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 in the Dryad FAQ.

= General cases =

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

Good reusability practice
See Best practices for creating reusable Dryad data packages

A very thoroughly documented data package: Lai (2011), Willerslev (2014)

A data package with a great ReadMe file: Westermann (2015)

ReadMe display examples

 * Data packages with a ReadMe file: [2], [3], [4], [5], [6]
 * ReadMe for each data file: [7], [8], [9]

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

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

Data packages that have been versioned

 * Cooke deposit from Molecular Ecology Cooke GM, Chao NL, Beheregaray LB (2012) Data from: Divergent natural selection with gene flow along major environmental gradients in Amazonia: insights from genome scans, population genetics and phylogeography of the characin fish Triportheus albus. Dryad Digital Repository.

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 packages that are portions of a larger dataset

 * Payne JL, Boyer AG, Brown JH, Finnegan S, Kowaleski M, Krause Jr. RA, Lyons SK, McClain CR, McShea DW, Novack-Gottshall PM, Smith FA, Stempien JA, Wang SC (2008) Data from: Two-phase increase in the maximum size of life over 3.5 billion years reflects biological innovation and environmental opportunity. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.223

Data package that links to/uses another data package in Dryad

 * Dokter AM, Fokkema W, Ebbinge BS, Olff H, van der Jeugd HP, Nolet BA. Data from: Agricultural pastures challenge the attractiveness of natural saltmarsh for a migratory goose. Dryad Digital Repository. https://doi.org/10.5061/dryad.j8cm402
 * (link to other data package is presented as a file in the package)
 * Hiddink JG, Moranta J, Balestrini S, Sciberras M, Cendrier M, Bowyer R, Kaiser MJ, Sköld M, Jonsson P, Bastardie F, Hinz H (2016) Data from: Bottom trawling affects fish condition through changes in the ratio of prey availability to density of competitors. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.g3qh8
 * (link to other data package is presented as a file in the package)
 * Mastretta-Yanes A, Zamudio S, Jorgensen TH, Arrigo N, Alvarez N, Piñero D, Emerson BC (2014) Data from: Gene duplication, population genomics and species-level differentiation within a tropical mountain shrub. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.n3jk5
 * (link to other data package is presented as a file in the package)
 * Lessios HA (2015) Data from: Appearance of an early closure of the Isthmus of Panama is the product of biased inclusion of data in the metaanalysis. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.b29k1
 * (link to other data package is in the abstract)
 * Zuur AF, Ieno EN (2016) Data from: A protocol for conducting and presenting results of regression-type analyses. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.v4t42
 * "Modified baboon data taken from Dryad Digital Repository: Sick C, Carter AJ, Marshall HH, Knapp LA, Dabelsteen T, Cowlishaw G (2014) Data from: Evidence for varying social strategies across the day in chacma baboons. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.n4k6p"
 * Schlamp F, van der Made J, Stambler R, Chesebrough L, Boyko AR, Messer PW (2015) Data from: Evaluating the performance of selection scans to detect selective sweeps in domestic dogs. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.hf46s
 * (link to other data package is presented as a file in the package) Raw Genotyping Data: Shannon LM, Boyko RH, Castelhano M, Corey E, Hayward JJ, McLean C, White ME, Abi Said M, Anita BA, Bondjengo Ikombe N, Calero J, Galov A, Hedimbi M, Imam B, Khalap R, Lally D, Masta A, Oliveira KC, Pérez L, Randall J, Tam NM, Trujillo-Cornejo FJ, Valeriano C, Sutter NB, Todhunter RJ, Bustamante CD, Boyko AR (2015) Data from: Genetic structure in village dogs reveals a Central Asian domestication origin. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.v9t5h

Data packages that link to more than one publication

 * Jefferson T, Jones MA, Doshi P, Del Mar CB, Hama R, Thompson MJ, Spencer EA, Onakpoya I, Mahtani KR, Nunan D, Howick J, Heneghan CJ (2014) Data from: Neuraminidase inhibitors for preventing and treating influenza in healthy adults and children. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.77471
 * Kraemer MUG, Sinka ME, Duda KA, Mylne A, Shearer FM, Brady OJ, Messina JP, Barker CM, Moore CG, Carvalho RG, Coelho GE, Van Bortel W, Hendrickx G, Schaffner F, Wint GRW, Elyazar IRF, Teng H, Hay SI (2015) Data from: The global compendium of Aedes aegypti and Ae. albopictus occurrence. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.47v3c
 * Kotrc B, Knoll AH (2015) Data from: A morphospace of planktonic marine diatoms, parts I and II. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.js64t
 * Guisan A, Dubuis A, Vittoz P (2011) Data from: Predicting spatial patterns of plant species richness: a comparison of direct macroecological and species stacking modelling approaches. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.28d4k
 * Djurhuus A, Boersch-Supan PH, Mikalsen S, Rogers AD, Giebel H (2017) Data from: Microbe biogeography tracks water masses in a dynamic oceanic frontal system. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.qh767
 * Mayo-Wilson E, Li T, Fusco N, Bertizzolo L, Canner JK, Cowley T, Doshi P, Ehmsen J, Gresham G, Guo N, Haythornthwaite JA, Heyward J, Hong H, Pham D, Payne JL, Rosman L, Stuart EA, Suarez-Cuervo C, Tolbert E, Twose C, Vedula S, Dickersin K (2017) Data from: Cherry-picking by trialists and meta-analysts can drive conclusions about intervention efficacy. Dryad Digital Repository. https://doi.org/10.5061/dryad.mp26fb1

Data packages associated with serials that do not use DOIs

 * Mudappa D, Raman TRS (2009) Data from: A conservation status survey of hornbills (Bucerotidae) in the Western Ghats, India. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.63s7r
 * Aidar IF, Santos AOR, Bartelli BF, Martins GA, Nogueira-Ferreira FH (2013) Data from: Nesting ecology of stingless bees (Hymenoptera, Meliponina) in urban areas: the importance of afforestation. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.k54hk
 * Aliabadian M, Nijman V, Mahmoudi A, Naderi M, Vonk R, Vences M (2014) Data from: ExcaliBAR: a simple and fast software utility to calculate intra- and interspecific distances from DNA barcodes. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.r458n
 * Lendemer JC, Harris RC (2014) Data from: Studies in lichens and lichenicolous fungi – No. 19: further notes on species from the Coastal Plain of southeastern North America. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.8g55g

Harvested item in Japanese

 * http://datadryad.org/handle/10255/dryad.17753

Data from non-journal publications

 * thesis: http://dx.doi.org/10.5061/dryad.7tr51, http://dx.doi.org/10.5061/dryad.202d4, http://dx.doi.org/10.5061/dryad.d772v, http://dx.doi.org/10.5061/dryad.541q2
 * thesis chapter: http://dx.doi.org/10.5061/dryad.n193d, https://doi.org/10.5061/dryad.25m10
 * book: http://dx.doi.org/10.5061/dryad.n48cm, https://doi.org/10.5061/dryad.b6c45, https://doi.org/10.5061/dryad.1tn7123
 * book chapter: http://dx.doi.org/10.5061/dryad.0kn60
 * report: http://dx.doi.org/10.5061/dryad.p5t21, http://dx.doi.org/10.5061/dryad.412nn

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. http://doi.org.10.5061/dryad.12734

Reproducible papers with the software & data bundled together in Dryad

 * Rajon E, Desouhant E, Chevalier M, Débias F, Menu F (2014) Data from: The evolution of bet hedging in response to local ecological conditions. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.g7jq6
 * Drake JM, Kaul RB, Alexander LW, O'Regan SM, Kramer AM, Pulliam JT, Ferrari MJ, Park AW (2015) Data from: Ebola cases and health system demand in Liberia. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.17m5q

Data packages with software snapshots available from an external repository

 * de Oliveira Martins L, Mallo D, Posada D (2014) Data from: A Bayesian supertree model for genome-wide species tree reconstruction. Dryad Digital Repository. doi:10.5061/dryad.74922
 * Kaehler BD, Yap VB, Zhang R, Huttley GA (2014) Data from: Genetic distance for a general non-stationary Markov substitution process. Dryad Digital Repository. doi:10.5061/dryad.g7g0n
 * Clifford J, Adami C (2015) Data from: Discovery and information-theoretic characterization of transcription factor binding sites that act cooperatively. Dryad Digital Repository. doi:10.5061/dryad.8b203

A somewhat representative sampling of the variety of disciplines, file types, complexity, etc. in Dryad (as of August 2017)

 * http://dx.doi.org/10.5061/dryad.7kt3h
 * http://dx.doi.org/10.5061/dryad.cf137
 * http://dx.doi.org/10.5061/dryad.03003
 * http://dx.doi.org/10.5061/dryad.vv53d
 * http://dx.doi.org/10.5061/dryad.800tj
 * http://dx.doi.org/10.5061/dryad.47n27
 * http://dx.doi.org/10.5061/dryad.8t55d
 * http://dx.doi.org/10.5061/dryad.7nk99
 * http://dx.doi.org/10.5061/dryad.vg7r3
 * http://dx.doi.org/10.5061/dryad.f9v80

Some popular data packages

 * A Running list is located on the Dryad homepage under the "Popular" button.
 * 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 =


 * Large data files: Laurie Stevenson's sequence alignments, Cossio (2010) PLOS Computational Biology, Geraldes (2011) Molecular Ecology Resources, Kartzinel (2015) Metabarcode sequence data (~100GB package), Hettne (2016) PLOS ONE (compressed gz file - 17.23 GB csv file when uncompressed)
 * 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
 * Non-CC0 licenses: Swenson (2011) Systematic Biology (file consists of code with GNU GPL 3.0 license), Sally Otto's package under Dryad's original license [17], items in the BIRDD collection under Dryad's original license (at least some of these can probably be moved to CC0)
 * Many authors: D'Hont (2012) Nature
 * Retractions: Pryke et al (2014), Laskowski et al (2020)

= Connections with other repositories and platforms =

TreeBASE
Data packages with related content in TreeBASE: Balboni et al. Rocha et al. 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.

Code/software in Github, Bitbucket
Package with links to content in Bitbucket: Alvarado-Serrano (2016) Methods in Ecology and Evolution

Package with links to content in Github: Moore (2016) PNAS

Open Tree of Life
Specialized resource that curates, synthesizes, visualizes, and exposes phylogenetic information from various sources, including (but not exclusively) Dryad, e.g. [1]

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

Indexed or harvested by institutional or other repositories

 * Indexed by DataBris at U Bristol. Multiple examples: 1, 2

= 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:


 * Animated GIF Hoffman (2015) International Journal of Image and Data Fusion
 * CT scans: Schachner (2013) Nature
 * Dinosaur animations: Allen (2013) Nature
 * Hosted HTML Revell et al (2015) Evolution, Cohen et al (2013) Journal of Paleontology
 * Multilayer Temporal Network of Public Transport in Great Britain. Multilayer node-list and edge-list, where each layer is associated to a mode of transport and each node is geo-referenced: Gallotti (2015) Scientific Data

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
 * cel Olarte (2015) Molecular Ecology
 * csv Bradshaw (2012) Heredity, Pyron (2009) Molecular Ecology, Chun (2009) Molecular Ecology, Krist (2007) Behavioral Ecology and Sociobiology
 * cvw Caro (2014) eLife
 * 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
 * gdb (Geodatabase) Sochi (2015) Journal of Applied Ecology
 * gtx (Genetix file) Adjeroud (2013) Marine Biology
 * hdr/img pair Li (2014) PLOS One
 * ics/ids pair Takemura (2016) Journal of Cell Science
 * jar Jalasvuori (2014) Molecular Ecology
 * jpg Jansen (2013) Palaeontology
 * kml Kawada (2011) ZooKeys
 * lsm Takemura (2016) Journal of Cell Science
 * m (Matlab file) Runemark (2013) Molecular Ecology, Prunier (2013) Molecular Ecology
 * map Feulner (2013) Molecular Ecology
 * mas Petrović (2015) BMC Evolutionary Biology
 * 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
 * nii Murphy (2016) Philosophical Transactions of the Royal Society B
 * 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
 * psf Napolitano (2015) Journal of Heredity
 * py Encinas-Viso (2014) Journal of Evolutionary Biology
 * qgd Crawford (2015) Biology Letters
 * R Viricel (2013) Molecular Ecology Resources
 * Rmd Boettiger (2015) Proceedings of the Royal Society B
 * raw McNulty (2013) PLoS Biology
 * rtf Wu (2013) PLoS ONE
 * sff Botnen (2014) Molecular Ecology, Peay (2012) Molecular Ecology
 * spf Meilink (2015) Molecular Ecology
 * tps Stubbs (2013) Proceedings of the Royal Society B
 * tre Chatelet (2013) International Journal of Plant Sciences
 * tsv Vijaykrishna (2015) eLife
 * txt Henry (2009) Molecular Ecology, Anderson (2010) Paleobiology
 * xls Pichlmüller (2013) Amphibia-Reptilia
 * xlsx Baker (2013) Marine Ecology Progress Series
 * xml Colombo (2014) Journal of Evolutionary Biology
 * 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

Corrections based on data reanalysis

 * http://bmjopen.bmj.com/content/2/3/e000311corr1.full

Use in classes, textbooks, and other educational contexts

 * Physics 722, a graduate statistical physics class at NCSU. The Neudecker et al. 2012 data on tetrahedral packing is used for problem set #4. (Disclosure: The NCSU professor is married to TJV)
 * Used to teach quantitative biology to undergraduates: QUBES DryadLab Network and other uses by the QUBES community https://qubeshub.org/members/1018
 * Introductory R textbook: on p4 "I'd just like to take this opportunity to point out the fabulous resource that is the Dryad digital repository"

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