Policies and publication ethics

AASTEMERs' policies

This section provides general guidance to authors on their responsibilities and the code of conduct. It also describes what are considered to be conflicts of interest, and outlines AASTEMERs policy on human and animal welfare. 

Open access and copyright

All AASTEMER articles are published with open access under the Creative Commons CC-BY license (the current version is CC-BY, version 4.0). The author(s) retains copyright, but the content is free to download, distribute, and adapt for commercial or non-commercial purposes, given appropriate attribution to the original article.

Upon submission, the author(s) grants AASTEMER a license to publish, including to display, store, copy, and reuse the content. The CC-BY Creative Commons attribution license enables anyone to use the publication freely, given appropriate attribution to the author(s) and citing AASTEMER as the original publisher. The CC-BY Creative Commons attribution license does not apply to third-party materials that display a copyright notice to prohibit copying. Unless the third-party content is also subject to a CC-BY Creative Commons attribution license, or an equally permissive license, the author(s) must comply with any third-party copyright notices.

Registration with AASTEMER

Corresponding author(s) must register with AASTEMER before submitting an article. You must be logged in to your personal AASTEMER account to submit an article.

Authorship and author responsibilities

In order to qualify for authorship of a manuscript, the following criteria should be observed:

  • take responsibility for a particular section of the study
  • substantial contributions to the conception or design of the work; or the acquisition, analysis, or interpretation of data for the work 
  • drafting the work or revising it critically for important intellectual content 
  • provide approval for publication of the content 
  • agree to be accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved

Contributors who do not meet these criteria, but nonetheless provided important contributions to the final manuscript, should be included in the acknowledgement section. It is the author’s responsibility to get written approval by persons named in the acknowledgment section. 

Manuscripts prepared and written by commercial entities on behalf of researchers listed as authors on the manuscript do not meet AASTEMERs’ policies and will not be considered for publication. AASTEMER will take proactive actions to reject suspicious manuscripts before peer review.

Author contributions

To provide appropriate credit to all authors, as well as assigning responsibility and accountability for published work, individual contributions should be specified as an Author Contributions statement. The Author Contributions Statement is mandatory. It should represent all the authors and is to be included upon submission. It can be up to several sentences long and should briefly describe the tasks of individual authors. Please list only 2 initials for each author, without full stops, but separated by commas (for example CM, CP). In the case of two authors with the same initials, please use their middle initial to differentiate between them (for example CMM, CTM) or second letter of the last name (for example SKi, SKa). Please see an example here:

“SL, AV, and CM contributed to conception and design of the study. CM organized the database. AV performed the statistical analysis. SL wrote the first draft of the manuscript. SL, AV, DM and NK wrote sections of the manuscript. All authors contributed to manuscript revision, read, and approved the submitted version.”

Corresponding authors

The corresponding author takes primary responsibility for communication with the journal and editorial office during the submission process, throughout peer review, and during publication. The corresponding author is also responsible for ensuring that the submission adheres to all journal requirements including, but not exclusive to, details of authorship, study ethics and ethics approval, clinical trial registration documents, and conflict of interest declaration. The corresponding author should also be available post-publication to respond to any queries or critiques.

Requests to modify the author list after submission should be made to the editorial office.

Research integrity: how to reuse text

Material submitted to AASTEMER must comply with the following policies to ensure ethical publication of academic work.

Original content and duplicate publication

AASTEMER only publishes original content. Authors confirm the submission of original content in the terms and conditions upon submission. Manuscripts submitted to AASTEMER must not have been previously published or be under consideration for publication elsewhere, either in whole or in part. If an article has been previously submitted for publication elsewhere, AASTEMER will only consider publication if the article has been definitively rejected by the other publisher(s) at the point of submission to AASTEMER.

Fabrication and falsification

AASTEMER opposes both the fabrication of data or images (that is, fake or made-up data) and falsification of data or images (that is, the intentional misrepresentation or deceptive manipulation of data).

Redundant publication

AASTEMER considers the submission and publication of very similar articles based on the same experiment or study to be unethical.

Plagiarism

Plagiarism occurs when an author attempts to present previously published work as original content. Every manuscript submitted to AASTEMER is screened for textual overlap by the software CrossCheck, powered by iThenticate. Manuscripts found to contain textual overlap are not considered for publication by AASTEMER. 

We reserve the right to contact the affiliated institutions of authors who have not acted according to good research and publication practices.

Plagiarism and duplication

AASTEMER checks all submitted manuscripts for plagiarism and duplication, and publishes only original content. Those manuscripts where plagiarism or duplication is shown to have occurred will not be considered for publication in a AASTEMER journal. It is required that all submissions consist of content that has not been published previously. In accordance with COPE guidelines, AASTEMER expect that “original wording taken directly from publications by other researchers should appear in quotation marks with the appropriate citations.” This condition also applies to an author’s own work.

Theses and dissertations

AASTEMER allows the inclusion of content which first appeared in an author’s thesis so long as this is the only form in which it has appeared, is in line with the author’s university policy, and can be accessed online. If the thesis is not archived online, it is considered original, unpublished data and is subject to the unpublished data restrictions of some article types. Inclusion of material from theses or dissertations should be noted in the Acknowledgements section of the manuscript and cited accordingly in the reference list. For some examples, please check the ‘References’ section of our author guidelines.

Conferences, proceedings, and abstracts

Manuscripts that first appeared as conference papers must be expanded upon if they are to be considered as original work. Authors are required to add a substantial amount of original content in the form of new raw material (experiments, data) or new treatment of old data sets which lead to original discussion and/or conclusions, providing value that significantly exceeds the original conference version. As a rule of thumb, at least 30% of the content must be original. Authors submitting such work to AASTEMER are required to:

  • seek permission for reuse of the published conference paper if the author does not hold the copyright
  • cite the conference in the acknowledgements section, or the references section if applicable

Blogs

Although permissible, extended manuscript content which previously appeared online in non-academic media, such as blogs, should be declared at the time of submission in the acknowledgements section of the manuscript.

Preprints

Our supportive preprint policy encourages full open access at all stages of a research paper, to share and generate knowledge researchers need to support their work. Authors publishing in AASTEMER journals may share their work ahead of submission to a peer-reviewed journal, as well as during the AASTEMER’s review process, on repositories or preprint servers, provided that the server imposes no restrictions upon the author’s full copyright and re-use rights. Also note that any manuscript files shared after submission to AASTEMER journals, during the review process, cannot contain the AASTEMER logo or branding.

Correct attribution of the original source in repositories or preprint servers must be included within the manuscript on submission or added at re-submission if the deposition is done during the review process. We ask that the preprint is both listed within the acknowledgement section and the full citation included in the reference list.

If the article is published, authors are then strongly encouraged to link from the preprint server to the AASTEMER publication to enable readers to find, access, and cite the final peer-reviewed version. Please note that we cannot consider for publication content that has been previously published, or is already under review, within a scientific journal, book or similar entity.

Corrections

AASTEMER recognizes our responsibility to correct scientifically relevant errors in previously published articles. Corrections can be submitted if:

  • a small portion of an otherwise reliable publication proves to be misleading OR 
  • there is an error in a figure that does not alter the conclusions OR 
  • there is an error in statistical data not altering conclusions OR 
  • there are mislabeled figures OR 
  • the wrong slide of microscopy was provided OR 
  • the author / contributor list is incorrect when a deserving author has been omitted or somebody who does not meet authorship criteria has been included. 

A correction must be submitted through our submission system.

If the error was introduced during the publishing process, the AASTEMER production office should be contacted.

Retractions

AASTEMER abides by following key principles in cases of potential retraction, in accordance with the guidelines and recommendations of the Committee on Publication Ethics (COPE).

  • retractions are not about punishing authors
  • retraction statements should be public and linked to the original, retracted article

All potential retractions will be judged on their own merits and will be the subject of an internal investigation or, where satisfactory, the recommendations from the institutional investigation of the author(s). AASTEMER considers the following reasons as giving cause for concern and potential retraction:

  • clear evidence that findings are unreliable, either as a result of misconduct (such as data fabrication) or honest error (such as miscalculation or experimental error)
  • findings have previously been published elsewhere without proper attribution, permission or justification (that is, cases of redundant publication)
  • major plagiarism
  • the reporting of unethical research, the publication of an article that did not have the required ethics committee approval
  • legal issues pertaining to the content of the article, such as libelous content
  • major authorship issues, such as proven or strongly suspected cases of ghostwriting or sold (‘gift’) authorship
  • politically motivated articles where objectivity is a serious concern
  • the singling out of individuals or organizations for attack
  • faith issues (such as intelligent design)
  • articles that have made extraordinary claims without concomitant scientific or statistical evidence (such as pseudoscience)

Readers who would like to draw the editors’ attention to published work that might require retraction should contact the authors of the article and write to the journal, making sure to include copies of all correspondence with authors.

Ethical concerns

For any ethical concerns, please contact us at research.integrity@pubs.aastemer.org.

Editorial policies

Conflicts of interest

A conflict of interest can be anything potentially interfering with, or that could be perceived as interfering with, full and objective peer review, decision-making or publication of articles submitted to AASTEMER. Personal, financial, and professional affiliations or relationships can be perceived as conflicts of interest.

All authors and members of AASTEMER editorial boards are required to disclose any actual and potential conflicts of interest at submission or upon accepting an editorial or review assignment.

Anything that can be perceived as a potential conflict of interest should be disclosed, during submission.

What should I disclose?

As an author, disclosure of any potential conflicts of interest should be done during the submission process. Consider the following questions and make sure you disclose any positive answers.

Potential conflicts of interest: authors

  • Did you or your institution at any time receive payment or services from a third party for any aspect of the submitted work?
  • Do you have financial relationships with entities that could be perceived to influence, or that give the appearance of potentially influencing, what you wrote in the submitted work?
  • Do you have any patents and copyrights, whether pending, issued, licensed, and/or receiving royalties, related to the research?
  • Do you have other relationships or activities that readers could perceive to have influenced, or that give the appearance of potentially influencing, what you wrote in the submitted work?
  • If you failed to disclose potential conflicts of interest during submission, or in case of doubt, please contact the AASTEMER editorial office at editorial.office@pubs.aastemer.org with the details of the potential conflicts as soon as possible.
  • For commercial affiliations, all authors must be accounted for. We recommend using the following template:
  • [AUTHOR NAME] was employed by [COMPANY]. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
  • For commercial funding, the role of the funder must be declared. We recommend the following statements:

The authors declare that this study received funding from [FUNDER NAME]. The funder had the following involvement with the study: [DESCRIPTION OF INVOLVEMENT]
The authors declare that this study received funding from [FUNDER NAME]. The funder was not involved in the study design, collection, analysis, interpretation of data, the writing of this article, or the decision to submit it for publication.

Conflicts of interest: editors and reviewers

Handling editors and reviewers will be asked to consider the following potential conflicts of interest before accepting any editing or review assignment.

Potential conflicts of interest: editors and reviewers

Family

  • Are any of the authors a spouse or significant other, a member of the same family, or a very close personal friend?
  • Review editors should also not be a member of the same family as the handling editor.

Collaborations

  • Are you currently hosting or have hosted a AASTEMER Research Topic with any of the authors within the past 2 years?
  • Are you currently collaborating or have you collaborated on a research project or a publication with any of the authors within the past 2 years?
  • Are you currently collaborating or have you collaborated with any of the authors as an advisor or in any other direct supervisory capacity in the past 5 years?
  • Are you currently collaborating or have you collaborated with any of the authors as a student or in any other direct subordinate capacity in the past 5 years?
  • Note: Review editors should not accept assignments if they have a close professional relationship with the handling editor, which in their view could affect the objectivity of the review.

Affiliation

Are you affiliated with the same institution as any of the authors? If so, has this resulted in interactions, collaborations, or mutual interests with the authors that would compromise your impartiality in conducting this review?

Are you a current member of a committee or department that coincides with an affiliation with any of the authors?

Financial

  • Do you have a business or professional partnership with any author?
  • Do you have financial interests or business relations with any organization involved in this research or in the preparation of the manuscript?
  • Do you have any financial interest or competing interests in the content of the manuscript that might affect your ability to perform an objective review?

Funding disclosure

Details of all funding sources must be provided in the funding section of the manuscript, including grant numbers, if applicable. All AASTEMER articles are published with open access under the CC-BY Creative Commons attribution license. Articles published with AASTEMER automatically fulfil or exceed the requirements for open access mandated by many institutions and funding bodies, including the National Institutes of Health, the Medical Research Council, Research Councils UK, and the Wellcome Trust. AASTEMER submits funding data to the Open Funder Registry, which is a funder identification service from CrossRef resulting from collaboration between scholarly publishers and funding agencies.

Disclaimer

Any necessary disclaimers which must be included in the published article should be clearly indicated in the manuscript.

Bioethics

All research submitted to AASTEMER for consideration must have been conducted in accordance with AASTEMER guidelines on study ethics. In accordance with COPE guidelines, AASTEMER reserves the right to reject any manuscript that editors believe does not uphold high ethical standards, even if authors have obtained ethical approval or if ethical approval is not required. AASTEMER encourages authors to follow the ARRIVE guidelines for the design, analysis, and reporting of scientific research.

Studies involving animal subjects

All research involving regulated animals (that is, all live vertebrates and higher invertebrates) must have been reviewed and approved by an ethics committee prior to commencing the study and performed in accordance with relevant institutional and national guidelines and regulations. AASTEMER follows the International Association of Veterinary Editors (AVMA) guidelines for publication of studies including animal research. Clinical studies involving animals and interventions outside of routine care require ethics committee oversight as per the American Veterinary Medical Association. Authors must provide ethics approval information within the submission system, which generates an ethics statement to be included in the submission. The generated ethics statement will be included in the reviewer file, in the following format:

“The animal study was reviewed and approved by [Full name and affiliation of ethics committee].”

If the study is exempt from ethics approval, authors need to state the reasons for exemption within the generated statement. Studies involving client-owned animals (non-commercially available animals such as pets or livestock) should demonstrate the best practice veterinary care and confirm that written informed consent has been granted by the owner(s), or the legal representative of the owner(s). Here is an example of a generated statement for a study involving client-owned animals:

“The animal study was reviewed and approved by [Full name and affiliation of ethics committee]. Written informed consent was obtained from the owners for the participation of their animals in this study.”

Studies involving animals should be conducted according to internationally accepted standards and are expected to comply with the three Rs principle (Replace, Reduce, Refine). AASTEMER endorses the ARRIVE guidelines (Animal Research: Reporting In Vivo Experiments) for reporting experiments involving live animals. Authors are encouraged to use the ARRIVE checklist and to submit this checklist with manuscripts involving animal research; AASTEMERs’ editors reserve the right to request this checklist.

Editors can request additional documentation, including approval forms and/or relevant citations from the literature, if experimental details described in a study deviate from common practice in animal research. Editors also reserve the right to reject a manuscript if research involves protocols that are inconsistent with commonly accepted norms for animal welfare, independent of ethics committee approval or previously published articles using such protocols.

Authors are advised to consult the American Veterinary Medical Association (AVMA) guidelines for the Euthanasia of Animals (2020) for guidance on veterinary best practice for the anesthesia and euthanasia of animals. Studies involving euthanasia protocols involving chloral hydrate, ether and chloroform overdose are strongly discouraged. Authors are encouraged to provide a full description of any anesthetic, surgical or euthanasia procedures performed during a study.

Humane endpoints

All manuscripts describing studies where death is an endpoint will be subject to additional ethical considerations. AASTEMER reserves the right to reject manuscripts lacking appropriate justification.

Studies involving human subjects

Research involving human subjects should have been conducted in accordance with the World Medical Association’s Declaration of Helsinki. Studies involving human participants must be performed in accordance with relevant institutional and national guidelines, with the appropriate institutional ethics committee’s prior approval and informed written consent from all human subjects involved in the study including for publication of the results. Confirmation of this approval is required upon submission of a manuscript to AASTEMER; authors must provide ethics committee information within the submission system, which generates an ethics statement to be included in the submission. Information regarding subjects’ (or when appropriate, the parent’s or guardian’s) consent for participation should be provided within the submission system. AASTEMER requires that consent for participation is both informed and written, unless waived by an ethics committee or otherwise not required as per local legislation. The submission system will generate an ethics statement in the following format (the statement will also be included in the final manuscript version for publication):

“The studies involving human participants were reviewed and approved by [Full name and affiliation of ethics committee]. The patients/participants provided their written informed consent to participate in this study.”

If the study is exempt from ethics approval or consent procedures, authors need clearly to state the reasons in the generated statement. AASTEMER may request a letter from the authors, obtained from an ethics committee in cases where full review and approval has been waived by the committee.

To protect subject anonymity, identifying information should not be included in the manuscript unless such information is absolutely necessary for scientific purposes AND explicit approval has been granted by the subjects.

Inclusion of identifiable human data

AASTEMER follows the ICMJE recommendations on the protection of research participants, which state that patients have a right to privacy that should not be violated without informed consent. We require nonessential identifiable details to be omitted from all manuscripts, and written informed consent will be required if there is any doubt that anonymity can be maintained.

It is the responsibility of the researchers and authors to ensure that these principles are complied with, including the obtaining of written informed consent for publication of any potentially identifiable data or images.

Written informed consent can be documented on a form provided by an institution or ethics committee, and it must clearly state how the identifiable data will be used. Consent form meeting the ICMJE recommendations may be used for this purpose. Author’s should encourage participants or patients whose consent for publication is required to read and understand the ICMJE guidelines, for their information prior to completing the consent form. Participants should also be encouraged to ask any questions and to ensure they are comfortable before they sign the consent form.

The completed consent forms should be stored by authors or their respective institutions, in accordance with institutional policies. Completed forms should not be included with your AASTEMER submission. However, consent forms should be made available upon request from the editor or editorial office, during the review process or post-publication.

The determination of what constitutes identifiable data lies with our editors and editorial office staff, and manuscripts may be rejected if the required consent documents cannot be provided. Please note that written informed consent for publication is required for all case report articles where the patient or subject is identified or identifiable. Information regarding participant/patient consent for publication of identifiable data should be provided within the submission system. This will generate an ethics statement that will be directly included in the manuscript.

Clinical trials

The World Health Organization (WHO) International Clinical Trials Registry Platform (ICTRP) defines a clinical trial as “any research study that prospectively assigns human participants or groups of humans to one or more health-related interventions to evaluate the effects on health outcomes.” In accordance with the Clinical Trial Registration Statement from the International Committee of Medical Journal Editors (ICMJE), all clinical trials must be registered in a public trials registry at or before the onset of participant enrolment. To meet the requirements of the ICMJE and AASTEMER, clinical trials can be registered with any Primary Registry in the WHO Registry Network or an ICMJE approved registry.

Clinical trial reports should be compliant with the Consolidated Standards of Reporting Trials (CONSORT) by including a flow diagram presenting the enrolment, intervention allocation, follow-up, and data analysis with number of subjects for each and taking into account the CONSORT Checklist of items to include when reporting a randomized clinical trial.

The information on the clinical trial registration (Unique Identifier and URL) must be included in the manuscript Abstract.

Materials and data policies

AASTEMER is committed to open science and open data; we require that authors make available all data relevant to the conclusions of the manuscript. Generated data should be publicly available and cited in accordance with our ‘Data citation guidelines’ below. We aim to achieve the best community standards regarding data availability, ensuring increased levels of transparency and reproducibility in our published articles.

Our policies on data availability are informed by community-driven standards, which AASTEMER endorses, such as the Transparency and Openness (TOP) guidelines and the joint declaration of data citation principles produced by FORCE11.

Availability of materials

Authors are required to make all materials used to conduct their research available to other researchers. Research materials necessary to enable the reproduction of an experiment should be clearly indicated in the Materials and Methods section. Relevant materials such as protocols, analytic methods, and study material should preferably be uploaded to an online repository providing a global persistent link/identifier. If this is not possible, authors are strongly encouraged to make this material available upon request to interested researchers, and this should be stated in the manuscript.

Resource identification initiative

Authors wishing to participate in the FORCE11 Resource Identification Initiative should cite antibodies, genetically modified organisms, software tools, data, databases, and services using the corresponding catalog number and Research Resource Identifier (RRID) in your current manuscript.

Availability of data

AASTEMER requires that authors make the “minimal data set” underlying the findings described and used to reach the conclusions of the manuscript, available to any qualified researchers. The data should be FAIR – findable, accessible, interoperable, and reusable – so that other researchers can locate and use the data. However, exceptions are granted if data cannot be made publicly available for legal or ethical reasons.

To comply with best practice in their field of research, authors are required to make certain types of data available to readers at the time of publication in specific, stable, community-supported repositories such as those listed below. Authors are encouraged to contact our data availability office at datapolicy@pubs.aastemer.org prior to submission with any queries concerning data reporting.

Exceptions related to availability of data

We strongly encourage sharing the maximal amount of data; however where ethical, legal or privacy issues are present the data should not be shared. In cases where some or all data cannot be shared for legal, ethical or privacy restrictions, the authors should make these limitations clear in the Data Availability Statement at the time of submission.

Possible limitations to making data publicly available include patient confidentiality and participant privacy. Authors should ensure that the data shared are in accordance with the ethical consent provided by participants on the use of confidential/identifiable human data. We require that the authors demonstrate that publication of such data does not compromise the anonymity of the participants or breach local data protection laws.

In situations where access is restricted to protect confidential or proprietary information, authors are required to explain the restrictions on the dataset and make the data available upon request with permission of the third party. The Data Availability Statement should include all necessary contact information to request access to the dataset.

Data citation guidelines

Authors are encouraged to cite all datasets generated or analyzed in the study. Where datasets are cited, they should be included in the references list to maximize future usability.

The following format should be used:

[DATASET] Author names. (year) Data Title. Repository name. Version. Persistent identifier

Data availability statements

Data availability statements are required for all articles published with AASTEMER. During the submission process, authors will be asked to detail the location of the raw data underlying the conclusions made in the manuscript, and whether it will be made available to other researchers following publication. Authors will also be asked for the details of any existing datasets that have been analyzed in the manuscript. These datasets should be cited in accordance with our data citation guidelines.

A statement will be automatically generated using the information provided in the submission form; however, manuscripts containing incomplete or incorrect statements will be prevented from entering the review process.

Examples of acceptable statements

Original datasets are available in a publicly accessible repository: The original contributions presented in the study are publicly available. This data can be found here: [link/accession number].

Existing datasets are available in a publicly accessible repository: Publicly available datasets were analyzed in this study. This data can be found here: [link/accession number].

Information for existing publicly accessible datasets is contained within the article (such as for studies using more than 10 accession numbers): The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/supplementary material.

All relevant data is contained within the article: The original contributions presented in the study are included in the article/supplementary material, further inquiries can be directed to the corresponding author/s.

Restrictions apply to the datasets: The datasets presented in this article are not readily available because [VALID REASON]. Requests to access the datasets should be directed to [text input].

Data has been obtained from a third party: The data analyzed in this study was obtained from [SOURCE], the following licenses/restrictions apply [RESTRICTIONS]. Requests to access these datasets should be directed to [NAME, EMAIL].

Datasets are available on request: The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.

Mandatory data and recommended repositories

Authors are required to deposit the following mandatory data types in public, community-supported repositories, such as those listed below, prior to publication of an associated AASTEMER manuscript.

Mandatory data repositories

Genetic and genomic sequence (DNA/RNA)*

Required repositories 

  • GenBank
  • DNA Data Bank of Japan (DDBJ)
  • European Nucleotide Archive (ENA)
Metadata standard
  • MiXS 

Metagenomic sequenceRequired repositories

Required repository
  • EBI Metagenomics
Metadata standard
  • MiXS 

DNA and RNA trace or short-read sequencing data

Required repositories
  • NCBI Trace Archive NCBI 
  • Sequence 
  • Read Archive
Metadata standard
  • MiXS 

Genetic polymorphism data, including SNP and CNV data

Required repositories
  • dbSNP 
  • dbVar 
  • European Variation Archive 
  • DGVa
Metadata standard
  • MiXS 

Gene expression data; chromatin immunoprecipitation data (deep-sequencing or microarray)

Required repositories
  • ArrayExpress 
  • Gene Expression Omnibus (GEO)
Metadata standard
  • MIAME / MINSEQE

Data linking genotype to phenotype

Required repository
  • dbGaP

Protein sequence data

Required repositories
  • UniProt

Proteome profiling data

Required repositories 

  • PRIDE 
  • PeptideAtlas 
  • ProteomeXchange

Metadata standard

  • MIAPE

Small molecule, protein, protein complex data structural data

Required repositories 

  • Crystallography Open Database 
  • Cambridge Structural Database 
  • wwPDB (Protein DataBank) 
  • Electron Microscopy Databank

Metadata standard

  • CIF

Taxonomy data

Required repository

  • Zoobank

*Genetic sequence variants should be annotated according to the guidelines established by the Human Variome Project.

Authors are encouraged to consider deposition in public, community-supported repositories of the data-types listed below.

Recommended data repositories

Protein-protein interaction data

Recommended repositories

Database of Interacting Proteins (DIP)

Metadata standard

MIMIx

Metabolite and metabolome profiling data

Recommended repositories
  • MetaboLights
  • Human Metabolome Database
Metadata standard

MSI

Small-molecule screening data; chemical compound data

Recommended repositories

PubChem 

Metadata standard

CIF

Flow cytometry data

Recommended repositories 

Flow Repository 

Brain imaging data; neuroimaging data

Recommended repositories 
  • OpenNeuro 
  • INDI 
  • NITRC 
  • NeuroVault [Statistical maps]
Metadata standard 

BIDS

Trait data

Recommended repositories

TRY database

Phenology data

Recommended repositories

National Phenology Network

Any data

Recommended repositories
  • Figshare 
  • Dryad Digital Repository
Metadata standard

None

Inclusion of RNAseq data

Studies employing RNASeq for comparative transcriptomic analyses must contain at least three biological replicates (unless otherwise justified). Each biological replicate should be represented in an independent library, each with a unique barcode if libraries are multiplexed for sequencing. Validation on a number of key transcripts highlighted in the study is also highly recommended.

Full data accompanying these experiments must be made available to reviewers at the time of submission in a freely accessible resource, e.g the Sequence Read Archive (SRA) or European Nucleotide Archive (ENA). Depending on the question addressed in a manuscript, de novo assemblies of transcriptomes may also require multiple replicates, and assembled sequences together with sequence annotation must be made freely available, such as in figshare or Dryad.

Inclusion of proteomics data

Authors should provide relevant information relating to how peptide/protein matches were undertaken, including methods used to process and analyze data, false discovery rates (FDR) for large-scale studies, and threshold or cut-off rates for peptide and protein matches. Further information should include software used, mass spectrometer type, sequence database and version, number of sequences in database, processing methods, mass tolerances used for matching, variable/fixed modifications, allowable missed cleavages, etc.

Authors should provide as supplementary material the information used to identify proteins and/or peptides. This should include information such as accession numbers, observed mass (m/z), charge, delta mass, matched mass, peptide/protein scores, peptide modification, miscleavages, peptide sequence, match rank, matched species (for cross-species matching), number of peptide matches, etc. Ambiguous protein/peptide matches should be indicated.

For quantitative proteomics analyses, authors should provide information to justify the statistical significance, including biological replicates, statistical methods, estimates of uncertainty, and the methods used for calculating error.

For peptide matches with biologically relevant post-translational modifications (PTMs) and for any protein match that has occurred using a single mass spectrum, authors should include this information as raw data or annotated spectra, or submit data to an online repository (recommended option; see table below).

Raw or matched data and 2-DE images should be submitted to public proteomics repositories such as those participating in ProteomeXchange. Submission codes and/or links to data should be provided within the manuscript.

Code

AASTEMER is committed to open science and open data; we require that authors make available all code used to conduct their research available to other researchers. Code necessary to enable the reproduction of an experiment should be clearly indicated in the Materials and Methods section, and where possible code should be uploaded to an online repository (such as github.com or code ocean) providing a global persistent link/identifier.

Our policies on code availability are informed by community-driven standards, which AASTEMER endorses, such as the Transparency and Openness (TOP) guidelines and the joint declaration of data citation principles produced by FORCE11.

Exceptions related to code availability

We strongly encourage sharing original code where possible. In situations where custom code is proprietary, an exception will be granted providing that all relevant software needed to replicate the results of the study are available commercially for researchers. Details of the proprietary software used should be listed in the materials and methods section.

At submission, authors should declare any intellectual property relating to the code and themselves in a conflict of interest statement.

Statistics

AASTEMER requires that all statements concerning quantitative differences should be based on quantitative data and statistical testing. For example, if a quantitative statement is made regarding the abundance of a certain protein based on a western blot, we request that the blot be scanned and the abundance assessed quantitatively using the correct analytic software (such as ImageJ) and statistics in order to support that statement.

Statistics should/must be applied for independent experiments. The number of independent samples and the deviation parameters (such as standard error of the mean, standard deviation, confidence intervals) should be clearly stated in the Methods or the Figure legends. In general, technical replicates within a single experiment are not considered to be independent samples. Where multiple comparisons are employed (such as microarray data or genome-wide association studies), any analysis should correct for false positive results. Descriptions of statistical procedures should include the software and analysis used, and must be sufficiently detailed to be reproduced.

Experiments

Authors are required to specifically state in their legends how many times experiments were performed (in general we require n=3 as a minimum) and what specific statistical analysis was performed.

Image manipulation

AASTEMER takes concerns regarding image manipulation seriously. We do not accept that individual features within an image are modified (including enhanced, obscured, moved, recycled, removed, or added). Image processing methods (such as changes to the brightness, contrast, or color balance) must be applied to every pixel in the image and the changes should not alter the information illustrated in the figure. Cropped images should be avoided where possible for gels and blots. Where cropped images are shown in figures, a full scan of the entire original gel(s) must be submitted as part of the supplementary material. Where control images are re-used for illustrative purposes, this must be clearly declared in the figure legend. If any form of image processing is legitimately required for the interpretation of the data, the software and the enhancement technique must be declared in the methods section of the manuscript. Image grouping and splicing must be clearly stated in the manuscript and the figure text.

Any concerns raised over undeclared image modifications will be investigated and the authors will be asked to provide the original images and data. Failure by authors to adequately address such concerns will result in rejection of the manuscript, and the issue may be raised with the authors’ institutions.

Support

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