Sample Dryad Content

This page lists examples of Dryad content with specific properties. Recommendations for authors on what to deposit and general suggestions on data management can be found on the Dryad site here.

=General cases=

Dryad content that may be useful as models for depositors and journals.

Models for depositors
A very thoroughly documented data package:

Sample journal articles illustrating links to data:
 * Article with Dryad link in Data Accessibility statement
 * Article with links to Dryad data in Materials and Methods, Figures, and Reference list
 * Article with Dryad link in Materials and Methods

There are two ways to include a ReadMe with your data:


 * Data packages with a ReadMe file:, , , ,
 * ReadMe for each data file:, ,

Examples of embargoed packages:


 * Data packages under embargo: ,
 * 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

Different types of content
Examples to highlight a variety of possible submission formats.

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, 336(6087): 1408. 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 from: Cladograms, phylogenies and the veracity of the conodont fossil record - two authors on the article, one on the data.

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

Harvested item in Japanese:

Data from non-journal publications:
 * thesis:
 * book:

Data papers with content in Dryad:
 * 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
 * from the Journal of Open Public Health Data: Alexander NS, Wint W (2013) Data from: Projected population proximity indices (30km) for 2005, 2030 & 2050. Dryad Digital Repository.

Some popular data packages

 * 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.doi:10.5061/dryad.8384
 * Highly cited: 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. doi:10.5061/dryad.234 - the Global Wood Density Database file is highly downloaded and cited.

=Extreme cases=

A reference for curators and developers when testing functionalities or thinking about design.

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

Packages 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

Packages 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

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, items in the BIRDD collection under Dryad's original license (at least some of these can probably be moved to CC0)

Items with many authors: D'Hont (2012) Nature

=Connections with other repositories and platforms=

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

GenBank
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.

ScienceDirect
Sample articles in Elsevier journals with data in Dryad; these are publicly accessible and show off the ScienceDirect link to Dryad:


 * R. Alexander Pyron, John J. Wiens, A large-scale phylogeny of Amphibia including over 2800 species, and a revised classification of extant frogs, salamanders, and caecilians, Molecular Phylogenetics and Evolution, Volume 61, Issue 2, November 2011, pp. 543-583, http://dx.doi.org/10.1016/j.ympev.2011.06.012.


 * Peter J. Unmack, Gerald R. Allen, Jerald B. Johnson, Phylogeny and biogeography of rainbowfishes (Melanotaeniidae) from Australia and New Guinea, Molecular Phylogenetics and Evolution, Volume 67, Issue 1, April 2013, pp. 15-27, http://dx.doi.org/10.1016/j.ympev.2012.12.019.


 * James Starrett, Marshal Hedin, Nadia Ayoub, Cheryl Y. Hayashi, Hemocyanin gene family evolution in spiders (Araneae), with implications for phylogenetic relationships and divergence times in the infraorder Mygalomorphae, Gene, Volume 524, Issue 2, July 2013, pp. 175-186, http://dx.doi.org/10.1016/j.gene.2013.04.037.


 * Mercy Y. Akinyi, Jenny Tung, Maamun Jeneby, Nilesh B. Patel, Jeanne Altmann, Susan C. Alberts, Role of grooming in reducing tick load in wild baboons (Papio cynocephalus), Animal Behaviour, Volume 85, Issue 3, March 2013, pp. 559-568, http://dx.doi.org/10.1016/j.anbehav.2012.12.012

=Examples by file type=

See http://wiki.datadryad.org/Opening_Files for a list of programs that we use to open, view, or edit different file types.

Data packages with unusual or interesting content:
 * CT scans: Schachner (2013) Nature
 * Dinosaur animations: Allen (2013) Nature

Data of specific file types; non-proprietary file formats are preferable:
 * asc (ASCII grid files) Munshi-South (2012) Molecular Ecology
 * avi Dennenmoser (2012) Evolution (battling fiddler crab video!)
 * bam Parchman (2013) Molecular Ecology, Malenfant (2013) Molecular Ecology Resources
 * csv Bradshaw (2012) Heredity, Pyron (2009) Molecular Ecology, Chun (2009) Molecular Ecology, Krist (2007) Behavioral Ecology and Sociobiology
 * doc (with table) Tezanos-Pinto (2009) Journal of Heredity
 * docx Neave (2013) PLoS ONE
 * dta (Stata data file) Harris (2013) BMJ Open
 * fdi (Network Draw file) Burzyński (2014) Heredity
 * fasta Muñoz (2013) PeerJ
 * fna Peay (2012) Molecular Ecology
 * gtx (Genetix file) Adjeroud (2013) Marine Biology
 * jar Jalasvuori (2014) Molecular Ecology
 * jpg Jansen (2013) Palaeontology
 * kml Kawada (2011) ZooKeys
 * m (Matlab file) Runemark (2013) Molecular Ecology, Prunier (2013) Molecular Ecology
 * map Feulner (2013) Molecular Ecology
 * mat Liu (2013) Proceedings of the National Academy of Sciences of the United States of America
 * mov Carter (2011) Biological Journal of the Linnean Society
 * mp3 MacCallum (2012) Proceedings of the National Academy of Sciences of the United States of America, Abraham (2013) Zootaxa
 * mp4 (an interesting data animation) Clune (2013) Proceedings of the Royal Society B
 * nb (Mathematica files) Hill (2007) Genetics
 * nexus Blackburn (2008) Molecular Phylogenetics and Evolution
 * nwk Martin (2013) Genome Research
 * obj Brassey (2012) Journal of the Royal Society Interface 3D scan format from Geomagic Studio
 * ods (OpenDocument Spreadsheet) Latour (2014) Proceedings of the Royal Society B
 * Origin files Leng (2011) Molecular Ecology
 * pbs Stanton-Geddes (2012) PLoS ONE
 * pdf Reeves (2013) PLoS ONE
 * ped (for use with PLINK, a free, open-source whole genome association analysis toolset) Murray (2013) BMC Evolutionary Biology
 * phy DeBiasse (2014) Molecular Ecology
 * png Aguilar (2013) Zookeys
 * prm Feulner (2013) Molecular Ecology
 * py Encinas-Viso (2014) Journal of Evolutionary Biology
 * R Viricel (2013) Molecular Ecology Resources
 * raw McNulty (2013) PLoS Biology
 * rtf Wu (2013) PLoS ONE
 * sff Botnen (2014) Molecular Ecology, Peay (2012) Molecular Ecology
 * tps Stubbs (2013) Proceedings of the Royal Society B
 * tre Chatelet (2013) International Journal of Plant Sciences
 * txt Henry (2009) Molecular Ecology, Anderson (2010) Paleobiology
 * xls Pichlmüller (2013) Amphibia-Reptilia
 * xlsx Baker (2013) Marine Ecology Progress Series
 * wav Francis (2011) PLoS ONE

Compressed formats:
 * gz Gross (2013) BMC Genomics
 * rar Aquilino (2011) Molecular Ecology Resources
 * tgz Parchman (2013) Molecular Ecology
 * zip Jay (2012) Molecular Ecology

=Reuse of Dryad data=

Large scale search and automated monitoring
There is currently a lack of good tools for tracking reuse of datasets archived in Dryad. Some cases can be found by searching scholarly databases such as the Data Citation Index, Google Scholar, and through publisher's websites.

While we work toward solutions to this problem, we are collecting cases of reuse in a Google spreadsheet accessible to Dryad staff. The most frequently downloaded data package is also frequently cited:
 * Zanne AE, Lopez-Gonzalez G, Coomes DA, Ilic J, Jansen S, Lewis SL, Miller RB, Swenson NG, Wiemann MC, Chave J (2009) Data from: Towards a worldwide wood economics spectrum. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.234

Other examples
Articles which reuse and cite earlier data from Dryad:
 * Lanfear et al (2014) Selecting optimal partitioning schemes for phylogenomic datasets BMC Evolutionary Biology 2014, 14:82 doi:10.1186/1471-2148-14-82
 * Gilbert KJ, Andrew RL, Bock DG, Franklin MT, Kane NC, Moore J, Moyers BT, Renaut S, Rennison DJ, Veen T, Vines TH (2012) Recommendations for utilizing and reporting population genetic analyses: the reproducibility of genetic clustering using the program structure. Molecular Ecology 21(20): 4925–4930. http://doi.org/10.1111/j.1365-294X.2012.05754.x
 * Robinson JD, Hall DW, Wares JP (2013) Approximate Bayesian estimation of extinction rate in the Finnish Daphnia magna metapopulation. Molecular Ecology 22(10): 2627–2639. http://doi.org/10.1111/mec.12283
 * Robinson MR, Beckerman, AP (2013) Quantifying multivariate plasticity: genetic variation in resource acquisition drives plasticity in resource allocation to components of life history. Ecology Letters 16(3) http://dx.doi.org/10.1111/ele.12047
 * Rota CT, Millspaugh JJ, Kesler DC, Lehman CP, Rumble MA, Jachowski CMB. (2013), A re-evaluation of a case–control model with contaminated controls for resource selection studies. Journal of Animal Ecology, 82: 1165–1173. http://dx/doi.org/10.1111/1365-2656.12092
 * Weinreich DM, Knies JL (2013) Fisher's geometric model of adaptation meets the functional synthesis: data on pairwise epistasis for fitness yields insights into the shape and size of phenotype space. Evolution 67(10) http://dx.doi.org/10.1111/evo.12156