Integrating manuscript processing
with the Dryad data repository
A step-by-step overview
June 2011
Submit manuscript
Author submits
manuscript to journal
Submit manuscript
Manuscript metadata
Journal sends…
1. notification to Dryad of
new manuscript
2. request to author to
upload data to Dryad,
including URL with ms #
Dryad creates provisional
record for the manuscript,
with authors, title,
abstract, etc.
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: 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. Thirty-five populations originating from five continents were
compared. In agreement with previous microsatellite studies, sub-Saharan African populations were the most variable ones.
Consistent with previous reports of a single ‘out of Africa’ habitat expansion, we found that non-African populations contained a
subset of the African alleles. The pattern of variation detected for the mitochondrial sequences differed substantially. The most
divergent haplotypes were detected in the Mediterranean region while Africa harbored most haplotypes, which were all closely
related. In the light of the well-established African origin of D. melanogaster, our results cast severe doubts about the suitability of
mtDNA for biogeographic inference in this model organism.
Sample email from journal to author
encouraging data deposit & providing the Dryad URL
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,
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.
Submit manuscript
Submit data
Submission notification
Author submits data to Dryad,
using the link sent by the
journal to the provisional
record
Submit manuscript
Submit data
Submission notification
Review passcode
Peer review
Dryad sends reviewer
passcode to journal, for
dissemination to peer
reviewers
NOTE: this step only applies if
the journal has chosen to
make data available for the
peer review process
Sample email notice from Dryad indicating reviewer access 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.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
Submit manuscript
Submit data
Submission notification
Review passcode
Peer review
Acceptance notification
Curation
Production
Dryad curator…
1. reviews &
approves the
data files
2. notifies journal
and author of
DOI
Data DOI
Upon final article acceptance,
journal…
1. notifies Dryad
2. includes Dryad DOI in
final article
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: 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. Thirty-five populations originating from five continents were
compared. In agreement with previous microsatellite studies, sub-Saharan African populations were the most variable ones.
Consistent with previous reports of a single ‘out of Africa’ habitat expansion, we found that non-African populations contained a
subset of the African alleles. The pattern of variation detected for the mitochondrial sequences differed substantially. The most
divergent haplotypes were detected in the Mediterranean region while Africa harbored most haplotypes, which were all closely
related. In the light of the well-established African origin of D. melanogaster, our results cast severe doubts about the suitability of
mtDNA for biogeographic inference in this model organism.
Sample email notice Dryad 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 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
Submit manuscript
Submit data
Submission notification
Review passcode
Peer review
Acceptance notification
Curation
Production
Data DOI
Data
publicatio
n
Article
Publication
Dryad
publishes data
files with link
to article
Journal article
is published
with link to
data DOI
Submit manuscript
Submit data
Submission notification
Review passcode
Peer review
Acceptance notification
Curation
Production
Data DOI
Data
publicatio
n
Article metadata
Article
Publication
Curation
At article
publication, journal
notifies Dryad of
final bibliographic
details
Submit manuscript
Submit data
Submission notification
Review passcode
Peer review
Acceptance notification
Curation
Production
Data DOI
Article metadata
Curation
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.
Submit manuscript
Peer review
Submit data
Acceptance notification
Curation
Production
Data DOI
Article metadata
Curation
Simplified process
(without peer
review)
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
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