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...
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| Veröffentlicht in: | Gigascience 2020-05, Vol.9 (5) |
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| creator | Gonzalez-Beltran, Alejandra N Masuzzo, Paola Ampe, Christophe Bakker, Gert-Jan Besson, Sébastien Eibl, Robert H Friedl, Peter Gunzer, Matthias Kittisopikul, Mark Dévédec, Sylvia E Le Leo, Simone Moore, Josh Paran, Yael Prilusky, Jaime Rocca-Serra, Philippe Roudot, Philippe Schuster, Marc Sergeant, Gwendolien Strömblad, Staffan Swedlow, Jason R van Erp, Merijn Van Troys, Marleen Zaritsky, Assaf Sansone, Susanna-Assunta Martens, Lennart |
| description | 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. |
| doi_str_mv | 10.1093/gigascience/giaa041 |
| format | Article |
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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.</description><identifier>ISSN: 2047-217X</identifier><identifier>EISSN: 2047-217X</identifier><identifier>DOI: 10.1093/gigascience/giaa041</identifier><identifier>PMID: 32396199</identifier><language>eng</language><publisher>United States: Oxford University Press</publisher><subject>Algorithms ; Biological activity ; Cell migration ; Data integration ; Data mining ; Datasets ; Review ; Standardization</subject><ispartof>Gigascience, 2020-05, Vol.9 (5)</ispartof><rights>The Author(s) 2020. Published by Oxford University Press. 2020</rights><rights>The Author(s) 2020. Published by Oxford University Press.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c510t-b70907e6e3077040a27b06a5c53a3cde3715575268d89d4121f3a520e8abd1943</citedby><cites>FETCH-LOGICAL-c510t-b70907e6e3077040a27b06a5c53a3cde3715575268d89d4121f3a520e8abd1943</cites><orcidid>0000-0003-3602-0014 ; 0000-0002-9642-9789 ; 0000-0002-1477-5478 ; 0000-0002-2198-1958 ; 0000-0003-3499-8262 ; 0000-0002-0615-9616 ; 0000-0003-4028-811X ; 0000-0001-9544-6213 ; 0000-0002-7019-0191 ; 0000-0001-8783-1429 ; 0000-0002-0119-4041 ; 0000-0002-9558-6248 ; 0000-0001-6632-8728 ; 0000-0001-9869-3826 ; 0000-0003-4277-658X ; 0000-0002-1236-6339 ; 0000-0002-6687-5286 ; 0000-0002-8554-3594 ; 0000-0003-4283-8103 ; 0000-0002-5534-6055 ; 0000-0001-8271-5429 ; 0000-0002-7751-7708 ; 0000-0003-3699-1195 ; 0000-0001-9853-5668 ; 0000-0001-5306-5690</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7317087/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7317087/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,550,723,776,780,881,1598,27901,27902,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/32396199$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttp://kipublications.ki.se/Default.aspx?queryparsed=id:143880863$$DView record from Swedish Publication Index$$Hfree_for_read</backlink></links><search><creatorcontrib>Gonzalez-Beltran, Alejandra N</creatorcontrib><creatorcontrib>Masuzzo, Paola</creatorcontrib><creatorcontrib>Ampe, Christophe</creatorcontrib><creatorcontrib>Bakker, Gert-Jan</creatorcontrib><creatorcontrib>Besson, Sébastien</creatorcontrib><creatorcontrib>Eibl, Robert H</creatorcontrib><creatorcontrib>Friedl, Peter</creatorcontrib><creatorcontrib>Gunzer, Matthias</creatorcontrib><creatorcontrib>Kittisopikul, Mark</creatorcontrib><creatorcontrib>Dévédec, Sylvia E Le</creatorcontrib><creatorcontrib>Leo, Simone</creatorcontrib><creatorcontrib>Moore, Josh</creatorcontrib><creatorcontrib>Paran, Yael</creatorcontrib><creatorcontrib>Prilusky, Jaime</creatorcontrib><creatorcontrib>Rocca-Serra, Philippe</creatorcontrib><creatorcontrib>Roudot, Philippe</creatorcontrib><creatorcontrib>Schuster, Marc</creatorcontrib><creatorcontrib>Sergeant, Gwendolien</creatorcontrib><creatorcontrib>Strömblad, Staffan</creatorcontrib><creatorcontrib>Swedlow, Jason R</creatorcontrib><creatorcontrib>van Erp, Merijn</creatorcontrib><creatorcontrib>Van Troys, Marleen</creatorcontrib><creatorcontrib>Zaritsky, Assaf</creatorcontrib><creatorcontrib>Sansone, Susanna-Assunta</creatorcontrib><creatorcontrib>Martens, Lennart</creatorcontrib><title>Community standards for open cell migration data</title><title>Gigascience</title><addtitle>Gigascience</addtitle><description>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.</description><subject>Algorithms</subject><subject>Biological activity</subject><subject>Cell migration</subject><subject>Data integration</subject><subject>Data mining</subject><subject>Datasets</subject><subject>Review</subject><subject>Standardization</subject><issn>2047-217X</issn><issn>2047-217X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><sourceid>TOX</sourceid><sourceid>D8T</sourceid><recordid>eNqNkU1LAzEQhoMoKrW_QJAFL15WZ5Ldze5FkOIXCF4UvIXpblpTu0lNdpX-e1NapXoylwyZZ97JzMvYMcI5QiUupmZKoTba1jrGRJDhDjvkkMmUo3zZ3YoP2DCEGcQjZVlKsc8OBBdVgVV1yGDk2ra3plsmoSPbkG9CMnE-cQttk1rP50lrpp4642zSUEdHbG9C86CHm3vAnm-un0Z36cPj7f3o6iGtc4QuHUuoQOpCi9gVMiAux1BQXueCRN1oITHPZc6LsimrJkOOE0E5B13SuMEqEwOWrnXDp170Y7XwpiW_VI6M2jy9xUirTKIoVvzlmo-ZVje1tp2n-a-y3xlrXtXUfSgpUEJcy4CdbQS8e-916FRrwmoBZLXrg-IZYIl5ASv09A86c723cR2Kx7lKLFBApMSaqr0LwevJz2cQ1MpEtWWi2pgYq0625_ip-bYsAudrwPWLfyl-AQfwq9Y</recordid><startdate>20200501</startdate><enddate>20200501</enddate><creator>Gonzalez-Beltran, Alejandra N</creator><creator>Masuzzo, Paola</creator><creator>Ampe, Christophe</creator><creator>Bakker, Gert-Jan</creator><creator>Besson, Sébastien</creator><creator>Eibl, Robert H</creator><creator>Friedl, Peter</creator><creator>Gunzer, Matthias</creator><creator>Kittisopikul, Mark</creator><creator>Dévédec, Sylvia E Le</creator><creator>Leo, Simone</creator><creator>Moore, Josh</creator><creator>Paran, Yael</creator><creator>Prilusky, Jaime</creator><creator>Rocca-Serra, Philippe</creator><creator>Roudot, Philippe</creator><creator>Schuster, Marc</creator><creator>Sergeant, Gwendolien</creator><creator>Strömblad, Staffan</creator><creator>Swedlow, Jason R</creator><creator>van Erp, Merijn</creator><creator>Van Troys, Marleen</creator><creator>Zaritsky, Assaf</creator><creator>Sansone, Susanna-Assunta</creator><creator>Martens, Lennart</creator><general>Oxford University Press</general><scope>TOX</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>JQ2</scope><scope>K9.</scope><scope>7X8</scope><scope>5PM</scope><scope>ADTPV</scope><scope>AOWAS</scope><scope>D8T</scope><scope>ZZAVC</scope><orcidid>https://orcid.org/0000-0003-3602-0014</orcidid><orcidid>https://orcid.org/0000-0002-9642-9789</orcidid><orcidid>https://orcid.org/0000-0002-1477-5478</orcidid><orcidid>https://orcid.org/0000-0002-2198-1958</orcidid><orcidid>https://orcid.org/0000-0003-3499-8262</orcidid><orcidid>https://orcid.org/0000-0002-0615-9616</orcidid><orcidid>https://orcid.org/0000-0003-4028-811X</orcidid><orcidid>https://orcid.org/0000-0001-9544-6213</orcidid><orcidid>https://orcid.org/0000-0002-7019-0191</orcidid><orcidid>https://orcid.org/0000-0001-8783-1429</orcidid><orcidid>https://orcid.org/0000-0002-0119-4041</orcidid><orcidid>https://orcid.org/0000-0002-9558-6248</orcidid><orcidid>https://orcid.org/0000-0001-6632-8728</orcidid><orcidid>https://orcid.org/0000-0001-9869-3826</orcidid><orcidid>https://orcid.org/0000-0003-4277-658X</orcidid><orcidid>https://orcid.org/0000-0002-1236-6339</orcidid><orcidid>https://orcid.org/0000-0002-6687-5286</orcidid><orcidid>https://orcid.org/0000-0002-8554-3594</orcidid><orcidid>https://orcid.org/0000-0003-4283-8103</orcidid><orcidid>https://orcid.org/0000-0002-5534-6055</orcidid><orcidid>https://orcid.org/0000-0001-8271-5429</orcidid><orcidid>https://orcid.org/0000-0002-7751-7708</orcidid><orcidid>https://orcid.org/0000-0003-3699-1195</orcidid><orcidid>https://orcid.org/0000-0001-9853-5668</orcidid><orcidid>https://orcid.org/0000-0001-5306-5690</orcidid></search><sort><creationdate>20200501</creationdate><title>Community standards for open cell migration data</title><author>Gonzalez-Beltran, Alejandra N ; 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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.</abstract><cop>United States</cop><pub>Oxford University Press</pub><pmid>32396199</pmid><doi>10.1093/gigascience/giaa041</doi><orcidid>https://orcid.org/0000-0003-3602-0014</orcidid><orcidid>https://orcid.org/0000-0002-9642-9789</orcidid><orcidid>https://orcid.org/0000-0002-1477-5478</orcidid><orcidid>https://orcid.org/0000-0002-2198-1958</orcidid><orcidid>https://orcid.org/0000-0003-3499-8262</orcidid><orcidid>https://orcid.org/0000-0002-0615-9616</orcidid><orcidid>https://orcid.org/0000-0003-4028-811X</orcidid><orcidid>https://orcid.org/0000-0001-9544-6213</orcidid><orcidid>https://orcid.org/0000-0002-7019-0191</orcidid><orcidid>https://orcid.org/0000-0001-8783-1429</orcidid><orcidid>https://orcid.org/0000-0002-0119-4041</orcidid><orcidid>https://orcid.org/0000-0002-9558-6248</orcidid><orcidid>https://orcid.org/0000-0001-6632-8728</orcidid><orcidid>https://orcid.org/0000-0001-9869-3826</orcidid><orcidid>https://orcid.org/0000-0003-4277-658X</orcidid><orcidid>https://orcid.org/0000-0002-1236-6339</orcidid><orcidid>https://orcid.org/0000-0002-6687-5286</orcidid><orcidid>https://orcid.org/0000-0002-8554-3594</orcidid><orcidid>https://orcid.org/0000-0003-4283-8103</orcidid><orcidid>https://orcid.org/0000-0002-5534-6055</orcidid><orcidid>https://orcid.org/0000-0001-8271-5429</orcidid><orcidid>https://orcid.org/0000-0002-7751-7708</orcidid><orcidid>https://orcid.org/0000-0003-3699-1195</orcidid><orcidid>https://orcid.org/0000-0001-9853-5668</orcidid><orcidid>https://orcid.org/0000-0001-5306-5690</orcidid><oa>free_for_read</oa></addata></record> |
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| source | Oxford Journals Open Access Collection; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central; SWEPUB Freely available online |
| subjects | Algorithms Biological activity Cell migration Data integration Data mining Datasets Review Standardization |
| title | Community standards for open cell migration data |
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