Literature

nanos gigantum umeris insidentes Bernhard of Chartres

If I have seen further it is by standing on y^e shoulders of giants. Isaac Newton

At least every scientific work needs proper dealing with its sources and therefore a bibliography¹⁾.

From the above, a number of fundamental questions arise about how to organise the informations necessary for a bibliography, and, if applicable, the literature itself²⁾:

• How to store information about references?
  • The easiest case would be to have a manually updated list. Nevertheless, this is the clearly not recommended.
  • There are different kinds of literature databases (BibTeX, EndNote, …).
  • There are different programs to access and use the different databases (JabRef, EndNote, EndNote Web, …)
• How to organise and store the literature itself (if it is electronically available)?
  • Ideally, access is easy and fast even without using the associated literature database.
  • Although many articles are accessible via internet (at least in a university), the relevant literature should be stored locally on the file system (for details and reasons see below).
• How to connect the literature list/database with the (electronically available) actual literature?

All these aspects will be dealt with in more details in the following.

This topic can be divided in two aspects: Formats and their associated interfaces.

Although there are many more, two formats are of particular interest here:

• EndNote
• BibTeX

While EndNote is a commercial (and binary) format and therefore its user depends on a (only) commercially available (and quite expensive) software, BibTeX is a complete free and open-source software and a pure text format (that can be read and modified very easily).

Those who use Word (or other word processing software) will usually use EndNote or one of its relatives (EndNote Web).

Those who write their (scientific) publications and texts with LaTeX (highly recommended!) normally tend to use BibTeX.

Note: It is possible to convert between both formats, EndNote and BibTeX. But be aware of the fact that such conversions are normally never completely perfect and without any errors.

Many websites (journals, literature search portals such as “Web of Science” and “PubMed”) allow to export the records in both (and even more) formats.

Whereas EndNote comes with its own interface, in case of BibTeX, the interface is - in the easiest case - a standard text editor capable of displaying and saving pure (ASCII) text³⁾.

Besides this “classic” way to use a text editor of your choice to directly edit your BibTeX files, nowadays there are a number of programs that allow for a more comfortable editing of BibTeX databases and provide further functionality (such as searching, etc.).

One program that is especially useful (given its platform independence) and easy to use should be highlighted here and is recommended for use for all those who dislike the idea of having to use a text editor and manually edit their BibTeX files:

• JabRef

Nevertheless, especially when using BibteX there are good reasons for the old-fashioned way of editing the literature database using a text editor. For details, see below.⁴⁾

Especially in science most of the references are articles from scientific journals. Nowadays, probably the vast majority of these articles are accessible online in electronic form (as PDF files).

Why then bother to save these files locally, and how to organise the files?

In former times, it was the filing cabinet, nowadays it is the hierarchy of folders on your file system of your local hard drive. Even though most of the articles can be accessed easily and comfortably using internet and search engines (given that you're currently connected to a university network), there are good reasons for saving the literature relevant to you locally on your hard drive:

• Accessibility
  • You can access your literature independend of your internet connection and access to the publishers websites.
  • Some articles may not be accessible via your local university network. But you have colleagues with different access that might provide you with such articles.⁵⁾
  • There is no guarantee that your university will permanently give you access to a given article or journal.⁶⁾
• Overview
  • Sometimes it is much easier to look through your locally saved files of you want to find a given article, than to search for it via internet.

Idea: Even without using the literature database, access to the actual literature (i.e., PDF file) should be as easy as possible.

One, if not the most prominent access to (scientific) literature is via the name of the first author of a publication. This is the normal way of referencing in a text, if you don't use numeric references there.

For a complete description of an article published in a journal (the common case for literature that you have access to in electronic form), you need four⁷⁾ pieces of information:

• First author's name
• Journal name
• Volume
• Page number (starting page)

Accordingly, the file name should contain these four pieces of information.⁸⁾ A scheme for file names that is consistent with the criteria named here will be introduced later.

A few hints for how to organise your files:

• One directory for all articles
  • Advantage: You can easily search for a given file⁹⁾
  • Topical directories have the disadvantage that you normally cannot assing a unique topic to a given file/article.
• Perhaps additional directories for other kinds of literature (thesis, chapters from books, etc.)

Of course, all those hints are not obligatory, but only stem from personal experience (although experience of quite some time).

How to connect your literature list/database with your (electronically available) literature?

A few of the interfaces between database and user (EndNote, JabRef) allow you to directly set links to files within the respective program. But beware of the obvious disadvantages that might have¹⁰⁾.

A far more robust way would be to create and use a generic scheme for naming your files and then add these file names (without extension) as “keys” to the respective records. In case that your generic scheme allows furthermore to directly extract the full citation (author, journal name, volumne, first page, see above) from the key/file name, than it will be very easy for you to look for a specific reference in your files starting out from a citation in an article (or elsewhere)¹¹⁾.

What follows is a scheme for naming files (and corresponding (BibTeX) keys) that has been used for quite some time and proved to be useful. It follows all criteria named above.

Key of the concept is to name the (PDF) files in the exact same way as the (BibTeX) keys. Additionally, from the file/key names, you can extract all necessary information for a full reference and vice versa.

A (bibtex) key for an article in a (scientific) journal consists of the following four parts, each followed by a short explanation:

First author's name

The first four letters of the first author's name

Journal

A unique abbreviation of the journal.

If you use BibTeX, you could/should create files that contain assignments of these abbreviations to either the full or the abbreviated name of the journal. The idea: Easy switching between full and abbreviated journal names in your (LaTeX) bibliographies without having to alter the actual BibTeX records. Besides that, this scheme helps you to keep your journal names consistent.

Volumne

The volume of the respective journal the article appeared in.

Page

The first page of the article.

To demonstrate the scheme introduced above, a short example using BibTeX:

literature.bib

@STRING{LASTEDIT = {25/NOV/2011}}
 
@Article{bisk-aciee-48-404,
  author = 	 {Till Biskup AND Erik Schleicher AND Asako Okafuji AND Gerhard Link AND Kenichi Hitomi AND Elizabeth D. Getzoff AND Stefan Weber},
  title = 	 {Direct Observation of a Photoinduced Radical Pair in a Cryptochrome Blue--Light Photoreceptor},
  journal =	 ACIEE,
  year = 	 {2009},
  volume = 	 {48},
  pages = 	 {404--407}
}

fulljrnl.bib

@STRING{LASTEDIT = {25/NOV/2011}}
 
@STRING{ACIEE = {Angewandte Chemie International Edition English}}

abbrjrnl.bib

@STRING{LASTEDIT = {25/NOV/2011}}
 
@STRING{ACIEE = {Angew. Chem. Int. Ed.}}

The corresponding file name of the PDF file is therefore: bisk-aciee-48-404.pdf

If you use BibTeX together with LaTeX, include the bibliography as follows:

\bibliography{fulljrnl,literatur}

or:

\bibliography{abbrjrnl,literatur}

In both cases, it is important to load the file with the assignments of abbreviations and actual journal names before loading the bibliography itself. Otherwise, BibTeX cannot do the necessary replacement of strings.

Please note: The abbreviations given here for the journal names (i.e., the abbreviations used in the file and key names) are no “official” abbreviations, but rather user-defined short string. Therefore, it might be useful if you plan to share BibTeX and PDF files within a group to agree not only about the general naming scheme of the keys and files, but as well about the abbreviations used for the journals.

A well-maintained literature database is very useful for your own scientific publications, be it a thesis or any arbitrary other publication (article in a journal, chapter in a book, etc.).

As literature databases grow over time, it is important and helpful to follow a few general rules straight from the beginning.

• Never directly take over references from other sources without proper checking of the original reference.
  • Besides other things, that prevents you from including references that don't exist at all.¹²⁾
  • Note: References/bibliographies are normally not well-maintained. Therefore, they contain usually lots of mistakes and typos. But nothing can be more frustrating than not to be able to access a reference due to such avoidable mistakes.
• If you add a record to your literature database/library, carefully check every field of the entry (and compare directly with the original reference).
  • Note: Never trust the records in databases on the web. Web of Science and others often contain typos and simply wrong or at least inconsistent entries.
• Check for correct display of special characters (especially in case of LaTeX, use the appropriate commands).
• If available electronically, add the reference as a (PDF) file to your own library/directory.
• Check for consistency of records within your library.
  • Capitalising of titles.
  • Completeness of the fields for a record.
  • Identical names of journals, titles of books, etc.

If you apply these rules consequently and straight from the beginning, that will save you lots of tedious work later on. Furthermore, it allows you to rely on your own library/literature database without restrictions and without having to check every time.