Difference between revisions of "Sample Dryad Content"

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This page lists samples of Dryad content with specific properties. These items are often needed to test new functionality, and are useful as models for depositors.  Recommendations for authors on what to deposit and general suggestions on data management can be found on the Dryad site [http://datadryad.org/depositing here.]
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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 [http://datadryad.org/pages/faq Dryad FAQ].
  
A large data file: [http://hdl.handle.net/10255/dryad.488 Brian Sidlauskas's fish jaw image], [http://dx.doi.org/10.5061/dryad.1877/3 Laurie Stevenson's sequence alignments], [http://datadryad.org/handle/10255/dryad.1923 Cossio (2010) PLoS Computational Biology], [http://dx.doi.org/10.5061/dryad.7990/1 Geraldes (2011) Molecular Ecology Resources]
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= General cases =
  
Package containing many data files: [http://hdl.handle.net/10255/dryad.25 Mike Taylor's paleo package], [http://datadryad.org/handle/10255/dryad.1926 Janies (2011) Systematic Biology], [http://dx.doi.org/10.5061/dryad.f1cb2 Gardner (2011) Molecular Ecology Resources] with 51 separate fasta formatted files, data package with [http://dx.doi.org/10.5061/dryad.125 many files for different species]
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Dryad content that may be useful as models for depositors and journals.
  
Package containing ZIP files with many aggregated files: [http://hdl.handle.net/10255/dryad.12 Chris Zmasek's apoptosis package], [http://datadryad.org/handle/10255/dryad.1923 Cossio (2010) PLoS Computational Biology], [http://dx.doi.org/10.5061/dryad.7990/1 Geraldes (2011) Molecular Ecology Resources]
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== Models for depositors ==
  
Package with related content in TreeBASE: [http://hdl.handle.net/10255/dryad.82 Sam Price's hunting package], [http://datadryad.org/handle/10255/dryad.7978 Melo (2011) Molecular Ecology] (TB link in article Data Accessibility section)
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=== Good reusability practice ===
  
Package with related content in GenBank: [http://datadryad.org/handle/10255/dryad.8437 Rocha-Olivares (2011) JHered], [http://datadryad.org/handle/10255/dryad.7978 Melo (2011) Molecular Ecology] (GenBank accession numbers in article Data Accessibility section)
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See [https://datadryad.org/pages/reusabilityBestPractices Best practices for creating reusable Dryad data packages]
  
Data packages with a ReadMe file:  [http://www.datadryad.org/handle/10255/dryad.1150], [http://datadryad.org/handle/10255/dryad.1758], [http://datadryad.org/handle/10255/dryad.1205], [http://datadryad.org/handle/10255/dryad.2020] and with a ReadMe for each data file, [http://datadryad.org/handle/10255/dryad.1295], [http://dx.doi.org/10.5061/dryad.87ht85rs], [http://dx.doi.org/10.5061/dryad.j512f21p].
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A very thoroughly documented data package: [http://dx.doi.org/10.5061/dryad.cm7td Lai (2011)], [http://dx.doi.org/10.5061/dryad.ph8s5 Willerslev (2014)]
  
Most popular data packages:
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A data package with a great ReadMe file: [http://dx.doi.org/10.5061/dryad.7g02r Westermann (2015)]
*Most highly viewed data package: [http://dx.doi.org/10.5061/dryad.8384 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.
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*Most frequently downloaded data file: [http://datadryad.org/handle/10255/dryad.234 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.
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=== ReadMe display examples ===
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*Data packages with a ReadMe file: [http://dx.doi.org/10.5061/dryad.9tb73 [2]], [http://www.datadryad.org/handle/10255/dryad.1150 [3]], [http://datadryad.org/handle/10255/dryad.1758 [4]], [http://datadryad.org/handle/10255/dryad.1205 [5]], [http://datadryad.org/handle/10255/dryad.2020 [6]]
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*ReadMe for each data file: [http://datadryad.org/handle/10255/dryad.1295 [7]], [http://dx.doi.org/10.5061/dryad.87ht85rs [8]], [http://dx.doi.org/10.5061/dryad.j512f21p [9]]
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=== Sample journal articles illustrating links to data ===
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*[http://dx.doi.org/10.1098/rsbl.2014.0040 Article with Dryad link in Data Accessibility statement]
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*[http://dx.doi.org/10.1007/s11557-011-0800-z Article with links to Dryad data in Materials and Methods, Figures, and Reference list]
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*[http://dx.doi.org/10.1371/journal.pone.0077467 Article with Dryad link in Materials and Methods]
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== Different types of content ==
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Examples to highlight a variety of possible submission formats.
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=== Data packages that have been versioned ===
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*[http://datadryad.org/resource/doi:10.5061/dryad.v5gp1233 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.
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=== Data packages with different authors from their corresponding articles ===
  
Data packages with different authors from corresponding articles:
 
 
*[http://datadryad.org/handle/10255/dryad.234 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.
 
*[http://datadryad.org/handle/10255/dryad.234 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.
* [http://dx.doi.org/10.5061/dryad.4dn793t6 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, online in advance of print. doi:10.1126/science.1215065
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*[http://dx.doi.org/10.5061/dryad.4dn793t6 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.
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*[http://dx.doi.org/10.5061/dryad.h0jg4 Data from: Development of an ultra-dense genetic map of the sunflower genome] - seven authors on the article, one on the data.
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*[http://dx.doi.org/10.5061/dryad.4067d Data from: Cladograms, phylogenies and the veracity of the conodont fossil record] - two authors on the article, one on the data.
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=== Data packages that are portions of a larger dataset ===
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*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/doi:10.5061/dryad.223 http://dx.doi.org/10.5061/dryad.223]
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=== Data package that links to/uses another data package in Dryad ===
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*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
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**(link to other data package is presented as a file in the package)
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*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 http://dx.doi.org/10.5061/dryad.g3qh8]
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**(link to other data package is presented as a file in the package)
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*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 http://dx.doi.org/10.5061/dryad.n3jk5]
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**(link to other data package is presented as a file in the package)
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*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 http://dx.doi.org/10.5061/dryad.b29k1]
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**(link to other data package is in the abstract)
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*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 
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**"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"
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*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 http://dx.doi.org/10.5061/dryad.hf46s]
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**(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 http://dx.doi.org/10.5061/dryad.v9t5h]
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=== Data packages that link to more than one publication ===
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*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 http://dx.doi.org/10.5061/dryad.77471]
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*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 http://dx.doi.org/10.5061/dryad.47v3c]
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*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 http://dx.doi.org/10.5061/dryad.js64t]
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*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 http://dx.doi.org/10.5061/dryad.28d4k]
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*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 http://dx.doi.org/10.5061/dryad.qh767]
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*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 https://doi.org/10.5061/dryad.mp26fb1]
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=== Data packages associated with serials that do not use DOIs ===
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*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 http://dx.doi.org/10.5061/dryad.63s7r]
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*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 http://dx.doi.org/10.5061/dryad.k54hk]
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*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 http://dx.doi.org/10.5061/dryad.r458n]
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*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 http://dx.doi.org/10.5061/dryad.8g55g]
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=== Harvested item in Japanese ===
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*[http://datadryad.org/handle/10255/dryad.17753 http://datadryad.org/handle/10255/dryad.17753]
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=== Data from non-journal publications ===
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*thesis: [http://dx.doi.org/10.5061/dryad.7tr51 http://dx.doi.org/10.5061/dryad.7tr51], [http://dx.doi.org/10.5061/dryad.202d4 http://dx.doi.org/10.5061/dryad.202d4], [http://dx.doi.org/10.5061/dryad.d772v http://dx.doi.org/10.5061/dryad.d772v], [http://dx.doi.org/10.5061/dryad.541q2 http://dx.doi.org/10.5061/dryad.541q2]
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*thesis chapter: [http://dx.doi.org/10.5061/dryad.n193d http://dx.doi.org/10.5061/dryad.n193d], [https://doi.org/10.5061/dryad.25m10 https://doi.org/10.5061/dryad.25m10]
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*book: [http://dx.doi.org/10.5061/dryad.n48cm http://dx.doi.org/10.5061/dryad.n48cm], [https://doi.org/10.5061/dryad.b6c45 https://doi.org/10.5061/dryad.b6c45], [https://doi.org/10.5061/dryad.1tn7123 https://doi.org/10.5061/dryad.1tn7123]
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*book chapter: [http://dx.doi.org/10.5061/dryad.0kn60 http://dx.doi.org/10.5061/dryad.0kn60]
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*report: [http://dx.doi.org/10.5061/dryad.p5t21 http://dx.doi.org/10.5061/dryad.p5t21], [http://dx.doi.org/10.5061/dryad.412nn http://dx.doi.org/10.5061/dryad.412nn]
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=== Data papers with content in Dryad ===
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*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. [http://dx.doi.org/10.5061/dryad.c213h doi:10.5061/dryad.c213]
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*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 http://doi.org.10.5061/dryad.12734]
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=== Reproducible papers with the software & data bundled together in Dryad ===
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*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 http://dx.doi.org/10.5061/dryad.g7jq6]
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*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 http://dx.doi.org/10.5061/dryad.17m5q]
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=== Data packages with software snapshots available from an external repository ===
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*de Oliveira Martins L, Mallo D, Posada D (2014) Data from: A Bayesian supertree model for genome-wide species tree reconstruction. Dryad Digital Repository. [http://doi.org/10.5061/dryad.74922 doi:10.5061/dryad.74922]
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*Kaehler BD, Yap VB, Zhang R, Huttley GA (2014) Data from: Genetic distance for a general non-stationary Markov substitution process. Dryad Digital Repository. [http://dx.doi.org/10.5061/dryad.g7g0n doi:10.5061/dryad.g7g0n]
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*Clifford J, Adami C (2015) Data from: Discovery and information-theoretic characterization of transcription factor binding sites that act cooperatively. Dryad Digital Repository. [http://dx.doi.org/10.5061/dryad.8b203 doi:10.5061/dryad.8b203]
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=== A somewhat representative sampling of the variety of disciplines, file types, complexity, etc. in Dryad (as of August 2017) ===
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*http://dx.doi.org/10.5061/dryad.7kt3h
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*http://dx.doi.org/10.5061/dryad.cf137
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*http://dx.doi.org/10.5061/dryad.03003
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*http://dx.doi.org/10.5061/dryad.vv53d
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*http://dx.doi.org/10.5061/dryad.800tj
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*http://dx.doi.org/10.5061/dryad.47n27
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*http://dx.doi.org/10.5061/dryad.8t55d
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*http://dx.doi.org/10.5061/dryad.7nk99
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*http://dx.doi.org/10.5061/dryad.vg7r3
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*http://dx.doi.org/10.5061/dryad.f9v80
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== Some popular data packages ==
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*A [http://datadryad.org/#most-viewed-data Running list] is located on the Dryad homepage under the "Popular" button.
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*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.[http://dx.doi.org/10.5061/dryad.8384 doi:10.5061/dryad.8384]
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*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. [http://doi.org/10.5061/dryad.234 doi:10.5061/dryad.234] - the Global Wood Density Database file is highly downloaded and cited.
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= Extreme cases =
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*Large data files: [http://dx.doi.org/10.5061/dryad.1877/3 Laurie Stevenson's sequence alignments], [http://datadryad.org/handle/10255/dryad.1923 Cossio (2010) PLOS Computational Biology], [http://dx.doi.org/10.5061/dryad.7990/1 Geraldes (2011) Molecular Ecology Resources], [http://dx.doi.org/10.5061/dryad.f18k5 Kartzinel (2015) Metabarcode sequence data (~100GB package)],&nbsp;[http://datadryad.org/handle/10255/dryad.91061 Hettne (2016) PLOS ONE]<span style="line-height: 20.8px;">&nbsp;(compressed gz file - 17.23 GB csv file when uncompressed)</span>
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*Packages containing many data files: [http://hdl.handle.net/10255/dryad.25 Mike Taylor's paleo package], [http://datadryad.org/handle/10255/dryad.1926 Janies (2011) Systematic Biology], [http://dx.doi.org/10.5061/dryad.f1cb2 Gardner (2011) Molecular Ecology Resources] with 51 separate fasta formatted files, data package with [http://dx.doi.org/10.5061/dryad.125 many files for different species]
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*Packages containing ZIP files with many aggregated files: [https://datadryad.org/resource/doi:10.5061/dryad.12 Chris Zmasek's apoptosis package], [http://datadryad.org/handle/10255/dryad.1923 Cossio (2010) PLOS Computational Biology], [http://dx.doi.org/10.5061/dryad.7990/1 Geraldes (2011) Molecular Ecology Resources], Acavedo et al. [http://datadryad.org/resource/doi:10.5061/dryad.g4n13 sound files]
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*Non-CC0 licenses: [http://dx.doi.org/10.5061/dryad.879st Swenson (2011) Systematic Biology] (file consists of code with GNU GPL 3.0 license), Sally Otto's package under Dryad's original license [http://datadryad.org/handle/10255/dryad.18 [17]], items in the [http://datadryad.org/handle/10255/dryad.148 BIRDD collection] under Dryad's original license (at least some of these can probably be moved to CC0)
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*Many authors: [http://doi.org/10.5061/dryad.mm54f D'Hont (2012) Nature]
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*Retractions: [http://datadryad.org/resource/doi:10.5061/dryad.fv21r Pryke et al (2014)], [https://doi.org/10.5061/dryad.33f0n Laskowski et al (2020)]
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= Connections with other repositories and platforms =
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== TreeBASE ==
  
Data package that is a portion of a larger dataset: [http://dx.doi.org/doi:10.5061/dryad.223 Payne]
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Data packages with related content in TreeBASE: [https://doi.org/10.5061/dryad.nr2h5 Balboni et al.] [https://doi.org/10.5061/dryad.0164h Rocha et al.] [http://dx.doi.org/10.5061/dryad.82 Sam Price's hunting package], [http://datadryad.org/handle/10255/dryad.7978 Melo (2011) Molecular Ecology] (TB link in article Data Accessibility section)
  
Data packages under embargo: [http://dx.doi.org/10.5061/dryad.jh87h], [http://dx.doi.org/10.5061/dryad.1fm3f]
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== GenBank ==
  
Data packages with extended embargoes: [http://datadryad.org/handle/10255/dryad.33566 Meirmans (2011) Molecular Ecology] (three years by request of journal editors), [http://datadryad.org/handle/10255/dryad.33775 Mueller (2011) Evolution] (three years by request of journal editors), [http://datadryad.org/handle/10255/dryad.33824 Mueller (2011) Molecular Ecology] (three years by request of journal editors), [http://datadryad.org/handle/10255/dryad.33972 Dewar (2011) Molecular Ecology] (two years by request of journal editors), [http://datadryad.org/handle/10255/dryad.33979 Rode (2011) Evolution] (three years by request of journal editors), [http://datadryad.org/handle/10255/dryad.37584 Morrissey (2012) Evolution] (ten years by request of journal editors
+
Package with links to content in GenBank: [http://datadryad.org/handle/10255/dryad.8437 Rocha-Olivares (2011) JHered]
  
Data packages with non-CC0 licensing: [http://dx.doi.org/10.5061/dryad.879st Swenson (2011) Systematic Biology] (file consists of code with GNU GPL 3.0 license), Sally Otto's package under Dryad's original license [http://datadryad.org/handle/10255/dryad.18], items in the [http://datadryad.org/handle/10255/dryad.148 BIRDD collection] under Dryad's original license (at least some of these can probably be moved to CC0)
+
Package in which article lists GenBank records in Data Accessibility section: [http://datadryad.org/handle/10255/dryad.7978 Melo (2011) Molecular Ecology] (no direct link from Dryad to GenBank)
  
Harvested item in Japanese: [http://datadryad.org/handle/10255/dryad.17753]
+
GenBank record with LinkOut to Dryad: [http://www.ncbi.nlm.nih.gov/nuccore/316925971 http://www.ncbi.nlm.nih.gov/nuccore/316925971]
 +
 
 +
[http://www.ncbi.nlm.nih.gov/pubmed?LinkName=nuccore_pubmed&from_uid=316925971 PubMed record] with LinkOut to Dryad package.
 +
 
 +
== Code/software in Github, Bitbucket ==
 +
 
 +
Package with links to content in Bitbucket: [http://dx.doi.org/10.5061/dryad.48hq1 Alvarado-Serrano (2016) Methods in Ecology and Evolution]
 +
 
 +
Package with links to content in Github: [http://dx.doi.org/10.5061/dryad.mb0sd 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. [http://tree.opentreeoflife.org/curator/study/view/ot_237 [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 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 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 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 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: [http://data.bris.ac.uk/data/dataset/cef0e89d595144212006a31cf822cd55 1], [http://data.bris.ac.uk/data/dataset/2fb9ff5e7fd6bc3191bef815311c5272 2]
 +
 
 +
= Examples by file type =
 +
 
 +
See [http://wiki.datadryad.org/Opening_Files 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&nbsp;[http://dx.doi.org/10.5061/dryad.879c0 Hoffman (2015) &nbsp;International Journal of Image and Data Fusion]
 +
*CT scans:&nbsp;[http://datadryad.org/resource/doi:10.5061/dryad.v1d30 <span data-cke-bookmark="1" style="display: none;">&nbsp;</span>Schachner (2013) Nature<span data-cke-bookmark="1" style="display: none;">&nbsp;</span>]
 +
*Dinosaur animations: [http://datadryad.org/resource/doi:10.5061/dryad.hh74n Allen (2013) Nature]
 +
*Hosted HTML [http://dx.doi.org/10.5061/dryad.1st98 Revell et al (2015) Evolution], [http://dx.doi.org/10.5061/dryad.79411 Cohen et al (2013) Journal of Paleontology]
 +
*Multilayer Temporal Network of Public Transport in Great Britain.&nbsp;Multilayer node-list and edge-list, where each layer is associated to a mode of transport and each node is geo-referenced: [http://datadryad.org/resource/doi:10.5061/dryad.pc8m3 Gallotti (2015) Scientific Data]
  
 
Data of specific file types; non-proprietary file formats are preferable:
 
Data of specific file types; non-proprietary file formats are preferable:
* csv  [http://dx.doi.org/10.5061/dryad.87ht85rs], [http://datadryad.org/handle/10255/dryad.1254], [http://datadryad.org/handle/10255/dryad.1300], [http://datadryad.org/handle/10255/dryad.2017]
 
* nexus [http://www.datadryad.org/handle/10255/dryad.1159], [http://datadryad.org/handle/10255/dryad.1310]
 
* txt [http://datadryad.org/handle/10255/dryad.1237], [http://datadryad.org/handle/10255/dryad.2021], [http://datadryad.org/handle/10255/dryad.2020]
 
* Word doc with table [http://datadryad.org/handle/10255/dryad.1146]
 
* Mathematica files [http://datadryad.org/handle/10255/dryad.18]
 
* Origin files [http://datadryad.org/handle/10255/dryad.8729]
 
* mov [http://datadryad.org/handle/10255/dryad.33701] (both files in this package)
 
* kml [http://datadryad.org/handle/10255/dryad.33804]
 
* wav [http://datadryad.org/handle/10255/dryad.35457]
 
* mp3 [http://dx.doi.org/10.5061/dryad.h0228]
 
  
[[Category:Software]]
+
*asc (ASCII grid files) [http://datadryad.org/resource/doi:10.5061/dryad.7gh65757 Munshi-South (2012) Molecular Ecology]
[[Category:Metadata]]
+
*avi [http://datadryad.org/resource/doi:10.5061/dryad.2m65j Dennenmoser (2012) Evolution] (battling fiddler crab video!)
[[Category:Usability]]
+
*bam [http://datadryad.org/resource/doi:10.5061/dryad.85078/2 Parchman (2013) Molecular Ecology], [http://datadryad.org/resource/doi:10.5061/dryad.79kh0/1 Malenfant (2013) Molecular Ecology Resources]
[[Category:Public Relations]]
+
*cel [http://dx.doi.org/10.5061/dryad.1pj04 Olarte (2015) Molecular Ecology]
 +
*csv [http://dx.doi.org/10.5061/dryad.87ht85rs Bradshaw (2012) Heredity], [http://datadryad.org/handle/10255/dryad.1254 Pyron (2009) Molecular Ecology], [http://datadryad.org/handle/10255/dryad.1300 Chun (2009) Molecular Ecology], [http://datadryad.org/handle/10255/dryad.2017 Krist (2007) Behavioral Ecology and Sociobiology]
 +
*cvw [http://dx.doi.org/10.5061/dryad.vb855 Caro (2014) eLife]
 +
*doc (with table) [http://datadryad.org/resource/doi:10.5061/dryad.1146/1 Tezanos-Pinto (2009) Journal of Heredity]
 +
*docx [http://datadryad.org/resource/doi:10.5061/dryad.322bb/1 Neave (2013) PLoS ONE]
 +
*dta (Stata data file) [http://datadryad.org/resource/doi:10.5061/dryad.80q86/1 Harris (2013) BMJ Open]
 +
*fdi (Network Draw file) [http://datadryad.org/handle/10255/dryad.59441 Burzyński (2014) Heredity]
 +
*fasta [http://datadryad.org/resource/doi:10.5061/dryad.7kb11/1 Muñoz (2013) PeerJ]
 +
*fna [http://datadryad.org/resource/doi:10.5061/dryad.b70pn/3 Peay (2012) Molecular Ecology]
 +
*gdb (Geodatabase) [http://dx.doi.org/10.5061/dryad.4n86v Sochi (2015) Journal of Applied Ecology]
 +
*gtx (Genetix file) [http://datadryad.org/resource/doi:10.5061/dryad.b5r86/3 Adjeroud (2013) Marine Biology]
 +
*hdr/img pair [http://dx.doi.org/10.5061/dryad.1642b Li (2014) PLOS One]
 +
*ics/ids pair [http://dx.doi.org/10.5061/dryad.90ps4 Takemura (2016) Journal of Cell Science]
 +
*jar [http://datadryad.org/resource/doi:10.5061/dryad.848ks/1 Jalasvuori (2014) Molecular Ecology]
 +
*jpg [http://datadryad.org/resource/doi:10.5061/dryad.3231b/1 Jansen (2013) Palaeontology]
 +
*kml [http://datadryad.org/resource/doi:10.5061/dryad.1t32v/1 Kawada (2011) ZooKeys]
 +
*lsm [http://dx.doi.org/10.5061/dryad.90ps4 Takemura (2016) Journal of Cell Science]
 +
*m (Matlab file) [http://datadryad.org/resource/doi:10.5061/dryad.nh3d2/8 Runemark (2013) Molecular Ecology], [http://datadryad.org/resource/doi:10.5061/dryad.490p9/4 Prunier (2013) Molecular Ecology]
 +
*map [http://datadryad.org/resource/doi:10.5061/dryad.p88q8/1 Feulner (2013) Molecular Ecology]
 +
*mas [http://dx.doi.org/10.5061/dryad.9t0g2 Petrović (2015) BMC Evolutionary Biology]
 +
*mat [http://datadryad.org/resource/doi:10.5061/dryad.2j9p4/1 Liu (2013) Proceedings of the National Academy of Sciences of the United States of America]
 +
*mov [http://datadryad.org/handle/10255/dryad.33701 Carter (2011) Biological Journal of the Linnean Society]
 +
*mp3 [http://dx.doi.org/10.5061/dryad.h0228 MacCallum (2012) Proceedings of the National Academy of Sciences of the United States of America], [http://dx.doi.org/10.5061/dryad.pm166 Abraham (2013) Zootaxa]
 +
*mp4 (an interesting data animation) [http://datadryad.org/bitstream/handle/10255/dryad.45430/modularity.mp4?sequence=1 Clune (2013) Proceedings of the Royal Society B]
 +
*nb (Mathematica files) [http://datadryad.org/handle/10255/dryad.18 Hill (2007) Genetics]
 +
*nexus [http://datadryad.org/handle/10255/dryad.1310 Blackburn (2008) Molecular Phylogenetics and Evolution]
 +
*nii [http://dx.doi.org/10.5061/dryad.3s06b Murphy (2016) Philosophical Transactions of the Royal Society B]
 +
*nwk [http://datadryad.org/resource/doi:10.5061/dryad.dk712/2 Martin (2013) Genome Research]
 +
*obj [http://dx.doi.org/10.5061/dryad.9ct2f Brassey (2012) Journal of the Royal Society Interface] 3D scan format from Geomagic Studio
 +
*ods (OpenDocument Spreadsheet) [http://datadryad.org/handle/10255/dryad.56875 Latour (2014) Proceedings of the Royal Society B]
 +
*Origin files [http://datadryad.org/handle/10255/dryad.8729 Leng (2011) Molecular Ecology]
 +
*pbs [http://datadryad.org/resource/doi:10.5061/dryad.pq143/7 Stanton-Geddes (2012) PLoS ONE]
 +
*pdf [http://datadryad.org/resource/doi:10.5061/dryad.dc25r/3 Reeves (2013) PLoS ONE]
 +
*ped (for use with PLINK, a free, open-source whole genome association analysis toolset) [http://datadryad.org/resource/doi:10.5061/dryad.bc598/1 Murray (2013) BMC Evolutionary Biology]
 +
*phy [http://datadryad.org/resource/doi:10.5061/dryad.hn104/6 DeBiasse (2014) Molecular Ecology]
 +
*png [http://datadryad.org/resource/doi:10.5061/dryad.0q7pc/1 Aguilar (2013) Zookeys]
 +
*prm [http://datadryad.org/resource/doi:10.5061/dryad.p88q8/5 Feulner (2013) Molecular Ecology]
 +
*psf [http://dx.doi.org/10.5061/dryad.65pm3 Napolitano (2015) Journal of Heredity]
 +
*py [http://datadrayd.org/resource/doi:10.5061/dryad.92kg0 Encinas-Viso (2014) Journal of Evolutionary Biology]
 +
*qgd [http://dx.doi.org/10.5061/dryad.ps70b Crawford (2015) Biology Letters]
 +
*R [http://datadryad.org/resource/doi:10.5061/dryad.mk364/2 Viricel (2013) Molecular Ecology Resources]
 +
*Rmd [http://dx.doi.org/10.5061/dryad.mj226 Boettiger (2015) Proceedings of the Royal Society B]
 +
*raw [http://datadryad.org/handle/10255/dryad.50267 McNulty (2013) PLoS Biology]
 +
*rtf [http://datadryad.org/handle/10255/dryad.53596 Wu (2013) PLoS ONE]
 +
*sff [http://datadryad.org/resource/doi:10.5061/dryad.45pv2 Botnen (2014) Molecular Ecology], [http://datadryad.org/resource/doi:10.5061/dryad.b70pn/4 Peay (2012) Molecular Ecology]
 +
*spf [http://dx.doi.org/10.5061/dryad.1fj75 Meilink (2015) Molecular Ecology]
 +
*tps [http://datadryad.org/resource/doi:10.5061/dryad.61s1n/1 Stubbs (2013) Proceedings of the Royal Society B]
 +
*tre [http://datadryad.org/resource/doi:10.5061/dryad.457f7/1 Chatelet (2013) International Journal of Plant Sciences]
 +
*tsv [http://dx.doi.org/10.5061/dryad.n940b Vijaykrishna (2015) eLife]
 +
*txt [http://datadryad.org/handle/10255/dryad.1237 Henry (2009) Molecular Ecology], [http://datadryad.org/handle/10255/dryad.2021 Anderson (2010) Paleobiology]
 +
*xls [http://datadryad.org/resource/doi:10.5061/dryad.fv487/1 Pichlmüller (2013) Amphibia-Reptilia]
 +
*xlsx [http://datadryad.org/resource/doi:10.5061/dryad.708j7/1 Baker (2013) Marine Ecology Progress Series]
 +
*xml [http://dx.doi.org/10.5061/dryad.5jt5j Colombo (2014) Journal of Evolutionary Biology]
 +
*wav [http://datadryad.org/resource/doi:10.5061/dryad.75nn1932/2 Francis (2011) PLoS ONE]
 +
 
 +
Compressed formats:
 +
 
 +
*gz [http://datadryad.org/resource/doi:10.5061/dryad.h5t68 Gross (2013) BMC Genomics]
 +
*rar [http://datadryad.org/resource/doi:10.5061/dryad.8416/1 Aquilino (2011) Molecular Ecology Resources]
 +
*tgz [http://datadryad.org/resource/doi:10.5061/dryad.85078/1 Parchman (2013) Molecular Ecology]
 +
*zip [http://datadryad.org/resource/doi:10.5061/dryad.777jk760/1 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 [https://docs.google.com/spreadsheet/ccc?key=0AqchxCiDYmMzdElBTWN0S01sQm5FakVRYjhRX1NHS3c&usp=sharing 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 http://dx.doi.org/10.5061/dryad.234]
 +
 
 +
== Corrections based on data reanalysis ==
 +
 
 +
*[http://bmjopen.bmj.com/content/2/3/e000311corr1.full http://bmjopen.bmj.com/content/2/3/e000311corr1.full]
 +
 
 +
== Use in classes, textbooks, and other educational contexts ==
 +
 
 +
*[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)
 +
*Used to teach quantitative biology to undergraduates: &nbsp;[https://qubeshub.org/groups/dryadlabnetwork QUBES DryadLab Network]&nbsp;and other uses by the QUBES community&nbsp;[https://qubeshub.org/members/1018 https://qubeshub.org/members/1018]
 +
*[https://books.google.com/books?id=3UWIGK8A594C&pg=PA4&lpg=PA4&dq=datadryad#v=onepage&q=datadryad&f=false 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 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 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 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 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 http://dx.doi.org/10.1111/evo.12156]
 +
[[Category:Software]]<br/>[[Category:Metadata]]<br/>[[Category:Usability]]<br/>[[Category:Public Relations|Public_Relations]]

Latest revision as of 11:59, 21 January 2020

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

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

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

  • 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

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

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

Some popular data packages

  • 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: 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:

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