Scholarly Publishing Fundamentals
This is an orientation cluster for readers who need grounding in scholarly publishing before engaging with the more specific sub-topics elsewhere in this section. It covers the basic structure of the scholarly publishing system: what a peer-reviewed journal is, how the journal article became the dominant unit of research output, the roles of authors, editors, reviewers, and publishers, and the general lifecycle of a manuscript from writing through publication and indexing. Because this is a fundamentals page rather than a page tied to a single standard or regulation, it draws on the same landscape of organizations referenced throughout this section without narrowing to any one of them: standards bodies such as ANSI/NISO and the STM Association, which shape terminology and practice around peer review; open-access organizations such as DOAJ and OASPA, which define what counts as a legitimate open-access publication; and research-integrity bodies such as COPE, which set expectations for editorial conduct and authorship. Readers are pointed to the more specific clusters — peer review, open access, bibliometrics, preprints, evidence synthesis, AI editorial standards, and editorial workflow — for the detailed treatment of each area. For a research administrator new to scholarly communication, or supporting researchers across disciplines with varying publishing norms, this page functions as a map: it explains why the section is organized the way it is, what distinguishes a journal article from other research outputs like preprints or datasets, and where to look for guidance on a specific publishing question. It intentionally avoids duplicating the detailed definitions found in the more specific sub-clusters, instead providing the connective context that makes those pages easier to use in sequence.
Guides
COUNTER 5.1.1: The New Access_Method: Agent Category for AI Usage Reporting
COUNTER Code of Practice Release 5.1.1 (30 June 2026) adds an optional Access_Method: Agent category and five new AI Metric_Types, letting publishers and platforms report AI/agentic usage separately from human browsing and text-and-data-mining access.
JATS4R: The NISO Recommended Practices for Reuse-Ready Journal Article Tagging
JATS4R (JATS for Reuse) is a NISO working group publishing Recommended Practices that pick one preferred JATS XML tagging pattern per element — covering funding, data citations, authors and affiliations, CRediT roles, and more — so tagged articles are consistently machine-reusable across publishers and archives.
Crossref Research Nexus: Linking Articles, Preprints, Grants, Data, and Protocols
Crossref’s Research Nexus connects journal articles, preprints, grants, datasets, and protocols through declared relationship metadata rather than isolated DOIs. Here is how the relationship types work, who benefits, and how it fits alongside Crossref Event Data.
BELS Certification for Manuscript Editors: What ELS Means
BELS certification (the ELS credential) is an exam-based credential from the Board of Editors in the Life Sciences that verifies a manuscript editor’s proficiency in life-sciences editing, terminology, and publication ethics. This guide explains eligibility, exam format, the advanced Distinguished Editor level, and what the credential actually signals to journals, PIs, and employers.
JATS XML Explained: The Metadata Standard Behind Every Journal Article
What JATS XML (ANSI/NISO Z39.96) is, its three tag sets, how it structures article full text and metadata, how it relates to Crossref XML, and why it matters to PMC deposit and research-office workflows.
Crossref Metadata Deposit Workflow: What to Submit, and When
A practical walkthrough of how a Crossref member registers a DOI and keeps its metadata current: the deposit methods available, the metadata a record needs to resolve and to be useful, and when registration and updates are actually expected to happen.
ROR IDs Explained: Why Research Organizations Need One and How to Get One
What a ROR ID is, why it matters for funders, publishers, and CRIS systems, who is eligible to register, and the step-by-step process an institution follows to request and start using one.
Funding Acknowledgement Statement: Format, Required Elements, and Example Wording by Funder
A funding acknowledgement statement names the funder and award number in a resulting publication. This guide covers required elements, how format varies by NIH, NSF, Wellcome, UKRI, and Horizon Europe, and illustrative example wording for each.
Journal Article Types: A Guide to the Manuscript Taxonomy
A practical guide to the taxonomy of journal article types — original research, review, case report, brief communication, letter, commentary, editorial, correction, and Registered Report — and why the choice affects peer review, indexing, and citation metrics.
How to Search for Peer-Reviewed Articles in Academic Databases
A practical walkthrough of searching PubMed, Scopus, Web of Science, and library discovery layers for peer-reviewed articles: Boolean logic, MeSH/subject headings, and peer-review filters.
How to Find Peer-Reviewed Journals: Databases, Filters, and Verification
How to find peer-reviewed journals for a literature search or manuscript submission, using database filters, DOAJ, indexing checks, and journal-verification steps.
What Does It Mean for a Journal to Be Indexed?
“Indexed journal” means a specific database — Scopus, Web of Science, PubMed/MEDLINE, or DOAJ — evaluated a journal against its own published criteria and accepted it for ongoing inclusion. This guide covers what indexing means, why it matters for discoverability and legitimacy, each database’s real criteria, and how indexing differs from a journal’s impact factor.
How to Get Permission to Reuse a Published Figure or Text
A practical, decision-based process for reusing a published figure or block of text: check the license first, use RightsLink/the Copyright Clearance Center for traditionally copyrighted content, know when fair use or fair dealing actually applies, and attribute reused material correctly.
Citation Styles and Referencing Formats: A Practical Overview
A practical, decision-support comparison of APA, MLA, Chicago, Vancouver/ICMJE, AMA, and IEEE citation styles: which fields and journals typically require which, and what structurally differs between them.







