Cruising the Biomedical Scientific Literature: Managing References


So you have spent time searching, screening and have a number of articles that you want to gather. However, you don’t have time to screen all the articles? How do you capture the citations? What is the best way to save the search results? Do you have to download all the articles? Fortunately, both PubMed and Google Scholar allow you to create a profile, login and use tools that allow you to save searches, search results and even run the same search repeatedly. Plus, by using free Reference Management Software, you can download article citations and manage your local personal resource library.

PubMed’s “My NCBI” dashboard provides access to a number of features for archiving and record keeping of search strategies. From this dashboard you can specifically search any of the 30+ NCBI databases. The last six-months of search activity is saved in the “Recent Activity” section. Records and searches are stored by date and include the search string terms used or a link to the specific record viewed. Searches can be “saved” from the PubMed search results page and appear in the “Saved Searches” section of the dashboard.  Saved searches can be scheduled for execution on a regular basis with outputs formatted in a variety of ways and delivered to your email account of choice.  The “Filters” section allows you to create custom filters in addition to dozens of pre-existing filters capable of running on any of the NCBI databases. “Collections” allows you to save search results indefinitely, plus save records from different searches in one collection. 

Google Scholar has a limited set of archiving and tracking attributes.  Signing into your Google account provide access to Google Scholars “My Library” feature.  Articles can be “Starred” on the main search page and retained in My Library.  “Labels” can be created and articles tagged to appear under different (multiple) labels for collecting and organizing citations.

The development of online resources databases, search tools such as PubMed and Google Scholar and the rapid increase in biomedical literature has driven the need for individual Reference (Citation or Bibliographic) Management software.  These locally created databases are similar to their online relatives except much smaller in scale. Almost all connect to NCBI (PubMed) databases and several have integrated searching of external databases from within the software itself. More importantly, with management software you can download citations and build libraries that can be used to automatically generate, embed and format bibliographies in word processing programs. Many have advanced features that enable finding, downloading and integrating open-access PDFs, adding citation data by DOI and even retrieving publication data from downloaded PDFs.

There are over 25 different Reference Management software tools available. Commercial software packages such as EndNote, Paperpile and ReadCube have a variety of pricing options for both individual and institutional purchase. Of the free software, the most well-known and perhaps most widely used is Zotero ( Created in 2006, Zotero is an open source tool and undergoes regular updates. It has free online storage (up to 300MB) and purchase additional storage space at .  Zotero also supports cloud-based local database storage (Google Drive, Dropbox), has a forum based online support system and runs on Windows, Apple and Linux operating systems.  Zotero exports and imports in multiple standard file formats enabling references to be shared among multiple users and connects to PubMed and open access ArVix archive for direct importing.   Word Processor integration for Word (Windows and Macintosh), Word Online, OpenOffice and Google docs is supported and there are over 9000 citation styles including APA (American Psychological Association), numbered and author-date styles available for use. 

Downloading and importing article citations into Zotero from both PubMed and Google Scholar is relatively straight forward.  From PubMed, select the articles you want to download from the PubMed search results page and choose “Send To” and “Create File”.  Save the file to your local computer. From the “My Library” page on Google Scholar, select the article citations you want download and select the “Export” button.   Choose the output format (BibTeX or RIS) and the citation file is downloaded.  To import the citations, open Zotero, select import and chose the file that contains the citations you wish to import.  The citations will appear in the main database window and include all the metadata available (depending on source database).  After installing the appropriate plugin Zotero will integrate with your word processor so that you can add in-text citations. Inserting citations is easy by 1) insert the cursor where you want to add the citation, 2) select “Add Citation” from the word processor “Add-Ins” menu to pick the citation style you want to use, and 3) choose the reference. Zotero inserts the style formatted citation in that location.  You can add as many in-text citations as needed. Once you have completed writing your document, create a bibliography at the end of your document by selecting the “Insert Bibliography” from the word processor “Add-Ins” menu. Zotero adds a bibliography, formatted in the style originally selected, at the end of the document.

From finding and reading articles to saving and using references, literature review is an important and critical step of preparing to undertake any research project. This goal of this series was to provide a brief overview of some methods to capture, interpret and utilize biomedical literature and to provide context to utilize these tools in your day-to-day activity.     

Written by Luis Chiriboga, PhD, HT(ASCP), QIHC