The Bibtex database is a plain text format. Each field is identified by a descriptive label. The following entry is an example of a Bibtex article entry.

@ARTICLE{Smith2011,

author = {Smith, Iam; Jones, U.R.},

title = {This is the document title.},

journal = {International Journal of Scientific Findings},

year = {2011},

volume = {1},

pages = {22-33},

abstract = {This field represents the abstract that would appear with the article.},

crossref = {,},

owner = {bob},

timestamp = {2011.08.12} }

The following paragraph is a real entry that doesn't use all of the parts used by the previous example.

@ARTICLE{abend2002,

author = {Abend, S.M. and Kulish, N.},

title = {The psychoanalytic method from an epistemological viewpoint.},

journal = {Int J Psychoanal},

year = {2002},

volume = {83},

pages = {491-5},

number = {Pt 2},

owner = {bob},

timestamp = {2011.05.13} }

The @ symbol indicates the start of a new record. This is followed by the author's last name and the year of publication. This is the key that is used to retrieve or refer to the article. It is like your SSN. It refers uniquely to the individual. The rest of the fields are self explanatory.

There are other fields that have value. Number of the article or item, month, part, Eid, Note, Annote, Crossref, Keywords, File, Doi, Url, Citeseerurl, Comment, owner, timestamp, abstract, review, plus a display of the Bibtex entry that results from your entries.

You can google Bibtex database and find lists of programs to operate on Bibtex. Pick one you like. JabRef is a good one, and I like and recommend it. You can use whatever you like. I want to let you know there are pitfalls with commercial software. For years I used a commercial product and then they went out of business. They still operate a rather busy blog filled with requests to help users get their data back. I won't do that again.

I like and recommend JabRef because it is written in Java which means it will work in any computer. Mac, Windows, Linux, Unix, everything supports Java and JabRef.

JabRef is mature and has been in use for years by scholars the world over.

JabRef is free and open source software (FOSS). You will not be constantly nagged to upgrade for only a few hundred dollars more. Data written 20 years ago is readable today.

The Bibtex standard that JabRef manipulates is plain text. There are no binary files. Anyone can read this file.

The basic operation of JabRef resembles filling in a form. There are various tabs one can navigate. The first tab has the majority of the information required for a journal or book citation. See Figure 1.

Figure 1: Opening screen of JabRef.

Items such as author name(s), title, journal name, pages, volumes. You fill in the form, and a Bibtex database entry is recorded and saved. This can be converted to multiple journal styles using other tools. The first problem with a reference list is collecting the data. JabRef does all of that nicely.

JabRef can search Medline (PubMed) database for you.

Figure 2: Search Medline.

You can enter your search terms and just watch the hits roll back in. All of the data is imported to the proper fields for you. You don't have to do any manual typing to enter data. You can search for a broad term (malaria for example) and just sit back and watch thousands of hits accumulate. Now you begin to appreciate the use of search terms to narrow the field a little bit. See figures Figure 2 and Figure 3.

Figure 3: Articles matching search terms return to user screen.

Incorporate New References Into Your Collection

After you have selected references that seem interesting to you and have generated keys (authorname and date), you will find these new references highlighted at the top of your display off all records. See Figure 4.

Figure 4: New Records Highlighted Yellow.

At this point, you can begin collecting the new references from your library. Our institution has a nice service that returns PDF files of requested articles. As you read these articles, you can use JabRef to keep your notes about the content. I am going to suggest a non-traditional use of the Abstract field. If an abstract is returned as part of the search you will have text in the Abstract tab. Move to the end of that field. You might want to enter a marker like a line of equal signs etc. Below this marker you can enter your personal notes about the article. You might comment about where this paper fits in your subject. You might summarize points you learned. All of these personal observations are now irrevocably linked to the article that spawned them. See Figure 5.

Generate the Annotated Bibliography

JabRef has a very nice built-in export feature that can generate an annotated bibliography that will contain the full Bibtex citation, the abstract and your personal comments in an interactive HTML format. You generate this with a few mouse clicks.

Figure 5: Display of Abstract Field. You Could Append Your Notes Here.

Select File > Export > (a new input box will appear). Select the type of export you want. You should select HTML table (with Abstract & Bib)(*.html).

Figure 6: Select type of file to export.

Supply the filename of your choice. Save the file. Navigate to your new bibliography and click on it. It should open in your browser and will appear as an HTML table. See figures Figure 6 and Figure 7.

Figure 7: Select Name For Exported Database.

Figure 8: HTML Output of Bibliography Export. Note Search box, Top Left.

See Figure 8. Examine this display. It has a search box at the top. Give it a try. You can search for terms contained in this HTML report. Notice the end of the Title cell there is a link to either Bib or Abstract or both. Click on those entries and the Bib entry or the Abstract will appear. If you print these you have a hard copy of a beautifully formatted annotated bibliography complete with abstract, Bib citation and your personal notes. This can be very useful when it is time to assemble your paper and begin writing. You will have all of the data and its proper citation at your fingertips. This is so much nicer than 3x5 cards. And it is really simple. See Figure 9.

Figure 9: Smith Record Selected, Abstract and BibTex Display Options Selected.

Many students use Microsoft Word (MSWord). This will supply some instructions for incorporating JabRef references into your MSWord document.

Once you have collected a set of references and begin writing, your focus will shift to MSWord. Before you leave JabRef, export your database or select the references you want to use in the current writing project and export only that subset of references. See Figure 10.

Figure 10: Export JabRef File to Word Format.

The file format you should select is: MS Office 2007 (*.xml). See Figure 11.

Figure 11: Select filename and export style (Word for this example).

Keep track of the storage location. You will have to direct MSWord to this location in the next step.

Open MSWord. Click on the References tab. Click on Manage Sources. In the box at the left, browse to the storage location of the JabRef export. Everything you exported from JabRef will appear in the left box. Select items from this left side and click on copy. These references will be available in word. Close that box.

Now from inside MSWord, if you want to insert a citation, click on the References tab, then Insert Citation. References you transferred to the right side box in the previous step will appear. Select the reference you want to cite.

At the end of your paper, Insert a heading such as References or Bibliography. Click on the References tab, Bibliography, choose one of the styles shown, click on Insert Bibliography.

Your references will appear in your paper.

You may have to hand edit or do some additional work to get minor format issues corrected. I would hope that your reader is more concerned with content than the format. However, this is often not the case.

This will do the largest part of the work. You can go from finding the citation in a literature search, to adding the reference to your collection, take notes on the article, produce an annotated bibliography, cite references in your paper, and place the bibliography at the end - all without retyping a single article.