Difference between revisions of "Sample Dryad Content"

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==Use in classes, textbooks, and other educational contexts==
==Use in classes, textbooks, and other educational contexts==
* [http://nile.physics.ncsu.edu/py722/ Physics 722], a graduate statistical physics class at NCSU. [http://datadryad.org/resource/doi:10.5061/dryad.qv331 Neudecker et al.] data is used for problem set #4.  (Disclosure: The NCSU professor is married to TJV)
* [http://nile.physics.ncsu.edu/py722/ Physics 722], a graduate statistical physics class at NCSU. The [http://datadryad.org/resource/doi:10.5061/dryad.qv331 Neudecker et al. 2012] data on tetrahedral packing is used for problem set #4.  (Disclosure: The NCSU professor is married to TJV)
==Other examples==
==Other examples==

Revision as of 12:37, 29 November 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 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

Data package that links to another data package in Dryad [12]

Harvested item in Japanese: [13]

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. [16]

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. doi:10.5061/dryad.g7jq6

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

Some popular data packages

  • Running list
  • 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 [17], 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:

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

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)

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