
\section{Scientific publications and bibliographic software}
\label{sec:SciPubBibSoftware}

\subsection{General conventions, terminology}
\label{sec:GeneralReferencesMS}

\index{scientific publishing!general terms}
\index{scientific publishing!bibliographic software}
\index{scientific publishing!personal bibliographic management software}

This section explains basic \emph{terms related to scientific publishing} 
often used in the context of
\emph{personal bibliographic management software}%
  \cite{i06177,m00513,NatbibPackage,HarvardPackage,i06135,i03285}. 
These terms will also be used in the following
chapters of this manual.
  \index{citation}% 
  \index{in-text citations}%
  \index{author-date citations}%
  \index{numeric citations}%
  \index{References!part of scientific manuscript}%
  \index{list of references}%

The text body of scientific manuscripts will contain \textbf{citations} or 
\textbf{in-text citations} % referring to references  
either in \textbf{author-date} format (as an example: \dots
Ebel and Bliefert, 1998; Grossmann, 1993\dots)
or as \textbf{numerical citations} (for example: \dots 
\cite{i06135,i06177}\dots). 
The text is usually
followed by a detailed \textbf{list of references} 
(\textbf{Literature Cited}, or \textbf{Works Cited}) with full bibliographic
information of quoted work. 
References lists usually must contain all sources cited in the
text. In books containing chapters from different (groups of) authors, lists
of references oftem follow the chapters to which they apply. 
Lists of references may
be \emph{sorted alphabetically} (according to
authors' or editors' names) or references have
the same \emph{order} as they \emph{appear in the text}.


\index{bibliographic databases}
\index{bibliographic software}
\index{bibliographic record}
\index{knowledge management}
\index{keywords}
\index{thesaurus}
Computer programs used to manage \textbf{bibliographic databases} are often
referred to as \textbf{bibliographic software},
\textbf{personal bibliographic management software},
\textbf{citation management software},
or \textbf{reference management software}
  \cite{WikipediaDefBibliographicSoftware}. 
A \textbf{bibliographic record}
within a bibliographic database is the set of data describing a single
published work. Using bibliographic software will often become an essential
part of your knowledge management. Work significant to your interests
has to be collected, e.\,g, by filing copies from articles, obtaining books
and creating ``bookmarks'' to electronic documents. Retrieval of 
bibliographic records is made easier by \textbf{reference numbers} 
assigned to records in
a bibliographic database which may be used at ``pointers'' to the location of a
filed copy in your working environment. In order to make work pertinent to a
certain problem accessible in the future, 
you should enter \textbf{keywords} as part of
bibliographic records. Standardized collections of keywords within a field of
interest are often called \textbf{thesauri}\footnote{\emph{pl.} of thesaurus}.
You will search in bibliographic databases with \textbf{queries}: keywords, text
fragments or (author) names to be searched for in the appropriate \textbf{fields} 
(keywords, title, authors' or editors' fields) in the database.
\index{field}
\index{database field}



\index{document type}
\index{article in a journal}
\index{chapter or article in a book}
\index{complete book}
In the process of writing a manuscript you will enter in-text citations in a
raw format (e.\,g. by entering reference numbers using a certain convention). 
If you have finished writing, you will (1) extract all reference numbers cited,
(2) generate a list of references which will be appended to the text body
and (3) convert the ``raw'' in-text
citation into their final format. Automatic execution of these processes is
a typical tasks for bibliographic
software. Work cited in a scientific manuscript can usually be classified in
into at least three main \textbf{document types}:
 \emph{article in a journal},
 \emph{chapter or article in a book},
 \emph{complete book}. 
As \emph{electronic documents}, e.\,g. those distributed via the internet are
becoming more and more important, publishing conventions for citing such
material are required \cite{NLMInternetFormats}.



\subsection{Features of the \texttt{References} implementation}
\label{sec:SpecialReferencesMS}

\index{scientific publishing!features implemented by References}
\index{scientific publishing!bibliographic software}

As \texttt{References} has been planned with publishing conventions in
medicine and natural sciences in
mind, certain decisions have been made for the initial implementation of
this software. As this implies (lack of) certain features, the short
description provided here may help your decision, if \texttt{References} can
be useful for your work.

\index{authors!first names}
\index{editors!first names}
\index{editors!institutional}
\index{authors!institutional}
\index{editors!personal}
\index{authors!personal}
%%
\textbf{Authors'/editors' names:} In the current version of 
\texttt{References} only initials of
\emph{first names} can be processed\footnote{If support of full forenames will
  be added to future versions depends upon requirements of users}. 
A list of authors/editors may
comprise up to 999 items\footnote{This will probably almost never be used in
real life situations}. Use of \emph{institutional authors/editors}%
 \footnote{also called corporate authors: group of authors
 with authorship responsibility} 
(as opposed to \emph{personal authors or editors}) is supported in distinct
document types (table \ref{tab:DocumentTypesAuEd}, 
page \pageref{tab:DocumentTypesAuEd}).

\textbf{Journal names:} Journal names are stored in a separate table
(file). The journal data records including journal names, one field for an
abbreviated form are linked to bibliographic records by
a key (``journal code''). 

\textbf{Keywords thesaurus:} Each bibliographic database includes one
thesaurus (which is only accessible from its ``own'' database). 
During entering or
editing bibliographic records, the user may enter keywords by their numeric
code in the database.

\textbf{Text field:} All bibliographic records may contain a text field which
can be used for notes, comments or abstracts (field width of approximately
30\,000 characters).

\textbf{Document types:} Document types supported by the current version of
\texttt{References} are listed in table \ref{tab:DocumentTypes} (page
\pageref{tab:DocumentTypes}). \texttt{References} addresses these document
types with codes as 
\texttt{j1} (article in a journal with personal authors), 
\texttt{j2} (article in a journal with institutional authors), 
\texttt{b1} (complete book with personal authors or editors), 
\texttt{m1} (document type for ``miscellanea'', personal authors). All
document types are listed in table \ref{tab:DocumentTypes}, page
\pageref{tab:DocumentTypes}.

\textbf{Databases:} One \texttt{References} installation may be used to run
more than one database. Databases are realized as directories 
(cf. section \ref{sec:InstallDirectTree}, page
\pageref{sec:InstallDirectTree}) 
on the same level as the \texttt{tutorial} and \texttt{data}
directories\footnote{containing the example databases} of
the standard installation (figure \ref{fig:DirectTree}, page
\pageref{fig:DirectTree}). Installation of new databases is described in
section \ref{Sec:ConfigCreateNewDatabase}, page
\pageref{Sec:ConfigCreateNewDatabase}. 

\textbf{Mode of interaction with text processors:} \texttt{References} only
reads, produces and manipulates external document files in text 
format\footnote{i.\,e.
  it does not read/create binary data, e.\,g. documents files produced by text
  processors. Data of \texttt{References} databases, however are processed in
  a binary format as described in the source code, especially \texttt{refs.h}.
  The internal structures of \texttt{References} databases can be ignored by
  the normal user}.  Lists of references may be generated as pure text files,
in html or \LaTeX-format. Html-files (or \LaTeX-files) 
have to be used if different fonts are required in a list
of references. \texttt{References} can be used to generate macros 
for text processors like OpenOffice.org Writer or Microsoft Word 
\index{OpenOffice.org Writer} which
convert raw citations in a manuscript into formatted \emph{in-text citations}.
Thus References does not depend upon changes of the internal document format
of these text processors.

\textbf{Formatted lists of references:} \texttt{References} has a powerful
function, which allows the user to write his own bibliographic format
definitions to generate lists of references in any format\footnote{More import
or export options can be implemented upon request of users, if sufficient
information on the format is available}.

\index{online resources!import into References}
\index{PubMed MEDLINE display format}
\index{MEDLINE format}
\textbf{Export, import of data (from online resources):}
Import of data in the PubMed MEDLINE display format 
% as issued by the PubMed database 
\cite{PubMedWebsite} has been implemented. For export of bibliographic data 
into other formats the user may create his own bibliographic format
definitions. A bibliographic database may be exported into text format
  \index{archive-files}
  \index{arr-file}
(archive files, arr-files) so that
data can be transferred into a later \texttt{References} version or a
\texttt{References} version compiled for another platform.

\textbf{Support:} New versions of the software, supplementary data and general
information related to bibliographic computing may be found on the
\texttt{References} project homepage \cite{ReferencesWebsite}. The program
author can be reached by email (\texttt{kiev AT users DOT sourceforge DOT
net}).

%% Informationen zu Feld-Tags bei Medline
%% http://www.ncbi.nlm.nih.gov/entrez/query/static/help/pmhelp.html#SearchFieldDescriptionsandTags

\clearpage

\section{What can References do for me?}

\label{secWhatCanRefsDoForMe}

This short section describes essential features of \texttt{References} and it
refers to sections where you can find pertinent information.

\subsection{Installation and configuration of \texttt{References}}

You may use \texttt{References} on Linux- or on win32-systems. Installation is
described in section  \ref{sec:Installation}, page \pageref{sec:Installation}
(win32) and section 
\ref{sec:InstallationLinux}, page \pageref{sec:InstallationLinux}
(Linux). Modifications of a \texttt{References} installation 
which require editing
of the configuration file are described in section \ref{SecConfigFile}, page
\pageref{SecConfigFile}. 
Necessary steps to create 
a new database are discussed in 
\ref{Sec:ConfigCreateNewDatabase}, page \pageref{Sec:ConfigCreateNewDatabase}. 
In its current version (4.3b or later) 
\texttt{References} requires that your Linux
installation uses utf-8, latin-1 or latin-9 encoding for text files.

\subsection{Writing scientific documents}

As you enter or import references into the database, you will assign
\textbf{reference numbers} (unique strings with which you identify records in
your database and citations in your manuscript) to these database records.
If you write a manuscript, you will have to insert these references numbers as
``raw'' in-text citations
In
the most simple situations you will write these raw in-text citations in the
following format using ``\texttt{refscite()}'':

\begin{quote}
  \dots \\
  Platelet glycoproteins with single nucleotide polymorphisms may be
  responsible for immunization if platelets are transfused into a genetically
  different individual refscite(b00366). Such polymorphic variants are
  referred to as platelet alloantigens refscite(b03622),
  refscite(z03333), refscite(z03335), refscite(z03339).\\
  \dots 
\end{quote}

Section \ref{sec:FormattedCitationsMS}, page
\pageref{sec:FormattedCitationsMS}  explains the methods by which
\texttt{References} can process manuscripts with raw in-text citations of the
\texttt{refscite()}-type.  In brief, \texttt{References} can (1) ``extract''
these references numbers, it can (2) create the list of references to be
included into the manuscript (in general, this will be inserted at the end of
the manuscript) and (3) is able to generate macros for the text processor
which converts raw \emph{in-text citations} in the text into \emph{formatted
citations}. 

\subsubsection{Generate a list of references}

Section \ref{SecListReferences}, page \pageref{SecListReferences} describes
how a list of references is generated. Therefore, you will have to provide a
list of reference numbers of those references which are to be included in this
list.  These lists are called \textbf{batch files} and they are described in
\ref{SecBatchFiles}, page \pageref{SecBatchFiles}. You may wish to create your
own style in which a list of references is formatted. These styles are termed
\textbf{bibliographic format definitions}.  You can get some bibliographic
format definitions from the \texttt{References} web site, and some format are
included in the standard \texttt{References} installation. Administration of
bibliographic format definitions is described in section \ref{secBibFD}, page
\pageref{secBibFD}. If you wish to write your own bibliographic format
definitions, please follow the step by step description in the tutorial
(section \ref{secTutorialBFD}, page \pageref{secTutorialBFD}).


\subsubsection{Generate formatted citations in the text}

The text fragment described above is probably intended to appear as

\begin{quote}
  \dots \\
  Platelet glycoproteins with single nucleotide polymorphisms may be
  responsible for immunization if platelets are transfused into a genetically
  different individual [1]. Such polymorphic variants are
  referred to as platelet alloantigens [2-4,7].\\
  \dots 
\end{quote}

or

\begin{quote}
  \dots \\
  Platelet glycoproteins with single nucleotide polymorphisms may be
  responsible for immunization if platelets are transfused into a genetically
  different individual (Meyer, 2001). Such polymorphic variants are
  referred to as platelet alloantigens (Karl et al., 1999, Mueller et al.,
  2000, Clausen et al., 2002, Thomas, 2006).\\
  \dots 
\end{quote}



What you have to do if you wish to create such formatted 
citations is descibed in section \ref{sec:PrinciplesFormattedCitations},
page \pageref{sec:PrinciplesFormattedCitations}. Either
OpenOffice.org/StarOffice writer (section \ref{sec:OOOMacros}, 
page \pageref{sec:OOOMacros}), MS Word (section \ref{sec:MSWordMacros}, page
\pageref{sec:MSWordMacros}) or \LaTeX{} (section \ref{sec:LaTeXWithRefscite},
page \pageref{sec:LaTeXWithRefscite}) are supported.


\subsection{Retrieve records in a \texttt{References} database}

You may wish to search your \texttt{References} database for 
records meeting certain
criteria, e.\,g. those from a certain author, with certain keywords, published
in a (range of) year(s). Principles of such queries are described in section
\ref{SecSearch}, (page \pageref{SecSearch}), a reference of search command
terms (the ``search command syntax'') is given in section
\ref{SecSearchCommand} (page \pageref{SecSearchCommand}).

\subsection{Enter records into a \texttt{References} database}

You can enter records manually: therefore you have to create an empty ``form''
(a text file), edit it with your text editor, save the form and transfer the
record from this form into the \texttt{References} database:
section \ref{SecEnterReferences} (page \pageref{SecEnterReferences}).

Before entering a record you will have to decide which \texttt{References}
document format (e.\,g. chapter in a book, 
journal article, complete book electronic document) 
fits best. Document types processed by \texttt{References} are discussed 
in section \ref{secDocumentTypes}, page \pageref{secDocumentTypes}.

The procedure to
edit an existing database record (reference) is outlined in section
\ref{secEditExistingReferences} (page \pageref{secEditExistingReferences}).
An automated conversion of records from the medline format 
of the \emph{journal article} type is described in section
\ref{sec:ImportFromMedline} (page \pageref{sec:ImportFromMedline}).

If you use the \textbf{PubMed} website/database, \texttt{References} offers
utilities to import records into your databases. Details are described in
section~\ref{sec:ImportFromMedline}, page~\pageref{sec:ImportFromMedline}.

\subsection{Support \LaTeX-users}

\texttt{References} supports writing of manuscripts with \LaTeX{} in many
aspects. 
All \texttt{References} databases or subsets of records from databases can
directly be exported into \texttt{.bib} files for Bib\TeX. You may, however,
create your own lists in a \texttt{thebibliography}-environment using 
\verb+\cite{}+ for citation of references in the manuscript and you may
generate lists of references and citations in \LaTeX-documents without usion
Bib\TeX{} and \verb+\cite{}+-commands.
\LaTeX-relatex items are 
described in section \ref{LaTeXRefsGeneralDescription} 
(page \pageref{LaTeXRefsGeneralDescription}).

\clearpage

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