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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.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats: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<jats:italic>noSQL<\/jats:italic>database) as a flexible data store and PowerLoom<jats:sup>\u00ae<\/jats:sup>(a mature First Order Logic reasoning system) to execute queries using spatial reasoning over the BAMS neuroanatomical ontology.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats: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).<\/jats:p><\/jats:sec>","DOI":"10.1186\/1471-2105-12-351","type":"journal-article","created":{"date-parts":[[2011,8,23]],"date-time":"2011-08-23T06:39:31Z","timestamp":1314081571000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":28,"title":["Knowledge engineering tools for reasoning with scientific observations and interpretations: a neural connectivity use case"],"prefix":"10.1186","volume":"12","author":[{"given":"Thomas A","family":"Russ","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cartic","family":"Ramakrishnan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eduard H","family":"Hovy","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mihail","family":"Bota","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gully APC","family":"Burns","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2011,8,22]]},"reference":[{"key":"4769_CR1","volume-title":"Workshop on Semantic Web Applications in Scientific Discourse (SWASD 2009)","author":"B Mons","year":"2009","unstructured":"Mons B, Velterop J: Nano-publication in the e-science era. 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