Terminology for neuroscience data discovery: multi-tree syntax and investigator-derived semantics

Abstract

The Neuroscience Information Framework (NIF), developed for the NIH Blueprint for Neuroscience Research and available at http://nif.nih.gov and http://neurogateway.org , is built upon a set of coordinated terminology components enabling data and web-resource description and selection. Core NIF terminologies use a straightforward syntax designed for ease of use and for navigation by familiar web interfaces, and readily exportable to aid development of relational-model databases for neuroscience data sharing. Datasets, data analysis tools, web resources, and other entities are characterized by multiple descriptors, each addressing core concepts, including data type, acquisition technique, neuroanatomy, and cell class. Terms for each concept are organized in a tree structure, providing is-a and has-a relations. Broad general terms near each root span the category or concept and spawn more detailed entries for specificity. Related but distinct concepts (e.g., brain area and depth) are specified by separate trees, for easier navigation than would be required by graph representation. Semantics enabling NIF data discovery were selected at one or more workshops by investigators expert in particular systems (vision, olfaction, behavioral neuroscience, neurodevelopment), brain areas (cerebellum, thalamus, hippocampus), preparations (molluscs, fly), diseases (neurodegenerative disease), or techniques (microscopy, computation and modeling, neurogenetics). Workshop-derived integrated term lists are available Open Source at http://brainml.org ; a complete list of participants is at http://brainml.org/workshops.

Fig. 1

The proto-Framework catalog at http://neurogateway.org includes a broad set of detector controlled vocabulary terms that specify resources’ scope and focus, here shown in an early version exposing segments of each of eight controlled-vocabulary detector trees

Fig. 2

NIF Detector Terms Search the Neuroscience Web. Neurogateway.org, a NIF prototype resource provides access to hundreds of neuroscience Web resources. From possible detector search terms for data type, technique, organism, and others, the example shows search for a specific disease type using selected NIF terminology. The same underlying terminologies seen in Fig. 1 are here shown in an alternate drop-down menu format, emphasizing that the content is adaptable to multiple presentation schemas

Fig. 3

Neurodatabase.org, the Laboratory of Neuroinformatics-developed archive of neurophysiology data, now incorporates the Open Source NIFv1 terminology for brain area and other descriptors. Exportable NIF terminology, available at http://brainml.org, standardizes metadata, aids future development of descriptors and query terms for databases, and can facilitate direct database access via NIF query screens