RefDB Examples: Data

Creating bibliographies for structured texts isn't straightforward, but it isn't rocket science either. This page tries to explain what the input, intermediate, and output files look like. For the exact processing instructions, please consult the manual or the tutorial. For an overview over the bibliography and citation styles available, see the style gallery.

On this page
RIS datasets
risx datasets
getref output
XML source documents
Generated output

We'll start with the structure of the datasets, that is the bibliographic input for the reference database. You can either write the datasets from scratch, or use one of the supplied input filters to convert electronic data to one of the input formats.

RIS datasets

RIS is a kind of bibliography interchange format that is understood by most Windows-based reference tools. It is a simple tagged file format: each piece of data is preceded by a tag that explains what it is. Each RIS file can hold several references. The character encoding is assumed to be UTF-8 (which is a superset of ASCII), but you can specify a different encoding when importing the references into a database. RIS files are plain text, so you can use just about any text editor to author them. RefDB also provides a ris mode for (X)Emacs which makes editing these datasets a little more convenient.

AU  - Miller,A.
AU  - Myers,B.
BT  - My first book about dinosaurs
SN  - 1-56592-580-7
PB  - O'Reilly
CY  - Sebastopol
PY  - 1999
T3  - My first book series
A3  - Smith,K.
N1  - In my opinion this is not bad, after all
N2  - Dinosaurs were big animals that ate a lot
KW  - dinosaurs
KW  - evolution
KW  - animals
UR  -
ER  - 

risx datasets

risx, the alternative reference data input format, is sort of an XML representation of the RIS format, however with a few useful additions. The <libinfo> element allows to store the personal information like notes, availability, and reprint status for each user individually, something that RIS is not capable of. As the file format is XML according to a provided DTD, you can use any SGML or XML editor to conveniently write and modify these datasets.

<?xml version="1.0" encoding="UTF-8" ?>
<!DOCTYPE ris PUBLIC "-//Markus Hoenicka//DTD Ris V1.0.2//EN"
<entry type="BOOK" id="31" citekey="MILLER1999">
<title>My first book about dinosaurs</title>
<pubdate type="primary">
<title>My first book series</title>
<libinfo user="markus">
<notes>Not bad, after all</notes>
<reprint status="ONREQUEST">
<availability type="useroot">palaeontology/dinosaurs/millera2002.pdf</availability>
<abstract>Dinosaurs were big animals that ate a lot</abstract>

getref output

getref is the client command which retrieves reference data from your database. There are various output formats to choose from. The two most common formats are the plain-text screen output shown below, and the (X)HTML output to view the results in a web browser. The latter is fully customizable by CSS stylesheets.

refdbc: getref -s ALL :ID:=3 OR :ID:=5
ID*:3 (1994)
Key: Phadke1994
Phadke,Arun G.
Application of global positioning systems to electrical systems synchronized pha
sor measurements techniques and uses
Colloquium on Developments in the Use of Global Positioning Systems (GPS) in Pow
er Systems,Feb 8 1994; part of: IEE Colloquium (Digest)
ABSTRACT: GPS navigational satellites provide an ideal method for distributing a
 common timing pulse at any point in the power network. Receivers of GPS transmi
ssion can reproduce the 1 pulse-per-second at any location on earth with better 
than 1 μsec accuracy.  [...]
ADDRESS: Virginia Tech, Blacksburg, VA, USA
ISSN: 0963-3308
PUBLISHER: IEE,Stevenage,Engl
CITY: London,USA

ID*:5 (2002)
Key: Wang2002
Wang,J.P., Chang,L.C., Raung,S.L., Hsu,M.F., Huang,L.J., Kuo,S.C.
Inhibition of superoxide anion generation by YC-1 in rat neutrophils through cyc
lic GMP-dependent and -independent mechanisms
Biochem.Pharmacol. 63(4):577-85
ABSTRACT: 3-(5'-Hydroxymethyl-2'-furyl)-1-benzyl indazole (YC-1), a soluble guan
ylyl cyclase (sGC) activator, inhibited formyl-methionyl-leucyl-phenylalanine (f
MLP)-induced superoxide anion (O(2)*(-)) generation and O(2) consumption in rat 
neutrophils (IC(50) values of 12.7+/-3.1 and 17.7+/-6.9 microM, respectively). [...]
ADDRESS: Department of Education and Research, Taichung Veterans General Hospita
l, 160 Chung Kang Road, Sec. 3, 407, ROC, Taichung, Taiwan.

XML source document

RefDB supports DocBook SGML and XML as well as TEI XML documents out of the box. TeX/LaTeX support is available too. In order to get a bibliography for your document, all you need to do is to enter the citations into the text. This is done within the limits of the original DTDs, so the documents that you write will validate against the unaltered DTDs. When the document is processed with the RefDB tools, a list of cited references is extracted from your document. RefDB will then look up these references in the database and create a suitable bibliography file. This file can be inserted as an external entity or via xinclude into your document.

<?xml version="1.0"?>
<!DOCTYPE book PUBLIC "-//OASIS//DTD DocBook XML V4.1.2//EN"
                    "/usr/local/share/xml/docbook/4.1.2/docbookx.dtd" [
<!ENTITY bibliography SYSTEM "refdbtest.bib.xml">
  <title>RefDB bibliography test document</title>
    <title>Some example citations</title>
    <para>This is a citation <citation role="REFDB">Nakane2002</citation>.</para>
    <para>This is a multiple citation <citation role="REFDB"
    <para>This is a book <citation role="REFDB">Miller1999</citation>
    and this is a book chapter <citation role="REFDB">Walsh1999</citation>.</para>
    <para><citation role="REFDB">A:Nakane2002</citation>
    reported recently <citation role="REFDB">Y:Nakane2002</citation>,
    that textual citations also work.</para>

Generated output

RefDB provides custom driver files for the stock DocBook (DSSSL and XSL) and TEI (XSL) stylesheets. These driver files provide the extended formatting capabilities for citations and bibliographies and allow to create output suitable for submission to scientific journals and publishers. Depending on the input file format, the output formats are HTML, XHTML, PDF, Postscript, and RTF. If you use the refdbnd tool, all you need to do to create the bibliography and transform your document is to type something like "make pdf".

The following PDF documents were created using data and documents similar to the ones shown above. Each source document was transformed using two different citation and bibliography styles. Please compare the citations in the text as well as the bibliographic listings at the end of each document.