Deploying the BioScholar System

What do you need to do to deploy the BioScholar system to a server.

June 2016

  1. Dry Run II Papers from MITRE

July 2015

  1. Two-Hop Ras BioPax Model

May 2015


April 2015

  1. Open Access Pathway Logic Papers and Figures
  2. Extended Coprecipitation Frames v2

January 2015

  1. Coprecipitation Frames v2
  2. List of Experimental Motif Types + Definitions
  3. KEfED Database Construction

December 2014

  1. KEfED Modeling of Coprecipitation Ras Papers
  2. Initial Extraction Study of Results-Based Epistemics

October 2014

  1. Pathway Logic Experiment Types
  2. Building a Database of Observations from Result Text
  3. Deploying the BioScholar System
  4. Reading Against a Model of Experimental Evidence

August 2014

  1. Developing NL Annotations for KEfED Elements
  2. Epistemics and Fragments
  3. Generating the Big Mechanisms Evaluation Corpus
  4. A Generative Story for Scientific Text from Experimental Data

Here we just document the various pieces needed to run the BioScholar system within Tomcat on a Linux server.


You will need to place a file that you will need to refer to when you run Tomcat.


This refers to several pieces that we will elaborate on here:

1.1 workingDirectory

This is where all the *.pdf, *.xml and *.txt files go. Typically, a working directory will have the following substructure.

+ wd
  +=> pdfs
    +=> journal
      +=> year
        +=> vol
          +=> 12345.pdf
          +=> 12345.swf
          +=> 12345_pmc.xml
          +=> 12345.txt
  +=> lod
  +=> owl
  +=> elsevierKeyFile.txt

The format is as shown below:

  1. MySQL installation

Update the /etc/my.cnf configuration file with the following:

max_allowed_packet = 10485760
innodb_log_file_size = 125242880

The file must have a current login to the local MySQL system with sufficient permissions to add and delete data.

  1. VPDMf data

The BioScholar system uses the ‘View-Primitive-Data-Modeling framework’ as its basis This is a local system developed within the BMKEG (see which permits a data archive to be easily installed into the underlying MySQL database (or saved from an existing database).

VPDMf Binary jar file: data/vpdmfCore-1.1.5-SNAPSHOT-jar-with-dependencies.jar (34MB)

Installing the database is then pretty easy using this command:

java -cp vpdmfCore-1.1.5-SNAPSHOT-jar-with-dependencies.jar

Dumping a VPDMf database to a zip file is also pretty easy with this command (you need to refer to a previous vpdmf archive to build the system):

java -cp vpdmfCore-1.1.5-SNAPSHOT-jar-with-dependencies.jar

4. Running tomcat

In order to inform Tomcat where the working directory is, you need to set some environment variables.

export TOMCAT_HOME=/path/to/tomcat
export CATALINA_OPTS="-Dbmkeg.propertiesfile=/path/to/ -Xmx1096M -Xms512M"

You will then need to build the BioScholar *.war file (and place it into the $TOMCAT_HOME/webapps directory). This is 111MB in size and so is a little too big for this site.

Then all you do is TOMCAT_HOME/bin/ to start up the system.