Sample Dryad Content

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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.

Models for depositors

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

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

Sample journal articles illustrating links to data:

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

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

Examples of embargoed packages:

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

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

  • 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

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

Data from non-journal publications

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

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

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.

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:

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

Compressed formats:

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

Use in classes, textbooks, and other educational contexts

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




































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