Integrating manuscript processing with the Dryad Digital Repository

Integrating manuscript processing with the Dryad Digital Repository A step-by-step overview March 2014 datadryad. org 1

BASIC PROCESS – ARCHIVING AT ARTICLE ACCEPTANCE datadryad. org 2

Author submits manuscript to journal Submit manuscript datadryad. org 3

Submit manuscript Peer review Acceptance notification Journal sends… 1. notification to Dryad system of manuscript acceptance 2. request to author to deposit data to Dryad, including custom link for the manuscript datadryad. org Dryad creates provisional record for the manuscript, with authors, title, abstract, etc. 4

Sample email notice from integrated journal to Dryad, sent upon ms acceptance: Journal Name: Molecular Ecology Journal Code: XXXX Print ISSN: 0962 -1083 Online ISSN: 1365 -294 X 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: Contrasting pattern of natural variation in global Drosophila melanogaster populations MS Authors: Nunes, Maria; Neumeier, Hannah; Schlötterer, Christian Contact Author: Maria Nunes Contact Author Email: (removed) Contact Author 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: Molecular Evolution, Phylogeography, Population Dynamics, Population Genetics – Empirical Abstract: Despite the popularity of Drosophila melanogaster in functional and evolutionary genetics, the global pattern of natural variation has not yet been comprehensively described in this species. For the first time, we report a combined survey using neutral microsatellites and mitochondrial sequence variation jointly. . . . Bolded fields are mandatory datadryad. org 5

Sample email from journal to author inviting data deposit, providing the custom Dryad link: Dear XXXXXX, Congratulations again on the acceptance of your manuscript, XXXXXX We would like to encourage you to deposit the data underlying this article in the Dryad Data Repository, at http: //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 datadryad. org/depositing. Please use the following link: EXAMPLE: http: //datadryad. org/submit? journal. ID=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 datadryad. org 6

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

Submit manuscript Peer review Submit data Acceptance notification Curation Production Data DOI Dryad curator… 1. reviews & approves the data files 2. notifies journal and author of DOI datadryad. org 8

Sample email notice from Dryad to author indicating data package DOI: Thank you for your recent submission to the Dryad repository titled "Data from: Contrasting pattern of natural variation in global Drosophila melanogaster populations". 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 available from the Dryad Digital Repository: http: //dx. doi. org/10. 5061/dryad. 123 abc 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 journal’s 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 for 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 datadryad. org 9

Weekly report to journal In the week since the last report (2013 -06 -14), Dryad has received the following. New notifications of accepted publications in this journal: 2 New deposits associated with publications in this journal: 2 Please find the data DOIs for new deposits below, for inclusion in the published articles. Layton Smith-Rodel EVA-2013 -048 -OA. R 1 EVA-2013 -104 -OA doi: 10. 5061/dryad. 13 j 34 doi: 10. 5061/dryad. m 9 st 63 The DOI may be presented as below: Data available from the Dryad Digital Repository: http: //dx. doi. org/10. 5061/dryad. NNNN Dryad links the data files to the published articles; it is up to journals to link published articles to their supporting data. Journal staff and authors collaborate to ensure that data DOIs are included in the appropriate locations for the print and online versions of published articles. datadryad. org 10

Submit manuscript Peer review Submit data Acceptance notification Curation Production Article Publication Data DOI Data publication Journal article is published with link to data DOI datadryad. org Dryad publishes data files with reference to article 11

Submit manuscript Peer review Submit data Acceptance notification Curation Production Data DOI Data publication Article Publication Curation datadryad. org After article publication, Dryad updates the article citation to include final bibliographic details 12

Submit manuscript Peer review Submit data Acceptance notification Curation Production Data DOI Data publication Article Publication Journals are only responsible for the notification circled in red. datadryad. org Curation 13

REVIEW WORKFLOW datadryad. org 14

Author submits manuscript to journal Submit manuscript datadryad. org 15

Submit manuscript Manuscript metadata Journal sends… 1. notification to Dryad of submitted manuscript 2. request to author to upload data to Dryad, including URL datadryad. org Dryad creates provisional record for the manuscript, with authors, title, abstract, etc. 16

First email notice from integrated journal to Dryad, sent at manuscript submission: Journal Name: Molecular Ecology Journal Code: XXXX Print ISSN: 0962 -1083 Online ISSN: 1365 -294 X Journal Admin Email: editorial. office@molecol. com Journal Editor: Tim Vines Journal Editor Email: managing. editor@molecol. com Article Status: Submitted MS Reference Number: XXXXX MS Title: Contrasting pattern of natural variation in global Drosophila melanogaster populations MS Authors: Nunes, Maria; Neumeier, Hannah; Schlötterer, Christian Contact Author: Maria Nunes Contact Author Email: (removed) Contact Author 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: Molecular Evolution, Phylogeography, Population Dynamics, Population Genetics – Empirical Abstract: Despite the popularity of Drosophila melanogaster in functional and evolutionary genetics, the global pattern of natural variation has not yet been comprehensively described in this species. For the first time, we report a combined survey. . . . . Bolded fields are mandatory datadryad. org 17

Sample email from journal to author, inviting data deposit & providing the custom Dryad URL: Dear XXXXXX, Thank you for submission of your manuscript, XXXXXX We would like to encourage you to deposit the data underlying this article in the Dryad Data Repository, http: //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? journal. ID=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 datadryad. org 18

Submit manuscript Submit data Submission notification Author submits data to Dryad, using the link sent by the journal to the provisional record. datadryad. org 19

Submit manuscript Submit data Submission notification Peer review Review passcode Dryad sends review passcode to journal. datadryad. org 20

Sample email notice from Dryad with review passcode URL: Dryad has received the following data package: Title: Data from: Contrasting pattern of natural variation in global Drosophila melanogaster populations 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. 123 abc Journal editors and anonymous peer reviewers may view the submission for review purposes using the following url: http: //datadryad. org/submission-review? wf. ID=517&token=d 8420534 -3477 -4986 -9366 -bb 17856 d 818 b Many thanks! The Dryad Team datadryad. org 21

Submit manuscript Submit data Submission notification Peer review Review passcode Acceptance notification Production Curation Data DOI Dryad curator… 1. reviews & approves data files 2. notifies journal and author of DOI At article acceptance, journal… 1. notifies Dryad 2. includes Dryad DOI in article datadryad. org 22

Second email notice from integrated journal to Dryad, sent upon ms acceptance: Journal Name: Molecular Ecology Journal Code: XXXX Print ISSN: 0962 -1083 Online ISSN: 1365 -294 X 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: Contrasting pattern of natural variation in global Drosophila melanogaster populations MS Authors: Nunes, Maria; Neumeier, Hannah; Schlötterer, Christian Contact Author: Maria Nunes Contact Author Email: (removed) Contact Author 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: Molecular Evolution, Phylogeography, Population Dynamics, Population Genetics – Empirical Abstract: Despite the popularity of Drosophila melanogaster in functional and evolutionary genetics, the global pattern of natural variation has not yet been comprehensively described in this species. For the first time, we report a combined survey using neutral microsatellites and mitochondrial sequence variation jointly. . . . Bolded fields are mandatory datadryad. org 23

Sample email notice from Dryad to author indicating data package DOI Thank you for your recent submission to the Dryad repository titled "Data from: Contrasting pattern of natural variation in global Drosophila melanogaster populations". 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 available from the Dryad Digital Repository: http: //dx. doi. org/10. 5061/dryad. 123 abc 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 datadryad. org 24

Weekly report to journal In the week since the last report (2013 -06 -14), Dryad has received the following. New notifications of manuscripts in review: 9 New deposits of data in review: 0 New notifications of accepted publications in this journal: 4 New archived deposits associated with publications in this journal: 2 Please find the data DOIs for new deposits below, for inclusion in the published articles. Almira JRL-2013 -002924. R 1 doi: 10. 5061/dryad. jv 45 h Magnusson JRL-2013 -002791. R 2 doi: 10. 5061/dryad. 58 vg 9 The DOI may be presented as below: Data available from the Dryad Digital Repository: http: //dx. doi. org/10. 5061/dryad. NNNN Dryad links the data files to the published articles; it is up to journals to link published articles to their supporting data. Journal staff and authors collaborate to ensure that data DOIs are included in the appropriate locations for the print and online versions of published articles datadryad. org 25

Submit manuscript Submit data Submission notification Peer review Review passcode Acceptance notification Production Curation Data DOI Data publication Article Publication Journal article is published with Dryad data DOI datadryad. org Dryad publishes data files with link to article 26

Submit manuscript Submit data Submission notification Peer review Review passcode Acceptance notification Production Article Publication Curation Data DOI This may look complicated, but journals are only responsible for the two notifications circled in red, and the first is only required if the review workflow is used. datadryad. org Data Curation publication 27

DATA CITATION datadryad. org 28

Dryad cites the article and its DOI, and the article cites the data and 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. PLo. S ONE 6(3): e 18011. 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. http: //dx. doi. org/10. 5061/dryad. 8384 datadryad. org 29

For more information… • Complete documentation & examples are on the Dryad wiki: http: //wiki. datadryad. org/Submission_Integration • Contact the Dryad team: – Ryan Scherle admin@datadryad. org – Peggy Schaeffer pschaeffer@datadryad. org – Jamie Lamkin jlamkin@datadryad. org – journalsetup@datadryad. org 30