Structured nanopublications pertaining to the drugome: A Knowledge Engineering from Experimental Design (KEfED) model

Gully Burns*, Tom Russ, Alan Ruttenberg
* Information Sciences Institute, University of Southern California, Marina del Rey, CA, USA


The ’Beyond the PDF Workshop’ (to be held January 2011) is based on a challenge: to develop software and tools that demonstrate an improvement in the utility of knowledge pertaining to a predefined body of scientific work. The corpus of work selected for this effort is centered around a grant proposal, a data set and an eventual publication (Kinnings et al. 2010, [1]) from the laboratory of Prof. Philip Bourne. This work is based on the development of a computational dataset referred to as a drugome (the drug-target interaction network for Mycobacterium tuberculosis). Within this short paper we provide a preliminary vision document for the formulation and development of an overarching knowledge engineering framework to support automated scientific reasoning over a collection of assertions in order to generate testable hypotheses that may be then tested experimentally. This framework is based on a high-level construct referred to here as the ’Cycle of Scientific Investigation’ (’CoSI’) and will be explained here only as a theoretical construct. The primary technical contribution of this work is to showcase the ’Knowledge Engineering from Experimental Design’ KEfED model as a part of the CoSI architecture. The KEfED modeling approach was originally developed as an object-oriented design with a web-based editor [2,3]. Within this study we use this tool to formulate a model of the workflow design from the final paper of the study [1]. We have also migrated the design of the KEfED formalism to the OWL semantic web standard (for compatibility and use by other attendees to the workshop).


1. Kinnings SL, Xie L, Fung KH, Jackson RM, Bourne PE (2010) The mycobacterium tuberculosis drugome and its polypharmacological implications. PLoS Comput Biol 6: e1000976.

2. Burns G, Russ T (2009) Biomedical knowledge engineering tools based on experimental design: a case study based on neuroanatomical tract-tracing experiments. In: KCAP 2009. Long Beach CA.

3. Burns G, Russ T, Ingulfsen T, Hovy E (2009) Bioscholar: A knowledge engineering system for biology and it’s application to neural connectivity data. In: 2nd Congress of the International Neuroinformatics Coordinating Facility (INCF2009). Pilsen, Czech Republic.