Zubair Khalid

Virologist/Molecular Biologist | Veterinarian | Bioinformatician

Conventional & Molecular Virology • Vaccine Development • Computational Biology

Dr. Zubair Khalid is a veterinarian and virologist specializing in conventional and molecular virology, vaccine development, and computational biology. Dedicated to advancing animal health through innovative research and multi-omics approaches.

Dr. Zubair Khalid - Veterinarian, Virologist, and Vaccine Development Researcher specializing in Computational Biology, Multi-omics, Animal Health, and Infectious Disease Research

Category: Guides

Open Access Practices for Researchers: A Guide

Open access publishing makes research articles freely available to readers without subscription barriers. For researchers, the practical question is not whether to engage with open access but how to choose the right route, manage costs, and meet funder requirements. This guide covers the two main pathways, green and gold open access, journal selection criteria, article processing charge management, and a compliance checklist that applies across disciplines and funding contexts.

At a Glance

Route What It Means Typical Cost to Author Funder Compliance
Green open access Author deposits the accepted manuscript in a repository, often after an embargo period Usually none Often accepted by funders, but embargo periods may conflict with mandates
Gold open access Article is published openly in the journal itself, sometimes after payment of an article processing charge APC required by many journals, though some waive fees Generally satisfies funder requirements immediately
Diamond open access Journal publishes openly with no APC charged to authors None Satisfies funder requirements when the journal meets quality standards

The choice between these routes depends on your funder's specific policy, the journal's offerings, your available budget, and the speed with which your work needs to be publicly visible.

Understanding Open Access Routes

Green Open Access

Green open access involves depositing a version of your manuscript in a repository, typically an institutional repository or a subject-based repository. The deposited version is often the accepted manuscript, which is the peer-reviewed version before final typesetting. Many publishers permit this deposit after an embargo period that can range from zero to 24 months.

The practical advantage of green open access is that it usually costs nothing. Researchers who lack funding for article processing charges can still make their work openly available. The main limitation is the embargo period, during which only subscribers can access the published version. If your funder requires immediate access, a lengthy embargo can create compliance problems.

Repository deposits also require attention to version identification. Depositing the wrong version, such as the submitted manuscript before peer review, may not satisfy funder requirements. Check your funder's policy on which version is acceptable and whether the embargo period is counted from acceptance or publication.

Gold Open Access

Gold open access means the final published version is freely available on the journal's website from the time of publication. This route often involves an article processing charge, which is a fee paid by the author, their institution, or their funder to cover the journal's publishing costs.

Some gold open access journals charge no fees at all. These are sometimes called diamond open access journals. The diamond model has received increasing attention in scholarly publishing discussions, with recognition that many such journals operate outside large commercial publishing systems. The distribution of diamond journals varies across disciplines and regions, and not all are indexed in major databases.

Gold open access provides immediate visibility and typically satisfies funder mandates without additional steps. The cost is the main barrier. Article processing charges vary widely by journal and discipline, and some researchers cannot access sufficient funding to cover them.

Hybrid Journals and Transformative Agreements

Hybrid journals are subscription journals that offer an open access option for individual articles. Authors can pay an APC to make their specific article open while the rest of the journal remains behind a paywall. This option can be useful when you want to publish in a particular journal that does not offer full open access.

Transformative agreements are contracts between institutions or consortia and publishers that shift subscription payments toward open access publishing. Under these agreements, researchers at participating institutions may publish open access without paying individual APCs. If your institution has signed such an agreement, you may have a cost-free gold route available. Check with your library or research office before assuming you must pay an APC.

Funder Mandates and Compliance

What Funders Require

Many research funders now require that peer-reviewed articles resulting from funded work be made openly available. The specifics vary by funder, including the acceptable routes, embargo limits, and which versions must be deposited. Some mandates apply to all funded research, while others apply only to specific programs.

The U.S. Department of Energy mandate provides an example of how such policies operate in practice. From 2014 onward, the DOE required its 17 National Laboratories to publish all peer-reviewed scientific articles without a paywall. Analysis of more than 300,000 publications between 2012 and 2018 showed that articles subject to the mandate were used 42% more in patents, despite embargo periods of up to 12 months. Interestingly, the same analysis found no increase in citations from other academic articles. The mandate primarily contributed to technological development instead of additional academic research, and small firms were the main beneficiaries of the increased diffusion of scientific knowledge.

This finding matters for researchers who want to demonstrate the broader impact of their work. Open access can extend the reach of your research beyond the academic community into industry and application, even when it does not change citation patterns within academia.

Plan S and International Coordination

Plan S is an open access initiative that has influenced funder policies across Europe and beyond. The initiative requires that research funded by participating organizations be published in compliant open access journals or platforms. The policy has generated substantial discussion about how it reshapes publishing practices, particularly regarding the acceptability of hybrid journals and the role of transformative agreements.

If you collaborate with researchers funded by Plan S signatories, you may need to ensure that joint publications comply with those requirements even if your own funder has different rules. Discuss open access plans early in collaborations to avoid last-minute compliance problems.

Checking Your Specific Obligations

Funder policies change, and individual programs within the same funder may have different requirements. Before submitting a manuscript, verify the current policy for your specific grant. Key questions to answer include:

  • Which versions of the manuscript are acceptable for deposit?
  • What is the maximum permitted embargo period?
  • Is there a preferred repository?
  • Are APCs an allowable expense under your grant?
  • What documentation of compliance does the funder expect?

Your institution's library or research support office can help answer these questions. Many institutions maintain current summaries of major funder policies.

Choosing a Journal

Quality Indicators

Journal quality matters for both career advancement and compliance. Publishing in a low-quality journal can harm your reputation and may not satisfy funder requirements if the journal is not recognized as legitimate.

The Directory of Open Access Journals provides a starting point for identifying legitimate open access journals. Journals listed there have met basic quality standards, including peer review and editorial oversight. However, not all quality open access journals are listed, and listing alone does not guarantee that a journal is appropriate for your work.

For biomedical and life sciences research, check whether the journal is indexed in PubMed or other major databases. The National Center for Biotechnology Information provides literature resources that can help you verify a journal's standing. PubMed, maintained by the National Library of Medicine, indexes journals that meet specific quality and scope criteria.

Reporting Guidelines

For health research, the EQUATOR Network provides reporting guidelines that many journals require or recommend. These guidelines specify what information must be included in a manuscript to ensure transparent and complete reporting. Following the appropriate guideline for your study type improves the likelihood of acceptance and contributes to research quality.

Experimental Design Considerations

For animal research and other studies where experimental design is critical, the NC3Rs Experimental Design Assistant can help you plan your experiments rigorously. This tool supports researchers in designing studies that are robust and reproducible, which is important regardless of where you publish.

Avoiding Predatory Journals

Predatory journals charge fees without providing legitimate peer review or editorial services. Warning signs include unsolicited email invitations, promises of rapid publication, unclear peer review processes, and fees that are not disclosed until after submission.

Before submitting to an unfamiliar journal, verify its editorial board, check whether it is indexed in databases you trust, and look for evidence of actual published articles that underwent visible peer review. If a journal's practices seem opaque, seek advice from colleagues or your institution's library.

Managing Article Processing Charges

Understanding APC Costs

Article processing charges vary enormously. Some journals charge a few hundred dollars, while others charge several thousand. The fee is typically due upon acceptance, and some journals offer discounts for reviewers, society members, or researchers from low-income countries.

Before submitting, confirm the APC amount and whether it applies to your article type. Some journals waive fees for certain article types, such as editorials or commentaries, while charging for original research. Others offer waivers based on geographic location or financial need.

Funding Sources for APCs

Several funding sources can cover article processing charges:

  • Your research grant, if the funder allows APC expenses
  • Institutional open access funds
  • Library agreements with publishers
  • Society or association publication funds
  • Co-author contributions from institutions with transformative agreements

Apply for APC funding before submission when possible. Some funds have limited budgets and operate on a first-come basis. If you wait until acceptance, the funding may no longer be available.

Negotiating and Requesting Waivers

Many publishers offer automatic waivers for authors from low-income countries and discretionary waivers for others. If your institution lacks resources, contact the journal before submission to ask about waiver options. Some journals also offer discounts for reviewers who have completed reviews for that journal.

When requesting a waiver, provide clear information about your funding situation. Be prepared to document that you lack alternative funding sources.

Budgeting for Open Access

If your research program regularly produces publications, include APC costs in your grant budgets. Some funders allow APCs as a direct cost, while others expect them to be covered by institutional funds. Check your funder's cost policy and plan accordingly.

Practical Workflow for Open Access Compliance

Before Submission

  1. Identify your funder's open access requirements and note the compliance deadline
  2. Check whether your institution has transformative agreements with target journals
  3. Verify the journal's open access options and APC amount
  4. Confirm the journal's quality indicators and reporting guideline requirements
  5. Determine which manuscript version you will deposit and where
  6. Secure APC funding or a waiver before submission if needed

At Submission

  1. Disclose your funder and grant number in the submission system
  2. Note your open access intentions in the cover letter
  3. Confirm the journal's policy on preprint posting
  4. Record the submission date and expected timeline

After Acceptance

  1. Pay the APC or confirm the waiver
  2. Deposit the accepted manuscript in the required repository
  3. Include the funder grant number in the deposit metadata
  4. Link the repository record to the published article
  5. Keep records of all compliance steps for your final report

After Publication

  1. Verify that the published version is accessible without a paywall
  2. Check that the repository record is complete and accurate
  3. Update your ORCID record and institutional profiles with the publication
  4. Share the open access link through appropriate channels

Records and Measurements

What to Track

Maintain a record of your open access activities for each publication. Useful information includes:

  • Funder policy version and compliance deadline
  • Journal name and open access route
  • APC amount and funding source
  • Manuscript version deposited and repository name
  • Deposit date and embargo period
  • Confirmation of compliance from the funder

This record supports your final research reports and helps you plan future submissions.

Measuring Impact

Open access can affect how your work is used. Article-level metrics, such as downloads and altmetrics, can show engagement beyond citations. The analysis of the DOE mandate found that open access articles were used more in patents, suggesting that industry and technology developers benefit from access to your work.

If your funder or institution requires impact reporting, collect data on downloads, social media mentions, policy citations, and patent citations. These measures can demonstrate the broader value of your research.

Common Failure Patterns

Missing the Embargo Deadline

Funder policies often require deposit within a specific time frame after acceptance or publication. Missing this deadline can make your work noncompliant even if you eventually deposit the manuscript. Set calendar reminders for the deposit deadline and complete the deposit as soon as possible after acceptance.

Depositing the Wrong Version

Some researchers deposit the submitted manuscript instead of the accepted version. Funders typically require the accepted manuscript, which includes peer review changes. Check your funder's version requirements and ensure your repository deposit matches.

Assuming All Open Access Journals Are Free

Not all open access journals waive fees. Some charge APCs that can be substantial. Always confirm the APC before submission, and secure funding or a waiver in advance.

Overlooking Institutional Agreements

Researchers sometimes pay APCs unnecessarily when their institution has a transformative agreement that would cover the cost. Check with your library before paying any APC.

Ignoring Funder Requirements Until the Final Report

Compliance is much easier to manage during the publication process than after the fact. If you discover a compliance problem at the final report stage, you may need to deposit manuscripts retroactively or explain the noncompliance to your funder.

Limitations and Professional Escalation

When to Seek Help

Consult your institution's library or research support office when:

  • You are unsure about your funder's current requirements
  • You cannot determine whether a journal is legitimate
  • You need help identifying transformative agreements
  • You are applying for APC funding or waivers
  • You have received a compliance notice from a funder

When to Escalate

Escalate to your institution's research integrity office or legal counsel when:

  • A publisher demands payment for services that were not disclosed before submission
  • You suspect a journal is operating fraudulently
  • A funder disputes your compliance documentation
  • You are asked to sign an agreement that conflicts with your funder's requirements

Handling Disputes

If a journal charges an APC you did not agree to, or if a publisher refuses to release your manuscript after you withdraw it, document all communications and seek institutional support. Most disputes can be resolved through the publisher's customer service, but persistent problems may require escalation.

Open Science Practices Beyond Publishing

Data Sharing

Open access to articles is one component of open science. Many funders also require data sharing plans that describe how research data will be made available. The National Institute of Standards and Technology Research Data Framework provides guidance on managing research data throughout its lifecycle, including documentation, storage, and sharing practices.

When planning your data sharing approach, consider what data can be shared ethically and legally, where it will be deposited, and how it will be documented. Data availability statements in your articles should point readers to the actual data.

Preprints

Preprints are manuscript versions posted to public servers before or during peer review. Many journals allow preprint posting, and some funders encourage it as a way to accelerate dissemination. The Royal Society's Open Biology journal has established a preprint team and supports preprint posting as part of its publishing model.

Before posting a preprint, check the target journal's policy. Some journals have specific requirements about preprint versions and licensing.

Open Educational Resources

Beyond research articles, open access applies to educational materials. Open educational resources include blog posts, podcasts, infographics, and videos that support learning. The quality of these resources varies considerably, and users should critically appraise them before relying on them for clinical or educational decisions.

If you create educational materials, consider publishing them under open licenses that allow reuse and adaptation. This approach extends the reach of your teaching materials and supports colleagues in resource-limited settings.

Open Access Textbooks

Traditional textbooks are often expensive and inaccessible in developing countries. Open access textbooks can address this gap. One otolaryngologist's experience with self-publishing open access textbooks demonstrated the simplicity and popularity of this approach, particularly for colleagues in developing countries. Medical societies can support quality control by evaluating open access texts and videos for their members.

If you are considering an open access textbook, investigate the publishing platforms available and the licensing options that will maximize accessibility.

Quality and Welfare Considerations

Research Quality and Open Access

Open access does not change the underlying quality of your research, but it can increase scrutiny. Making your work openly available means more readers can examine your methods and results. This transparency supports research integrity and can improve the reproducibility of your work.

The EQUATOR Network reporting guidelines and the NC3Rs Experimental Design Assistant support rigorous research design and reporting. Using these resources before submission can improve your manuscript and reduce the likelihood of post-publication criticism.

Ethical Publishing Practices

Open access publishing should follow the same ethical standards as any scholarly publishing. This includes accurate reporting of funding sources, conflicts of interest, and author contributions. Some open access journals have adopted open peer review, where reviews and author responses are published with the paper, as described in the Royal Society's Open Biology journal. This practice increases transparency but may not suit all researchers.

Protecting Participant Privacy

If your research involves human participants, open access does not override your obligations to protect privacy. De-identify data before sharing, and ensure that your data sharing plans comply with ethical approvals and legal requirements.

Frequently Asked Questions

What is the difference between green and gold open access?

Green open access means depositing a version of your manuscript in a repository, usually the accepted manuscript after peer review. It typically costs nothing but may involve an embargo period. Gold open access means the final published version is freely available on the journal's website, often after payment of an article processing charge. Gold provides immediate access but can be expensive.

How do I know if my funder requires open access?

Check your grant agreement and your funder's current policy. Many funders require open access for peer-reviewed articles resulting from funded research, but the specific requirements vary. Your institution's library or research support office can help you identify the applicable policy.

What is an article processing charge and who pays it?

An article processing charge is a fee that some open access journals charge to cover publishing costs. The author, their institution, or their funder typically pays it. Some journals waive fees for authors from low-income countries or for certain article types. Check the journal's policy before submission.

Can I publish in a subscription journal and still comply with open access mandates?

Yes, through green open access. Most subscription journals allow authors to deposit the accepted manuscript in a repository after an embargo period. Check the journal's policy and your funder's embargo limits to ensure compliance.

What is a transformative agreement?

A transformative agreement is a contract between an institution or consortium and a publisher that shifts subscription payments toward open access publishing. Under these agreements, researchers at participating institutions may publish open access without paying individual APCs. Check with your library to see if your institution has such agreements.

How can I tell if an open access journal is legitimate?

Check whether the journal is listed in the Directory of Open Access Journals, indexed in PubMed or other major databases, and has a visible editorial board and peer review process. Be cautious of unsolicited invitations and journals that promise rapid publication without clear editorial oversight.

What should I do if I cannot afford an article processing charge?

Consider green open access through a repository, which costs nothing. Look for diamond open access journals that charge no fees. Apply for institutional open access funds or request a waiver from the journal. Some journals offer discounts for reviewers or society members.

Do open access articles receive more citations?

Evidence is mixed. Analysis of the U.S. Department of Energy mandate found that open access articles were used more in patents but were not cited more frequently by other academic articles. Open access can increase the broader use of your work even when it does not change academic citation patterns.

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References and Further Reading

This article is educational and does not replace institutional policy, professional advice, or applicable safety and regulatory requirements.