Working with a reference manager

A reference manager is a database of reference records that a writer fills from literature databases and PDFs, keeps free of duplicates, and drives from the word processor to insert citations and build the reference list in the style the destination requires. Practitioners differ on how essential it is, and the products differ in what they offer and what they cost. The hidden field codes it writes into a document, the way its library syncs and is shared, and the licence it is sold under each limit how a writer can use it. Tools that map a literature from a writer's own collection extend the library toward finding what to read next.

What the software saves

Keeping track of references and citing and formatting them correctly is a particularly time-consuming job during manuscript writing, and reference-management software is very useful for automating it. ^{1, 2, 3} In the longer term, a reference management system can save time and money: it keeps references organised and ensures they are correctly cited. ⁴

Collecting, organising, citing and sharing references used to take an enormous amount of time, and reference-management software has made the task much simpler. ^{5, 6}

Every journal has its own idea of how an in-text citation and a reference-list entry should look, ⁷ and no two are alike. ⁸

To EndNote's European distributor, formatting by hand is a waste of intellectual resources, leaving a researcher to decide whether something is italic or bold. ⁹ The distributor holds that whichever product is chosen, references should be handled with software. ¹⁰ In the distributor's 2021 webinar, handling and reformatting the references of a journal article by hand was put at around two full working weeks. ¹¹

How essential it is

Practitioners disagree about how essential a reference manager is. ^{12, 13} One experienced writer finds it useful for manuscripts, review articles and monographs with many references but does not consider it essential, though many others do. ¹² In that writer's account, in regulatory work it is not needed for clinical study reports but may be useful for investigator's brochures and other comprehensive summaries that need a longer bibliography. ¹² Some journals specifically request that EndNote not be used, but it can still organise and format the references, which are then copied and pasted into the document. ¹² Another writer finds it essential and could not imagine managing references without it. ¹³

Two writers asked in 2021 for the pros and cons both favoured the software. ¹⁴ For anyone who does not relish typing references and renumbering citations by hand, one of them judges that the pros far outweigh the cons. ¹⁴ That writer moved from the now defunct Reference Manager to EndNote, made by the same company, learned the open-source Zotero for one client who later switched to EndNote, and was using EndNote X8 with an upgrade in view. ¹⁴ The few times that writer needed technical support, it responded quickly, and a strong incentive to use EndNote is that every client of that writer's who uses citation management software uses EndNote. ¹⁴ The pros that writer lists are time saved by automated renumbering and reformatting of citations and reference lists; easy capture of citations from major databases, standardised formatting of reference lists and reformatting of a manuscript for submission to a different journal; and easier management and sharing of citation databases with their PDFs. ¹⁴ The cons are cost, except for some free programs such as Zotero; a learning curve; the occasional need to edit database entries and journal styles to fix capitalisation or the number of authors listed; and the need to remember to remove the codes before submission to certain journals, an easy automated step. ¹⁴ That writer considers the software an essential, time- and headache-saving tool for medical writers who write scientific articles and other manuscripts and reports with many citations. ¹⁴

The other writer lists the platforms as including EndNote, Zotero, Reference Manager, Mendeley, EasyBib.com, Cite This for Me, Sciwheel, Refworks and cite4me.org, and prefers EndNote after decades of use, updating it with each new computer at a 50% discount from the company and valuing its knowledgeable technical team. ¹⁴ Because that writer works for several clients, they do not use EndNote online, which may merge the files of different clients, though at a university this may not be an issue. ¹⁴ The advantages they find run through the literature search, the writing, the formatting and the deliverables: harvesting potentially relevant references during the supplementary literature search; single-click retrieval of most open-access articles and downloadable citations from PubMed and other databases; a searchable database of relevant references while writing; faster formatting of in-text citations and an accurate reference list during writing and after client-requested revisions; relatively rapid conversion to other citation formats; editable styles for client-specific needs; and a library file that can be handed to a client who may have further rounds of review, as for a professional society's guidelines. ¹⁴ The advantages grow with the length of the document and the number of citations. ¹⁴ Many clients prefer the use of reference-management software and also want the location of the specific information cited, so depending on the client's preferred style, that writer often gives the page, paragraph, table or figure in a comment bubble. ¹⁴ Where a client's in-house style puts the page and paragraph into the in-text citation itself, the software may treat each entry as a new reference. ¹⁴ If needed, the EndNote codes can be removed before the deliverable is sent. ¹⁴

In a live poll of attendees at a 2021 EMWA webinar on EndNote, ¹⁵ 82% said they used a reference citation management system and 18% said they did not. ¹⁶ In a follow-up poll, 70% of those who used a system said they used EndNote and 27% said they did not, figures that do not sum to 100. ¹¹

What a manager does

EndNote's main functions are holding reference records together with full-text PDFs and other attachments, searching online databases and collecting the bibliographic details, inserting citations and building bibliographies in the word processor, fetching full-text articles automatically, sharing a library with colleagues, and suggesting journals to publish in. ^{10, 7}

The basic function of reference-management software is to produce formatted bibliographies, in-text citations and footnotes suitable for journal publication, and some programs have plug-ins that give direct access from word processors such as Word, Open Office and Pages. ³ Around that function, the software can:

• build an electronic library for an article or research topic that keeps research documents, websites and articles in one place; some programs let the library be sent to a client or team member, and otherwise it can be shared online, and references can be copied from one library to another
• search online databases, import existing PDF collections and upload websites to the library; some programs also give access to the PDFs, so that key phrases or sections can be highlighted and annotated
• complete reference information automatically where a reference is incomplete, or check that a reference exists and is correctly cited
• apply the exact citation and bibliographic style the target journal requires; most packages contain typical journal styles, and more can be obtained from an internet database and saved
• change the citation and bibliography style with one click when the target journal changes, with no retyping or reformatting

^{3, 4}

The library as a database

EndNote is a database with an interface for handling references built on top of it, ⁸ and organisations also use it for more than references: medical companies share one reference library worldwide so that their representatives give the same answers to the same questions, and others use it for knowledge bases, support and inventories, museums among them. ^{8, 17} In its reference view each row is a reference and each column one of its information fields; the edit tab shows every field, and not all of them need to be filled. ¹⁸ A preview pane summarises the selected reference, a paperclip marks an attachment, ¹⁸ and an attached PDF can be read inside the application. ¹⁹

Everything added to EndNote is indexed, attached full-text PDFs included, so the library can be searched across the text of the articles as well as their reference information. ²⁰ Zotero's search bar likewise reaches the text inside attached PDFs. ²¹ A Zotero library can be organised in collections, like the folders on a computer, and files, notes, links and full texts can be attached to each reference. ²¹

Up to a million references can be synced to an EndNote online account, and for a library of more than 100,000 references the recommendation is to consider splitting it into several libraries; customers run libraries of around 12,000 references with attached PDFs without trouble. ²² Attaching a large number of full-text articles does not slow the connection between EndNote and Word or make updating the references take longer. ²³

EndNote 20 has a new database format and a redesigned interface, one reason being that Apple stopped supporting 32-bit software, so the program had to be rebuilt as 64-bit software. ^{19, 24, 25} In EndNote 20, a preview pane that has been closed can be brought back only by double-clicking a reference. ²⁶

Importing references

Exporting from the database's own interface. The records are selected in the database's web interface and sent with its send-to-citation-manager command, which creates a file; a helper application installed with EndNote receives the file and can be set to do so automatically from then on. ^{27, 26} The command differs from database to database. ²⁷ Apple's Safari browser does not support the mechanism, so on a Mac the export works in Firefox or Chrome. ²⁷

A database without direct support for EndNote can normally still save its results as a text file, and EndNote ships with thousands of import filters, so exporting and then importing should work. ²⁸ For an unfamiliar database, the quickest answer is a web search for the database's name together with "export to EndNote". ²⁹

Searching the database from inside the manager. EndNote's online search connects directly to a database such as PubMed. ²⁰ Its results are staged rather than added, so only the records selected enter the library. ³⁰ The search does not apply the web interface's filters: the same term returned 620 records in EndNote against 327 in PubMed's web interface with a free-full-text filter applied. ^{30, 24}

EndNote probably reaches PubMed through a connection file, and when PubMed changes how connections are made, the file goes out of date. ³¹ An installation of EndNote X7 that had stopped connecting to PubMed should work again once a current connection file is downloaded, without a new version of the software. ^{32, 31}

The owner of the data decides which search options are offered. Connected to PubMed, EndNote offered only the field operator "contains", because that is all PubMed allows; searching the local library offered the full set of operators, because EndNote then decides. ³³ The in-app search accepts the Boolean operators AND, OR and NOT, and additional search lines are evaluated from top to bottom. ^{22, 33} A simple search gives the same results either way, but an advanced search is better run in the database's own web interface, which offers far more options. ³⁴

Importing PDFs already held. Told to import a PDF, EndNote scans it for a DOI, goes online for the reference information and attaches the PDF to the record it creates. ^{35, 36} Zotero recovers the metadata from the PDF of a published article, at least for articles from around 2000 onward, or from an identification number such as a DOI, ISBN or PubMed ID, and it also collects the metadata automatically when a citation is read on a computer, tablet or mobile device. ^{21, 37}

Importing a folder tree. The same import can take a top folder, include everything in its subfolders and create a group set mirroring the folder structure, so a structure already built on disk becomes the library's groups. ^{36, 38}

Bringing over an existing library. An older EndNote library is converted when it is opened in EndNote 20. ²³ Zotero imports libraries from other reference managers, and its libraries are compatible with other reference management programs. ^{21, 6}

Fetching full text for records already in the library. EndNote's find-full-text command searches online for each selected reference, downloads the full text it finds, indexes it so that it is searchable, and renames each attachment to a configurable pattern, such as author, year and part of the title. ^{38, 39, 40} Where it finds no full text it may still record the article's URL, which opens the publisher's page in a browser. ⁴⁰ What it reaches depends on the network: on a university's network it has access to the university's subscriptions and finds many more articles than without an affiliation. ^{39, 24} Zotero automatically downloads PDFs that are available, such as open-access articles, and can rename them by first author, year and title, and its locate button finds items online. ²¹ Its metadata retrieval tool can tidy up PDF files already stored on a computer, which helps when their file names are unclear. ⁴¹

Duplicate records

EndNote's duplicate search sits with its other library tools, such as a search for broken file attachments. ⁴² Matched records are shown side by side with any differing field highlighted, and either record can be kept. ^{42, 43} Two records that differ only in their issue number are still shown as a pair, with that field highlighted, so whether they really are duplicates is the user's decision. ⁴³

Comparing pairs one at a time works for 10 or 20 duplicates but is tedious for a thousand. ⁴⁴ Cancelling the side-by-side review instead collects the matches into a duplicate-references group with all but one of each set highlighted for deletion. ^{45, 44} The copy it highlights is the one added most recently, because that is the one least likely to have been used in a document already. ⁴⁴

For removing duplicates from just one of two groups, selecting a reference in a group highlights it in the full list, but whether the reverse works was uncertain in the demonstration, and EndNote has no way to show which group a reference belongs to. ⁴⁶ EndNote 20 opens each library in its own window, so two libraries can be placed side by side and references dragged between them. ⁴⁵

Citing from the word processor

The EndNote tab in Word shows which library it is driving. ⁴⁷ A version number in the tab name, such as EndNote 20, means the installed desktop version; the name alone means it is connected to the EndNote online account. ⁴⁷

A citation can be inserted by two routes. ^{48, 49} From Word, a quick search matches its text anywhere in a reference rather than only in one field, so a year finds every reference with that year anywhere in it and a fragment of a surname is enough to find an author; the search is broad and very fast. ⁴⁸ Switching to EndNote and selecting the references there gives more control, and a command inserts a citation for each selected reference at the cursor. ⁴⁹ The bibliography is built automatically as citations go in, by instant formatting, which is on by default and can be turned off. ⁴⁹

Zotero inserts citations in Microsoft Word, LibreOffice, OpenOffice and NeoOffice through its buttons in the word processor and creates the reference list automatically. ⁵⁰ Its word-processor plugin is installed separately, and citations cannot be inserted until it is. ⁵¹

EndNote's citation-management dialog lists every citation in the document with the number of times each has been used, and selecting one jumps to its location, which makes a reference easy to find in a long document. ⁵² An extra citation inserted from it in the first sentence of a numbered document renumbers the whole document and its bibliography once confirmed. ^{53, 54, 52} By hand, the same insertion means renumbering the whole document, reference list included. ⁵³

Where the field codes break

Each EndNote citation is a hidden field code, highlighted when clicked. ^{54, 55} Cutting and pasting a whole citation moves its field codes with it, and nothing is lost; selecting only part of the field, though that is hard to do, can corrupt it, after which EndNote no longer recognises it as a citation. ^{54, 55}

EndNote's European distributor therefore recommends not sending a reviewer a document with active references. ⁵⁵ Converting the citations and bibliography to plain text creates an identical copy with no connection to EndNote, in which a reviewer can cut and paste without damaging the references. ^{55, 56} The active document is kept, and the plain-text copy can be edited as text. ⁵⁶

Two reference managers on one computer conflict only in Word. ⁵⁷ They write into the same hidden field codes, and some block other applications from writing into theirs, so the other one stops working there; any number can be installed as long as they are not used in Word at the same time. ⁵⁷

Two people cannot add or edit EndNote citations in the same document simultaneously, even on a shared platform such as Google Docs or OneDrive, because every insertion makes EndNote scan the whole document and update all its reference information, and two scans at once conflict. ^{29, 58} Two people using different versions of EndNote on one document generally works but is not recommended: EndNote 20 has a new database format, and some functions of a newer version do not exist in an older one such as X7. ⁵⁹ In Zotero, several authors can each edit citations in a shared document, provided the references cited come from a group library. ³⁷

Citation styles

In 2021 EndNote shipped with more than 7,000 styles, and because many are generic styles that serve a group of journals, the number of journals covered ran to tens of thousands. ⁸ The program itself listed more than 7,200 styles. ⁶⁰ Zotero's online style repository held more than 6,700 styles in 2014. ⁵⁰ When EndNote is installed, its styles can be restricted to fields such as medicine, biology or science, so that styles for journals in fields such as accounting need not be kept. ^{60, 61}

Changing the style restyles the whole document: a numbered document became author–date in a single step. ⁶¹ Zotero lets the citation format be switched as often as needed. ⁵⁰

Two arrangements go beyond choosing a style. ^{62, 63} A reference list can be grouped under custom category headings, with references dragged into each and any uncategorised reference shown, to produce a categorised bibliography. ⁶² With section breaks in the document, a custom output style can produce a reference list after each section as well as a combined list at the end, with the numbering consecutive across sections or set otherwise, which suits a document divided into chapters. ^{63, 60}

Where the exact style is not in Zotero's repository, its search-by-example tool finds a similar one. ⁵⁰ In-text citations and bibliographies can be personalised, for example by removing the author or adding page numbers, journal titles can be abbreviated automatically, and some styles include a translator that renders terms such as available at and accessed in a specific language. ⁵⁰

Syncing and sharing the library

An EndNote licence covers a desktop installation and an EndNote online account, and syncing the library to the account makes it reachable from another computer and shareable with colleagues. ¹⁷ Libraries are compatible between Windows and Mac, so a writer who uses both can sync one library between them. ^{15, 32} Sync is switched on, and its login entered, in the application's preferences, where an online account can also be created. ⁶⁴

Syncing merges libraries rather than replacing one with the other. ⁶⁵ Syncing a library to an account that already holds references merges the two, so the demonstration created a new, empty library before syncing. ⁶⁵

Zotero offers the same reach through a free account. ³⁷ A personal account comes with 300 MB of free online storage, which can be increased for a small fee. ³⁷ Zotero synchronises the computer with it, so several computers share the latest version of the bibliography and the library can be reached from anywhere through zotero.org. ³⁷ Group libraries let the owner invite anyone with a Zotero account and set reading and editing rights for each member. ³⁷ Groups can be public or private, and a public group is a free and easy way to list individual or collective publications and make them more widely known; because Zotero is open source, a developer can easily post such a list online and keep it up to date. ³⁷

How the products differ

A 2015 summary of the main pros and cons of several programs, drawn from library comparison websites, set them out as follows. ⁴

Program	Pros	Cons
RefWorks	Internet-based; mobile device access; large number of citation styles; citation styles easy to edit; free access for students and alumni with a Bodleian Libraries subscription	Cannot extract metadata from PDFs; word-processor plug-in compatible only with MS Word; very limited offline access
EndNote	Desktop-based, with plug-in for Pages, MS Word and Open Office; copes well with a very large library; large number of citation styles; journal abbreviation recognition; can search and upload references from online databases such as PubMed, or from PDFs; can highlight and annotate PDFs	Incompatible with Linux; advanced features require buying the software
EndNote online	Online collaboration; mobile device access; direct reference download button in the Web of Science database; free with EndNote	Word-processor plug-in not compatible with Linux; limited citation styles and storage
Reference Manager	Desktop-based, with plug-ins for MS Word; can share references; can search and upload from online databases	Incompatible with Mac; limited citation styles; limited organisational facility
Zotero	Separate collections can be made from one source library; iPhone and Android apps; useful tools for creating references from websites; notes can be made on the go and stored in a library collection; free access; compatible with Mac, Windows and Linux	Limited free storage space (300 MB)
Mendeley	Collaborative PDF annotation and notes; iPhone and iPad interface; work can be showcased and reading lists shared with a social network; free access; keywords can be searched in references	Manual syncing of desktop application to web account; limited free storage space
ColWiz and Papers, in one row	Nested folders; PDF annotation; iPhone, iPad and Android apps; social network; collaborative research management tools; reading lists can be shared with a social network; large number of citation styles; access available with some university libraries	Direct export of references only with the desktop application; software must be bought; not compatible with Linux; cannot sync across several computers

⁶⁶

Zotero is a free, open-source reference manager for Linux, Mac and Windows whose libraries are backed up online, which allows sharing between computers and between users, and for these reasons it can be a valuable resource to medical writers. ⁶ It was originally developed by the Center for History and New Media at George Mason University and the Corporation for Digital Scholarship in the United States. ⁶ Other programs available in 2014 included Mendeley, which Elsevier acquired in 2013, EndNote and Biblioscape. ⁶

Zotero began as an add-on to the Firefox browser and also exists as Zotero Standalone, completed by a browser extension for Safari or Chrome or by a bookmarklet for other browsers. ⁵¹ Both offer exactly the same services; the add-on opens as a window inside the browser, while Zotero Standalone runs as an independent application. ⁵¹ Unlike Zotero Standalone, the Firefox installation does not require administrator rights on the computer. ⁵¹

Zotero's further strengths are continuous improvement by developers worldwide, and a quick-start guide and numerous tutorials in several languages, with online forums where difficulties and style requests are answered quickly. ⁴¹ Its limitations in 2014 were that editing or creating a style can be difficult, for which the visual editor at citationstyles.org is recommended; that the quick search bar searches one group library at a time, not all of them at once; and that the computer may slow while citations are inserted or the library synchronises. ⁶⁷

A 2012 review described Mendeley as an up-and-coming online reference manager and scientific social community, similar to and compatible with EndNote but possibly slightly less robust, and then still in beta. ⁶⁸ Its strengths were that it could be completely mobile while also having a desktop icon, synced with EndNote, let PDFs be annotated and shared, showed what colleagues were currently reading so that collaborations could be built, inserted and formatted citations on many platforms including text editors, email and blogs, and let users explore current trends in research. ⁶⁸

Buying a licence

In 2021 a single-user EndNote licence allowed installation on three computers for personal use and worked on both Windows and Mac, so a writer changing from a PC to a Mac did not need to buy again, though the old computers still counted toward the three. ⁶⁹

Some universities provide continued alumni access to reference-management software, which is worth exploring before buying; some programs provide free tutorials and after-sales assistance; and several packages provide telephone and tablet access for freelancers on the go. ⁴ Because modern programs offer various features beyond the basic function, the market is worth surveying before purchasing. ³

Uses beyond the bibliography

An EndNote library can be imported into NVivo, a tool for analysing unstructured data such as text, video and audio, so that the references can be analysed during a literature review; NVivo is also used to analyse material such as drug side effects or interviews. ⁷⁰

Citation maps for finding what to read next

Literature review and mapping tools such as Research Rabbit, Connected Papers and Litmaps do more or less the same thing, and one practitioner finds them especially useful in the research and discovery phase. ⁷¹ With ResearchRabbit and Connected Papers, the user supplies specific citations as seeds, and the models search for similar work and map it visually, which greatly speeds up and deepens the discovery phase at any stage of research. ⁷²

The same practitioner singles out Litmaps as versatile, performant and easy to use. ⁷³ One or more papers are added, and it draws a seed map from which related papers can be discovered, read and shared. ⁷³ A free tier is most probably enough, and a subscription adds, for example, monitoring of papers of interest, with what it finds placed in storage for later review. ^{73, 74} Litmaps also has an AI semantic similarity search, which finds similar papers by title, abstract or keywords beyond the citation network. ⁷⁴ Its own suggested workflow is to collect the papers in one place, export them as BibTeX, create a new collection in the Litmaps library, import the selected articles from the reference manager, and create a map from them. ⁷⁴ From the map, papers of interest are added to a new collection, the newly organised work is reviewed and adapted, further papers are explored, and what is found is added back to the collection. ⁷⁵ In that practitioner's view, a visual presentation is much better than a text-based one for literature review. ⁷⁵

Research Rabbit is a reference manager that uses AI to surface unexpected connections and widen the field of search, visualising relationships between papers, authors and fields in a way likened to the discovery that happens at a conference or in brainstorming with colleagues. ⁷⁶ At its surface it works like other reference managers: papers are found by title or keyword and added to collections, which sync with Zotero to generate a bibliography. ⁷⁷ For one freelance writer, its best feature is the visualisation map. ⁷⁸ Adding a paper to a collection opens a sidebar for exploring similar work, and an AI-powered algorithm maps related articles from the papers in the collection, each added seed paper updating the map. ⁷⁸ Seed papers show in green and suggestions in blue, and clicking one shows its title, abstract, authors and a link to the full text, to read at once or add to the collection for later review. ⁷⁸ References can be deselected to zoom in on a topic or an author; other work by the seed authors and cross-referenced papers can be found without digging through whole bibliographies; timeline plots order the works by publication date; collections can be built with other writers; and references from an earlier manual search can be imported from Zotero through two-way syncing. ⁷⁸ Manual literature reviews are prone to error because they leave an overwhelming number of open browser tabs and an overflowing downloads folder, and the map gives structure to a search that would otherwise become tangled and confusing. ⁷⁸

Writers often raise two concerns about AI tools: hallucination and losing touch with the comprehension of the work. ⁷⁹ Hallucinations are rare in Research Rabbit because it is not a large language model and its references come mainly from scholarly publications, and it does not summarise papers: its algorithm only suggests similar works, so reading and understanding them remains the writer's responsibility. ⁷⁹ For the same writer, efficiency is the main reason to use it, since it quickly delivers thousands of papers for documents that need hundreds of references. ⁸⁰ Among its competitors, Connected Papers has no Zotero integration and accepts only a single seed paper, and Litmaps, which that writer ranks second, prioritises its suggestions better and has a friendlier interface but is slow and shows only ten papers at a time; in 2025 Research Rabbit was the only one of the three that was always free. ⁸⁰