NeuroScholar\'s Electronic Laboratory Notebook and Its Application to Neuroendocrinology

Abstract

Scientists continually relate information from the published literature to their current research. The challenge of this essential and time-consuming activity increases as the body of scientific literature continues to grow. In an attempt to lessen the challenge, we have developed an Electronic Laboratory Notebook (ELN) application. Our ELN functions as a component of another application we have developed, an open-source knowledge management system for the neuroscientific literature called NeuroScholar (http://www.neuroscholar.org/). Scanned notebook pages, images, and data files are entered into the ELN, where they can be annotated, organized, and linked to similarly annotated excerpts from the published literature within Neuroscholar. Associations between these knowledge constructs are created within a dynamic node-and-edge user interface. To produce an interactive, adaptable knowledge base. We demonstrate the ELN's utility by using it to organize data and literature related to our studies of the neuroendocrine hypothalamic paraventricular nucleus (PVH). We also discuss how the ELN could be applied to model other neuroendocrine systems; as an example we look at the role of PVH stressorresponsive neurons in the context of their involvement in the suppression of reproductive function. We present this application to the community as open-source software and invite contributions to its development.

Infrastructure for Annotation-Driven Information Extraction from the Primary Scientific Literature: Principles and Practice

“…Importantly, we seek to provide a framework that supports the development of biomedical databases in subjects that currently are not supported with informatics systems. We envisage that the development of low-cost IE systems such as this may permit the creation of smallscale databases that significantly assist scholarly work in the biosciences (see [43,44] for preliminary software constructs to support this vision).…”

The NeuARt II system: a viewing tool for neuroanatomical data based on published neuroanatomical atlases

“…Data persistence in NeuARt II is handled under the NeuroScholar knowledge management platform [60-64]. The NeuroScholar project is an open-source, research prototype that uses the MySQL open-source relational database and can therefore scale to contain hundreds of thousands of data instances.…”

Mapping Molecular Datasets Back to the Brain Regions They are Extracted from: Remembering the Native Countries of Hypothalamic Expatriates and Refugees

“…4 of [49]; [216]). As greater sophistication is brought to bear using methods that combine neuroanatomical tract tracing with molecular analysis of the traced projection neurons (e.g., see [346]), both the mapping and management of data concerning such projection systems will become even more streamlined.…”

“…We have chosen to use the hypothalamus as an exemplar structure to illustrate the possibilities of such an effort, a choice that is predicated in part on our own experiences in mapping and modeling multi-scale data for this brain region (e.g., [215, 216, 217, 219, 484]), and because a review of “-omics” work on the hypothalamus in the context of spatial mapping has not yet, to our knowledge, been attempted. So far, molecule extraction from hypothalamus has been focused primarily on mining either the whole hypothalamus or its well-defined sub-regions to the virtual exclusion of parts that are less well understood.…”