Knowledge engineering tools for reasoning with scientific observations and interpretations: a neural connectivity use case.

Thomas A Russ,Mihail Bota,Eduard H Hovy,Cartic Ramakrishnan,Gully Apc Burns

doi:10.1186/1471-2105-12-351

Abstract

BackgroundWe 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.ResultsThe 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.ConclusionsWe 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).

Highlights

We address the goal of curating observations from published experiments in a generalizable form; reasoning over these observations to generate interpretations and querying this interpreted knowledge to supply the supporting evidence
If the user chooses to edit a model, they are taken to the main Knowledge Engineering from Experimental Design’ (KEfED) model editor panel, where they may draw a model on a graphical palette
This study describes a detailed analysis of the connectional topology of neural systems associated with spatial navigation in the rat based on manually-curated connectivity data from the primary neuroanatomical research literature as part of [8]. This information was contributed to the Brain Architecture Management System (BAMS) repository and subsequently augmented with a small number of subsequently published studies

Summary

Introduction

The term nanopublication refers to a citable unit of published knowledge that refers to a scientific assertion with accompanying provenance metadata that permits a reader to understand where the assertion was made (author, source, format, etc.) [1,2] An example of such an assertion ‘Hippocampo-hypothalamic connections: origin in subicular cortex, not ammon’s horn’ was unusually made in a paper’s title in [3], describing the localized origin of neuroanatomical projections from the study). We describe a formulation called ‘Knowledge-Engineering from Experimental Design’

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Conclusion