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README.md

BioAssay Template

An editor for specifying how the BioAssay Ontology, and other related vocabularies, are to be used to describe bioassays.

Primary author: Dr. Alex M. Clark (alex@collaborativedrug.com)

Released under the Gnu Public License 2.0

Based on Java 8 using Eclipse, JavaFX and Apache Jena.

The BioAssay Ontology is included as part of the distribution. Latest content can be obtained from the GitHub repository.

This project has been described in the scientific literature: A.M. Clark, N.K. Litterman, J.E. Kranz, P. Gund, K. Gregory, B.A. Bunin. BioAssay templates for the semantic web. PeerJ Computer Science 2:e61 (2016) link

The source code contains functionality for manipulating the data model used for templates, which guide the use of the BioAssay Ontology (BAO) for annotating bioassay protocols. It also includes the BioAssay Schema Editor, which is an interactive desktop application that allows editing of template schemata, and a preliminary interface for using the current template to annotate assays.

The project is a continuation of the work begun in: "Fast and accurate semantic annotation of bioassays exploiting a hybrid of machine learning and user confirmation": Alex M. Clark; Barry A. Bunin; Nadia K. Litterman; Stephan C. Schürer; Ubbo Visser, PeerJ 524 (2014) link

A second manuscript, which describes this application, has been published in PeerJ CompSci link

Installation

To compile and run the package, download the files or synchronize with git. The deliverable can be compiled using ant (the build.xml file is provided), or it can be opened as an Eclipse project. Java 8 is required, but all other dependencies are included in the project.

To get started quickly without compiling, download two files:

Run the application by double clicking on the BioAssayTemplate.jar file within the appropriate file manager tool, or run it with the command line syntax: java -jar BioAssayTemplate.jar. As long as you have Java 8 installed, the interface should appear, with a blank schema window as the default. Use File|Open to locate and load the schema.json file.

When executing a build version with raw Java .class files, it is useful to add the command line parameter -Dlog4j.configuration=file:cfg/log4j.properties in order to prevent the logging mechanism from complaining needlessly.