integrating manuscript processing with the dryad data repository
DESCRIPTION
Integrating manuscript processing with the Dryad data repository. A step-by-step overview June 2011. Basic Process – Archiving at Article Acceptance. Author submits manuscript to journal . Submit manuscript. Submit manuscript. Peer review. Acceptance notification. - PowerPoint PPT PresentationTRANSCRIPT
Integrating manuscript processing with the Dryad data repository
A step-by-step overview
June 2011
BASIC PROCESS – ARCHIVING AT ARTICLE ACCEPTANCE
Submit manuscript Author submits manuscript to journal
Peer review Acceptance notification
Submit manuscript
Journal sends…1. notification to Dryad of
manuscript acceptance2. request to author to
upload data to Dryad, including URL with ms #
Dryad creates provisional record for the manuscript, with authors, title, abstract, etc.
Journal Name: Molecular EcologyPrint 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. 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 from an integrated journal to Dryad (acceptance)
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 data
Peer review Acceptance notification
Submit manuscript
Author submits data to Dryad, using the link sent by the journal to the provisional record
Submit data
Peer review Acceptance notification
Curation
Data DOIProduction
Submit manuscript
Dryad curator…1. reviews &
approves the data files
2. notifies journal and author of 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
Sample email notice Dryad indicating data package DOI
Submit data
Peer review Acceptance notification
Curation
Data DOIProduction
Submit manuscript
ArticlePublication
Data publication
Journal article is published with link to data DOI
Dryad publishes data files with reference to article
Submit data
Peer review Acceptance notification
Curation
Data DOIProduction
Submit manuscript
ArticlePublication
Data publication
Article metadata
Curation
At article publication, journal notifies Dryad of final bibliographic details
Dryad updates reference to article
Submit data
Peer review Acceptance notification
Curation
Data DOIProduction
Submit manuscript
ArticlePublication
Data publication
Article metadata
Curation
Journals are only responsible for the two notifications circled in red.
PROCESS INCLUDING PEER REVIEW
Submit manuscript Author submits manuscript to journal
Manuscript metadata
Submit manuscript
Journal sends…1. notification to Dryad of
new manuscript2. request to author to
upload data to Dryad, including URL with ms #
Dryad creates provisional record for the manuscript, with authors, title, abstract, etc.
Journal Name: Molecular EcologyPrint ISSN: 0962-1083Online ISSN: 1365-294XJournal Admin Email: [email protected] Editor: Tim VinesJournal Editor Email: [email protected] Status: in reviewMS 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. 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 from an integrated journal to Dryad (at manuscript submission)
Sample email from journal to author encouraging data deposit & providing the 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://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 data
Submission notification
Submit manuscript
Author submits data to Dryad, using the link sent by the journal to the provisional record
Submit data
Submission notification
Peer reviewReview passcode
Submit manuscript
Dryad sends reviewer passcode to journal, for dissemination to peer reviewers
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 indicating reviewer access URL
Submit data
Submission notification
Peer reviewReview passcode
Acceptance notification Curation
Data DOIProduction
Submit manuscript
Dryad curator…1. reviews &
approves the data files
2. notifies journal and author of DOI
Upon final article acceptance, journal…1. notifies Dryad 2. includes Dryad
DOI in article text
Journal Name: Molecular EcologyPrint 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. 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 from an integrated journal to Dryad (acceptance)
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
Sample email notice Dryad indicating data package DOI
Submit data
Submission notification
Peer reviewReview passcode
Acceptance notification Curation
Data DOIProduction
ArticlePublication
Data publication
Submit manuscript
Journal article is published with link to data DOI
Dryad publishes data files with link to article
Submit data
Submission notification
Peer reviewReview passcode
Acceptance notification Curation
Data DOIProduction
Article metadataArticle
Publication
Data publication
Submit manuscript
At article publication, journal notifies Dryad of final bibliographic details
Curation
Submit data
Submission notification
Peer reviewReview passcode
Acceptance notification Curation
Data DOIProduction
Article metadata Curation
Submit manuscript 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.
DATA CITATION
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
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.
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 [email protected]– Peggy Schaeffer [email protected]