Work / Technology & tools ILLUSTRATION BY THE PROJECT TWINS THE PROJECT BY ILLUSTRATION THE COLLABORATIVE REFERENCE LIBRARY A suite of tools can help researchers to manage citations for grants and papers — and share those references with colleagues. By Jeffrey M. Perkel or such utilitarian tools, reference and supplementary materials; generating the citations. She had been using Google management software can inspire strong bibliographies; and fostering collaboration. Scholar, which can output references in only reactions. Physician Ben Goldacre, for There are dozens of options, including End- a small number of styles. But for her exam, she instance, has tweeted at least five times Note, Mendeley Reference Manager, ReadCube needed a format that Google Scholar didn’t about Paperpile, a subscription-based Papers, RefWorks, Sciwheel and Zotero. (Read- support, and she had no time to learn to use a Freference manager that integrates tightly with Cube Papers is supported by Digital Science — new piece of software that did. So she turned Google Docs, calling it “amazing”, “fantastic, part of Holtzbrinck, the majority shareholder to an online bibliography generator, and “used best ever”, and “unbeLIEVably good”. Goldacre, in Nature’s publisher, Springer Nature.) as few citations as possible to save myself some who is also director of the DataLab at the Centre For Goldacre, Paperpile’s seamless compat- pain”, she says. Weeks later, on the advice of a for Evidence-Based Medicine at the University ibility with Google Docs, which the team uses university librarian, she was using Zotero to of Oxford, UK, explains: “Paperpile is the first for collaborative writing, is what tipped the insert citations in an online magazine when she time I’ve used a reference manager where it scales towards its use. For PhD student Emily was moved to tweet: “HOW AM I JUST USING A didn’t make me want to punch myself in the Wissel, who studies how the microbiome CITATION MANAGER FOR THE FIRST TIME??” face on a regular basis out of sheer rage. It’s just affects pregnancy, it was Zotero’s status as a glorious and perfect.” freely available, open-source project that led Reference features That’s because it dovetails nicely with his her to favour it over other software. Michael Francavilla, a paediatric radiologist team’s workflow. Reference-management tools, When Wissel took the preliminary exami- at the Children’s Hospital of Philadelphia, also called citation managers, perform a hand- nations required by her department at Emory Pennsylvania, uses his reference manager as ful of related functions: searching the literature; University in Atlanta, Georgia, to advance in an electronic brain — a place where he can storing and organizing PDFs of papers her doctoral programme, she struggled with store what he’s learnt about the conditions he Nature | Vol 585 | 3 September 2020 | 149 ©2020 Spri nger Nature Li mited. All rights reserved. Work / Technology & tools treats, as well as informative graphics that he and that flag retracted articles, thanks to a features to allow for threaded discussions in can share with patients and trainees. “Having partnership with the Retraction Watch blog. the reference library, according to company a reference manager versus not having a ref- ReadCube can also flag retracted articles. And representatives. Because of the coronavirus erence manager is just a sea change,” he says. RefWorks is adding integration with Unpay- pandemic, “Right now everyone needs to be Francavilla catalogued some basic criteria wall, says Shalhevet Bar-Asher, product man- able to collaborate on their research efforts, for choosing a reference manager in a 2018 ager at the Ex Libris Group, based in Jerusalem, and we need to be able to do that when we’re review (M. L. Francavilla Pediatr. Radiol. 48, Israel, which develops RefWorks. not sitting right next to each other,” Neff says. 1393–1398; 2018). The variables considered Reference managers are mainly organiza- include cost, cloud-storage limits, operat- tional tools. But for many users, their truly Fit for purpose ing-system compatibility and support for must-have features have nothing to do with How much weight users assign to each annotating PDFs (for a list of various reference organization. feature varies. In 2018, Renner co-authored a managers and their features, see Supplemen- Integration with word-processing soft- study illustrating how different users require tary table at go.nature.com/2d7athc). ware, for instance, allows authors to find and different functions from a reference manager Reference managers are typically desktop insert citations into documents as they write, (L. Murphree et al. Med. Ref. Serv. Q. 37, 219–233; applications with an associated web inter- and to build and reformat bibliographies in 2018). Whereas medical doctors might value face that allows researchers to remotely any of thousands of journal styles with just mobile access and the ability to access their ref- access their own user ‘libraries’ — curated erence library after they leave the institution, lists of references and associated PDFs — as “Having a reference manager for instance, wet-laboratory researchers tend well as browser plug-ins that make it easy to to prioritize collaborative writing, recommen- import references from a journal web page or versus not having a reference dations and use of the program offline. other online source. Some (including Paper- manager is just a sea change.” For Gavamukulya, the choice of reference pile, RefWorks and Sciwheel) are exclusively manager came down to cost. While writing his web-based, meaning there is no installation master’s thesis, he test-drove EndNote, but or cloud syncing required, and most provide a click of the mouse. In the absence of such opted for Mendeley because it could do what mobile apps that allow users to read and add tools, even minor revisions can throw manu- he needed and was free to use. “The key thing is references from their smartphones or tablets. scripts into disarray, to say nothing of refor- its integration with different word processors Juliana Soares Lima, a reference librar- matting an article for a different journal. “It and ease of importation of references from ian at the Federal University of Ceará in can really be quite a nightmare,” says Yahaya online sources,” he says. (Gavamukulya is a Brazil, is a Mendeley Advisor — a volun- Gavamukulya, a biochemist at Busitema Mendeley Advisor, too.) teer regional ambassador for Mendeley’s University in Mbale, Uganda. Francavilla uses Sciwheel, the reference reference-management software. She uses EndNote has offered a Microsoft Word manager his department adopted. That deci- Mendeley’s mobile app, and found that the plug-in since 1993, says Gillian Neff, product sion was based both on price and practicality: convenience of saving references that she manager for Endnote Desktop at Clarivate in because Sciwheel is a web-based tool, team found on Twitter helped with her doctoral Philadelphia, Pennsylvania; many other tools members could use it anywhere, no installa- dissertation. (Other reference managers also have since followed suit. Paperpile, Sciwheel, tion required. But to others he recommends have this option.) “It facilitated the tracking Zotero, ReadCube Papers and RefWorks all Mendeley, which is free like Zotero, but offers of updated, recently published and curated support Google Docs; the latter two also sup- 2 gigabytes of online storage. (Zotero caps scientific literature,” she says. port Microsoft’s web-based version of Word, as attachments at 300 megabytes; users can pur- With most reference managers, users can does Mendeley Reference Manager. Sciwheel chase extra storage starting at US$20 per year.) organize their libraries with folders and tags, is currently developing this feature. Those researchers who just want to create and search for articles by author name, key- Also increasingly essential, says Barbara bibliographies have other options. These word, text and notes. Built-in PDF viewers ena- Rochen Renner, a librarian at the University include BibTeX for documents created using ble them to read and annotate documents, to of North Carolina at Chapel Hill, is support for the LaTeX manuscript-preparation system, highlight key passages and take notes. External team-based workflows. “I’d definitely urge a and Manubot, a GitHub-based authoring tool search functions let them import articles — for researcher to think about how well a particular for documents written using the formatting instance, from PubMed or Google Scholar, or product facilitates collaboration of the type language Markdown. in Mendeley’s case, from a custom catalogue they do, anticipate doing, or would like to do.” There are also online bibliography genera- of more than 100 million papers. ReadCube Reference managers typically allow research- tors. ZoteroBib, for instance, is a free web tool Papers offers an ‘enhanced PDF’ experience, ers to share all or part of their library with that allows users to create and format a bibliog- which fleshes out the PDF with supplementary colleagues, which they can use when writing raphy in any of nearly 10,000 styles, then copy material and hyperlinks. manuscripts as a team or as a shared knowl- the result to the clipboard or publish it online. edge base. As of May this year, Zotero users In choosing a reference-management tool, Recommended reading have created some two million public and pri- consider your workflow, and that of your col- Some reference-management tools recom- vate groups, according to Sean Takats at the laborators. Think about usability, customer mend articles of interest on the basis of what’s University of Luxembourg, who has led Zotero support and the ease of migration from one already in the user’s library. Sciwheel flags arti- development since 2006. Sharing attach- reference manager to another. And, Renner cles in searches that have been recommended ments, such as PDFs, is usually reserved for advises, consult your librarian.