Difference between revisions of "Sample Dryad Content"

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A large data file: [http://hdl.handle.net/10255/dryad.488 Brian Sidlauskas's fish jaw image], [http://dx.doi.org/10.5061/dryad.1877/3 Laurie Stevenson's sequence alignments], [http://datadryad.org/handle/10255/dryad.1923 Cossio (2010) PLoS Computational Biology], [http://dx.doi.org/10.5061/dryad.7990/1 Geraldes (2011) Molecular Ecology Resources]
 
A large data file: [http://hdl.handle.net/10255/dryad.488 Brian Sidlauskas's fish jaw image], [http://dx.doi.org/10.5061/dryad.1877/3 Laurie Stevenson's sequence alignments], [http://datadryad.org/handle/10255/dryad.1923 Cossio (2010) PLoS Computational Biology], [http://dx.doi.org/10.5061/dryad.7990/1 Geraldes (2011) Molecular Ecology Resources]
  
Package containing many data files: [http://hdl.handle.net/10255/dryad.25 Mike Taylor's paleo package], [http://datadryad.org/handle/10255/dryad.1926 Janies (2011) Systematic Biology], [http://dx.doi.org/10.5061/dryad.f1cb2 Gardner (2011) Molecular Ecology Resources] with 51 separate fasta formatted files.
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Package containing many data files: [http://hdl.handle.net/10255/dryad.25 Mike Taylor's paleo package], [http://datadryad.org/handle/10255/dryad.1926 Janies (2011) Systematic Biology], [http://dx.doi.org/10.5061/dryad.f1cb2 Gardner (2011) Molecular Ecology Resources] with 51 separate fasta formatted files, data package with [http://dx.doi.org/10.5061/dryad.125 many files for different species]
  
 
Package containing ZIP files with many aggregated files: [http://hdl.handle.net/10255/dryad.12 Chris Zmasek's apoptosis package], [http://datadryad.org/handle/10255/dryad.1923 Cossio (2010) PLoS Computational Biology], [http://dx.doi.org/10.5061/dryad.7990/1 Geraldes (2011) Molecular Ecology Resources]
 
Package containing ZIP files with many aggregated files: [http://hdl.handle.net/10255/dryad.12 Chris Zmasek's apoptosis package], [http://datadryad.org/handle/10255/dryad.1923 Cossio (2010) PLoS Computational Biology], [http://dx.doi.org/10.5061/dryad.7990/1 Geraldes (2011) Molecular Ecology Resources]

Revision as of 09:08, 20 July 2012

This page lists samples 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

Package containing ZIP files with many aggregated files: Chris Zmasek's apoptosis package, Cossio (2010) PLoS Computational Biology, Geraldes (2011) Molecular Ecology Resources

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

Package with related content in GenBank: Rocha-Olivares (2011) JHered, Melo (2011) Molecular Ecology (GenBank accession numbers in article Data Accessibility section)

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

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 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

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

Data packages under embargo: [8], [9]

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 [10], 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: [11]

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