Sample Dryad Content

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This page lists examples of Dryad content with specific properties. These items are often needed to test new functionality, and are useful as models for depositors. Recommendations for authors on what to deposit and general suggestions on data management can be found on the Dryad site here.

A large data file: Brian Sidlauskas's fish jaw image, Laurie Stevenson's sequence alignments, Cossio (2010) PLOS Computational Biology, Geraldes (2011) Molecular Ecology Resources

Package containing many data files: Mike Taylor's paleo package, Janies (2011) Systematic Biology, Gardner (2011) Molecular Ecology Resources with 51 separate fasta formatted files, data package with many files for different species

A data paper for content in Dryad, this one from the Hindawi journal 'Dataset Papers in Ecology': Roopnarine PD, Hertog R (2013) Data from: Detailed food web networks of three Greater Antillean coral reef systems: the Cayman Islands, Cuba, and Jamaica. Dryad Digital Repository. doi:10.5061/dryad.c213

Package containing ZIP files with many aggregated files: Chris Zmasek's apoptosis package, Cossio (2010) PLOS Computational Biology, Geraldes (2011) Molecular Ecology Resources, Acavedo et al. sound files

Package with related content in TreeBASE: Sam Price's hunting package, Melo (2011) Molecular Ecology (TB link in article Data Accessibility section)

Package with links to content in GenBank: Rocha-Olivares (2011) JHered

Package in which article lists GenBank records in Data Accessibility section: Melo (2011) Molecular Ecology (no direct link from Dryad to GenBank)

GenBank record with LinkOut to Dryad: http://www.ncbi.nlm.nih.gov/nuccore/316925971

PubMed record with LinkOut to Dryad package.

Data packages with a ReadMe file: [1], [2], [3], [4], [5] and with a ReadMe for each data file, [6], [7], [8].

Most popular data packages:

  • Most highly viewed data package: Eisen paper Wu D, Wu M, Halpern A, Rusch DB, Yooseph S, Frazier M, Venter JC, Eisen JA (2011) Data from: Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in phylogenetic trees of phylogenetic marker genes. PLOS ONE 6(3): e18011.
  • Most frequently downloaded data file: Global Wood Density Database from Chave J, Coomes D, Jansen S, Lewis SL, Swenson NG, Zanne AE (2009) Towards a worldwide wood economics spectrum. Ecology Letters 12: 351-366.

Data packages with different authors from their corresponding articles:

  • Global Wood Density Database from Chave J, Coomes D, Jansen S, Lewis SL, Swenson NG, Zanne AE (2009) Towards a worldwide wood economics spectrum. Ecology Letters 12: 351-366.
  • Massive phytoplankton blooms under Arctic sea ice from Arrigo KR, Perovich DK, Pickart RS, Brown ZW, van Dijken GL, Lowry KE, Mills MM, Palmer MA, Balch WM, Bahr F, Bates NR, Benitez-Nelson C, Bowler B, Brownlee E, Ehn JK, Frey KE, Garley R, Laney SR, Lubelczyk L, Mathis J, Matsuoka A, Mitchell BG, Moore GWK, Ortega-Retuerta E, Pal S, Polashenski CM, Reynolds RA, Schieber B, Sosik HM, Stephens M, Swift JH (2012) Massive phytoplankton blooms under Arctic sea ice. Science, online in advance of print. doi:10.1126/science.1215065 - over 30 authors on the article, one on the data.
  • Data from: Development of an ultra-dense genetic map of the sunflower genome - seven authors on the article, one on the data.

Data package that is a portion of a larger dataset: Payne

Data packages under embargo: [9], [10]

Data packages with extended embargoes: Meirmans (2011) Molecular Ecology (three years by request of journal editors), Mueller (2011) Evolution (three years by request of journal editors), Mueller (2011) Molecular Ecology (three years by request of journal editors), Dewar (2011) Molecular Ecology (two years by request of journal editors), Rode (2011) Evolution (three years by request of journal editors), Morrissey (2012) Evolution (ten years by request of journal editors

Data packages with non-CC0 licensing: Swenson (2011) Systematic Biology (file consists of code with GNU GPL 3.0 license), Sally Otto's package under Dryad's original license [11], items in the BIRDD collection under Dryad's original license (at least some of these can probably be moved to CC0)

Harvested item in Japanese: [12]

Data from non-article publications:

  • thesis: [13]
  • book: (pending publication)

Data of specific file types; non-proprietary file formats are preferable:

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