Journal open-data policies: Difference between revisions

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Revision as of 15:13, 13 October 2012

This list is part of the Open Access Directory.

This list is still under development. Every part of it may change before the official launch, including its title, URL, and method of organization.

  • This is a list of journals with data-sharing mandates for their published articles.
  • When possible, please annotate each journal with its URL, its publisher, its ISSN, and the URL of its data policy. When possible, please annotate the data policies in the following ways:
    • When was the policy adopted and last revised?
    • Does it apply to some kinds of data and not other kinds? If so, which kinds?
    • Does it require (as opposed to encourage, request, invite, or accommodate) open data? If the language is vague or ambiguous, then quote it.
    • Does it specify a data repository? If so, which one?
    • Does it specify an open license or licensing terms? If so, which license or terms?
  • Alphabetical by journal title.

A

  • African Journal of Ecology
    • Publisher: Wiley Blackwell
    • ISSN: 0141-6707
    • Policy text: Data that is integral to the paper must be made available in such a way as to enable readers to replicate, verify and build upon the conclusions published in the paper. Any restriction on the availability of this data must be disclosed at the time of submission.
  • Animal Conservation
    • Publisher: Wiley Blackwell
    • ISSN: 1367-9430
    • Policy text: DNA sequence data published in Animal Conservation should be deposited in one of the EMBL/GenBank/DDBJ nucleotide sequence databases, and accession numbers must be included in the final version of the manuscript. Genetic data from sources other than the manuscript must either be publicly available (with accession numbers or citations provided) or the authors must have appropriate permission to use unpublished data. Such permission should be described explicitly in the covering letter
    • Type of data: DNA sequences
    • Repository: EMBL, GenBank, DDBJ
  • Aquatic Microbial Ecology
    • Publisher: Inter Research.
    • ISSN: 0948-3055
    • Policy text: Novel nucleotide or protein sequences must be deposited in the GenBank, EMBL or DDBJ databases and an accession number obtained
    • Type of data: New nucleotide or protein sequences.
    • Repository: EMBL, GenBank, DDBJ

B

  • BMC Evolutionary Biology
    • Publisher: Biomed Central (Note: guidelines across BMC journals are similar but not identical)
    • ISSN: 1471-2148
    • Policy text: Submission of a manuscript to BMC Evolutionary Biology implies that readily reproducible materials described in the manuscript, including all relevant raw data, will be freely available to any scientist wishing to use them for Non-commercial purposes. Nucleic acid sequences, protein sequences, and atomic coordinates should be deposited in an appropriate database in time for the accession number to be included in the published article. In computational studies where the sequence information is unacceptable for inclusion in databases because of lack of experimental validation, the sequences must be published as an additional file with the article… (continued)
    • Type of data: All raw data supporting publication.

C

D

  • Diversity and Distributions
    • Publisher: Wiley Blackwell
    • ISSN:1366-9516
    • Policy text: It is a condition of publication that papers using new molecular sequences must place the sequences in an appropriate database (e.g. GenBank). Relevant accession numbers should be provided in the final manuscript. Accession numbers are required for all sequences used in analyses, including existing sequences in databases... appendices may be provided for important primary data, which needs to be included in the paper. If, however, these data are very extensive, or if they are of only indirect relevance to the paper, they will normally be made available in an electronic form through the Journal's web pages
    • Types of data: All new molecular sequences.

E

  • Environmental and Experimental Botany
    • Publisher: Elsevier.
    • ISSN: 0098-8472.
    • Policy text: Accession numbers are unique identifiers in bioinformatics allocated to nucleotide and protein sequences to allow tracking of different versions of that sequence record and the associated sequence in a data repository [e.g., databases at the National Center for Biotechnical Information (NCBI) at the National Library of Medicine ('GenBank') and the Worldwide Protein Data Bank]…
  • Evolution
    • Publisher: Wiley Blackwell
    • ISSN: 0014-3820
    • Policy text: We require authors to submit DNA sequence data to GenBank and phylogenetic data to TreeBase
    • Type of Data: DNA and phylogenetic data
    • Associated repository: GenBank and/ or TreeBase

I

  • ISME Journal
    • Publisher: Nature Publishing Group
    • ISSN: 1751-7362
    • Policy text: The ISME Journal will only review and publish manuscripts if the authors agree to make all data that cant be published in the journal itself (e.g. vel nucleotide sequences, structural data, or data from large-scale gene expression experiments) freely available in one of the public databases (see Submission to public databases below). Accession codes must be provided at the time a revised manuscript is returned to the Editorial Office. To avoid delays in publication of the manuscript, we encourage authors to deposit relevant data in public databases prior to submission. The authors may request that the data be stored in a confidential section of the database, in which they can request passwords from the database administrators, and these should be passed on to the Editorial Office to allow the editors and referees to anonymously access the information during the review process.
    • Type of data: All underlying data of publication

J

  • Journal of Exposure Science and Environmental Epidemiology
    • Publisher: Nature Publishing Group.
    • ISSN: 1559-0631.
    • Policy text: An inherent principle of publication is that others should be able to replicate and build upon the authors' published claims. Therefore, a condition of publication is that authors are required to make materials, data and associated protocols available in a publicly accessible database (as detailed in the sections below on this page). Where one does not exist, the information must be made available to referees at submission and to readers promptly on request. Any restrictions on materials availability or other relevant information must be disclosed in the manuscript‚ methods section and should include details of how materials and information may be obtained.

O

  • Organism Diversity and Evolution
    • Publisher: Elsevier
    • ISSN:1439-6092
    • Policy text: Molecular sequence data must be available from a public database (e.g. GenBank) when the corresponding paper is published. Whenever possible, sequences should be associable with publicly accessible morphological voucher specimens. Provide the respective accession and collection numbers. For phylogenetic data such as trees and matrices, the editors also sincerely recommend deposition in a public database (e.g. TreeBASE).
    • Type of data: DNA and phylogenetic

P

  • The Plant Cell
    • Publisher: American Society of Plant Biologists
    • ISSN: Print 1040-4651, Online 1532-298X
    • Policy Text (Last Updated June 22, 2011): "Large-scale data sets must be made available for review at the time of submission and must be deposited in an accepted format to a permanent public repository with open access (e.g., GEO http://www.ncbi.nlm.nih.gov/geo or Array-Express http://www.ebi.ac.uk/arrayexpress)."
    • Type of data: "Large-scale data sets (e.g., complete or draft genome sequences, genome annotations, genetic maps, EST data sets, transcript profiles, proteomic data sets, metabolic profiles, and next-gen sequencing data.")
  • Plant Physiology
    • Publisher: American Society of Plant Biologists
    • ISSN: Print 0032-0889, Online 1532-2548
    • Policy text (Last updated July 7, 2011): "At the time of publication, supplemental data must be placed in a permanent public repository if one is available, or if none is available, in Plant Physiology Online."
    • Type of data: microarray data, next-generation genome sequencing, "This includes data from small RNA, mRNA, specialized RNA libraries, ChIP-seq, whole-genome re-sequencing or genotyping, whole-genome bisulfite sequencing, etc."
  • Polar Research
    • Publisher: Wiley Blackwell
    • ISSN:0800-0395
    • Policy text: "Data that are integral to the published article must be made available in such a way as to enable readers to replicate, verify and build upon the conclusions published in the paper. Restrictions on the availability of this data must be disclosed at the time of submission. We recommend that data for which public repositories are widely used, and are accessible to all, should be deposited in such a repository prior to publication. The appropriate linking details and identifier(s) should then be included in the publication and, where possible, in the repository, to facilitate linking between the journal article and the data. If such a repository does not exist, data should be included as supporting information to the published paper or authors should agree to make their data available upon reasonable request."
    • Type of data: All underlying data

S

  • Systematic Biology
    • Publisher: Oxford Univesity Press
    • ISSN: 1063-5157
    • Policy text: All nucleotide sequence data and alignments must be submitted to GenBank or EMBL before the paper can be published. In addition, all data matrices and resulting trees must be submitted to TreeBASE. GenBank and TreeBASE reference numbers should be provided in the final version of the paper.
    • Type of data: Type of Data: DNA and phylogenetic data
    • Repository: GenBank and/ or TreeBase

T

  • Taxon
    • Publisher: International Association of Taxonomy.
    • ISSN: 0040-0262
    • Policy text: DNA or protein sequences must be deposited in public data repository.
    • Type of data: DNA or Protein sequences.
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