Difference between revisions of "Sample Dryad Content"

From Dryad wiki
Jump to: navigation, search
m (Models for depositors)
m (Models for depositors)
Line 11: Line 11:
Sample journal articles illustrating links to data:
Sample journal articles illustrating links to data:
*[http://dx.doi.org/10.1007/s11557-011-0800-z Article with links to Dryad data in Materials and Methods, Figures, and Reference list]
*[http://dx.doi.org/10.1007/s11557-011-0800-z Article with links to Dryad data in Materials and Methods, Figures, and Reference list]
*[http://dx.doi.org/10.1371/journal.pone.0077467 Article with link to Dryad data in Materials and Methods]
*[http://dx.doi.org/10.1371/journal.pone.0077467 Article with Dryad link in Materials and Methods]
*[http://dx.doi.org/10.1098/rsbl.2014.0040 Article with Dryad link in Data Accessibility statement]
*[http://dx.doi.org/10.1098/rsbl.2014.0040 Article with Dryad link in Data Accessibility statement]

Revision as of 11:20, 20 March 2014

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: [1]

Sample journal articles illustrating links to data:

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

Examples of embargoed packages:

Different types of content

Examples to highlight a variety of possible submission formats.

Data packages with different authors from their corresponding articles:

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

Harvested item in Japanese: [12]

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. [15]

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.

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 [16], 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


Data packages 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.


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:

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

Compressed formats:

Tracking reuse of Dryad data

It is currently difficult to effectively track reuse of datasets archived in Dryad. Some cases can be found by searching scholarly databases, such as Web of Science, and through publisher's websites. While we are working 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 in Dryad is also the most frequently cited one:

  • 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

Here are a few recent articles which reuse and cite earlier data from Dryad:

  • 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