The Biomedical Knowledge Engineering Group (BMKEG)

BMKEG is an academically-funded, applied computer science research group. We take cutting-edge computer science (CS) research in the field of artificial intelligence and apply it to biomedicine across multiple fields based on requirements of end-users. Our focus is on the development of practical tools that may be used by knowledge workers in their everyday work. We work in collaboration with specialized CS researchers to find innovative ways of applying their work within practical software tools.

View on GitHub BMKEG

The Biomedical Knowledge Engineering Research Group (BMKEG) is part of the Intelligent Systems Division at the University of Southern California's Information Sciences Institute


The BioScholar System

Working with the BioMedical literature is something that every scientist must grapple with and there exist relatively few practical tools that enable and support the construction of knowledge bases from published papers. BioScholar is designed to be a practical framework that a graduate student could use to track information in the literature to help build a database of known facts for their subject. The system is the first instantiation of a system using the 'KEfED' model.

[Lab Notes] [All Source] [Webapp Source] [Academia]

The SciKnowMine System

Even though text mining research is an active field in biomedicine ('BioNLP'), there are relatively few practical systems available for bioinformatics developers and biocurators that are easy to install and use. This initial implementation extends our basic digital library application to provide a `triage' function (identifying documents of interest to a specific database) using supervised machine learning techniques.

As an open source project that provides a set of basic, yet extensible functionality (document management, accurate PDF text-extraction, annotation, triage, document clustering etc.) that is intended support CS text mining techniques in other groups removing the need to reimplement these basic capabilities.

[Technical Documentation] [All Source] [Webapp Source] [Academia]

The Layout Aware PDF Text Extraction System

A low-level java library for accurately extracting text from PDF files and additional web-based tools to improve performance of the text extraction.

[Technical Documentation] [All Source] [App Source] [Academia]

Knowledge Engineering from Experimental Design

A general-purpose, ontology-aware knowledge engineering methodology for biomedical data that permits the construction of biomedical databases derived only from a description of the underlying experimental protocol used to gather the data.

[Academia] [All Source] [Previous Version]

The View Primitive Data Model framework

A system scaffolding set of java-libraries that permit the agile development of web-applications. This is the foundation for all of our software tools and permits us to develop specialized database applications for scientists rapidly and efficiently.

[Project Page] [Source Code]