Eight Ways to Clean a Digital Library

ILLUSTRATION BY THE PROJECT TWINS A now studying medicine at University the of says, has brought up gems. some unexpected light recommended tunes. And that feature, he some music-file-management programs high andhis library suggests related papers, rather as system of choice, scans ReadCube, periodically doingbe his research. But his electronic filing BY JEFFREYM.PERKEL that described awaythat to described entrap using fish the in zebrafish. ReadCube highlighted apaper Ottawa, was researching infections bacterial As agraduate student, Rocker, is who library to flag up to betterlibrary flag ways he could that managed reference his digital dam Rocker didn’t software the expect EIGHT WAYS TO CLEAN Scientists have asurfeit ofoptions to choose from inthe competitive A DIGITAL LIBRARY market ofreference-management software. - © 2015 Macmillan Publishers Limited. Allrights reserved ‘Reference-management software’). Some ing reference-management inthe market (see ReadCube, and RefME Zotero compet —all EndNote, F1000Workspace, Mendeley, Papers, offering an ever-evolving of features. set extra knife, tool each now appeals to customers by ple like electronic Rather aSwiss-army filing. management tools go above and beyond sim own project to adopt alternative the approach. although he was ultimately invested too inhis research was “really rewarding”, Rocker says, ier than to the his own alerted method. Being would not normally read — that was much eas microfluidics literature whose —afield he This article focuses on eightThis focuses article tools — colwiz, As Rocker discovered, today’s reference- TOOLBOX 5 NOVEMBER 2015 | VOL 2015 | NATURE 527| NOVEMBER 5 |123 - - - chaos can quickly hold, take with multiple — and dump into them any convenient folder, impenetrable alphanumeric as filenames codes websitesnal — where are they often assigned to that problem: grab PDFs as they from jour downloaded PDFs. Most scientists can relate and flotsam digital the of jetsam scattered, has ashare also which in operated by Holtzbrinck the Publishing Group, ReadCube, is owned by a firm Science, Digital workspaces or recommending papers. (One, ing collaboration through of use the shared others on focus creating bibliographies, aid and building literature libraries, whereas excel at streamlining process the of browsing Each tool existsEach to help researchers to tame Nature

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copies of files spread across hard disks. REFERENCE-MANAGEMENT SOFTWARE “In science, or at least in my experience, we Eight of the most popular tools. tend to end up with a folder in the desktop with 3,000 really weirdly named PDF files, which Product URL Platform Free? we can never find when we need them,” says colwiz colwiz.com Desktop/web/mobile Yes Raúl Delgado-Morales, a neuroscientist at EndNote endnote.com Desktop/web/mobile Yes, with some limited features the Bellvitge Biomedical Research Institute in F1000Workspace f1000.com/work/ Web No Barcelona, Spain. Reference-management tools address that Mendeley mendeley.com Desktop/web/mobile Yes, with some limited features confusion by indexing a hard disk. Typically, the Papers papersapp.com Desktop/web/mobile No process of dragging and dropping a PDF into ReadCube readcube.com Desktop/web/mobile Yes, with some limited features an application window triggers the software to RefME refme.com Web/mobile (only Yes try to identify it using the DOI or title, and to stores references) retrieve relevant metadata (such as title, keyword and author names) from online servers. Zotero zotero.org Desktop/web/mobile Yes, with some limited features Researchers can also assign software to See the online version of this article at go.nature.com/xbp9ot for a fuller comparison. monitor specific folders into which they drop their files. They can then find PDFs through the in-text reference. Later, the user can create articles into a shared library; others reading a simple search for author name, keyword a bibliography and in-text citations according them; still more adding annotations and tags or, in some cases, their own notes. Delgado- to several thousand journal styles, picking his and logging key data. Morales solved his problem, for example, by or her choice from a pull-down list. According to Wiernik, the process is akin organizing his literature library with Papers, Most tools include built-in PDF readers for to using a shared Dropbox folder, with the a user-friendly application that automatically reading and annotating articles — typically added benefit that Zotero tracks and maintains renames files according to any scheme he allowing users to search through comments metadata, notes and annotations. For instance, chooses. Other tools offer similar functions, and notes — as well as cloud-based capabili- researchers can use a dedicated tag to indicate except for RefME — a website and mobile app ties for syncing those comments (and the PDFs that they are processing an article, thereby sig- — which stores only lists of references and not themselves) between, for example, an iPad nalling to collaborators that they should work the PDFs themselves. and a desktop computer. But ReadCube and on a different article to avoid duplicated effort. colwiz try to offer richer PDF reading experi- F1000Workspace and colwiz both extend CORE FUNCTIONS ences. In ReadCube, for instance, in-line cita- sharing to include features for preparing Most of the tools help researchers to import tions and author names in PDFs are rendered manuscripts and managing projects. With literature from a variety of online sources. as active hyperlinks to provide direct access to F1000Workspace, researchers can use a plugin Many offer in-app searching of external data- cited articles and publication lists. The same to upload Microsoft Word manuscripts to a bases such as PubMed and Google Scholar, as functionality is available when viewing and secure location, thereby enabling team mem- well as web-browser plugins that grab refer- annotating PDFs on the websites of partnering bers to comment on the shared copy — although ence data (and some- publishers (including, for ReadCube, Nature the text cannot be edited in the browser, says times, associated “We tend to end and Wiley; and, for colwiz, Taylor & Francis). João Peres, the company’s product-development PDFs) from journal up with a folder Many of these tools can identify articles manager. Peres plans to implement a ‘one-click’ websites and other with 3,000 related to specific items in a library, or recom- article-submission feature that sends papers pages. really weirdly mend articles on the basis of the library’s con- directly from F1000Workspace to journal edi- Zotero — a free, named PDF tent overall. F1000Workspace — like ReadCube tors, starting with the journal F1000Research. open-source soft- files.” — uses an algorithm to do this. It also taps into And colwiz also permits users to share docu- ware project — was recommendations made by a community of ments to an online drive for team members to founded ten years ago specifically to tackle the 10,000 or so specialists. However, many other view and comment on. problem of extracting information from a web stand-alone software products also recommend Given the highly overlapping feature sets of browser, says project director Sean Takats of papers (see Nature 513, 129–130; 2014). these tools, a user’s choice often comes down George Mason University in Fairfax, Virginia. to particular individual priorities. Richard “That’s the key feature of Zotero, and remains SET TO SHARE Karnesky, a materials scientist at the Sandia one of its strongest compared to other reference Many tools now allow researchers to set up National Laboratories in Livermore, Califor- managers,” he says. RefME offers the unusual group libraries or share key papers with distant nia, supports Zotero for its open-source ethos, option of adding references by scanning a bar- collaborators, although this process is care- for example. code with a smartphone camera. fully managed to prevent violation of publish- Perhaps the best reason for using a reference One of the best-known features of reference- ers’ copyright. Those in public groups using manager is the technology’s ability to provide a management software is the ability to insert Mendeley, for instance, can share only infor- form of searchable memory. Imagine, says Boyd in-text references in a research paper and to mation about a paper — the equivalent of a Steere, a senior research scientist at pharma- create bibliographies in any format. EndNote, library-catalogue entry. Only users in pri- ceutical firm Eli Lilly in Indianapolis, Indiana, a widely used commercial package, has offered vate groups can share and modify PDFs (and a desk piled high with printed papers: Post-it this feature for decades, but now faces compe- groups must upgrade to a paid account to add notes hanging out, writing in the margins, doo- tition from many modern tools. more than three individuals). dles, notations, arrows and more. Today’s PDF- Many tools interface with common word- Brenton Wiernik, an organizational- filled, digital folders are in many ways no easier processing software (usually Microsoft Word, psychology PhD candidate at the University of to navigate. With a digital reference manager, but sometimes OpenOffice and related free- Minnesota in Minneapolis, uses a shared library however, buried knowledge is just a keyword ware suites as well) so that a user typing up in Zotero for collaborative projects involving search away. ■ a research article need only select the papers systematic reviews and meta-analyses of the that they want to mention and click a button to literature in his field. Such efforts might involve Jeffrey M. Perkel is a writer based in have codes inserted into the document to mark 15–20 people, he says: some downloading Pocatello, Idaho.