Musings on a Tool Every Academic Should Use

William Hersh, MD, Professor and Chair, OHSU
Blog: Informatics Professor
Twitter: @williamhersh

I often muse that there are few computer applications that truly save me time. For all the fun and productive things that computers enable me to do, they are just as often a time sink rather than a time saver, especially when hardware or software go wrong. The transition from being able to talk to a person on the phone to the use of chatbots and other ways to keep people with problems away from costly human support has added even more time, especially during the pandemic.

There is, however, one notable exception, a computer application that saves me a great deal of time. This is bibliographic management software. Any academic who writes a great deal, especially those who publish in journals and other venues across different disciplines, knows the time and effort required to maintain and format references.

As with all computer applications, one must choose their bibliographic management software package wisely. I was an early user of EndNote, back to Version 1 when it was first released in the 1990s. It had served me well over the years, but one challenge was that as the formats of bibliographic records changed, I was not able to take advantage of its automatic capture of metadata. I was also not able to easily merge my EndNote database with those of others, again due to the formatting issues. By the end of last year, my database of papers that I have cited once or more in research writing or teaching, had grown to over 12,000 entries, yet my effort to use the product put me in a silo.

This year I decided to make a decision to start over. My first decision was whether to continue with EndNote or move to a different package. One package that many of my colleagues seemed to be adopting was Zotero. This package has the advantage of being open-source, with a large developer community. I decided to make the switch.

The transition has not been simple, as my existing EndNote library had too many irregularities for me to simply import it into Zotero. However, I have been able to build up my new Zotero database relatively quickly due to its automated capture of metadata. (In fairness to EndNote, they have this feature as well.) The automated capture of metadata is not perfect, mainly because many Web sites and pages do not adhere to standards. But many key sources, such as PubMed, most journals, Amazon (for books), and others make entry into the database quick. One notable feature for someone concerned with the big picture of science is Zotero’s ability to flag that a scientific paper has been retracted.

Zotero is not perfect, and one feature I hope is added soon is the ability to easily update a record, such as when a journal paper goes from “online ahead of print” to actually being “in print,” i.e., having a volume, issue, and page numbers (even if many journals are not physically printed these days). The metadata of journal articles does change over time, and the ability to automate the capture of its changing as easily as its initial capture would be a great feature.

Nonetheless, bibliographic management software is a vitally important tool for those who write scientific papers, especially in inter-disciplinary fields like informatics. And the decision on which package to use is important, as changing from one to another can be time-consuming. But it is certainly an application whose proper use can save time overall.

This article post first appeared on The Informatics Professor. Dr. Hersh is a frequent contributing expert to HealthIT Answers.