Finding and Managing Literature
Scientists have to gather, read, and keep track of a huge range of
papers and source materials. Here I have gathered a few resources and
ideas for managing this without losing complete control.
Searching for Citations
There are a lot of databases out there for searching, more all the time.
We have a number of excellent ones available through the University of Utah
libraries and here are some pointers to my favorites.
The new policy from NIH on public access to publications will also
change the landscape as more and more papers start to populate the
General Search Sites
Note: please send me links to publicly accessible
literature databases in the areas of engineering and for conference
proceedings. Pubmed and Medline have the medical world covered very well
but Engineering is missing such a reference.
Journal Search Sites
Lots of journals now let you search and even download articles, a
wonderful way to avoid a trip to the library.
While we have access to many journals through the library (thank you,
University of Utah!) and PubMed Central (thank you, NIH) there are times
when we need additional resources. For this, we have ILLIAD. Here are the
steps to getting an article from this system.
- To do this, go to the ILLIAD website
- Login or click the First User link to set up an account.
- On the left is a menu bar, select the "Article" option under the
"New Request" Heading Fill in the required info about the article and
- Within a few days, they will send it to you. NOTE: You can only
request 10 per day and they will reject it if you can find it by some
other (free) means, so make sure that it isn't available over PubMed or
IEEE or google scholar. (I've also been rejected on one published by KIT
in a german journal).
Done stupidly, managing a literature database can be as much fun as
visiting the endodontist, but there are smarter ways to go. Use them and
your visit to the dentist becomes a chat with the nice lady who cleans your
Some sensible ways to manage references are:
- Mendeley, a free resource
with growing support.
- Zotero, it was a plug-in for
Firefox and not it is a standalone app that provides a complete
reference management system that saves the database in a central
site, accessible online. It is free!
- Papers3 (or version
3 of Papers) for both Mac OSX and Windows. This project manages the
pdf files we collect more and more often instead of paper. It is
very solid, has some nice search tools built into the app, and with
some clever use of Dropbox, it can sync across computers and IOS
devices. Inidividual licenses are $79.
- EndNote, a pretty nice and
very widely used commercial product for Macs and PCs. It fails
miserably when documents and databses get large but for small
projects, it is fine. At $250 (there are some educational
discounts), this is the most expensive of the tools.
- RefWorks, a new application for
managing references that is web based and hence accessible from any
computer on the network. Costs about $100 per year.
Sente for Mac, another entry in this ever busier market of tools
for managing references. THere is a free version with space for 100
refernces, i.e., useful only for testing and Academic individual
license is $60.
- BibTex , my clear
favorite. It is not a full featured tool like those above but a
simple text file database that interacts with LaTeX. In fact, many of
the products listed above will generate output in BibTex format.
- Parsing downloads from PubMed One
example of a tool to convert references into BibTex format is this
program I wrote in awk that will take the output of literature
PubMed Medline and convert them.
- Using EndNote together with BibTex
a utilty to searching PubMed and returning BibTex formatted hits. I
have no firsthand experience with this one.
Guidelines for Authors
Here are pointers to the guidelines that we use when submitting papers to
Last modified: Thu Jan 15 19:36:43 MST 2015