4.13. Set up your bibliographic database

If you don't want to use RefDB, there is nothing you have to do at this stage, so you can skip this section. However, you will have more work in the long run, as you will need to enter the bibliographic references each time by hand in pure SGML in a separate file, see Section 5.19.

If you want to use RefDB, to take advantage of all the automated processing offered to you by a bibliographic database, RefDB and the lyxtox script, there is some prelimnary work to do: before you use your bibliographic treasures in citations and the reference list, you have to import them into the RefDB database you created during installation of the RefDB package (see Section 3.11). Further, you must give the name of your database as the value of the RefDB_db variable in lyxtox and also set process_RefDB to “1”, indicating you wish bibliographic processing through RefDB.

Adding references boils down to running the addref command with proper input files. The input files have to be valid RIS files. They may contain one or more RIS datasets.

An example of a RIS file is refdb.ris. A typical bibliographic entry in the RIS format looks like:

TY  - ELEC
ID  - Walsh2002
AU  - Walsh,Norman
AU  - Muellner,Leonard
TI  - DocBook: The definitive Guide - Apendix
KW  - guide
KW  - docbook
RP  - NOT IN FILE
PB  - O'Reilly & Associates, Inc.
UR  - http://docbook.org/tdg/en/html/appa.html
N1  - Accessed 29.06.2003
PY  - 2002/06/17/Version 2.0.8
SN  - 156592-580-7
ER  -

Each line starts with a two-letter tag followed by the string “ - “ (two spaces, a dash, and another space). Each RIS dataset starts with the TY (type) tag and ends with the ER (End of Reference) tag. In between, tag sequence is arbitrary. The meaning of the tags is:

• ABST (abstract reference)

• BOOK (whole book reference)

• COMP (computer program)

• DATA (data file)

• ELEC (electronic citation)

• GEN (generic)

• JOUR (journal/periodical reference)

• IN FILE

• NOT IN FILE

• ON REQUEST MM/DD/YY

Multiple AU and KW tags are possible. For a complete list of the RIS tags and their possible values see Writing RefDB data input - here is a more elaborate example of a bibliographic entry in RIS format, taken from this document:

TY  - CHAP
T1  - Physiological studies of the natriuretic peptide family
A1  - Lewicki,J.A.
A1  - Protter,A.A.
Y1  - 1995///
N1  - Atrial Natriuretic Peptide   Cardiac synthesis and secretion of /
ANP   Regulation of ANP Gene Expression   Regulation of ANP Release /
  ANP Receptors   Biologic Actions of ANP Brain Natriuretic Peptide (BNP) /
  BNP Structure   Biosynthesis of BNP   Biological Actions of BNP C-Type /
 Natriuretic Peptide (CNP)   Biologic Actions of CNP Modulators of /
 Natriuretic Peptide Clearance   Effects of Clearance Receptor Blockers /
  Effects of Neutral Endopeptidase Inhibitors Role of the Natriuretic / 
 Peitedes in Physiology and Disease   Hypertension   Congestive Heart  /
Failure   Supraventricular Tachyarrhythmias   Acute Renal Dysfunction
KW  - natriuretic
KW  - ANF
KW  - ANP
KW  - receptors
KW  - BNP
KW  - CNP
KW  - hypertension
KW  - congestive heart failure
KW  - review
KW  - cardiac
KW  - regulation
KW  - gene expression
KW  - expression
KW  - brain
KW  - structure
KW  - biosynthesis
KW  - receptor
KW  - inhibitor
KW  - physiology
KW  - renal
KW  - study
KW  - Peptides
KW  - atrial natriuretic peptide
KW  - MODULATOR
KW  - secretion
KW  - Gene Expression Regulation
RP  - IN FILE
SP  - 1029
EP  - 1053
VL  - 2
T2  - Hypertension: Pathophysiology, Diagnosis, and Management
A2  - Laragh,J.H.
A2  - Brenner,B.M.
IS  - 61
CY  - New York
PB  - Raven Press, Ltd.
ER  -

To build your own bibliographic database, you thus need all your references in the RIS format. If you found your reference in the web edition of some scientific journal, or one of the specialized bibliographic databases on the Internet, like PubMed, chances are that you will be able to copy the RIS version of the bibliographic entry with a mouse click on some link. Otherwise, you will either have to import it with the use of one of the input filters shipped with RefDB, use the Web interface (which you installed in Section 3.11), or write all those tags and their values by hand.

For automatic import, RefDB offers the following input filters:

• dos2unix: A simple shell script to convert text files like RIS documents from DOS-style line endings to Unix-style line endings. Most refdb tools need their input files with Unix-style line endings. This is a valuable tool to import reference databases from Windows reference managers.

• med2ris.pl: A tool to convert Pubmed data in both the tagged and the XML format to RIS.

• bib2ris: A tool to convert BibTeX data to RIS.

• db2ris: A tool to convert reference data in DocBook SGML/XML documents to RIS.

• marc2ris.pl: A tool to convert references in MARC format to RIS.

To import all references from a RIS file called, say, refdb.ris, start refdbc and then type:

addref refdb.ris

Once you have populated your own bibliographic database with entries, you should export it to a file - it will serve you as a backup and reference. To export all entries in a file called refdb.ris (this will overwrite any existing refdb.ris file, so take care):

getref -t ris -o refdb.ris -s "ALL" :ID:>0

Open the refdb.ris file with a text editor and examine it. Pay special attention to the values of the ID field - we will use this field in a somewhat tricky way to refer to the bibliographic entries from LyX. How this is done, is explained in Section 5.19.