Best practice data life cycle approaches for the life sciences
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Ute Roessner | Maria Victoria Schneider | Suzanna E Lewis | Sandra Orchard | Saravanan Dayalan | Torsten Seemann | Jyoti Khadake | Simon Gladman | Andrew Treloar | Pasi K Korhonen | Neil D Young | Sonika Tyagi | Peter Neish | Gabriel Keeble-Gagnère | Mark F Richardson | Andrew Pask | Kelly L Wyres | Bernard Pope | Pasi K. Korhonen | S. Lewis | U. Roessner | S. Orchard | J. Khadake | M. Richardson | M. Schneider | A. Treloar | N. Young | A. Pask | G. Keeble-Gagnère | P. Korhonen | S. Hangartner | N. Watson-Haigh | H. Hayden | S. Dayalan | S. Tyagi | T. Seemann | Philippa C Griffin | Kate S LeMay | Keith Russell | Jeffrey H Christiansen | Sandra B Hangartner | Helen L Hayden | William W H Ho | Priscilla R Prestes | Nathan S Watson-Haigh | K. Wyres | Pip Griffin | Bernard J. Pope | Keith Russell | Jeffrey H. Christiansen | Peter Neish | P. Prestes | W. W. H. Ho | Simon L. Gladman | Kate S. LeMay | S. Lewis
[1] Lex Nederbragt,et al. Good enough practices in scientific computing , 2016, PLoS Comput. Biol..
[2] Amir Feizi,et al. Strategies to improve usability and preserve accuracy in biological sequence databases , 2016, Proteomics.
[3] Carole A. Goble,et al. State of the nation in data integration for bioinformatics , 2008, J. Biomed. Informatics.
[4] Daniel S. Katz,et al. Four simple recommendations to encourage best practices in research software , 2017, F1000Research.
[5] Menno Schilthuizen,et al. Specimens as primary data: museums and 'open science'. , 2015, Trends in ecology & evolution.
[6] Richard Gibson,et al. Value, but high costs in post-deposition data curation , 2016, Database J. Biol. Databases Curation.
[7] Amanda L. Whitmire,et al. Water, Water, Everywhere: Defining and Assessing Data Sharing in Academia , 2016, PloS one.
[8] Bradley Voytek,et al. The Virtuous Cycle of a Data Ecosystem , 2016, PLoS Comput. Biol..
[10] Ian M. Fingerman,et al. Database resources of the National Center for Biotechnology Information , 2010, Nucleic Acids Res..
[11] Allyson L. Lister,et al. BioSharing: curated and crowd-sourced metadata standards, databases and data policies in the life sciences , 2016, Database J. Biol. Databases Curation.
[12] Richard J. Edwards,et al. Establishing a distributed national research infrastructure providing bioinformatics support to life science researchers in Australia , 2017, Briefings Bioinform..
[13] Linda Naughton,et al. Making sense of journal research data policies , 2016 .
[14] John P. A. Ioannidis,et al. Reproducible Research Practices and Transparency across the Biomedical Literature , 2016, PLoS biology.
[15] James Taylor,et al. Next-generation sequencing data interpretation: enhancing reproducibility and accessibility , 2012, Nature Reviews Genetics.
[16] B. Björk,et al. The Development of Open Access Journal Publishing from 1993 to 2009 , 2011, PloS one.
[17] Nigel W. Hardy,et al. Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project , 2008, Nature Biotechnology.
[18] T. Magnuson,et al. Reproducibility: Use mouse biobanks or lose them , 2015, Nature.
[19] Chris Morris,et al. Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data , 2017, bioRxiv.
[20] Chris Morris,et al. Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data , 2017, bioRxiv.
[21] Jason Williams,et al. Unmet needs for analyzing biological big data: A survey of 704 NSF principal investigators , 2017, bioRxiv.
[22] Daniel S. Caetano,et al. Forgotten treasures: the fate of data in animal behaviour studies , 2014, Animal Behaviour.
[23] Walter G. Berendsohn,et al. Strategies for the sustainability of online open-access biodiversity databases , 2014 .
[24] Brian A. Nosek,et al. How open science helps researchers succeed , 2016, eLife.
[25] Peter N. Robinson,et al. Human genotype–phenotype databases: aims, challenges and opportunities , 2015, Nature Reviews Genetics.
[26] Wendy W. Chapman,et al. A review of journal policies for sharing research data , 2008, ELPUB.
[27] John P A Ioannidis,et al. Improving Validation Practices in “Omics” Research , 2011, Science.
[28] Carly Strasser,et al. The fractured lab notebook: undergraduates and ecological data management training in the United States , 2012 .
[29] D E Koshland,et al. The price of progress. , 1988, Science.
[30] Division on Earth. Sharing Publication-Related Data and Materials:: Responsibilities of Authorship in the Life Sciences , 2003 .
[31] David Gomez-Cabrero,et al. Data integration in the era of omics: current and future challenges , 2014, BMC Systems Biology.
[32] C. Richards,et al. Genebanks in the post-genomic age: Emerging roles and anticipated uses , 2008 .
[33] F. Arnaud,et al. From core referencing to data re-use: two French national initiatives to reinforce paleodata stewardship (National Cyber Core Repository and LTER France Retro-Observatory) , 2017 .
[34] I. Cuthill,et al. Reporting : The ARRIVE Guidelines for Reporting Animal Research , 2010 .
[35] D. Lipman,et al. Improved tools for biological sequence comparison. , 1988, Proceedings of the National Academy of Sciences of the United States of America.
[36] A. Ehrenhalt,et al. The price of progress , 2012, Nature.
[37] Toshihisa Takagi,et al. DNA Data Bank of Japan , 2016, Nucleic Acids Res..
[38] Oliver Horlacher,et al. The SIB Swiss Institute of Bioinformatics’ resources: focus on curated databases , 2015, Nucleic Acids Res..
[39] Brian A. Nosek,et al. An open investigation of the reproducibility of cancer biology research , 2014, eLife.
[40] Tudor Groza,et al. The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species , 2016, bioRxiv.
[41] Haruki Nakamura,et al. Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive. , 2017, Methods in molecular biology.
[42] Midori A. Harris,et al. Model organism databases: essential resources that need the support of both funders and users , 2016, BMC Biology.
[43] Evan Bolton,et al. Database resources of the National Center for Biotechnology Information , 2017, Nucleic Acids Res..
[44] Kristin Vanderbilt,et al. Completing the data life cycle: using information management in macrosystems ecology research , 2014 .
[45] Rachel G Liao,et al. A federated ecosystem for sharing genomic, clinical data , 2016, Science.
[46] Rachel G Liao,et al. Facilitating a culture of responsible and effective sharing of cancer genome data , 2016, Nature Medicine.
[47] Daniel L. Moody,et al. Measuring the Value Of Information - An Asset Valuation Approach , 1999, ECIS.
[48] Ute Roessner,et al. Best practice data life cycle approaches for the life , 2019 .
[49] Robert Stevens,et al. Ten Simple Rules for Selecting a Bio-ontology , 2016, PLoS Comput. Biol..
[50] P. Watson. Biospecimen Complexity—the Next Challenge for Cancer Research Biobanks? , 2016, Clinical Cancer Research.
[51] Santiago Schnell,et al. Ten Simple Rules for a Computational Biologist’s Laboratory Notebook , 2015, PLoS Comput. Biol..
[52] Jocelyn Kaiser,et al. BIOMEDICAL RESOURCES. Funding for key data resources in jeopardy. , 2016, Science.
[53] Matthew B Jones,et al. Ecoinformatics: supporting ecology as a data-intensive science. , 2012, Trends in ecology & evolution.
[54] Edward Baker,et al. Scratchpads 2.0: a Virtual Research Environment supporting scholarly collaboration, communication and data publication in biodiversity science , 2011, ZooKeys.
[55] Florence Debarre,et al. The Availability of Research Data Declines Rapidly with Article Age , 2013, Current Biology.
[56] Patricia C. Babbitt,et al. Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies , 2009, PLoS Comput. Biol..
[57] Rafael C. Jimenez,et al. Top 10 metrics for life science software good practices , 2016, F1000Research.
[58] Matej Oresic,et al. Data standards can boost metabolomics research, and if there is a will, there is a way , 2015, Metabolomics.
[59] Ryan P. Womack,et al. Research Data in Core Journals in Biology, Chemistry, Mathematics, and Physics , 2015, PloS one.
[60] Yann Joly,et al. Data Sharing in the Post-Genomic World: The Experience of the International Cancer Genome Consortium (ICGC) Data Access Compliance Office (DACO) , 2012, PLoS Comput. Biol..
[61] Ann J Wolpert,et al. For the sake of inquiry and knowledge--the inevitability of open access. , 2013, The New England journal of medicine.
[62] Stephen R. Piccolo,et al. Tools and techniques for computational reproducibility , 2016, GigaScience.
[63] Laura Christopherson,et al. Data Management Lifecycle and Software Lifecycle Management in the Context of Conducting Science , 2014 .
[64] W. Christopher Lenhardt,et al. The Tao of open science for ecology , 2015 .
[65] Anne E. Trefethen,et al. Toward interoperable bioscience data , 2012, Nature Genetics.
[66] Jonathan Cooper,et al. Where next for the reproducibility agenda in computational biology? , 2016, BMC Systems Biology.
[67] Heather A. Piwowar,et al. Data reuse and the open data citation advantage , 2013, PeerJ.
[68] Elizabeth D. Dalton,et al. Data management education from the perspective of science educators , 2016 .
[69] Oliver Butters,et al. DataSHIELD - New Directions and Dimensions , 2017, Data Sci. J..
[70] Anne E. Thessen,et al. Data issues in the life sciences , 2011, ZooKeys.
[71] Toni Kazic,et al. Ten Simple Rules for Experiments’ Provenance , 2015, PLoS Comput. Biol..
[72] Neil Beagrie,et al. The Value and Impact of the European Bioinformatics Institute , 2016 .
[73] Peter M. Rice,et al. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants , 2009, Nucleic acids research.
[74] Emily Walsh,et al. Using Evernote as an Electronic Lab Notebook in a Translational Science Laboratory , 2013, Journal of laboratory automation.
[75] M. Whitlock. Data archiving in ecology and evolution: best practices. , 2011, Trends in ecology & evolution.
[76] Scott D. Kahn. On the Future of Genomic Data , 2011, Science.
[77] Melissa Haendel,et al. A sea of standards for omics data: sink or swim? , 2013, J. Am. Medical Informatics Assoc..
[78] Christopher M. Buddle,et al. Distributed under Creative Commons Cc-by 4.0 Non-repeatable Science: Assessing the Frequency of Voucher Specimen Deposition Reveals That Most Arthropod Research Cannot Be Verified , 2022 .
[79] Carl Boettiger. Case Study 3: A Reproducible R Notebook Using Docker , 2019 .
[80] Luiz Olavo Bonino da Silva Santos,et al. Cloudy, increasingly FAIR; revisiting the FAIR Data guiding principles for the European Open Science Cloud , 2017, Inf. Serv. Use.
[81] François Michonneau,et al. Ten Simple Rules for Digital Data Storage , 2016, PeerJ Prepr..
[82] Marco Brandizi,et al. Updates to BioSamples database at European Bioinformatics Institute , 2014, Nucleic Acids Res..
[83] M. Placet,et al. Strategies for Sustainability , 2005 .
[84] Alban Gaignard,et al. Scientific workflows for computational reproducibility in the life sciences: Status, challenges and opportunities , 2017, Future Gener. Comput. Syst..
[85] Robert D. Finn,et al. The European Bioinformatics Institute in 2016: Data growth and integration , 2015, Nucleic Acids Res..
[86] K. Hinsen. ActivePapers: a platform for publishing and archiving computer-aided research , 2015, F1000Research.
[87] Laura Lyman Rodriguez,et al. The dbGaP data browser: a new tool for browsing dbGaP controlled-access genomic data , 2016, Nucleic Acids Res..
[88] Data's shameful neglect. , 2009, Nature.
[89] Kimberly Keeton,et al. Why traditional storage systems don't help us save stuff forever , 2005 .
[90] Barbara R. Jasny. Realities of data sharing using the genome wars as case study - an historical perspective and commentary , 2012, EPJ Data Science.