References Bibliographic Tools (RBT) v0.4

Volker Kiefel*

August 20, 2007

Contents

Introduction

The scripts of the RBT package have been tested on Linux and win32. For installation, copy the perl (.pl) scripts into a directory included in the string assigned to the PATH environment variable. The RBT-scripts require that a perl installation is installed on your system.

1  Extract citations from a LaTeX document – excite.pl

Writers insert bibliographic citations into LaTeX documents with \cite{} commands. Excite.pl processes the following formats of \cite{}:


   \cite{refno1}
   \cite[page 1-12]{refno1}
   \cite{refno1,refno2,refno3}
   \cite[page 1-12]{refno1,refno2,refno3}

Instructions for usage are shown if you call excite.pl with the `-h' option:


   Bibliographic tools v0.4
      excite.pl - extract citations from a LaTeX document

   Usage:
      excite.pl [-r|-a] -f input-file -o output-file

      -f input-file name
      -o output-file name
      -r replace existing output-file
      -a append to existing output-file
      -h this help

   Copyright (C) 2007 Volker Kiefel

An example (win32):


   perl -S excite.pl -r -f groot.tex -o out.txt

On Linux systems:


   excite.pl -r -f groot.tex -o out.txt

Excite extracts citations from the file `groot.tex' and writes them into `out.txt'. If `out.txt' already exists, the script overwrites the previous version of this file. If you wish to append citations from another TeX file to `out.txt', insert the `-a' option instead of `r'.

2  Convert bibliographic records from MEDLINE to BibTEX– medl2bib.pl

Medl2bib.pl converts bibliographc recods in MEDLINE format into a BibTeX (.bib) file of `article' type. Instructions for usage:


  Bibliographic tools v0.4
      medl2bib.pl - convert references from MEDLINE format to BibTeX (.bib)
   
   Usage:
      excite.pl [-r|-a] -f input-file -o output-file
   
      -f input-file name
      -o output-file name
      -r replace existing output-file
      -a append to existing output-file
      -h this help
   
   Copyright (C) 2007 Volker Kiefel

An example of a record in medline format obtained from PubMed (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed):


   PMID- 15943711
   OWN - NLM
   STAT- MEDLINE
   DA  - 20050609
   DCOM- 20050901
   PUBM- Print
   IS  - 0958-7578 (Print)
   VI  - 15
   IP  - 3
   DP  - 2005 Jun
   TI  - Anti-HPA-1a in a case of post-transfusion purpura: binding to
         antigen-negative platelets detected by adsorption/elution.
   PG  - 243-7
   AB  - Post-transfusion purpura (PTP) is a rare transfusion reaction almost
         exclusively observed in female patients. Affected patients develop severe
         immune-mediated thrombocytopenia in the course of a strong anamnestic
         alloimmune reaction against a platelet-specific antigen. The
         pathophysiology of thrombocytopenia has remained elusive. Immunological
         analysis in the HPA-1a-alloimmunized patient described in this report
         revealed an antibody with features considered typical of PTP: not only was
         anti-HPA-1a detectable in plasma, but it could also be eluted from the
         patients' (alloantigen negative) platelets, and anti-HPA-1a could be
         detected in eluates from both antigen positive and negative test
         platelets, which had been incubated in the patient's serum. This is in
         contrast to two sera with HPA-1a alloantibodies obtained from mothers of
         children with neonatal alloimmmune thrombocytopenia which were strictly
         HPA-1a specific. It is proposed that alloantibodies with HPA-1a-like
         specificity explain the patient's immune thrombocytopenia. The technique
         described in this report is proposed for further investigation, as it
         might be useful for discrimination of alloantibodes in PTP and
         alloantibodies of transfused thrombocytopenic patients.
   AD  - Department of Transfusion Medicine, University of Rostock, Germany.
         volker.kiefel@med.uni-rostock.de
   FAU - Kiefel, V
   AU  - Kiefel V
   FAU - Schonberner-Richter, I
   AU  - Schonberner-Richter I
   FAU - Schilf, K
   AU  - Schilf K
   LA  - eng
   PT  - Case Reports
   PT  - Journal Article
   PL  - England
   TA  - Transfus Med
   JT  - Transfusion medicine (Oxford, England)
   JID - 9301182
   RN  - 0 (Antigens, Human Platelet)
   RN  - 0 (Isoantibodies)
   RN  - 0 (Isoantigens)
   RN  - 0 (platelet specific antigen PL(A))
   SB  - IM
   MH  - Aged
   MH  - Antigens, Human Platelet/*immunology
   MH  - Female
   MH  - Humans
   MH  - Isoantibodies/immunology
   MH  - Isoantigens/immunology
   MH  - *Platelet Transfusion
   MH  - Purpura, Thrombocytopenic, Idiopathic/etiology/*immunology
   EDAT- 2005/06/10 09:00
   MHDA- 2005/09/02 09:00
   AID - TME578 [pii]
   AID - 10.1111/j.1365-3148.2005.00578.x [doi]
   PST - ppublish
   SO  - Transfus Med 2005 Jun;15(3):243-7.

It is converted to BibTeX file out.bib with the command (win32):


   perl -S medl2bib.pl -f pubmed-result.txt -o out.bib -r

On Linux, please call:


   medl2bib.pl -f pubmed-result.txt -o out.bib -r

which results in:


   @article{15943711,
     author = {Kiefel, V. and Schonberner-Richter, I. and Schilf, K.},
     title = {{Anti-HPA-1a in a case of post-transfusion purpura: binding to
     antigen-negative platelets detected by adsorption/elution.}},
     journal = {Transfus Med},
     year = {2005},
     month = jun,
     volume = {15},
     number = {3},
     pages = {243--247},
     abstract = {Post-transfusion purpura (PTP) is a rare transfusion reaction almost
     exclusively observed in female patients. Affected patients develop severe
     immune-mediated thrombocytopenia in the course of a strong anamnestic
     alloimmune reaction against a platelet-specific antigen. The
     pathophysiology of thrombocytopenia has remained elusive. Immunological
     analysis in the HPA-1a-alloimmunized patient described in this report
     revealed an antibody with features considered typical of PTP: not only was
     anti-HPA-1a detectable in plasma, but it could also be eluted from the
     patients' (alloantigen negative) platelets, and anti-HPA-1a could be
     detected in eluates from both antigen positive and negative test
     platelets, which had been incubated in the patient's serum. This is in
     contrast to two sera with HPA-1a alloantibodies obtained from mothers of
     children with neonatal alloimmmune thrombocytopenia which were strictly
     HPA-1a specific. It is proposed that alloantibodies with HPA-1a-like
     specificity explain the patient's immune thrombocytopenia. The technique
     described in this report is proposed for further investigation, as it
     might be useful for discrimination of alloantibodes in PTP and
     alloantibodies of transfused thrombocytopenic patients.}
   }


Tag in MEDLINEBibTEX fieldr, o
PMID[identifier]r
AUauthorr
TItitler
TAjournalr
DPyearr
VIvolumeo
IPnumbero
PGpageso
DPmontho
ABabstracto
Table 1: Medl2bib.pl: MEDLINE tags and BibTEX fields, r: required, o: optional. The abstract field is ignored by most BibTEX styles

Requirements for the input file:

Usually medl2bib.pl should generate syntactically correct BibTEX records, it will sometimes be necessary to expand the abbreviated form of the journal names.


*
kiev AT users DOT sourceforge DOT net

This document was translated from LATEX by HEVEA.