Zotero

Over the years, we have accumulated large number of pdf files. The old adage of if you don’t know you have it or you can’t find it when you need it, there’s no point having it. This is quite apt with the situation most of us researchers find ourselves in dealing with ever increasing number of pdf files.

I have thousands and thousands of scientific articles and hundreds of books in pdf format scattered across multiple folders. I tried to organise them using folders, subfolders, labelling library/journals/interesting read etc. Finding the right paper or piece of information when I want it from this huge pile of pdf haystack proves very difficult and time consuming.

Recently I’ve come across Zotero. It’s a sort of reference management software and pdf file management software. I find the latter quite useful. It’s a different concept of file organisation. Forget about folders and subfolders, now we search. The classic example would be legacy email system vs Gmail. 

Good file organisation system should be firstly, easy to file and secondly, easy to find. The way Zotero works is that we dump all pdf files in Zotero. It automatically scans the files and searches for relevant citation info of which from several databases on the internet. Once citation info is found, it links this info with the pdf files. The automatic process of scanning pdf file for identifier and download citation info from the internet to match the file is not perfect, but it’s reasonably good. If automatic process fails, we can look up article using PMID, ISBN etc on Pubmed or other databases, download citation info and manually link the pdf files. We don’t need to do this a lot and we shouldn’t as it defeats the purpose of using software to do the heavy lifting.

Once you start using Zotero, next time you download pdf file from your browser, you can set it up in such a way that it is saved directly to Zotero. This way the citation info gathered from the publisher/database websites is much more accurate and reliable than extracting directly from pdf files. Moving forward the quality of your pdf library will improve, so will the ease of retrieving pdf files based on search terms.

In other words, it’s like you have a private Pubmed for your private pdf library. If you are familiar with how to search articles on Pubmed, you can do the same on your pdf library using Zotero.

Features that I found useful

Collection: it’s like a playlist in iTune. A file can be in multiple collections. Removing files from collections doesn’t delete them. They remain in other collection and library until you actually delete them. This is useful as the same article may be required or referred to in different essays and projects.

Tag: Zotero automatically attaches keywords, subject headings to the file if you download pdf from browsers and save directly to the program. You can also create your own tag that makes sense to you. For example, ‘read’ tag can be applied to articles that you have read. Creating a smart collection, which has rule such as tag is not ‘read’ meaning all articles that don’t have tag ‘read’ and therefore have not been read will show up in this collection waiting to be read.

Note: once you read a paper, you may want to summarise key take away or you may develop some idea you want to jot down that link to the article, you can do so by creating note attached to that article.

Related: papers can be linked to other papers, if you find they have some forms of relevant relationship. This is how we naturally expand our knowledge base. We connect new information with prior knowledge. This happens constantly especially during literature review. Tracing this web of relationship will be easier with this feature.

Give Zotero a try, it’s open source and free.