How to Write a Literature Review Protocol: A Template for Biology Researchers
By Dr. Zubair Khalid, DVM, MS, PhD ·
Quick Answer
- A literature review protocol is a written plan that documents your research question, search strategy, inclusion criteria, and data extraction methods before you begin reviewing.
- Start by drafting the protocol sections in this template, register or share the plan with your team, then follow it consistently while tracking any deviations.
- The protocol does not guarantee a perfect review, but it reduces bias and makes your methods transparent enough for others to evaluate or reproduce.
At a Glance
| Protocol Section | Purpose | Minimum Content Required | Common Mistake |
|---|---|---|---|
| Research Question | Defines the scope and boundaries of the review | Population, intervention or exposure, comparison, outcome, and context | Writing a question too broad to search effectively |
| Search Strategy | Documents where and how you will find studies | Databases, search terms, Boolean operators, date limits, and language filters | Searching only one database or using vague keywords |
| Screening Criteria | Sets rules for including or excluding studies | Inclusion criteria, exclusion criteria, and screening workflow | Applying criteria inconsistently between reviewers |
| Data Extraction | Standardizes what information you collect from each study | Extraction form fields, data items, and handling of missing data | Collecting data without a predefined form |
| Quality Assessment | Evaluates the reliability of included studies | Assessment tool, scoring method, and resolution process for disagreements | Skipping quality checks or using an unvalidated tool |
| Reporting Plan | Describes how you will present findings | Synthesis method, tables or figures planned, and reporting guidelines | Writing the report before finalizing the protocol |
Why a Protocol Matters for Biology Research
Biology researchers face a distinctive challenge when reviewing literature. The field spans molecular mechanisms, organism-level studies, ecological observations, and clinical applications. Each subfield uses different terminology, study designs, and standards of evidence. Without a written protocol, a review can drift from its original question, include studies that do not actually address the problem, or miss important work because the search was not systematic.
A protocol serves as a fixed reference point. It records the decisions you made before seeing the results, which prevents the common problem of shaping the review around studies that support a preferred conclusion. The Committee on Publication Ethics Core Practices emphasize that transparency in research methods is a fundamental expectation of ethical scholarship. A protocol is one concrete way to meet that expectation because it shows reviewers and readers exactly what you planned to do.
For biology researchers, the protocol also supports collaboration. Many reviews involve multiple team members who screen titles, extract data, or assess quality. A written protocol ensures everyone applies the same rules. When disagreements arise, the protocol provides the framework for resolving them consistently.
Core Principles of a Review Protocol
Transparency
The protocol should describe your methods in enough detail that another researcher could replicate your search and screening decisions. This means naming the databases, listing the exact search terms, and specifying how you handled variations in terminology across biological subfields. For example, a review on gene expression in plant stress responses might need to include both "drought tolerance" and "water deficit stress" as search terms because different research communities use different language.
Reproducibility
A reproducible protocol is one that another team could follow and obtain similar results. This requires precise documentation of every step. The National Library of Medicine Research Methods Resources provide access to authoritative texts on research methodology that can help you understand what level of detail is expected in different review types.
Accountability
A protocol creates accountability for the research team. It establishes who is responsible for each task, how decisions will be made, and what records must be kept. This is particularly important in biology where studies may involve animal subjects, field data, or laboratory experiments that have their own documentation requirements.
Flexibility Within Boundaries
A protocol is not a prison. You can deviate from it when new information emerges, but you must document the deviation and explain why it was necessary. The key distinction is between a planned change and an unplanned drift. Planned changes are recorded, justified, and dated. Unplanned drift happens when reviewers unconsciously alter their criteria as they encounter studies, which undermines the validity of the review.
The Protocol Template
Section 1: Research Question and Objectives
The research question is the foundation of the entire protocol. It determines what you search for, what you include, and how you synthesize the findings. A well-formed question in biology typically includes several components.
For a review on the effects of a specific agricultural practice on soil microbial communities, the question might specify the practice, the soil type, the microbial outcome, and the comparison condition. Write the question in a single sentence that can be evaluated for clarity. If you cannot explain the question to a colleague in one sentence, it is probably too vague.
State the objectives separately from the question. Objectives are the specific things the review aims to accomplish. For example, one objective might be to identify all published studies on the topic, another might be to assess the methodological quality of those studies, and a third might be to summarize the direction and magnitude of reported effects.
Section 2: Eligibility Criteria
Eligibility criteria define which studies enter the review and which are excluded. These criteria must be specific enough to apply consistently but broad enough to capture relevant work.
Inclusion criteria typically cover study design, population or system studied, intervention or exposure, outcomes measured, and publication characteristics. For a biology review, you might specify that only peer-reviewed primary research articles are included, that studies must involve a particular organism or system, and that outcomes must be measured at a particular level.
Exclusion criteria remove studies that meet inclusion criteria but have characteristics that make them unsuitable. Common exclusions include conference abstracts without full data, studies published in languages the team cannot read, and studies with insufficient methodological detail.
The EQUATOR Network provides reporting guidelines that can help you think about what study characteristics matter for different research designs. While these guidelines are primarily for reporting completed research, they also help reviewers understand what information studies should contain.
Section 3: Search Strategy
The search strategy is the operational plan for finding studies. It must specify the information sources, the search terms, and the search process.
List every database you will search. Biology reviews commonly use PubMed, Web of Science, Scopus, and field-specific databases such as Agricola for agricultural topics or Zoological Record for animal studies. Each database has different search syntax and coverage, so the search strategy must be adapted for each one.
Document the search terms and how they are combined. Include the Boolean operators, truncation symbols, and field tags used. For biology topics, consider synonyms and variant spellings. A search for "tumor" should also include "tumour" and "neoplasm" depending on the database and the research community.
Record the date of each search and the number of results retrieved. This information is essential for the PRISMA-style flow diagram that many journals require in the final review report.
Section 4: Study Selection Process
The study selection process describes how you move from the full set of search results to the final set of included studies. This typically happens in stages.
The first stage is title and abstract screening. Two reviewers independently screen each record against the eligibility criteria. Records that clearly do not meet the criteria are excluded. Records that might meet the criteria proceed to full-text review.
The second stage is full-text review. Reviewers obtain the full text of potentially eligible studies and apply the eligibility criteria to the complete article. Studies that do not meet the criteria are excluded, and the reason for exclusion is recorded.
Disagreements between reviewers are resolved through discussion or by a third reviewer. The protocol should specify how many reviewers will screen, how disagreements will be resolved, and what records will be kept.
Section 5: Data Extraction
Data extraction is the process of collecting information from each included study. The protocol must specify what data will be extracted and how.
Create a data extraction form that lists every data item. For biology reviews, this might include study characteristics such as author, year, country, and study design. It might also include population characteristics such as species, strain, sample size, and experimental conditions. Outcome data should include the specific measurements taken, the statistical results, and any reported effect sizes.
The protocol should specify whether data extraction is done by one reviewer or two, and how discrepancies are handled. Some review teams extract data in duplicate and compare results. Others use a single reviewer with verification by a second reviewer. The choice depends on the complexity of the data and the resources available.
Section 6: Quality Assessment
Quality assessment evaluates the methodological soundness of included studies. The protocol must specify the assessment tool and the process for applying it.
Different study designs require different assessment tools. Randomized controlled trials have established tools such as the Cochrane Risk of Bias tool. Observational studies have tools such as the Newcastle-Ottawa Scale. Laboratory studies and ecological studies may require custom assessment criteria because standard clinical tools do not apply.
The protocol should specify how quality ratings will be used. Some reviews exclude low-quality studies. Others include them but weight them less in the synthesis. The decision should be made before data collection begins.
Section 7: Data Synthesis
Data synthesis describes how the extracted data will be combined and analyzed. The protocol must specify the synthesis method.
Narrative synthesis describes the findings of included studies in text and tables. This is appropriate when studies are too heterogeneous for statistical pooling. Thematic synthesis groups findings by theme or topic. Meta-analysis combines quantitative results statistically, but this requires sufficient homogeneity in study designs and outcome measures.
The protocol should specify which synthesis method will be used and under what conditions. For example, you might plan a meta-analysis but specify that a narrative synthesis will be used if statistical heterogeneity is too high.
Section 8: Reporting and Publication
The reporting plan describes how the review will be written and shared. The EQUATOR Network maintains a comprehensive collection of reporting guidelines that help researchers write transparent and complete reports. For systematic reviews, the PRISMA guideline is the most commonly used reporting standard.
The protocol should specify which reporting guideline will be followed, where the review will be registered, and how the final report will be disseminated. Registration of systematic reviews is expected in many fields, and some journals require it before considering a manuscript.
Practical Implementation Steps
Step 1: Draft the Protocol Early
Write the protocol before conducting the search. This is the defining characteristic of a protocol-based review. If you write the protocol after collecting data, it becomes a description of what you did instead of a plan for what you intended to do.
Step 2: Pilot the Search Strategy
Test your search strategy before finalizing the protocol. Run the search in one database and examine the results. Check whether known relevant studies appear in the results. If they do not, adjust the search terms. This pilot process helps you identify problems with terminology or database syntax before you commit to the full search.
Step 3: Pilot the Screening Criteria
Apply your eligibility criteria to a sample of search results. This tests whether the criteria are clear enough to apply consistently. If reviewers interpret the criteria differently, revise the criteria or add clarification notes.
Step 4: Pilot the Data Extraction Form
Extract data from two or three studies using your draft extraction form. This reveals missing fields, ambiguous items, and formatting problems. Revise the form before starting full data extraction.
Step 5: Register or Share the Protocol
Share the protocol with your team and, where appropriate, register it in a public registry. Registration creates a dated record of your plan. The National Institutes of Health Grants and Funding pages describe expectations for rigorous research planning in NIH-funded projects, and a protocol is part of that planning process.
Step 6: Follow the Protocol and Document Deviations
Execute the review according to the protocol. When you need to deviate, document the deviation, the reason, and the date. This documentation goes into the final report so readers can see how the actual process differed from the plan.
Records and Measurements
What to Record
The protocol should specify what records will be kept throughout the review process. At minimum, keep the following records.
Search records include the date of each search, the database searched, the exact search string used, and the number of results retrieved. Save the search strategies in a format that can be reproduced.
Screening records include the number of records screened at each stage, the number excluded, and the reasons for exclusion. A flow diagram is the standard way to present this information in the final report.
Data extraction records include the completed extraction forms for each study. These forms document what data were collected and from where.
Quality assessment records include the completed assessment forms and the resolution of any disagreements between reviewers.
How to Organize Records
Use a consistent file naming convention and folder structure. Create a folder for each stage of the review process. Store search strategies, screening decisions, extraction forms, and quality assessments in separate subfolders.
Consider using reference management software to organize the studies identified in the search. This software can help you track which records were screened, which were excluded, and which were included.
Version Control
The protocol itself should have version control. Number each version and record the date and the changes made. This is particularly important when multiple team members contribute to the protocol or when the protocol is revised after pilot testing.
Common Failure Patterns
Failure Pattern 1: The Question Is Too Broad
A broad question such as "What is known about climate change and agriculture?" produces thousands of search results and defies meaningful synthesis. The protocol cannot fix a question that is fundamentally unanswerable in a single review.
Prevention: Test the question by running a preliminary search. If the search returns more records than the team can reasonably screen, narrow the question by specifying the population, intervention, outcome, or context more precisely.
Failure Pattern 2: The Search Misses Key Studies
A search that misses important studies produces a review that is incomplete or biased. This often happens when the search terms do not capture the vocabulary used by the relevant research community.
Prevention: Pilot the search and check whether known key studies appear in the results. Consult with a librarian or a researcher in the field to identify additional search terms and databases.
Failure Pattern 3: Eligibility Criteria Are Applied Inconsistently
When reviewers apply criteria differently, the included studies do not reflect the stated scope of the review. This happens when criteria are vague or when reviewers interpret them differently.
Prevention: Pilot the screening process with a sample of records. Discuss disagreements and clarify the criteria before starting full screening.
Failure Pattern 4: Data Extraction Errors
Errors in data extraction propagate through the entire review. These errors are more likely when the extraction form is poorly designed or when extractors are not adequately trained.
Prevention: Pilot the extraction form, provide clear instructions, and consider dual extraction with verification for critical data items.
Failure Pattern 5: The Protocol Is Written After the Review
A protocol written after data collection is not a protocol. It is a description of methods that cannot prevent the biases that a protocol is designed to address.
Prevention: Treat the protocol as a required first step. Build time for protocol development into the project timeline.
Quality Controls and Professional Escalation
Quality Controls
Quality controls are checks built into the review process to maintain standards. These include dual screening, dual data extraction, and regular team meetings to discuss progress and problems.
Dual screening means that two reviewers independently apply the eligibility criteria to each record. This reduces the risk that one reviewer will make idiosyncratic decisions. Disagreements are resolved through discussion or by a third reviewer.
Dual data extraction means that two reviewers independently extract data from each included study. The extracted data are compared, and discrepancies are resolved. This is more resource-intensive but substantially reduces extraction errors.
When to Escalate
Some problems require escalation beyond the review team. Escalate when you encounter issues that the team cannot resolve internally.
Escalate to a librarian when the search strategy is not returning expected results or when you are unsure which databases cover your topic. Librarians have specialized training in database searching and can help you develop more effective search strategies.
Escalate to a statistician when you are planning a meta-analysis and are uncertain about the statistical methods or when you encounter unexpected heterogeneity in the data.
Escalate to an institutional review board or ethics committee when the review raises ethical concerns. While literature reviews typically do not require ethics approval, some aspects of the review process may raise questions about data handling or publication ethics.
Escalate to a research integrity officer when you suspect misconduct in the studies you are reviewing or when you encounter questions about authorship, data fabrication, or duplicate publication. The Committee on Publication Ethics Core Practices provide guidance on handling such concerns.
Limitations of a Protocol
A protocol cannot guarantee a perfect review. It is a tool for reducing bias and increasing transparency, but it has inherent limitations.
A protocol cannot fix a poorly conceived research question. If the question is not worth answering, the protocol will produce a well-documented review of an unimportant topic.
A protocol cannot compensate for missing or low-quality primary studies. If the literature on a topic is sparse or methodologically weak, the review will reflect those limitations regardless of how carefully the protocol is followed.
A protocol cannot eliminate all reviewer judgment. Screening decisions, quality assessments, and synthesis choices all involve judgment. The protocol makes those judgments visible and consistent, but it does not remove them.
A protocol can become outdated. New studies are published continuously, and a review that was current when the search was conducted may be incomplete by the time it is published. Some reviews address this by updating the search before publication or by conducting living reviews that are updated regularly.
Safety and Regulatory Context
Research Integrity
The Committee on Publication Ethics Core Practices describe the fundamental expectations for ethical research conduct. These include honesty in reporting, transparency in methods, and accountability for research outputs. A literature review protocol supports these expectations by documenting the methods before the results are known.
Data Management
The National Institutes of Health Data Management and Sharing Policy describes expectations for managing and sharing research data. While this policy applies to NIH-funded research, the principles of good data management apply broadly. A review protocol should specify how review data will be stored, organized, and made available to others.
Researcher Identity
The ORCID for Researchers pages describe how researchers can maintain a persistent identifier that links their work across publications and projects. Including ORCID identifiers in review protocols and reports helps ensure that the review is correctly attributed to its authors.
Funding and Grant Context
The National Institutes of Health Grants and Funding pages describe the expectations for research planning in NIH-funded projects. Grant applications often require a description of the proposed methods, and a review protocol can serve as the basis for the methods section of a grant application that includes a systematic review component.
Frequently Asked Questions
What is the difference between a literature review protocol and a literature review?
A protocol is the written plan that describes what you will do before you do it. The review is the actual work of searching, screening, extracting, and synthesizing. The protocol is completed first and serves as the reference point for the review process.
How long should a literature review protocol be?
The length depends on the complexity of the review and the requirements of the target journal or funder. A simple review for a class assignment might have a protocol of two to three pages. A systematic review intended for publication might have a protocol of ten or more pages. The content matters more than the length.
Do I need to register my literature review protocol?
Registration is expected for systematic reviews in many fields, and some journals require it before considering a manuscript. Registration creates a public record of your plan and helps prevent duplication of effort. Check the requirements of your target journal or funder.
Can I change my protocol after I start the review?
You can change the protocol, but you must document the change and the reason for it. A planned change that is recorded and justified is acceptable. Unplanned drift that happens without documentation undermines the validity of the review.
What software can I use to manage my literature review?
Reference management software such as Zotero, EndNote, or Mendeley can help you organize the studies identified in your search. Systematic review software such as Covidence or Rayyan can help with screening and data extraction. The choice depends on your budget and the complexity of your review.
How do I handle studies that are not in English?
The protocol should specify how you will handle non-English studies. Options include excluding them, translating them, or including them with the help of translators. The decision should be made before the search begins and documented in the protocol.
What is the role of a librarian in a literature review?
A librarian can help you develop and refine your search strategy, identify appropriate databases, and ensure that your search is comprehensive. Librarians have specialized training in database searching that most researchers do not have. Consulting a librarian early in the process can save substantial time and improve the quality of your search.
How do I know if my protocol is good enough?
Test the protocol by piloting each section. Run the search and check the results. Apply the screening criteria to a sample of records. Extract data from a few studies. If the pilot processes reveal problems, revise the protocol before starting the full review.
Using the Evidence
| Source | Best use in this topic | Important limitation |
|---|---|---|
| Research Methods Resources | official guidance | Check the linked page for current local requirements |
| EQUATOR Network | official guidance | Check the linked page for current local requirements |
| Core Practices | official guidance | Check the linked page for current local requirements |
Related Articles
- Data Management Plan Template: A Practical Guide for Researchers
- Scientific Literature Review Format: A Reproducible Structure for Researchers
- How to Write an Experiment Report: A Practical Template
- Scientific Literature Review: A Reproducible Search and Synthesis Workflow
- Responding to Peer Review: A Structured Revision and Response Process
References and Further Reading
- Research Methods Resources. National Library of Medicine.
- EQUATOR Network. EQUATOR Network.
- Core Practices. Committee on Publication Ethics.
- NIH Grants and Funding. National Institutes of Health.
- ORCID for Researchers. ORCID.
- Data Management and Sharing Policy. National Institutes of Health.
- NCBI Literature Resources. National Center for Biotechnology Information.
- PubMed. National Library of Medicine.
This article is educational and does not replace institutional policy, professional advice, or applicable safety and regulatory requirements.