Managing Literature

Managing and Citing Scientific Literature

Updated June 2021

“A few months in the laboratory can save a few hours in the library.”  Frank Westheimer

 

Overview

Reading and managing scientific literature is one of the most important skills you need to develop.  Scientific literature is the foundation upon which all future work must be built.   Climbing to the top of the mountain of literature is a must for PhD students.  For Master’s students and undergraduates, you must engage the literature.  Reading the literature is a skill, and if you do not develop a commitment to developing that skill then that quality of your science will suffer.  In the McEwan lab all project leaders are required to commit to reading the literature and using that literature to bolster your science.

Mendeley

We use Mendeley as the literature management software in the McEwan Lab.  There is a lab account that you can sign into.  It has a web-based application and a downloadable desktop application including a plug-in.  I use the plug-in for some literature work on manuscripts, but the more important thing is that it serves as a repository.  LINK

The Salty Seven

Every project leader in the lab should find seven peer-reviewed scientific articles that apply to their project.  Use Google Scholar or Web of Science.  Then save PDFs of these articles and place them into a folder that you create in Mendeley.  These articles are then the basis for your work going forward.  Read them carefully.  Look at the figures.  Look at the literature they are citing.  Look at how they are “framing” the project in terms of ideas and concepts.  These papers can serve as a model for your project. What techniques to use, how to analyze data and how to frame up the science in the broader scientific conversation.

 

Creating a well-organized literature cited page in your manuscript.

 Proper citation of literature is a fundamental task of writing a manuscript for a Thesis, Dissertation or scientific publication.  In the McEwan lab we use Mendeley to manage literature and this does have a function to automatically create a literature cited page!  This makes things much easier.  However, the Mendeley library itself has errors that are propagated into the Literature Cited page.  Later in the process, you will need to de-couple from Mendeley and finalize your references, which will require you to be sure that the citations are complete and formatted consistently.  Journal copyeditors have some responsibility in getting your format correct once your article is accepted and prior to publication; however, it is important that the manuscript be edited carefully prior to submission.  If a reviewer turns to the references and finds something missing, or a very messy formatting situation, they may take a negative view of the work. You do not want this though popping up in a reviewer’s mind: “If the authors are sloppy and irresponsible with their references, maybe they are sloppy and irresponsible with the data collection too….hmmmm.” 

 Here are some McEwan Lab Best Practices to checking your references.

(a) Choose a format and stick with it.

 You need for your Reference Cited page to be consistent.  This means you need to select a format and then use the identical format for all citations.  If you have a journal that you are targeting from early on you can use that journal’s “Instruction to Authors” to figure out your format.  Mendeley might have something that matches precisely that format, or you can actually create your own format within Mendeley.  Alternatively, you can chose a Mendeley format that is close to the final format you need and edit from there.  Ultimately, your goal is consistency.      

(b) Make sure all the literature cited in the manuscript appears as an entry in the Literature Cited pages, and that all literature listed in the Literature Cited pages are also referenced in the manuscript.

The reference program you are using (eg, Mendeley) should help you with this, but still mistakes happen and especially if you are working with multiple co-authors you are almost guaranteed to end up with a mis-match between literature cited and Literature Cited.  My recommendation is to literally print out the manuscript, and the Literature Cite page and go through one-by-one with a marker and check off each manuscript citation.  There really is no substitute for this kind of screening process. Then if you find a reference in the text that is not in the Literature Cited you can fill it in, and if you find Literature Cited that is not in the text you can add it, or delete.

(c) Edit for consistent formatting

As you are working on your manuscript and approaching the later stages in the editing process it is good to begin scanning your Literature Cited for formatting mistakes.  There will often be many mistakes of consistency.  Here are some things to look for:

———————-

Author names and initials

You want these to be consistent.  Below are three different ways to list the author names and initials, fix this if you find it!

Borth, EB, Custer KW and McEwan RW (2018) Lethal effects of leaf leachate from the non-native invasive shrub Amur honeysuckle (Lonicera maackii) on a model aquatic organism (Hyalella azteca). Ecoscience 25: 189–197.

Borth, E.B., K.W. Custer & R.W. McEwan (2018) Lethal effects of leaf leachate from the non-native invasive shrub Amur honeysuckle (Lonicera maackii) on a model aquatic organism (Hyalella azteca). Ecoscience 25: 189–197.

Borth, E.B., Custer K.W., McEwan R.W. (2018) Lethal effects of leaf leachate from the non-native invasive shrub Amur honeysuckle (Lonicera maackii) on a model aquatic organism (Hyalella azteca). Ecoscience 25: 189–197.

———————-

Date

You want to be consistent in the way the date is displayed.  Each citation must be the same.  Below are three different ways to display date, this is no good.

Borth, EB, Custer KW and McEwan RW.  2018. Lethal effects of leaf leachate from the non-native invasive shrub Amur honeysuckle (Lonicera maackii) on a model aquatic organism (Hyalella azteca). Ecoscience 25: 189–197.

Borth, E.B., K.W. Custer & R.W. McEwan (2018) Lethal effects of leaf leachate from the non-native invasive shrub Amur honeysuckle (Lonicera maackii) on a model aquatic organism (Hyalella azteca). Ecoscience 25: 189–197.

Borth, E.B., Custer K.W., McEwan R.W. Lethal effects of leaf leachate from the non-native invasive shrub Amur honeysuckle (Lonicera maackii) on a model aquatic organism (Hyalella azteca). (2018). Ecoscience 25: 189–197.

———————-

Article title

Make sure the title is consistent and watch out for capitalization in particular.  For example, these are inconsistent.  This is bad.  Make all of your references the same.

Borth, E.B., K.W. Custer & R.W. McEwan (2018) Lethal effects of leaf leachate from the non-native invasive shrub Amur honeysuckle (Lonicera maackii) on a model aquatic organism (Hyalella azteca). Ecoscience 25: 189–197.

Borth, E.B., K.W. Custer & R.W. McEwan (2018) Lethal Effects of Leaf Leachate From the Non-native Invasive Shrub Amur Honeysuckle (Lonicera maackii) on a Model Aquatic Organism (Hyalella Azteca). Ecoscience 25: 189–197.

Borth, E.B., K.W. Custer & R.W. McEwan (2018) Lethal effects of leaf leachate from the non-native invasive shrub Amur honeysuckle (Lonicera maackii) on a model aquatic organism (Hyalella azteca). Ecoscience 25: 189–197.

———————-

Latin names are in italics

 See below.  The bottom one is incorrect.

Borth, E.B., K.W. Custer & R.W. McEwan (2018) Lethal effects of leaf leachate from the non-native invasive shrub Amur honeysuckle (Lonicera maackii) on a model aquatic organism (Hyalella azteca). Ecoscience 25: 189–197.

Borth, E.B., K.W. Custer & R.W. McEwan (2018) Lethal effects of leaf leachate from the non-native invasive shrub Amur honeysuckle (Lonicera maackii) on a model aquatic organism (Hyalella azteca). Ecoscience 25: 189–197.

​———————-

There should not be random stuff at the end of a citation

Let the Journal decide if they want to DOI at the end.  We just put the proper citation.  Don’t have stuff, like below in the top example in maroon, hanging out at the end.

Gregory, SV, Swanson, FJ, Mckee, WA, Kenneth, W, Swanson, J, Cummins, KW (1991). An Ecosystem Perspective of Riparian Zones Focus on links between land and water. BioScience, 41(8), 540–551. URL : http://www.jstor.org/stable/

vs.

Miller KE, Gorchov DL (2004). The invasive shrub, Lonicera maackii, reduces growth and fecundity of perennial forest herbs. Oecologia 139: 359-375.

​​———————-

All​ journal names should be treated identically and spelled out

You should not have some abbreviated, others not, not some italics, others not.  Three below are three different articles where the journal title has been treated differently each time.  Just spell out the title.  

Tank, JL, Rosi-Marshall EJ, Griffiths NA, Entrekin SA, Stephen ML (2010). A review of allochthonous organic matter dynamics and metabolism in streams. Journal of the North American Benthological Society 29: 118-146.

Vannote RL, Minshall GW, Cummins KW, Sedell JR, Cushing CE (1980). The river continuum concept. Can. J. Fish. Aquat. Sci. 37: 130-137.

Voshell Jr., J. R. 2002. A Guide to common Freshwater Invertebrates of North America.

Wallace, JB (1996). The Role of Macroinvertebrates in Stream Ecosystem Function. Annual Review of Entomology, 41(1), 115–139

​​———————-

Be consistent in whether you have “and”  “&” or “nothing” at the end of your author list. 

Below we have these treated three different ways.  It has to be the same.

Lenth, R., Singmann, H., & Love, J. (2018). Emmeans: Estimated marginal means, aka least-squares means. R package version1(1).

Lieurance D, Cipollini D (2012). Damage levels from arthropod herbivores on Lonicera maackii suggest enemy release in its introduced range. Biological Invasions, 14(4), 863–873.

Likens FH, Bormann, R. S. Pierce and W. A. Reiners, G. E. (1978). Recovery of a deforested ecosystem. Science 199: 492–496.

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