If, as starting graduate students, you are following my first key advice of reading on a regular basis scientific manuscripts related to your field of research in general and your project in particular, you’ve probably reach an obvious observation: you are collecting a large number of PDF files very quickly.
There are, of course, a few more observations to be made:
- Simply filing these PDF in folders is not very useful. Face it, you will have to use some (most?) of the references for your own papers that you will be writing.
- Manually entering each manuscript information (title, authors, abstract, journal, pages, …) in a database is highly inefficient and not a very good use of time.
- Your PDF contents is not indexed by default i.e. you can not search by key words within your documents by default.
So action must be taken; Invest in a good manuscript management system!
Myself, I have abandon the use of a citation only software a few years ago and instead opted for PDF management software. Yes their first application is to work with scientific manuscript you get online. But now most will also allow you to:
- Grab a reference directly from a website (PubMed, Google, Amazon, …)
- If a PDF file is involved, it will also be transferred directly to your PDF library
- Extract the information from the metadata automatically
- Match a document to a repository (again PubMed, Scorpus, Google, …) and filled out much more information automatically into the software database.
- Handle also books, patents, abstracts, presentation documents and more.
- Allow you to use this information for direct building of your reference section in WORD, PAGE, OpenOffice, LaTeX (through BibTex export) and others.
The most advanced ones, will also allow you to read, annotate, comment, rank, tag each of your manuscript, have a perfect sync with your smartphone or tablet and even read and comments directly on your iPad and sync back with your main library afterward!. In this category, you will find Papers (Mac and Windows) and Sente (Mac). An excellent review can be found in the book Organizing Creativity (see here)
This bring another observation: At this stage of my career, time is becoming constraint and therefore expensive. Thus I do not mind investing 80$ for a state-of-the-art Mac/iPad software combination that I do not need to maintain. However, for graduate students, money is often hard to come by while time is “abundant” and cheap (at least until the last stretch before the thesis defense 😉 ).
Solution: the free Zotero software. I say free if you use it as is, without the offered cloud syncing (the annual fee alone is such that in that case, simply by one of the better app mentioned above).
I have used Zotero for over 6 months in my transition for the older Endnote and the newer Sente/Paper. It use to be only working as a plug-in for Firefox browser. Nowadays you can use Firefox, Chrome or Safari. Furthermore, Zotero now has a standalone application (displayed below)!
From the browser, you can:
- Grab references from the PubMed website or other website directly into your Zotero database.
- Attach PDF files to a reference entry
- Drop PDF file and have the metadata scan to make a citable entry.
- Index your PDF (for future search)
- Have other file types in your database, including web pages.
An example from the PubMed website is given below (click on the figure below to get a full resolution version)
Note that support of file types, in particular for indexing anything else than PDF or RTF, is nothing like DevonThink in my experience (but DT is not free either…)
Zotero, also come with modules that allow you to tap in your database for citation when writing your own documents in various word processors and even e-mails. It also has modules for BibTex export, link to Drupal and so on. Zotero support Citation Style Language and thus any journals citation format can be built (if it does not already exist)
The complete database structure is accessible, you can even chose when you want it to reside (preference) and can be easily backed-up.
Bottom line, you have no reason to handle manuscripts and building your citation lists manually. Get a free copy of Zotero and welcome to the 21st century!