integrating manuscript processing with the dryad digital repository a step-by-step overview march...

Integrating manuscript processing with the Dryad Digital Repository

A step-by-step overview

March 2014

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BASIC PROCESS – ARCHIVING AT ARTICLE ACCEPTANCE

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Submit manuscriptAuthor submits manuscript to journal

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Peer reviewPeer review

Acceptance notification

Submit manuscript

Journal sends…1.notification to Dryad system of manuscript acceptance2.request to author to deposit data to Dryad, including custom link for the manuscript

Dryad creates provisional record for the manuscript, with authors, title, abstract, etc.

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Journal Name: Molecular EcologyJournal Code: XXXXPrint ISSN: 0962-1083Online ISSN: 1365-294XJournal Admin Email: [email protected] Editor: Tim VinesJournal Editor Email: [email protected] Status: acceptedMS Reference Number: XXXXXMS Title: Contrasting pattern of natural variation in global Drosophila melanogaster populationsMS Authors: Nunes, Maria; Neumeier, Hannah; Schlötterer, ChristianContact Author: Maria NunesContact 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 – EmpiricalAbstract: 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........

Sample email notice from integrated journal to Dryad, sent upon ms acceptance:

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Bolded fields are mandatory

mailto:[email protected]

Sample email from journal to author inviting data deposit, providing the custom Dryad link:

Dear XXXXXXXXXXX,

Congratulations again on the acceptance of your manuscript, XXXXXXXXXXXX

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?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.

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Submit data

Peer reviewPeer review Acceptance notification

Submit manuscript

Author submits data to Dryad, using the link sent by the journal.

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Submit data


CurationCuration

Data DOIProductionProduction

Submit manuscript

Dryad curator…1. reviews & approves the

data files2. notifies journal and author

of DOI

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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.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 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

Sample email notice from Dryad to author indicating data package DOI:

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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: 2New deposits associated with publications in this journal: 2

Please find the data DOIs for new deposits below, for inclusion in the published articles.

Layton EVA-2013-048-OA.R1 doi:10.5061/dryad.13j34Smith-Rodel EVA-2013-104-OA doi:10.5061/dryad.m9st63

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.

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Submit data


CurationCuration


Submit manuscript

ArticlePublication

ArticlePublication

Data publication

Data publicationJournal article

is published with link to data DOI

Dryad publishes data files with reference to article

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Submit data


CurationCuration


Submit manuscript

ArticlePublication

ArticlePublication

Data publication

Data publication

CurationCuration

After article publication, Dryad updates the article citation to include final bibliographic details

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Submit data


CurationCuration


Submit manuscript

ArticlePublication

ArticlePublication

Data publication

Data publication

CurationCuration

Journals are only responsible for the notification circled in red. 13datadryad.org

REVIEW WORKFLOW

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Submit manuscriptAuthor submits manuscript to journal

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Manuscript metadata

Submit manuscript

Journal sends…1.notification to Dryad of submitted manuscript2.request to author to upload data to Dryad, including URL

Dryad creates provisional record for the manuscript, with authors, title, abstract, etc.

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Journal Name: Molecular EcologyJournal Code: XXXXPrint ISSN: 0962-1083Online ISSN: 1365-294XJournal Admin Email: [email protected] Editor: Tim VinesJournal Editor Email: [email protected] Status: SubmittedMS Reference Number: XXXXXMS Title: Contrasting pattern of natural variation in global Drosophila melanogaster populationsMS Authors: Nunes, Maria; Neumeier, Hannah; Schlötterer, ChristianContact Author: Maria NunesContact 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 – EmpiricalAbstract: 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 .....................

First email notice from integrated journal to Dryad, sent at manuscript submission:

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Sample email from journal to author, inviting data deposit & providing the custom Dryad URL:

Dear XXXXXXXXXXX,

Thank you for submission of your manuscript, XXXXXXXXXXXX

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?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.

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Submit data

Submission notification

Submit manuscript

Author submits data to Dryad, using the link sent by the journal to the provisional record.

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Submit data


Peer reviewPeer reviewReview passcode

Submit manuscript

Dryad sends review passcode to journal.

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Dryad has received the following data package:Title: Data from: Contrasting pattern of natural variation in global Drosophila melanogaster populationsSubmitted by: Jane User ([email protected])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

Journal editors and anonymous peer reviewers may view the submission for review purposes using the following url:http://datadryad.org/submission-review?wfID=517&token=d8420534-3477-4986-9366-bb17856d818b

Many thanks!

The Dryad Team

Sample email notice from Dryad with review passcode URL:

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Submit data



Acceptance notification CurationCuration


Submit manuscript

Dryad curator…1. reviews & approves data

files2. notifies journal and author

of DOI

At article acceptance, journal…1.notifies Dryad 2.includes Dryad DOI in article

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Journal Name: Molecular EcologyJournal Code: XXXXPrint ISSN: 0962-1083Online ISSN: 1365-294XJournal Admin Email: [email protected] Editor: Tim VinesJournal Editor Email: [email protected] Status: acceptedMS Reference Number: XXXXXMS Title: Contrasting pattern of natural variation in global Drosophila melanogaster populationsMS Authors: Nunes, Maria; Neumeier, Hannah; Schlötterer, ChristianContact Author: Maria NunesContact 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 – EmpiricalAbstract: 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........

Second email notice from integrated journal to Dryad, sent upon ms acceptance:

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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.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

Sample email notice from Dryad to author indicating data package DOI

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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: 9New deposits of data in review: 0New notifications of accepted publications in this journal: 4New 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.R1 doi:10.5061/dryad.jv45hMagnusson JRL-2013-002791.R2 doi:10.5061/dryad.58vg9

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

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Submit data





ArticlePublication

ArticlePublication

Data publicatio

n

Data publicatio

n

Submit manuscript

Journal article is published with Dryad data DOI

Dryad publishes data files with link to article

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Submit data





CurationCuration

Submit manuscript

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.

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ArticlePublication

ArticlePublication

Data publicatio

n

Data publicatio

n

DATA CITATION

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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. http://dx.doi.org/10.5061/dryad.8384

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.

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For more information…

• Complete documentation & examples are on the Dryad wiki: http://wiki.datadryad.org/Submission_Integration

• Contact the Dryad team:– Ryan Scherle [email protected]– Peggy Schaeffer [email protected] – Jamie Lamkin [email protected]– [email protected]

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integrating manuscript processing with the dryad digital repository a step-by-step overview march...

Documents

manuscript author

manuscript dryad

manuscript journal

data deposit

dryad data repository

contact author address

christian contact author

contact author country