transpose-publishing / policies-database Goto Github PK

BMJ appears in both romeo_1174 and romeo_25 which is its parent. At some point we may want to propagate missing info in the child policy from the parent policy and remove duplicate journals from the parent policies, in order to simplify the display.

Updated CONTRIBUTING.md with instructions on how to modify policy records. Does it look like the simplest solution, @dhimmel ?

The following MDPI journals use a version of open peer review where reviewer identities can be open (optionally - reviewer decides) and review reports can be published (optionally - author decides)

Life www.mdpi.com/journal/life
Animals www.mdpi.com/journal/animals
Medical Sciences www.mdpi.com/journal/medsci
Behavioral Sciences http://www.mdpi.com/journal/behavsci
Administrative Sciences http://www.mdpi.com/journal/admsci
Brain Sciences http://www.mdpi.com/journal/brainsci
Atoms http://www.mdpi.com/journal/atoms
Cosmetics http://www.mdpi.com/journal/cosmetics
Dentistry Journal http://www.mdpi.com/journal/dentistry
Economies http://www.mdpi.com/journal/economies
Condensed Matter http://www.mdpi.com/journal/condensedmatter
QuBS http://www.mdpi.com/journal/qubs
Sci http://www.mdpi.com/journal/sci
J http://www.mdpi.com/journal/j

To-do: update YAML files with this info

Moved from transpose-publishing/transpose-publishing.github.io#1

We are collecting evidence of demand for TRANSPOSE to help inspire people to contribute to the resource. The TRANSPOSE team have collated a series of potential use cases for the resource: website page on use cases and source file.

Does a use case apply to you? Would you use TRANSPOSE for the reason supplied? Do you have another reason for using TRANSPOSE? If yes, please tell us via this form. Thank you for your help!

This survey is currently in beta. Your feedback is welcome and appreciated. Please contribute feedback about the survey itself by commenting in this thread or by email to naomi dot penfold at asapbio dot org. Many thanks!

Hello from OpenCon! I met up with @npscience during the OpenCon do-a-thon and I would like to potentially add material sharing policies to the TRANSPOSE-publishing database.

To give you more context, I've started working on a project to engage in conversations with journals and publishers to discuss the possibility of updating their material sharing policies to recommend specific reagent repositories, much like how Data sharing journal policies are recommending specific data and code repositories. The goal is that by recommending authors to make their research materials available through different non-profit repositories, journals can help to ensure timely distribution of materials and improve scientific reproducibility.

My colleagues and I at Addgene have started collecting material sharing policies for several journals (so far we've documented ~75 policies). Would it be possible to add material sharing policies to the TRANSPOSE-publishing database? I realize that it may not be compatible with the new googleforms format of contributing, but would like to explore this possibility. Thanks so much!

The following publishers are partnered with Publons and listed as allowing their peer review reports to be published via the service. We should check each of these publishers and update their YAML files with the actual peer review practices on their website.

• USFQ Press
• MDPI
• MedCrave Group
• Annals of Medical Physiology
• Kowsar Medical Institute
• BMJ Publishing Group
• Wiley (Brain and Behavior, Developmental Science, European Journal of Neuroscience, International Journal of Quantum Chemistry, Weed Research)
• Check List
• Regional Association for Security and Crisis Management
• Endocrinology Research Centre
• eLife
• Department of English Studies of New Bulgarian University
• Sapientia Publishing Group
• f1000
• Danesh Negaran Owj
• Oxford University Press (GigaScience)
• Kowsar Publishing
• Hittite Journal of Science and Engineering
• Hoegskolan i Boraas
• iGlobal Research and Publishing Foundation
• Open BioMedical Publishing Corporation
• Elsevier (Journal of Applied Research on Medicinal and Aromatic Plants)
• OAE Publishing (Journal of Translational Genetics and Genomics, Plastic and Aesthetic Research)
• Hindawi (Journal of Chemistry, The Scientific World Journal)
• ITB Journal Publisher
• Universitas Muhammadiyah Ponorogo
• Universitas Negeri Surabaya
• Life Science Alliance LLC
• The Royal Society (Open Biology)
• PeerJ
• Horizon e-Publishing Group
• Public Library of Science
• Universitas Muhammadiyah Sidoarjo
• Pensoft Publishers
• Clinical Biotec
• Instituto Brasileiro de Direito Processual Penal
• Institut Catala d'Ornitologia
• SAGE Publishing
• Scientific Journal Publishers
• Centre for Medical Education (CenMED)
• International Medical Publisher
• Florida State University College of Medicine
• EEEIC International Publishing

2018-05-08 update: Please see this comment for a revised architecture and list of data fields.

For each journal record, we hope to assemble the following fields (draft; please edit):

Journal information

• Journal title (from SHERPA/RoMEO: jtitle)
• Journal ISSN (from SHERPA/RoMEO: issn)
• Publisher (from SHERPA/RoMEO: romeopub)
• Date SHERPA/RoMEO information was last updated (from SHERPA/RoMEO: dateupdated)

Peer review

Open Peer Review

• Peer review policy url
• Does the journal publish the content of peer reviews? (mandatory/optional/no)
• Are reviewer identities revealed to the author? (mandatory/optional/no)
• Are reviewer identities published? (mandatory/optional/no)

Co-reviewers

• Co-reviewer policy url
• Journal’s policy about co-reviewers (people who collaborate with an invited reviewer) (free text)
• Does the journal make it clear in the invite email that co-reviewers can contribute? (yes/no)
• Is there a dedicated place in the submission form to identify co-reviewers? (yes/no)

(NEW suggestion) Peer review transfer

• Transfer policy url
• Policy on transfer of peer reviews
• What is the structure of the review form (are there separate fields for technical & impact evaluation?)

(NEW suggestion after conversation with B. Konforti) Peer review credit

• Does the journal deposit peer review information into ORCiD? info

Preprints

• Preprint policy url
• Are preprints allowed? (from SHERPA/RoMEO: prearchiving) (can/cannot/restricted/unclear)
• Preprint restrictions (from SHERPA/RoMEO: prerestrictions)
• Copyright policy url (from SHERPA/RoMEO: copyrighturl)
• Conditions (from SHERPA/RoMEO: conditions)
• Version of the preprint that can be posted to a disciplinary server (first submission only, any, other, none)
• Time when a preprint can be posted (before acceptance only, anytime, other)
• Acceptable servers (or characteristics) of servers (specific names, non-commercial, “recognized, etc)
• Media policy on preprints (what type of coverage or discussion (scientific blog, etc) of preprints is allowed?) (free text)
• Policies on preprint licensing (recommended or restricted licenses (eg, CC etc) for preprints) (free text)
• “Scoop protection” policy (ie, submitted preprints will not be rejected if a competing work comes out in another journal after the date of preprinting) (free text)
• Preprint citation policy (can preprints be cited in the reference list? Is there a special format?) (free text)
• Policy on incorporating community reviews or comments on preprints into editorial assessment (free text)

All data from SHERPA RoMEO is released under a CC BY-NC-SA 2.5 license and we will follow the specified conditions for reuse.

Here is a prioritized list of journals to work on!

Prioritized journals

See source lists collapsed at bottom of post: these come from Crossref (sorted by number of records) and Google H-index lists (general and cell bio, biochem, and bioinformatics) sorted alphabetically

Read our instructions for contributing to get started!

• Accounts of Chemical Research
• ACS Applied Materials & Interfaces
• ACS Nano
• Acta Crystallographica Section E Structure Reports Online
• Acta Horticulturae
• Advanced Functional Materials
• Advanced Materials
• AJN, American Journal of Nursing
• American Journal of Obstetrics and Gynecology
• American Journal of Ophthalmology
• American Journal of Psychiatry
• Analytical Chemistry
• Anesthesiology
• Angewandte Chemie
• Angewandte Chemie International Edition
• Annals of Internal Medicine
• Annals of Oncology
• Annals of the New York Academy of Sciences
• Annual Review of Biochemistry
• Antioxidants & Redox Signaling
• Applied Mechanics and Materials
• Applied Physics Letters
• Archives of Internal Medicine
• Biochemical and Biophysical Research Communications
• Biochemical Journal
• Biochemistry
• Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms
• Biochimica et Biophysica Acta (BBA)-General Subjects
• Biochimica et Biophysica Acta (BBA)-Molecular and Cell Biology of Lipids
• Biochimica et Biophysica Acta (BBA)-Molecular Cell Research
• Bioinformatics
• Biomaterials
• Biophysical Journal
• Blood
• BMC Bioinformatics
• BMC Systems Biology
• Brain Research
• Briefings in Bioinformatics
• British Medical Journal
• Cancer
• Cancer Cell
• Cancer Research
• Cell
• Cell Death & Differentiation
• Cell Death and Disease
• Cell Metabolism
• Cell Reports
• Cell Research
• Cell Stem Cell
• Chemical communications (Cambridge, England)
• Chemical Physics Letters
• Chemical Reviews
• Chemical Society reviews
• Circulation
• Clinical Cancer Research
• Clinical Infectious Diseases
• Cold Spring Harbor Perspectives in Biology
• Current Biology
• Database
• Development
• Developmental Cell
• Diabetes Care
• DMW - Deutsche Medizinische Wochenschrift
• Electronics Letters
• Endocrinology
• Energy & Environmental Science
• Environmental Science & Technology
• European Heart Journal
• European Urology
• Experimental Biology and Medicine
• FEBS Journal
• FEBS Letters
• Fertility and Sterility
• Free Radical Biology and Medicine
• Gastroenterology
• Genes & Development
• Genomics, Proteomics & Bioinformatics
• GigaScience
• Gut
• Hepatology
• IEEE Conference on Computer Vision and Pattern Recognition, CVPR
• IEEE Transactions on Industrial Electronics
• IEEE Transactions on Magnetics
• IEEE Transactions on Pattern Analysis and Machine Intelligence
• IEEE Transactions on Power Electronics
• IEEE/ACM Transactions on Computational Biology and Bioinformatics
• Immunity
• Inorganic Chemistry
• International Conference on Research in Computational Molecular Biology
• International Journal of Radiation OncologyBiologyPhysics
• JAMA
• Japanese Journal of Applied Physics
• Japanese Journal of Radiological Technology
• Journal of Agricultural and Food Chemistry
• Journal of Allergy and Clinical Immunology
• Journal of Alloys and Compounds
• Journal of Applied Physics
• Journal of Biological Chemistry
• Journal of Biomedical Semantics
• Journal of Cell Biology
• Journal of Cell Science
• Journal of Chemical Education
• Journal of Chromatography A
• Journal of Clinical Oncology
• Journal of Computational Biology
• Journal of Financial Economics
• Journal of Geophysical Research
• Journal of Hepatology
• Journal of High Energy Physics
• Journal of Materials Chemistry
• Journal of Materials Chemistry. A
• Journal of Mathematical Biology
• Journal of Organometallic Chemistry
• Journal of the American Chemical Society
• Journal of the American College of Cardiology
• Journal of the American Medical Association
• Journal of The Electrochemical Society
• Journal of the Society of Mechanical Engineers
• Journal of Theoretical Biology
• Mathematical Biosciences
• Medicine & Science in Sports & Exercise
• Molecular and Cellular Biology
• Molecular Biology of the Cell
• Molecular Cell
• Monthly Notices of the Royal Astronomical Society
• Nano Letters
• Nanoscale
• Nature
• Nature Biotechnology
• Nature Cell Biology
• Nature Chemical Biology
• Nature Chemistry
• Nature Climate Change
• Nature Communications
• Nature Genetics
• Nature Immunology
• Nature Materials
• Nature Medicine
• Nature Methods
• Nature Nanotechnology
• Nature Neuroscience
• Nature Photonics
• Nature Physics
• Nature Reviews Cancer
• Nature Reviews Genetics
• Nature Reviews Immunology
• Nature Reviews Molecular Cell Biology
• Nature Reviews Neuroscience
• Nature Structural & Molecular Biology
• NeuroImage
• Neurology
• Neuron
• New England Journal of Medicine
• Nucleic Acids Research
• Nursing Standard
• Obstetrical & Gynecological Survey
• Oncogene
• Pacific Symposium on Biocomputing
• Physical Review A
• Physical Review B
• Physical Review D
• Physical Review E
• Physical Review Letters
• Physics Letters B
• Plastic and Reconstructive Surgery
• PLOS Computational Biology
• PLoS ONE
• Proceedings of the American Mathematical Society
• Proceedings of the National Academy of Sciences
• Radiology
• Renewable and Sustainable Energy Reviews
• RSC Advances
• Science
• Science Translational Medicine
• Scientific Reports
• Southern Medical Journal
• Tetrahedron Letters
• The American Economic Review
• The American Historical Review
• The American Journal of Cardiology
• The American Journal of the Medical Sciences
• The Annals of Thoracic Surgery
• The Astrophysical Journal
• The Boston Medical and Surgical Journal
• The Cochrane Database of Systematic Reviews
• The EMBO Journal
• The Journal of Chemical Physics
• The Journal of Clinical Investigation
• The Journal of Organic Chemistry
• The Journal of Pediatrics
• The Journal of Physical Chemistry
• The Journal of Physical Chemistry B
• The Journal of Physical Chemistry C
• The Journal of Physiology
• The Journal of the Acoustical Society of America
• The Journal of Urology
• The Lancet
• The Lancet Neurology
• The Lancet Oncology
• The New England Journal of Medicine
• Transplantation
• Trends in Biochemical Sciences
• Trends in Cell Biology
• Vacuum

@dhimmel & @cameronblandford, I was talking with @tonyR-H & @garymcdowell today about out editathon yesterday and wanted to get your perspective on some issues:

• The number of data fields we would like to have is growing (even without the recent bolus added in #20). As YAML files get longer they get harder and harder to read, and more and more overwhelming for people who might be coming into the project casually (ideally there might be a way of prioritizing or highlighting these?) It seems like putting a lot of explanation/documentation into them would negatively impact their readability as well
• It is more difficult than anticipated for contributors to add information; most of the PRs have come from people already experienced with GitHub, and even some of the very dedicated/motivated people on this team have not contributed.
• We will need a way to make our own child policies; current SHERPA/RoMEO policies do not accurately reflect peer review policy groups.

The features I think would be very useful:

• A user-friendly form-like interface allowing users to view and change existing fields. Ideally this could also offer additional help text to describe what a field is, or a way to highlight certain fields to prioritize them. Detailed policies around certain topics would ideally be collapsible.
• For each contribution, to know who made the change and when (of course, this is already nicely done with GitHub)
• The ability to create different ways of viewing the data (which I think Cam's project already does)
• Ideally a way for the less-technical among us to add new fields to all records, and create new child policies (and specify which journals belong to them)

I apologize that these issues were not more obvious earlier on! I would be really eager to hear your thoughts on how best to proceed. Would it be possible to create a way for users to input information through Cam's front end?

Thanks in advance....

We'll want encode the valid YAML structure from #1 into a schema so we can programmatically enforce it. I'm going to use this issue to jot down potential options.

• https://github.com/23andMe/Yamale
• http://rx.codesimply.com/
• https://github.com/Grokzen/pykwalify

We can also look to see what http://reusabledata.org does (source).

Here are some suggested changes/additions!

• Would it be possible to add some of the headers that are present in schema.yml - for example, OPEN PEER REVIEW, to the YAML files themselves? Furthermore, condensing down some of the white space (ie, between data fields that share the same reference url) might reduce the need to scroll so much. Each dsc could then be started with the name of the variable for disambiguation
• "Peer review policy url (valid url)" -> "Open peer review policy url (valid url)"
• Add url for preprint-citation
• In the later part of the files, preprint urls follow the data fields, but in the early part, they preceed them. Suggest standardizing these
• preprint url fields descriptions could be standardized as well
• would be good to add "unknown" to most fields to signify that this information can't be found. If users don't look for info, they can leave the field null. But if they do look and can't find, they could use unknown. The absence of public information is also important...
• From #25: split journals into two fields like journals and journals-subpolicies

Re: https://github.com/transpose-publishing/policies-database/edit/master/policies/policies/romeo_22.yml

We will need to split this policy; there are 3 types of peer review at BMC:

Single-blind: the reviewers know the names of the authors, but the authors do not know who reviewed their manuscript unless the reviewer chooses to sign their report.
Double-blind: the reviewers do not know the names of the authors, and the authors do not know who reviewed their manuscript.
Open peer: authors know who the reviewers are, and the reviewers know who the authors are. If the manuscript is accepted, the named reviewer reports are published alongside the article."

Source: https://www.biomedcentral.com/getpublished/peer-review-process
Journals that practice open peer review are marked here: https://www.biomedcentral.com/journals
Biology Direct is not listed among them but apparently has mandatory open reviews and identities: https://biologydirect.biomedcentral.com/about/how-it-works