The following terms appear throughout this text or are commonly encountered in the literature and practice of scientific publishing. Definitions aim to be concise and practical.
APC
An Article Processing Charge (APC) is a fee paid by the author, their institution, or their funder to a journal publisher in exchange for making a published article freely and immediately available under an open access license. APCs are the primary funding mechanism for gold open access journals and for hybrid open access options within subscription journals. Charges vary widely, from a few hundred dollars at some fully open access journals to several thousand at hybrid journals published by major commercial publishers.
Altmetrics
Altmetrics (alternative metrics) refers to indicators of scholarly attention and engagement beyond traditional citation counts, including mentions in news media, policy documents, social media posts, Wikipedia articles, and research blogs. The term was coined around 2010 and reflects the recognition that academic research influences society through channels that bibliographic databases do not capture. Altmetric scores, as provided by platforms such as Altmetric.com, aggregate these non-citation mentions into a composite indicator.
Boolean Operators
Boolean operators are logical terms — AND, OR, and NOT — used in database searching to combine search terms and control the scope of retrieval. AND narrows a search by requiring both terms to be present; OR broadens a search by retrieving records containing either term; NOT excludes records containing a specified term. Parentheses are used to group terms and control the order of operations in complex queries.
Citation Chasing
Citation chasing, also called snowballing, is a technique for finding additional relevant literature by reviewing the reference lists of known relevant articles (backward chasing) or by identifying articles that have subsequently cited a known article (forward chasing). Backward chasing is possible with any reference list; forward chasing requires a citation database such as Web of Science, Scopus, or Google Scholar that tracks citations over time.
CONSORT
CONSORT (Consolidated Standards of Reporting Trials) is a reporting guideline for randomized controlled trials that specifies the information that should be included in a published trial report to ensure transparency and completeness. The CONSORT checklist includes items covering the trial design, participant eligibility, randomization procedure, blinding, outcomes, statistical methods, and results. Journal endorsement of CONSORT is common in clinical and health sciences; authors submitting RCTs to CONSORT-endorsing journals must typically complete the checklist and submit it alongside the manuscript.
Controlled Vocabulary
A controlled vocabulary is a standardized set of terms used to index documents in a database, ensuring that all documents on a given concept are indexed with the same term regardless of the terminology used by individual authors. MeSH (Medical Subject Headings) is the controlled vocabulary applied to PubMed/MEDLINE; Emtree is used in Embase. Using controlled vocabulary terms in database searches improves recall by capturing documents that discuss a concept using different synonyms or terminologies.
COPE
COPE (Committee on Publication Ethics) is an international organization that provides guidance and resources to journal editors and publishers on ethical issues in scholarly publishing, including authorship disputes, plagiarism, data fabrication, undisclosed conflicts of interest, and duplicate publication. COPE publishes flowcharts and guidelines for handling suspected research misconduct and offers a forum in which editors can seek advice on challenging cases. Membership in COPE signals that a journal has committed to following best practices in publication ethics.
Data Management Plan
A data management plan (DMP) is a formal document describing how research data will be collected, organized, stored, shared, and preserved during and after a research project. Many major funding agencies, including the NIH and NSF, require DMPs as part of grant applications. A DMP typically specifies the types of data to be generated, the formats and standards used, the storage and backup arrangements, the access and sharing policies, and the long-term preservation plan. Institutional research libraries often provide guidance, templates, and tools (such as DMPTool) to help researchers write DMPs.
DOI
A DOI (Digital Object Identifier) is a persistent identifier assigned to a digital object — most commonly a journal article, dataset, book chapter, or other scholarly output — that provides a permanent, stable link to the object regardless of changes to its URL. DOIs are assigned by registration agencies (most commonly CrossRef for scholarly publications) and are expressed in the format 10.XXXX/XXXXX. A DOI URL takes the form https://doi.org/10.XXXX/XXXXX. Citing DOIs rather than URLs ensures that references remain resolvable even when publishers change their website structures.
Double-Blind Review
Double-blind review is a form of peer review in which both the reviewer’s identity and the author’s identity are withheld from each other. This contrasts with single-blind review, in which reviewers know the authors’ identities but are themselves anonymous to the authors. Double-blind review is intended to reduce biases related to author prestige, gender, or institutional affiliation. Its effectiveness is debated, in part because anonymizing authors is difficult in specialized fields where experts can often infer authorship from subject matter, methods, or writing style.
Eigenfactor
The Eigenfactor Score is a journal-level metric that measures a journal’s influence in the research literature by counting citations weighted by the prestige of the citing journal, drawing on an algorithm analogous to Google’s PageRank. Unlike the Journal Impact Factor, the Eigenfactor takes into account not just how many citations a journal receives but from which journals those citations come. Eigenfactor scores are freely available at eigenfactor.org and are also reported in the Web of Science Journal Citation Reports.
FAIR Data
FAIR is an acronym for Findable, Accessible, Interoperable, and Reusable — a set of principles articulated in 2016 to guide the management and publication of scientific data in ways that maximize its utility to both humans and machines. Findable means that data is assigned a persistent identifier and described by rich metadata. Accessible means that the data and metadata are retrievable via a standard protocol. Interoperable means that the data uses broadly applicable standards and vocabularies. Reusable means that the data is described with sufficient provenance and context that it can be understood and used by others.
Grey Literature
Grey literature refers to research outputs produced outside of commercial publishing channels, including technical reports, government documents, conference proceedings, theses and dissertations, preprints, working papers, policy briefs, and internal reports. Grey literature is an important source of evidence, particularly for systematic reviews in public health and policy contexts, because it may include findings that were never formally published (addressing publication bias) and because governments and agencies frequently release substantive research in report rather than journal format. Identifying and retrieving grey literature requires search strategies beyond standard database searching.
h-Index
The h-index is an author-level metric defined as the largest number h such that a researcher has published at least h papers that have each been cited at least h times. Proposed by physicist Jorge Hirsch in 2005, the h-index combines productivity and impact in a single number. It increases monotonically over time, is sensitive to field-level citation norms, and should not be compared across disciplines or career stages without careful contextualization.
Impact Factor
The Journal Impact Factor (JIF), calculated and published annually by Clarivate in the Journal Citation Reports, is the mean number of citations received in a given year by articles published in a journal during the two preceding years. It was designed as a tool for library journal selection, not as a measure of individual article or researcher quality. Its widespread misuse in research evaluation — applying a journal-level average to individual articles or researchers — has been extensively criticized by the scientific community, most formally in the San Francisco Declaration on Research Assessment (DORA).
IMRaD
IMRaD stands for Introduction, Methods, Results, and Discussion, the standard organizational structure for primary research articles in the natural and biomedical sciences. The Introduction establishes the research question and its significance; the Methods describes the experimental design and analytical approach in sufficient detail to permit replication; the Results presents findings without interpretation; the Discussion interprets findings, addresses limitations, and situates the work in the context of the existing literature. Some journals add an abstract before the introduction and a conclusion after the discussion.
Institutional Repository
An institutional repository (IR) is a digital archive maintained by a university or research institution for the purpose of collecting, preserving, and providing open access to the research outputs of its faculty and students. Institutional repositories accept a range of materials including journal articles (typically the accepted manuscript version), theses and dissertations, datasets, working papers, and other scholarly products. Depositing publications in an institutional repository is a common way of complying with green open access mandates while complying with publisher copyright policies.
IRB
An Institutional Review Board (IRB) is a committee formally designated to review, approve, and oversee research involving human subjects, in accordance with federal regulations and ethical principles. IRBs evaluate research proposals for risk to participants, adequacy of informed consent procedures, equitable selection of subjects, and protection of privacy and confidentiality. IRB approval must typically be obtained before a study begins and is reported in the methods section of published articles; most journals require a statement of IRB approval (or a determination of IRB exemption) for human subjects research.
IACUC
An Institutional Animal Care and Use Committee (IACUC) is the counterpart to the IRB for research involving non-human animals. IACUCs review animal research protocols for compliance with the Animal Welfare Act and the Public Health Service Policy on Humane Care and Use of Laboratory Animals. They evaluate the scientific justification for animal use, the choice of species, the number of animals, the procedures performed, and the measures taken to minimize pain and distress. IACUC approval must be obtained before animal experiments begin and is reported in published methods sections.
MeSH
MeSH (Medical Subject Headings) is the controlled vocabulary developed by the National Library of Medicine for indexing articles in PubMed/MEDLINE. The MeSH vocabulary includes approximately 30,000 terms organized in a hierarchical tree structure, with broader and narrower terms linked by parent-child relationships. Each indexed article in MEDLINE is assigned MeSH terms by trained indexers. Using MeSH terms in PubMed searches improves recall by capturing articles that discuss a concept using different terminologies and synonyms, all of which map onto a single standardized term.
Open Access
Open access (OA) refers to the practice of making scholarly research freely available on the internet without subscription fees, access barriers, or most copyright restrictions. Open access publishing encompasses a spectrum of models: green OA (self-archiving), gold OA (APC-funded publication), diamond OA (no-fee journals), and hybrid OA (individual article OA within a subscription journal). The defining characteristic is free, immediate, online availability; many OA definitions also require that the content carry a permissive license allowing reuse.
ORCID
ORCID (Open Researcher and Contributor ID) is a nonprofit organization that provides persistent digital identifiers (ORCID iDs) for researchers. An ORCID iD is a 16-digit number that uniquely identifies a researcher across databases and institutions, regardless of name changes or transliteration variations. ORCID iDs are increasingly required by journals and funders during manuscript submission and grant applications, and they serve as a connective layer linking a researcher’s publications, grants, and professional activities across systems.
Peer Review
Peer review is the process by which a journal editor solicits evaluation of a submitted manuscript by experts in the relevant field before making a publication decision. Reviewers assess the scientific rigor, novelty, significance, and presentation of the work and provide written comments to the editor and, typically, to the authors. Peer review serves as the primary quality control mechanism in academic publishing, though it is not infallible and has well-documented limitations including inconsistency, reviewer bias, and an inability to detect sophisticated data manipulation.
PICO
PICO is a framework for structuring clinical and health research questions. It stands for Population (the patient or participant group of interest), Intervention (the treatment, exposure, or test), Comparison (the alternative to which the intervention is compared), and Outcome (the measure of interest). The PICO framework helps researchers formulate precise, answerable research questions and translate those questions into effective database search strategies by identifying the key concepts that should be searched.
Plan S
Plan S is a coalition initiative launched in 2018 by cOAlition S, a group of research funding organizations led by the European Commission and national funders. Plan S requires that research funded by participating funders be published in fully open access journals or deposited in open access repositories with no embargo period. It also requires that published articles carry a Creative Commons Attribution (CC BY) license, permitting unrestricted reuse with attribution. Plan S has significantly accelerated the transition to open access in Europe and has influenced funder policies worldwide.
Predatory Journal
A predatory journal is a publication that claims to be a peer-reviewed academic journal but operates without genuine editorial standards, charging APCs in exchange for rapid, non-rigorous publication. Predatory journals often solicit submissions by unsolicited email, promise implausibly rapid peer review, list fabricated or non-consenting editors, and lack indexing in reputable databases. They damage scientific integrity by publishing unvetted work and exploit authors who are unaware of the warning signs. Resources for identifying predatory journals include the Directory of Open Access Journals (DOAJ), the Think. Check. Submit. checklist, and institutional library guidance.
Preprint
A preprint is a version of a scholarly manuscript that has been shared publicly — typically through a preprint server such as bioRxiv, medRxiv, arXiv, or SSRN — before or concurrently with submission for formal peer review. Preprints are freely accessible, assigned DOIs, and citable as soon as they are posted. They allow rapid dissemination of findings and establish priority, but they have not been peer reviewed and should be read with corresponding critical scrutiny.
Preregistration
Preregistration is the practice of registering the hypotheses, methods, and analysis plan of a study in a publicly accessible registry before data collection begins. Preregistration reduces the opportunity for post-hoc hypothesis adjustment and selective reporting, which are significant drivers of the replication crisis. Clinical trials are preregistered in ClinicalTrials.gov or equivalent registries; observational and experimental studies can be preregistered through platforms such as the Open Science Framework (OSF) or AsPredicted.
Retraction
A retraction is a formal withdrawal of a published article by the journal in which it appeared, typically due to findings of error, fraud, duplicate publication, or authorship misconduct. Retractions are announced in a retraction notice that specifies the reason for withdrawal and are indexed in databases so that readers can identify retracted work. The Retraction Watch database (retractionwatch.com) maintains a comprehensive record of retracted scientific publications. A retracted paper remains in the literature but is marked to indicate that it should not be relied upon.
Scoping Review
A scoping review is a type of evidence synthesis that maps the existing literature on a broad topic, identifies the range and nature of available evidence, and characterizes gaps in the literature. Unlike systematic reviews, scoping reviews do not typically include a formal quality appraisal of individual studies or a meta-analysis of pooled results. They are appropriate when the purpose is to survey what is known about a topic, identify key concepts and definitions, or assess the feasibility of a full systematic review.
Systematic Review
A systematic review is a type of evidence synthesis that uses explicit, reproducible methods to comprehensively identify, select, and critically appraise all available evidence on a focused research question. Systematic reviews follow a pre-specified protocol, conduct comprehensive searches across multiple databases, apply defined inclusion and exclusion criteria, and assess the risk of bias in included studies. They are the highest level of evidence in the evidence hierarchy for clinical and health research, and their methods are reported according to the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines.
STROBE
STROBE (Strengthening the Reporting of Observational Studies in Epidemiology) is a reporting guideline for observational studies in epidemiology, covering cohort studies, case-control studies, and cross-sectional studies. The STROBE checklist specifies the information that should be reported in each section of an observational study manuscript to ensure transparency and completeness. It is endorsed by many epidemiology and public health journals and is a required submission element for observational studies at journals that have adopted the guideline.
Vancouver Style
Vancouver style is the citation and reference formatting system used by many biomedical journals, based on the guidelines of the International Committee of Medical Journal Editors (ICMJE). In Vancouver style, references are numbered consecutively in the order in which they appear in the text, and in-text citations are denoted by superscript numbers or numbers in parentheses. The reference list at the end of the article presents references in numerical order. Vancouver style contrasts with author-date (Harvard) style, in which citations appear as author surnames and year within the text.
Web of Science
Web of Science is a citation indexing database operated by Clarivate that indexes a curated set of high-quality peer-reviewed journals across sciences, social sciences, and humanities. Its bidirectional citation tracking allows users to identify papers that have cited a given article (forward citation search), making it essential for systematic reviews and citation analysis. Web of Science data underlies Journal Impact Factors and related bibliometric products, and its ResearcherID system provides researcher-level citation profiles.
Zotero
Zotero is a free, open-source reference management software application that helps researchers collect, organize, cite, and share bibliographic references and associated full-text documents. It operates as a desktop application with browser extensions that allow one-click capture of citation metadata from journal databases, library catalogs, and websites. Zotero integrates with word processors including Microsoft Word and Google Docs to insert formatted citations and automatically generate reference lists in any citation style. Its sync and sharing features make it useful for collaborative projects.
Green OA
Green OA (green open access) refers to the practice of making a version of a published journal article freely available by depositing it in a repository — such as an institutional repository, a subject-specific archive, or PubMed Central — rather than through the journal itself. The deposited version is typically the author accepted manuscript (after peer review, before publisher formatting) or, where permitted, the final published version. Green OA does not require an APC and is permitted by the vast majority of publishers, though embargo periods and version restrictions vary.
Gold OA
Gold OA (gold open access) refers to publishing in a journal that makes all content — or, in the case of hybrid journals, individual articles — freely available immediately upon publication, funded primarily through APCs paid by authors, institutions, or funders. Fully gold OA journals make all published content open; hybrid journals offer individual-article open access within an otherwise subscription journal.
Diamond OA
Diamond OA (diamond open access), also called platinum OA, describes journals that provide free access to readers and charge no APCs to authors, funded instead through institutional support, society subsidy, volunteer labor, or government grants. Diamond OA journals remove financial barriers for both readers and authors, making them particularly important for researchers from low- and middle-income countries and for disciplines where APC costs are prohibitive.
Creative Commons
Creative Commons (CC) is a nonprofit organization that has developed a suite of standardized public copyright licenses that allow creators to specify the conditions under which their works may be reused. The most important Creative Commons licenses for academic publishing are CC BY (Attribution, allowing any reuse with credit), CC BY-NC (Attribution-NonCommercial, restricting commercial use), CC BY-ND (Attribution-NoDerivatives, prohibiting modification), and CC BY-SA (Attribution-ShareAlike, requiring derivative works to carry the same license). Most open access mandates require CC BY licensing to maximize the reusability of publicly funded research.