Terminology for neuroscience data discovery: multi-tree syntax and investigator-derived semantics.
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.
Gardner
Daniel
D
Laboratory of Neuroinformatics and Department of Physiology, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY, 10065, USA. dan@med.cornell.edu
Goldberg
David H
DH
Grafstein
Bernice
B
Robert
Adrian
A
Gardner
Esther P
EP
D022126:Access to Information; D000818:Animals; D019295:Computational Biology / Q000379:methods* / Q000639:trends; D019992:Databases as Topic / Q000592:standards* / Q000639:trends; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods / Q000592:standards / Q000639:trends; D020407:Internet / Q000458:organization & administration / Q000639:trends; D015201:Meta-Analysis as Topic; D009488:Neurosciences / Q000379:methods* / Q000639:trends; D012660:Semantics; D012984:Software / Q000592:standards / Q000639:trends; D009626:Terminology as Topic