title: Knowledge engineering tools for reasoning with scientific observations and interpretations: a neural connectivity use case.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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 noSQL 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.
  
  
  CONCLUSIONS
  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).
authors.affiliation: Information Sciences Institute, University of Southern California, Marina del Rey, CA, USA.
authors.forename: Thomas A
authors.initials: TA
authors.lastname: Russ
authors.forename: Cartic
authors.initials: C
authors.lastname: Ramakrishnan
authors.forename: Eduard H
authors.initials: EH
authors.lastname: Hovy
authors.forename: Mihail
authors.initials: M
authors.lastname: Bota
authors.forename: Gully A P C
authors.initials: GA
authors.lastname: Burns
mesh_terms: D000818:Animals; D001931:Brain Mapping / Q000379:methods*; D019295:Computational Biology / Q000379:methods; D006801:Humans; D020407:Internet; D051188:Knowledge Bases; D051381:Rats; D012984:Software