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Related Experiment Video

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Statistical Modelling of Cortical Connectivity Using Non-invasive Electroencephalograms

Statistical Modelling of Cortical Connectivity Using Non-invasive Electroencephalograms

Published on: November 1, 2019

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

Thomas A Russ¹, Cartic Ramakrishnan, Eduard H Hovy

¹Information Sciences Institute, University of Southern California, Marina del Rey, CA, USA.

BMC Bioinformatics

|August 24, 2011

Summary

This study introduces Knowledge Engineering from Experimental Design (KEfED) for curating and reasoning over experimental data. BioScholar software enables structured interpretation of neural connectivity from tract-tracing experiments.

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Area of Science:

Neuroscience
Bioinformatics
Computational Biology

Background:

Curating experimental observations for generalizable reasoning.
Developing methods to interpret and query experimental data for supporting evidence.
Focusing on rat brain neural connectivity using tract-tracing experiments.

Purpose of the Study:

To present the first instantiation of a knowledge representation for experimental observations called Knowledge Engineering from Experimental Design (KEfED).
To introduce web-application software, BioScholar, for curating, interpreting, and querying experimental data.
To apply these tools to the domain of rat brain neural connectivity.

Main Methods:

Developed the KEfED model editor for designing experimental protocols via flow diagrams.
Created the KEfED data interface for entering experimental data.
Implemented a neural connection matrix for visualizing and querying connectivity data.
Utilized Persevere (noSQL database) and PowerLoom® (First Order Logic reasoner) with the BAMS neuroanatomical ontology.

Main Results:

Successfully instantiated the KEfED knowledge representation for experimental observations.
Developed the BioScholar software with three integrated components: model editor, data interface, and connection matrix.
Demonstrated the ability to represent and query neural connectivity data from tract-tracing experiments.
Enabled viewing of experimental evidence supporting specific neural connections.

Conclusions:

Introduced KEfED as a general approach for structured reasoning in scientific publication models.
Described the design and implementation of the BioScholar software as a biocuration interface and reasoning toolkit.
Positioned BioScholar as a supplementary tool for the Brain Architecture Management System (BAMS).