Banish the PDF-hunting blues with these AI and digital tools

Since starting my PhD in veterinary pathobiology in 2014, I have looked for ways to streamline my literature-review workflow. Every day, I search for papers, import them into my citation manager, read them and take notes. I can then incorporate those references and insights into manuscripts. But the conventional approach of searching for and downloading PDF files is tedious and inefficient, involving multiple mouse clicks, scattered files and a large disconnect between my notes and the source. Ten years later, with the development of digital and artificial intelligence (AI) tools, I have finally landed on a process that can streamline my academic writing. I call it ACCU — the acquisition, collection, crystallization and utilization workflow.

Acquisition: how I find papers

For quick keyword searches, I use Google Scholar. In settings, under ‘search results’, I set the export format to RefMan for compatibility with my citation manager and add my university library under ‘library links’ so that I can retrieve the full text when it is available.

For systematic searches, I use the PubMed database’s advanced search function, coupled with the EasyPubMedicine Chrome browser extension to display the journal ranking, impact factor and citation count under each hit. On the PubMed search-results page, I can click ‘create RSS’ to turn the results into a web feed in an RSS reader, such as Feedly, which will then alert me to any new papers that fit the search criteria. This allows me to access all newly published papers in my field — as well as multiple journals’ most recent publications — anytime, anywhere, even on my phone.

To flesh out my research, I use the AI-powered academic search engines Perplexity and Consensus. These can provide answers to well-defined, natural-language questions, such as, ‘Is vitamin D beneficial for osteoporosis?’ They have a better user interface than ChatGPT, with hyperlinks to the original sources so that I can verify the results.

Alternatively, I can use ResearchRabbit, an AI-based tool that allows me to use papers in my literature collection as seeds to find related publications. I can add the newly identified papers to my reference manager with one click.

Collection: how I store my papers

I use the free and open-source reference manager Zotero because it is easy to use and compatible with many of my other digital tools.

Zotero covers all the basic functions of many available commercial tools and, in my experience, provides better solutions. The Zotero Connectors Chrome browser extension allows me to import papers from Google Scholar searches in batches. A right-click can save academic articles (or any web page) to my Zotero library in a ready-to-cite format. My university library provides the OpenURL link resolver, which I use in Zotero’s settings to automatically download full-text articles. I can double-click on Zotero entries to highlight and annotate the PDF.

Advanced users can expand Zotero with plugins. For example, I use Notero to import all the ‘What Is Your Diagnosis’ articles from the journal Veterinary Clinical Pathology into Notion, a productivity and note-taking app, to create a searchable database for veterinary clinical pathologists and trainees.