title: Tools and approaches for the construction of knowledge models from the neuroscientific literature.
abstract: Within this paper, we describe a neuroinformatics project (called "NeuroScholar," http://www.neuroscholar.org/) that enables researchers to examine, manage, manipulate, and use the information contained within the published neuroscientific literature. The project is built within a multi-level, multi-component framework constructed with the use of software engineering methods that themselves provide code-building functionality for neuroinformaticians. We describe the different software layers of the system. First, we present a hypothetical usage scenario illustrating how NeuroScholar permits users to address large-scale questions in a way that would otherwise be impossible. We do this by applying NeuroScholar to a "real-world" neuroscience question: How is stress-related information processed in the brain? We then explain how the overall design of NeuroScholar enables the system to work and illustrate different components of the user interface. We then describe the knowledge management strategy we use to store interpretations. Finally, we describe the software engineering framework we have devised (called the "View-Primitive-Data Model framework," [VPDMf]) to provide an open-source, accelerated software development environment for the project. We believe that NeuroScholar will be useful to experimental neuroscientists by helping them interact with the primary neuroscientific literature in a meaningful way, and to neuroinformaticians by providing them with useful, affordable software engineering tools.
authors.affiliation: K-Mechanics Research Group, 3641 Watt Way, Hedco Neuroscience Building, University of Southern California, Los Angeles, CA 90089-2520, USA. gully@usc.edu
authors.forename: Gully A P C
authors.initials: GA
authors.lastname: Burns
authors.forename: Arshad M
authors.initials: AM
authors.lastname: Khan
authors.forename: Shahram
authors.initials: S
authors.lastname: Ghandeharizadeh
authors.forename: Mark A
authors.initials: MA
authors.lastname: O'Neill
authors.forename: Yi-Shin
authors.initials: YS
authors.lastname: Chen
mesh_terms: D001185:Artificial Intelligence; D001921:Brain / Q000503:physiopathology; D001931:Brain Mapping; D007256:Information Systems; D009474:Neurons / Q000502:physiology; D009488:Neurosciences; D010286:Paraventricular Hypothalamic Nucleus / Q000166:cytology / Q000503:physiopathology; D013315:Stress, Psychological / Q000503:physiopathology; D009626:Terminology as Topic