Neuroscience Research Guide

An ontology is a formal representation of knowledge that consists of a set of classes that represent concepts defining a field and the relationships among these classes. (Larson & Martone, 2009)

The Cognitive Atlas is a collaborative knowledge building project that aims to develop a knowledge base (or ontology) that characterizes the state of current thought in cognitive science. The project is led by Russell Poldrack, Professor of Psychology at Stanford University and is funded by the National Institute of Mental Health.

NIF Standard ontology (NIFSTD) is a core component of Neuroscience Information Framework (NIF) project, a semantically enhanced portal for accessing and integrating neuroscience data, tools and information. NIFSTD includes a set of modular ontologies that provide a comprehensive collection of terminologies to describe neuroscience data and resources.

Format: OWL [to open .ttl files you will need to download Protege]

Github Repository | Documentation

KnowledgeSpace aims to be a globally-used, community-based, data-driven encyclopedia for neuroscience that links brain research concepts to data, models, and the literature that support them. KnowledgeSpace is a framework that combines general descriptions of neuroscience concepts found in wikipedia with more detailed content from NeuroLex. It then integrates the content from those two sources with the latest neuroscience citations found in PubMed and data found in some of the world’s leading neuroscience repositories. KnowledgeSpace is a joint development between the Human Brain Project (HBP), the International Neuroinformatics Coordinating Facility (INCF), and the Neuroscience Information Framework (NIF).

NeuroNames Ontology and Standard Nomenclature of some 3000 central nervous system structures in the human, macaque, rat and mouse.

Neural ElectroMagnetic Ontologies (NEMO) is an NIH funded project that aims to create EEG and MEG ontologies and ontology based tools.

Format: OWL [to open .ttl files you will need to download Protege]

Reference: Frishkoff, G., LePendu, P., Frank, R. et al. Development of Neural Electromagnetic Ontologies (NEMO): Ontology-based Tools for Representation and Integration of Event-related Brain Potentials. Nat Prec (2009). https://doi.org/10.1038/npre.2009.3458.1 

Neuroscience Knowledge Engine contains a data-driven ontology for neurobiological domains that synthesizes the texts and data of nearly 20,000 human neuroimaging articles. The data-driven ontology includes 6 domains, each defined by a circuit of brain structures and its associated mental functions.

Preprint: A computational knowledge engine for human neuroscience. Elizabeth Beam, Christopher Potts, Russell A. Poldrack, Amit Etkin
bioRxiv 701540; doi: https://doi.org/10.1101/701540

BioPortal is a comprehensive repository of biomedical ontologies