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<p>Abstract</p> <p>Background</p> <p>We address the goal of curating observations from published experiments in a generalizable form; reasoning over these observations to generate interpretations and then querying this interpreted knowledge to supply the supporting evidence. We present web-application software as part of the 'BioScholar' project (R01-GM083871) that fully instantiates this process for a well-defined domain: using tract-tracing experiments to study the neural connectivity of the rat brain.</p> <p>Results</p> <p>The main contribution of this work is to provide the first instantiation of a knowledge representation for experimental observations called 'Knowledge Engineering from Experimental Design' (KEfED) based on experimental variables and their interdependencies. The software has three parts: (a) the KEfED model editor - a design editor for creating KEfED models by drawing a flow diagram of an experimental protocol; (b) the KEfED data interface - a spreadsheet-like tool that permits users to enter experimental data pertaining to a specific model; (c) a 'neural connection matrix' interface that presents neural connectivity as a table of ordinal connection strengths representing the interpretations of tract-tracing data. This tool also allows the user to view experimental evidence pertaining to a specific connection. BioScholar is built in Flex 3.5. It uses Persevere (a <it>noSQL </it>database) as a flexible data store and PowerLoom^®(a mature First Order Logic reasoning system) to execute queries using spatial reasoning over the BAMS neuroanatomical ontology.</p> <p>Conclusions</p> <p>We first introduce the KEfED approach as a general approach and describe its possible role as a way of introducing structured reasoning into models of argumentation within new models of scientific publication. We then describe the design and implementation of our example application: the BioScholar software. This is presented as a possible biocuration interface and supplementary reasoning toolkit for a larger, more specialized bioinformatics system: the Brain Architecture Management System (BAMS).</p>