Integrating manuscript processing with the Dryad data repository

1. Integrating manuscript processing with the Dryad data repository A step-by-step overview June 2011

2. Basic Process – Archiving at Article Acceptance

3. Author submits manuscript to journal Submit manuscript

4. Submit manuscript Peer review Acceptance notification Dryad creates provisional record for the manuscript, with authors, title, abstract, etc. Journal sends… notification to Dryad of manuscript acceptance request to author to upload data to Dryad, including URL with ms #

5. Sample email notice from an integrated journal to Dryad (acceptance) Journal Name: Molecular Ecology Print ISSN: 0962-1083 Online ISSN: 1365-294X Journal Admin Email: editorial.office@molecol.com Journal Editor: Tim Vines Journal Editor Email: managing.editor@molecol.com Article Status: accepted MS Reference Number: XXXXX MS Title: Contrastingpattern of naturalvariation in global Drosophilamelanogasterpopulations MS Authors: Nunes, Maria; Neumeier, Hannah; Schlötterer, Christian ContactAuthor: Maria Nunes Contact Author Email: (removed) ContactAuthor Address 1: (removed) Contact Author Address 2: Contact Author Address 3: Contact Author City: (removed) Contact Author State: Contact Author Country: (removed) Contact Author ZIP/Postal Code: (removed) Keywords: MolecularEvolution, Phylogeography, Population Dynamics, Population Genetics – Empirical Abstract: Despitethepopularity of Drosophilamelanogaster in functionalandevolutionarygenetics, the global pattern of naturalvariation has not yet beencomprehensivelydescribed in thisspecies. Forthefirst time, wereport a combinedsurveyusingneutralmicrosatellitesandmitochondrialsequencevariationjointly. Thirty-fivepopulationsoriginatingfromfivecontinentswerecompared. Inagreementwithpreviousmicrosatellitestudies, sub-SaharanAfricanpopulationswerethemostvariableones. Consistentwithpreviousreports of a single ‘out of Africa’ habitat expansion, wefoundthatnon-Africanpopulationscontained a subset of theAfricanalleles. Thepattern of variationdetectedforthemitochondrialsequencesdifferedsubstantially. Themostdivergenthaplotypesweredetected in theMediterraneanregionwhileAfricaharboredmosthaplotypes, whichwereallcloselyrelated. Inthelight of thewell-establishedAfricanorigin of D. melanogaster, ourresultscast severe doubtsaboutthesuitability of mtDNAforbiogeographicinference in this model organism.

6. Sample email from journal to author encouraging data deposit & providing the Dryad URL Dear XXXXXXXXXXX,Congratulations again on the acceptance of your manuscript, XXXXXXXXXXXXWe would like to encourage you to deposit the data underlying this article in the Dryad Data Repository, http://www.datadryad.org. As you may recall, we ask all authors to agree to make data available. This is a way to achieve that.Advantages of depositing data in Dryad include: * Visibility: Making your data available online (and linking it back to the publication) provides a new pathway for others to learn about your work through topical searches. * Citability: all data packages and data files you deposit will receive persistent, resolvable Digital Object Identifiers (DOIs) that can be used in a citation as well as listed on your CV. * Workload reduction: if you receive individual requests for data, you can simply direct them to the items in Dryad. * Preservation: your data files will be permanently and safely archived in perpetuity. * Impact: you will garner citations through the reuse of your data, and you can monitor the use of your data through Dryad's usage statistics The link below will take you to the Dryad record for your article, so you won't have to re-enter its bibliographic information, and can upload your files directly. More information about depositing data in Dryad is available at http://www.datadryad.org/depositing . Please use the following link:EXAMPLE: http://datadryad.org/submit?journalID=NNNN&manu=XXXXX (where NNNN is replaced by journal ID and XXXXX is replaced with a real manuscript number). Once you deposit your data package, it receives a unique and stable DOI identifier, which is immediately sent back to you and to the journal for inclusion in the published article. Depositing your data in good time for this to happen, is optimal; if the Dryad DOI doesn't appear in the final published article, that of course greatly weakens its connection to the underlying data.

7. Submit manuscript Submit data Peer review Acceptance notification Author submits data to Dryad, using the link sent by the journal to the provisional record

8. Submit manuscript Submit data Peer review Acceptance notification Dryad curator… reviews & approves the data files notifies journal and author of DOI Curation Production Data DOI

9. Sample email notice Dryad indicating data package DOI Thank you for your recent submission to the Dryad repository titled "Data from: Contrastingpattern of naturalvariation in global Drosophilamelanogasterpopulations". Your data package has been archived in Dryad and assigned a unique identifier, called a DOI. Including the data DOI in the published article will make readers aware that the data files are available, and enable their access and citation.   The DOI may be presented as follows: Data deposited at Dryad: doi:10.5061/dryad.123abc Dryad links your data to your published article; it is up to authors and journals to link the published article to its supporting data. Please work with your journals editorial and production staff to ensure  that the data DOI is included. Many journals specify a particular location for such links to data in repositories, or have a section on Data Accessibility. You can also provide your data DOI in the text, just before the References. If your article has already been published, use this DOI to refer others to your data. Please let us know if you have any questions or concerns. The Dryad Team

10. Submit manuscript Submit data Peer review Acceptance notification Dryad publishes data files with reference to article Curation Production Data DOI Journal article is published with link to data DOI Data publication Article Publication

11. Submit manuscript Submit data Peer review Acceptance notification Curation Production Data DOI At article publication, journal notifies Dryad of final bibliographic details Data publication Article metadata Article Publication Dryad updates reference to article Curation

12. Submit manuscript Submit data Peer review Acceptance notification Curation Journals are only responsible for the twonotifications circled in red. Production Data DOI Data publication Article metadata Article Publication Curation

13. Process Including Peer review

14. Author submits manuscript to journal Submit manuscript

15. Submit manuscript Manuscript metadata Journal sends… notification to Dryad of new manuscript request to author to upload data to Dryad, including URL with ms # Dryad creates provisional record for the manuscript, with authors, title, abstract, etc.

16. Sample email notice from an integrated journal to Dryad (at manuscript submission) Journal Name: Molecular Ecology Print ISSN: 0962-1083 Online ISSN: 1365-294X Journal Admin Email: editorial.office@molecol.com Journal Editor: Tim Vines Journal Editor Email: managing.editor@molecol.com Article Status: in review MS Reference Number: XXXXX MS Title: Contrastingpattern of naturalvariation in global Drosophilamelanogasterpopulations MS Authors: Nunes, Maria; Neumeier, Hannah; Schlötterer, Christian ContactAuthor: Maria Nunes Contact Author Email: (removed) ContactAuthor Address 1: (removed) Contact Author Address 2: Contact Author Address 3: Contact Author City: (removed) Contact Author State: Contact Author Country: (removed) Contact Author ZIP/Postal Code: (removed) Keywords: MolecularEvolution, Phylogeography, Population Dynamics, Population Genetics – Empirical Abstract: Despitethepopularity of Drosophilamelanogaster in functionalandevolutionarygenetics, the global pattern of naturalvariation has not yet beencomprehensivelydescribed in thisspecies. Forthefirst time, wereport a combinedsurveyusingneutralmicrosatellitesandmitochondrialsequencevariationjointly. Thirty-fivepopulationsoriginatingfromfivecontinentswerecompared. Inagreementwithpreviousmicrosatellitestudies, sub-SaharanAfricanpopulationswerethemostvariableones. Consistentwithpreviousreports of a single ‘out of Africa’ habitat expansion, wefoundthatnon-Africanpopulationscontained a subset of theAfricanalleles. Thepattern of variationdetectedforthemitochondrialsequencesdifferedsubstantially. Themostdivergenthaplotypesweredetected in theMediterraneanregionwhileAfricaharboredmosthaplotypes, whichwereallcloselyrelated. Inthelight of thewell-establishedAfricanorigin of D. melanogaster, ourresultscast severe doubtsaboutthesuitability of mtDNAforbiogeographicinference in this model organism.

17. Sample email from journal to author encouraging data deposit & providing the Dryad URL Dear XXXXXXXXXXX,Thank you for submission ofyour manuscript, XXXXXXXXXXXXWe would like to encourage you to deposit the data underlying this article in the Dryad Data Repository, http://www.datadryad.org. As you may recall, we ask all authors to agree to make data available. This is a way to achieve that.Advantages of depositing data in Dryad include: * Visibility: Making your data available online (and linking it back to the publication) provides a new pathway for others to learn about your work through topical searches. * Citability: all data packages and data files you deposit will receive persistent, resolvable Digital Object Identifiers (DOIs) that can be used in a citation as well as listed on your CV. * Workload reduction: if you receive individual requests for data, you can simply direct them to the items in Dryad. * Preservation: your data files will be permanently and safely archived in perpetuity. * Impact: you will garner citations through the reuse of your data, and you can monitor the use of your data through Dryad's usage statistics The link below will take you to the Dryad record for your article, so you won't have to re-enter its bibliographic information, and can upload your files directly. More information about depositing data in Dryad is available at http://www.datadryad.org/depositing . Please use the following link:EXAMPLE: http://datadryad.org/submit?journalID=NNNN&manu=XXXXX (where NNNN is replaced by journal ID and XXXXX is replaced with a real manuscript number). Once you deposit your data package, it receives a unique and stable DOI identifier, which is immediately sent back to you and to the journal for inclusion in the published article. Depositing your data in good time for this to happen, is optimal; if the Dryad DOI doesn't appear in the final published article, that of course greatly weakens its connection to the underlying data.

18. Submit manuscript Submit data Submission notification Author submits data to Dryad, using the link sent by the journal to the provisional record

19. Submit manuscript Submit data Submission notification Review passcode Peer review Dryad sends reviewer passcode to journal, for dissemination to peer reviewers

20. Sample email notice from Dryad indicating reviewer access URL Dryad has received the following data package: Title: Data from:Contrastingpattern of naturalvariation in global Drosophilamelanogasterpopulations Submitted by: Jane User (jane@someuniversity.edu) Data file(s): Microsatellite data Microsatellite Primers Dryad has assigned the following provisional DOI to the submission. This DOI may be included in the article manuscript. Although this DOI is not yet fully registered with the DOI system, it will be registered when the manuscript is accepted for publication. doi:10.5061/dryad.123abc Journaleditorsandanonymouspeerreviewersmayviewthesubmissionforreviewpurposesusingthefollowingurl: http://datadryad.org/submission-review?wfID=517&token=d8420534-3477-4986-9366-bb17856d818b Manythanks! TheDryad Team

21. Submit manuscript Submit data Submission notification Upon final article acceptance, journal… notifies Dryad includes Dryad DOI in article text Review passcode Peer review Acceptance notification Curation Production Data DOI Dryad curator… reviews & approves the data files notifies journal and author of DOI

22. Sample email notice from an integrated journal to Dryad (acceptance) Journal Name: Molecular Ecology Print ISSN: 0962-1083 Online ISSN: 1365-294X Journal Admin Email: editorial.office@molecol.com Journal Editor: Tim Vines Journal Editor Email: managing.editor@molecol.com Article Status: accepted MS Reference Number: XXXXX MS Title: Contrastingpattern of naturalvariation in global Drosophilamelanogasterpopulations MS Authors: Nunes, Maria; Neumeier, Hannah; Schlötterer, Christian ContactAuthor: Maria Nunes Contact Author Email: (removed) ContactAuthor Address 1: (removed) Contact Author Address 2: Contact Author Address 3: Contact Author City: (removed) Contact Author State: Contact Author Country: (removed) Contact Author ZIP/Postal Code: (removed) Keywords: MolecularEvolution, Phylogeography, Population Dynamics, Population Genetics – Empirical Abstract: Despitethepopularity of Drosophilamelanogaster in functionalandevolutionarygenetics, the global pattern of naturalvariation has not yet beencomprehensivelydescribed in thisspecies. Forthefirst time, wereport a combinedsurveyusingneutralmicrosatellitesandmitochondrialsequencevariationjointly. Thirty-fivepopulationsoriginatingfromfivecontinentswerecompared. Inagreementwithpreviousmicrosatellitestudies, sub-SaharanAfricanpopulationswerethemostvariableones. Consistentwithpreviousreports of a single ‘out of Africa’ habitat expansion, wefoundthatnon-Africanpopulationscontained a subset of theAfricanalleles. Thepattern of variationdetectedforthemitochondrialsequencesdifferedsubstantially. Themostdivergenthaplotypesweredetected in theMediterraneanregionwhileAfricaharboredmosthaplotypes, whichwereallcloselyrelated. Inthelight of thewell-establishedAfricanorigin of D. melanogaster, ourresultscast severe doubtsaboutthesuitability of mtDNAforbiogeographicinference in this model organism.

23. Sample email notice Dryad indicating data package DOI Thank you for your recent submission to the Dryad repository titled "Data from: Contrastingpattern of naturalvariation in global Drosophilamelanogasterpopulations". Your data package has been archived in Dryad and assigned a unique identifier, called a DOI. Including the data DOI in the published article will make readers aware that the data files are available, and enable their access and citation.   The DOI may be presented as follows: Data deposited at Dryad: doi:10.5061/dryad.123abc Dryad links your data to your published article; it is up to authors and journals to link the published article to its supporting data. Please work with your journals editorial and production staff to ensure  that the data DOI is included. Many journals specify a particular location for such links to data in repositories, or have a section on Data Accessibility. You can also provide your data DOI in the text, just before the References. If your article has already been published, use this DOI to refer others to your data. Please let us know if you have any questions or concerns. The Dryad Team

24. Submit manuscript Submit data Submission notification Review passcode Peer review Dryad publishes data files with link to article Acceptance notification Curation Production Data DOI Journal article is published with link to data DOI Data publication Article Publication

25. Submit manuscript Submit data Submission notification Review passcode Peer review Acceptance notification Curation Production Data DOI At article publication, journal notifies Dryad of final bibliographic details Data publication Article metadata Article Publication Curation

26. Submit manuscript Submit data This may look complicated, but journals are only responsible for the three notifications circled in red, and the first is only required if the peer review process is used. Submission notification Review passcode Peer review Acceptance notification Curation Production Data DOI Article metadata Curation

27. Data CITATION

28. A recent example from a PLoS ONE paper. Dryad reports the article DOI, and the article reports the Dryad DOI. This establishes a permanent reciprocal linkage between the article and its data. Article: Wu D, Wu M, Halpern A, Rusch DB, Yooseph S, Frazier M, Venter JC, Eisen JA (2011) 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:10.1371/journal.pone.0018011 Dryad data package: 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. Dryad Digital Repository. doi:10.5061/dryad.8384

29. For more information… • Complete documentation & examples are on the Dryad wiki: https://www.nescent.org/wg_dryad/Submission_Integration • Contact the Dryad team: • Ryan Scherle rscherle@nescent.org • Peggy Schaeffer pschaeffer@nescent.org