Science is commonly defined as knowledge derived from the facts of experience. On this view, science is special because it rests not on personal opinion or speculation but on what we can see, hear and touch: facts established by careful, unprejudiced observation. From this secure, objective basis, sound reasoning leads to the laws and theories that make up scientific knowledge. Yet the slogan needs qualification: perceptions depend on the observer's knowledge and expectations, and observation statements presuppose a conceptual framework, so facts are fallible rather than an absolutely firm foundation [1].

The conscious and systematic effort to obtain information for a specific purpose is called "research." Information that cannot be acquired by chance can only be obtained through systematic and organized inquiry. In this text, the term "research" refers primarily to scientific research. Scientific research — or simply research — has been defined in various ways. According to a definition frequently cited in the literature, research is the planned and systematic process of collecting data, making it comprehensible, evaluating it through reasoning, and reporting the results in order to produce reliable solutions to problems [2].

A scientific publication is any formally disseminated output of scientific research, including journal articles, conference papers, books, book chapters, theses, and technical reports. The journal article is the most common and most cited type. It is distinct from popular science writing, which communicates research findings to a general audience without a formal citation apparatus [3].

An anonymous work is a publication whose author is unknown or unidentified. In APA 7, the word "Anonymous" is used in the author position only when the work is explicitly signed as Anonymous; otherwise, the title of the work moves into the author position in both the in-text citation and the reference entry. It is distinct from a pseudonymous work, in which the author publishes under an assumed name.

A scientific journal is a periodical that publishes original research articles and reviews in a scientific discipline, typically after peer review, with issues released at regular intervals and grouped into volumes. The broader umbrella terms academic journal and scholarly journal cover the same publication type across all disciplines. It is distinct from a popular magazine, which addresses a general audience and does not apply peer review.

The main reasons for citing sources in a scientific study can be listed as follows:

• To support and defend the validity of the claims made by the researcher;
• To indicate the source of the information, to distinguish the researcher's own contribution, and to give the original authors the credit they deserve;
• To enable the reader to verify the accuracy, reliability, and impartiality of the information presented;
• To provide accessible source information for those who wish to conduct further research on the topic [4].

A citation is a reference in which one scientific study acknowledges another as its source. Footnotes, on the other hand, serve to provide supporting evidence or explanations, or to indicate sources. In terms of content, there are two types of footnotes: content footnotes and copyright permission footnotes. A content footnote supplements or clarifies important information in the text. Such footnotes should not contain complicated, irrelevant, or trivial information, and they should be used only when they genuinely strengthen the discussion, since footnotes can distract the reader. Whenever possible, important information should be presented within the text itself rather than in a footnote. Content footnotes are numbered consecutively, beginning from the point where the first one appears. Copyright permission footnotes, by contrast, are used to acknowledge the source of quoted or reprinted material [5].

An ambiguous citation is an in-text citation that could refer to more than one entry in the reference list, most commonly because two or more sources share the same author surname and publication year. In APA 7, this ambiguity is resolved by adding lowercase letter suffixes to the year or by including first-author initials when different authors share a surname. It is distinct from an incomplete citation, which lacks the bibliographic elements needed to identify the source at all.

Etymologically, the word bibliography derives from the Greek biblion (book) and graphein (to write); in its broadest sense, it refers to the recording of book titles. The principles and conditions of this recording process remain the same today as in the past [6]. According to the renowned French historian and bibliographer P. Caron, bibliography is the branch of book science concerned with repertoires, providing tools for obtaining information about sources. Works lacking certain essential elements — such as a title page, a publication date, or a place of publication — are not included in bibliographies.

In the context of a scientific study, the bibliography is the list of sources used in the research and works cited in the text. Its content should be concise and limited to valuable sources that genuinely support the study [5]. According to another view, however, the bibliography need not be restricted to the sources actually cited: researchers may also include general reference sources they consulted, in order to better inform the reader [4].

Bibliographies fall into two categories: general and special. General bibliographies include bibliographies of bibliographies, universal bibliographies, printed library catalogs, union catalogs, national bibliographies, bibliographies of official publications, bibliographies of journal and newspaper articles, and encyclopedias. Special bibliographies, by contrast, are devoted to specific disciplines and can be further divided into the humanities and the applied sciences.

A bibliographic database is a database containing records of information resources such as books, journal and newspaper articles, conference proceedings, and audiovisual materials. Through its search interface, users can locate these records by criteria such as author, title, or subject [7].

An identifier is a unique code assigned to a document or publication that distinguishes it from all other works and can be used to retrieve its bibliographic information from the relevant databases. Examples include the ISBN, ISSN, DOI, PMID, and arXiv ID. Reference management programs provide dedicated fields for these identifiers and can often retrieve a complete bibliographic record from an identifier alone.

arXiv is an open-access repository maintained by Cornell University, containing scholarly resources in the fields of physics, mathematics, computer science, quantitative biology, quantitative finance, statistics, electrical engineering and systems science, and economics. Each item deposited in arXiv receives a unique identifier known as an arXiv ID, through which the resource can be accessed. Reference management programs include a dedicated field for this identifier and can retrieve bibliographic information automatically via the arXiv ID [8].

A DOI is a system used to identify information resources on digital networks permanently. It can be assigned to physical, digital, or abstract entities. When a DOI is entered into the resolver at https://doi.org/, the user is directed to the identified resource — typically the publisher's page, where the material can be accessed or downloaded. Reference management programs can also retrieve bibliographic information automatically via a DOI [9].

An ISBN is a unique, permanent commercial identifier assigned to a specific edition and format of a published book.

An ISSN is a unique, permanent eight-digit code used to identify a serial publication — a newspaper, journal, magazine, or other periodical — as a whole title, rather than its individual issues or articles. The print and electronic versions of the same serial are assigned separate ISSNs [10].

An NIHMSID is a temporary, unique identification number assigned to a peer-reviewed manuscript when it is submitted to the NIH Manuscript Submission (NIHMS) system. It is used to track the manuscript until processing is complete and the article receives its permanent PubMed Central identifier (PMCID), which then replaces the NIHMSID [11].

A PMID is a unique, permanent identification number assigned by the National Library of Medicine (NLM) to every record indexed in the PubMed database [11].

The PMCID (PubMed Central Identifier) is the unique, permanent identifier assigned to an article when it is made available in PubMed Central (PMC). The NIHMSID, by contrast, is a temporary identifier assigned to a manuscript when it is submitted through the NIH Manuscript Submission (NIHMS) system. The NIHMSID may be used only for the first 90 days after it is assigned, or until the article receives its PMCID, which then permanently replaces it. More information is available on the NIH public access policy page [11].

A bibliographic management program (also known as a reference management program) is a class of software used primarily by scientists and researchers to perform two main functions:

• creating a database of bibliographic records, and
• generating bibliographies that can be easily inserted into word-processing documents.

Citation records can be entered manually by the user or imported from online bibliographic databases [12].

These programs specialize in storing, managing, and searching bibliographic information within their own libraries, as well as sharing it with others. Users can also store charts, tables, figures, equations, and images, assigning each item its own title and keywords. In addition, the program can track the lists of references, figures, and tables inserted into a manuscript [13].

Modern reference management programs offer a range of further capabilities. They can extract bibliographic metadata automatically from imported PDF files, or retrieve it through identifiers such as a DOI or arXiv ID. Browser extensions (web importers) allow users to capture references and full texts directly from journal websites, databases, and library catalogs with a single click. Within the program, references can be organized into folders or collections, labeled with tags, and cleaned of duplicate records. Most programs also include a built-in PDF viewer with annotation tools for highlighting and note-taking, together with full-text search across the entire library. Through word-processor plugins, users can insert citations while writing and instantly reformat the entire document in any of thousands of citation styles, most of which are based on the open Citation Style Language (CSL). Finally, cloud synchronization keeps a user's library identical across desktop, web, and mobile devices, while shared group libraries enable research teams to build and maintain a common collection of sources [14].

EndNote, Mendeley, and Zotero each provide an add-in that works with the Microsoft Word word processor. All of these add-ins allow the user to insert and edit citations in the document and to generate a bibliography from the citations inserted. Functions beyond these core features are explained under the heading of each respective program [13], [15].

EndNote, Mendeley, and Zotero each provide a reference-import plugin that can be installed in a web browser. Using such a plugin, references from supported websites can be captured and transferred to the user's web library — and, if synchronization is enabled, on to the local library in the desktop program [14].

A connection file is a system file that enables a bibliographic management program to connect to an online database or library catalog, search it, and transfer the retrieved records into the user's reference library [16].

Importing is the process of bringing reference information from an external source into the database of a bibliographic management program. This operation is typically performed through the program's "Import" menu. Beyond the menu itself, several other tools can carry out the same operation: the program's web browser extensions, its connection files, and shortcut options for specific databases [16].

File formats commonly supported by reference management programs for import and export operations include BibTeX (.bib), EndNote XML (.xml), and RIS (.ris) [14].

Exporting is the process of transferring reference information stored in a bibliographic management program to another program, or more generally, of moving it out of the program in a usable file format. This operation is typically performed through the program's "Export" menu [16].

An import filter is a file that specifies which fields of the incoming reference information will be mapped to which data fields in the program's database during import. Import filters can also be used to exclude information that the user does not wish to bring into the program [16].

RIS, short for Research Information Systems, is a standardized tag format developed to enable bibliographic management programs to exchange data. References downloaded from online databases in this format can be saved into a bibliographic management program; conversely, references stored in one program can be exported as an RIS file and transferred to another for use [17].

In bibliographic management programs, a reference is a record representing an information resource of a predefined type — such as a book, journal article, newspaper article, or manuscript [16].

A reference type is a predefined category used by the program to classify the references added to the library according to the kind of resource they represent — for example, book, journal article, or newspaper article [16].

Some of reference types available at the reference managers are: Aggregated Database, Ancient Text, Artwork, Audiovisual Material, Bill, Blog, Book, Book Section, Case, Catalog, Chart or Table, Classical Work, Computer Program, Conference Paper, Conference Proceedings, Dataset, Dictionary, Discussion Forum, Edited Book, Electronic Article, Electronic Book, Electronic Book Section, Encyclopedia, Equation, Figure, Film or Broadcast, Generic, Government Document, Grant, Hearing, Interview, Journal Article, Legal Rule or Regulation, Magazine Article, Manuscript, Map, Multimedia Application, Music, Newspaper Article, Online Database, Online Multimedia, Pamphlet, Patent, Personal Communication, Podcast, Press Release, Report, Serial, Social Media, Standard, Statute, Television Broadcast, Thesis, Unpublished Work, Web Page, Working Paper.

A reference library is the database in which references are recorded and stored within the program [16].

EndNote, Mendeley, and Zotero can synchronize a user's library across their web, desktop, and mobile applications. This synchronization is made possible by a user account created on the program's website. Once the account's username and password are entered into the relevant application, synchronization is enabled. The amount of online storage available for synchronizing the local library varies depending on the reference management program used [14].

Reference management programs include functions for sharing the reference library with others. Either the entire library or selected groups within it can be shared. Through the sharing settings, the user can control who has access to the shared group — specific individuals or everyone. In addition, a reference library can be shared as a file by exporting it through the "Export" menu available in all three programs [14].

To connect to library catalogs and retrieve data over the internet, bibliographic management programs must meet certain technical requirements. One of these is support for the Z39.50 standard.

Z39.50 is an international standard — also published as ISO 23950 — that enables computer-to-computer information retrieval. It is used primarily for retrieving data from bibliographic databases [16]. The standard was first adopted in 1988 by the American National Standards Institute–accredited National Information Standards Organization (NISO) [13].

A citation output style is a system file that determines how the bibliographic information of a reference — such as the title of the work, the author's name, the year of publication, the place of publication, and the publisher — is formatted in citations and bibliographies [16]. Styles are typically named after, and defined by, the journal, publisher, or institution that requires them. The Nature style, for example, formats references according to the requirements of the journal Nature.

CSL (Citation Style Language) is an open, XML-based file format for defining citation output styles. It is one of the most widely used style formats, supported by programs such as Zotero and Mendeley [18].

A citation output style editor is a tool used to create new citation output styles, modify existing ones, and preview how the changes will appear in the document. EndNote and Zotero provide built-in style editors within the program, whereas Mendeley offers a web-based editor [13], [19].

EndNote, Mendeley, and Zotero can synchronize a user's library across their web, desktop, and mobile applications. This synchronization is made possible by a user account created on the program's website. Once the account's username and password are entered into the relevant application, synchronization is enabled [13], [14].

A local library is the reference library stored on the user's own computer by the reference management program [14].

An online library is the copy of the user's reference library stored on the internet, on the servers of the reference management program, and kept up to date through synchronization [14].

EndNote's term lists are used to store frequently occurring terms, such as author names, journal names, and keywords. When a new reference is entered, these stored terms are suggested automatically, which improves the consistency and accuracy of the information in the library [20].

Tags are keywords that the user assigns to references in order to categorize them. EndNote, Mendeley, and Zotero all provide a dedicated field for this information, and the references in the library can be filtered by the tags added to it [14].

A smart group is an EndNote feature that automatically collects the references matching criteria defined by the user. When the user sets up a smart group with keywords or other search conditions, every reference in the library that matches them is automatically assigned to that group — including references added later [21].

A citation key is a short, unique identifier used to refer to a specific source — such as a journal article or book — within a document. It acts as a bridge between the text being written and the full bibliographic record of the source, allowing software to generate correctly formatted citations and reference lists automatically.

Personally identifiable information (PII) is any data that can be used to identify, contact, or locate a specific individual, either on its own or when combined with other information [22].

In computational and artificial intelligence research, an SGR document is a structured template or file built according to the Schema-Guided Reasoning (SGR) approach. SGR itself is a technique that constrains a large language model (LLM) to follow a specific, predefined reasoning pattern or schema; the SGR document is the file in which that schema is defined [23].

Duplicates are multiple records in the reference library that represent the same source. The duplicate-detection function can be used to find such records and either merge them into a single record or delete the redundant copies from the library [14].

When a folder on the computer is designated as a watched folder in Mendeley, every document added to that folder is automatically imported into the Mendeley reference library. This makes it easy to add new sources to the library and to cite and browse them [14]. To see how this feature is used, see the Watched Folder guide [24].

A compressed library is a single file into which an EndNote library — the library's .enl file together with its associated .Data folder and all of its contents — can be saved. It is used to back up a library or to send a copy to a colleague. A compressed library can later be restored (opened) in EndNote, which extracts the original library files [25].

The Mendeley Web Catalog is a database operating on mendeley.com that allows users to search for references, update the information of records in their personal libraries, and receive recommendations for similar resources. The catalog is compiled from all the references that Mendeley users add to their personal libraries. In building this database, uploaded references are first anonymized — that is, a catalog entry is not associated with any individual user — and then saved as searchable catalog records. Each new record is compared with the entries that other users have added for the same resource, and the information is merged to produce the most accurate and detailed record available. As more users contribute information about a resource over time, its catalog record is continuously refined, and the result is a broad, interdisciplinary reference collection. Through the Web Catalog, Mendeley also makes these records — including their readership statistics — accessible to all users [14].

The Find a Journal feature in EndNote leverages advanced machine learning to assist researchers in identifying the most suitable academic journals for their manuscripts. This tool analyzes key components of a paper to recommend relevant journals, helping streamline the submission process [26].

The full text is the complete document itself — the entire content of an article from the introduction to the references. It is distinct from the bibliographic record (title, authors, journal, year) and from the abstract, both of which merely describe or summarize the document.

A citation report is a summary of citation activity generated for a set of records or an author, most notably the Citation Report feature in Web of Science, which displays total publications, total citations, average citations per item, and the h-index, together with year-by-year graphs. It is distinct from Journal Citation Reports, which measures whole journals rather than individual records or authors [27].

Journal Citation Reports is an annual analytical product from Clarivate, built on Web of Science data, that provides journal-level citation metrics — most notably the Journal Impact Factor (JIF) — along with quartile rankings (Q1–Q4) within subject categories. Researchers use it to evaluate and compare journals when deciding where to publish. It is distinct from Scopus-based journal metrics such as CiteScore and SJR [28].

A reprint is a copy of an article produced and distributed after publication, traditionally as a printed offprint supplied by the publisher to the author for sharing with colleagues, and today usually as a publisher PDF. Requesting reprints from authors was the standard way of obtaining articles before widespread electronic access. It is distinct from a preprint, which circulates before peer review. In book publishing, a reprint is a new printing of a book without substantive changes, and is distinct from a new edition [29].

A preprint is a version of a scholarly manuscript shared publicly before peer review, typically on a preprint server such as arXiv, bioRxiv, or SSRN. Preprints usually receive a DOI and are citable, and APA 7 defines a specific reference format for them. It is distinct from a postprint (the accepted, peer-reviewed manuscript) and from the version of record published by the journal [30].

A classification number is the notation a library assigns to a work to represent its subject and determine its shelf position, and it forms the core of the call number. The two dominant schemes are the Library of Congress Classification (LCC), which combines letters and numbers (e.g., Z for bibliography and library science), and the Dewey Decimal Classification (DDC), which uses purely numeric notation across ten main classes (e.g., 020 for library and information sciences). It is distinct from a call number, which adds author (Cutter) marks and other elements to the classification number to identify one specific item [31].

The NIH is the primary biomedical research agency of the United States government, operating under the Department of Health and Human Services and comprising 27 institutes and centers. It is the world's largest public funder of biomedical research, and its public access policy requires that funded research articles be deposited in PubMed Central. It is distinct from the NLM, which is the library institute operating within the NIH [32].

The NLM is the world's largest biomedical library and a component of the United States National Institutes of Health. It produces and maintains the core information resources of biomedical research, including PubMed, PubMed Central, MEDLINE, and the MeSH (Medical Subject Headings) controlled vocabulary. The NLM also defines the NLM citation style, the standard reference format in medicine, published in the guide Citing Medicine and used by PubMed and many biomedical journals. It is distinct from the NIH, which is its parent agency, and from PubMed, which is a database the NLM produces rather than the library itself [33].

LeapSpace is an AI-assisted workspace developed by Elsevier for academic and corporate researchers. It supports tasks such as generating ideas, planning projects, exploring the literature, finding collaborators, and identifying funding opportunities, as well as assisting with writing. In contrast to general-purpose AI chatbots, its answers are grounded in a curated body of scholarly content: more than 20 million full-text peer-reviewed articles and books from Elsevier and over 1,000 licensing partners, together with more than 100 million records from over 7,000 publishers indexed in Scopus. Each AI-generated result is referenced and traceable to its original sources. Users can also upload their own documents for analysis [34].

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