Source Code of Bibtex Graph Generator

Now I would like to release the source code of the software described in an earlier post. The package will be released under the GNU General Public License, any release of other software which includes the full source code or parts of it must also be released under the GPL.

The software is running with python 2.7.9 (Python 3 is not supported) and requires PyGraphViz 1.3rc2 and BibtexParser 0.6.2.

The program includes three main data structures: the list of all publications from the Bibtex file, a list of authors, and a list of relations. The latter two are implemented as python classes. As first step, the full bibtexfile is parsed into an array of dictionaries with the package BibtexParser. Second, the author list is created by iterating over all publications and authors in the bibtex database. Third, the relationsship array is created with entries for all combinations of two authors A and B by iterating over the publications list and checking if both A and B are author of a specific publication. The the graph is constructed by adding nodes for each author and edges for all relations. As a last step, the graph is compacted by constraints given as arguments. Two short examples follow to describe such kind of constraints. The parsed bibtexfile is included in the published package.

Starting it without any argument will show the license info and the help.

A Graph Display Software for bibtex databases
 
 Copyright (C) 2015 Benjamin Laemmle, jdmorise a t yahoo.com
 This program is free software: you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by
 the Free Software Foundation, either version 3 of the License, or
 (at your option) any later version.
 This program is distributed in the hope that it will be useful,
 but WITHOUT ANY WARRANTY; without even the implied warranty of
 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
 GNU General Public License for more details.
 You should have received a copy of the GNU General Public License 
along with this program. If not, see <http://www.gnu.org/licenses/>. 

usage: "Examples:

optional arguments:
 -h, --help show this help message and exit
-if INPUT_FILENAME, --input_filename INPUT_FILENAME 
          Filename of publication database in bibtex format
-gf GRAPH_FILENAME, --graph_filename GRAPH_FILENAME    
          Filename of graph output stored as png
-ma MAIN_AUTHOR_NAME, --main_author_name MAIN_AUTHOR_NAME
-ert EDGE_RELATION_THRES, --edge_relation_thres EDGE_RELATION_THRES
          Only add edges with ERT or more number of relations
-art AUTHOR_RELATION_THRES, --author_relation_thres AUTHOR_RELATION_THRES
          Only add authors with ART or more number of relations
-apt AUTHOR_PUBLICATION_THRES, --author_publication_thres AUTHOR_PUBLICATION_THRES
          Only add authors with APT number of publications
-lvl LEVEL, --level LEVEL
-b BEFORE, --before BEFORE     
          Only use Publications before YEAR for the graph
-a AFTER, --after AFTER
          Only use Publications after YEAR for the graph
-gp GRAPH_PROGRAMM, --graph_programm GRAPH_PROGRAMM
          Graph Programm for rendering the graph. one of the
          following: fdp,dot,sfdp,circo,twopi.

 

 

The first example was created without any filter, just specifying the input database and the output picture:

python graph_coaut_bibtex.py -if Darabi.bib -gf graph_plain.png

graph_plain

Now, in the second example the filters are explained in more detail. First, we would like to see only direct relations between an author and anybody else, so only direct collaboration. This is achieved by specifying the “main author” (-ma “A. Mirzaei” )  and the collaboration “level” (-lvl 1). Then, we would like to remove all authors with less than three publications (e.g. P. Suri) by adding an “author publication threshold” (-apt 3). To make it more readable, we also remove all edges with less than three relations by specyfing an “edge relation threshold” (-ert 3), which removes a couple of authors like K. Juan.

python graph_coaut_bibtex.py -if Darabi.bib -gf graph_red.png 
-ma "A. Mirzaei" -lvl 1 -apt 3 -ert 3

The reduced graph is shown below with only a limited amount of authors remaining.

graph_red

Additional arguments include an “author relation threshold”(-art) to remove all authors with only few relations, and you can filter by publication date by specifying a certain range. As a last argument, the graph generation programm can be selected (-gp) where fdp is chosen as default. The GraphViz documentation will give more details about the examples.

The python code can be found together with the example bibtexfile and the license file in my DropBox. Have fun!

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Graph Display Software for Author Relationships with Bibtex Files

Now, I just introduced last week the idea of looking at author relationsships by a graph with a short example. In this post I want to further explain my approach to create such kind of figures. The first requirement is a valid base of data in forms of bibliographic information.

As a bibliography file in form a bibtex database was readily available, the first version of my graph display software is working with bibtex files as source. In a later post, it will be shown how databases can be easily created by automatic parsing of google scholar or other sources.

The created python software reads the bibtexfile, creates a list of authors and a list of relationsships. From these two lists, it creates a graph with nodes and edges and invokes the graphviz software to draw the graph and export it as a png file. The python lib pygraphviz is used as interface for graphviz which includes classes for creation and analysis of graphs, nodes, and edges.

An example of a graph for my bibtex database from my phd thesis is shown below. We can see many different authors and a very complex structure of relationships (along with some bugs as authornames are written differently in publications, e.g. Jager and Jaeger).

graph6

We see most authors are in a cloud and only some authors have no connection to others at all. Now, in order to get a better visibility of the graph, the following simple filters are available:

1. Authors with number of publication under a specific thmmWave3_51reshold are filtered

2. Authors with number of relations lower than a threshold are removed

3. Edges with lower weight than a threshold are removed.

These filters are very powerful to reduce complexity of the figure. In order to find main contributors to an area, authors with small amount of publications can be removed, which are mostly PhD students with only a short time in research.

Additionaly, a specific author can be marked as main author and only authors with specific neighbourhood level are printed. In this way, only direct neighbors, or  authors over two edges are printed.

Here I wanted to study the network around professor S. Voinigescu from University of Toronto and his direct network and removed all authors with only one publication.

What kind of filters do you want to see for the graph display software? In what kind of research about research are you interested? I’m curious about your feedback.