Scientific Knowledge Engineering @ ISI


ISI's Scientific Knowledge Engineering ('SKE') group combines ontology/knowledge engineering, artificial intelligence, the semantic web, machine reading and science informatics techniques to support the development of next-generation scientific informatics infrastructure. We leverage general research techniques across information-intensive disciplines, focussing primarily on specialized subfields of biomedical informatics, but also generalizing to other fields. The group is lead by Gully Burns, a Research Lead at the Information Sciences Institute.

The SKE group currently is pursuing automatic machine reading systems for scientific evidence, unsupervised modeling of complex research literature, modeling experimental design to better understand the structure of scientific data, automated scientifically-aware web-agents, application of information integration and semantic web to biomedical databases and pedadogical systems to support improved technical knowledge acquisition. Our work focuses on solving real-world problems to bridge research and relevant applications by building and applying tools for working scientists.

Our work has included development of:

The SciKnowEngine 'swirl' logo represents the Cycle of Scientific Investigation as a group of combined threads that resembles a breaking ocean wave. The color scheme is derived from Van Gogh's Starry Night.


Here are some videos to provide a quick explanatory introduction to our work.

2013 INCF Annual Congress

Using experimental design to design neuroinformatics data structures

Google Tech Talk

Organizing the World's Scientific Knowledge

SKM Workshop Introduction

Introducing a day-long workshop on text mining + Biocuration


Developing Triage Capabilities for Biocuration

Flipping the Light Switch

Using the Cambrian Explosion as a Metaphor for Accelerated Scientific Discovery



May 2017

  1. Don't Be a Troll, Be a Wizard!
  2. What is Scientific Knowledge Engineering?





Evidence Extraction Systems for the Molecular Interaction Literature


Knowledge Engineering from Experimental Design

Big Mechanism

Machine Reading of the Cancer Literature

Educational Resource Discovery Index

Data science knowledge engineering (PIs: JL Ambite & K. Lerman)


Building Reading Lists from Technical Corpora


A neuroanatomical atlasing system based on Larry Swanson's brain atlas.


Building systems to accelerate biocuration with text mining

NIH Maps

Topic Maps of the NIH Funding Landscape