ampe, Christophe

AU - Bakker, Gert Jan

AU - Besson, Sébastien

AU - Eibl, Robert H.

AU - Friedl, Peter

AU - Gunzer, Matthias

AU - Kittisopikul, Mark

AU - Dévédec, Sylvia E.Le

AU - Leo, Simone

AU - Moore, Josh

AU - Paran, Yael

AU - Prilusky, Jaime

AU - Rocca-Serra, Philippe

AU - Roudot, Philippe

AU - Schuster, Marc

AU - Sergeant, Gwendolien

AU - Strömblad, Staffan

AU - Swedlow, Jason R.

AU - Van Erp, Merijn

AU - Van Troys, Marleen

AU - Zaritsky, Assaf

AU - Sansone, Susanna Assunta

AU - Martens, Lennart

PY - 2020/5/20

Y1 - 2020/5/20

N2 - 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.

AB - 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.

KW - CMSO

KW - FAIR data

KW - MIACME

KW - biotracks

KW - cell migration

KW - data standards

KW - frictionless data package

KW - metadata

UR - http://www.scopus.com/inward/record.url?scp=85084584598&partnerID=8YFLogxK

U2 - 10.1093/gigascience/giaa041

DO - 10.1093/gigascience/giaa041

M3 - Review article

C2 - 32396199

AN - SCOPUS:85084584598

SN - 2047-217X

VL - 9

JO - GigaScience

JF - GigaScience

IS - 5

M1 - giaa041

ER -

Community standards for open cell migration data

Abstract

Keywords

ASJC Scopus subject areas

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