SpringerProtocols: Abstract: XML for Data Representation and Model Specification in Neuroscience

XML for Data Representation and Model Specification in Neuroscience

By: Sharon M. Crook⁴, Fred W. Howell⁵

Abstract

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EXtensible Markup Language (XML) technology provides an ideal representation for the complex structure of models and neuroscience data, as it is an open file format and provides a language-independent method for storing arbitrarily complex structured information. XML is composed of text and tags that explicitly describe the structure and semantics of the content of the document. In this chapter, we describe some of the common uses of XML in neuroscience, with case studies in representing neuroscience data and defining model descriptions based on examples from NeuroML. The specific methods that we discuss include (1) reading and writing XML from applications, (2) exporting XML from databases, (3) using XML standards to represent neuronal morphology data, (4) using XML to represent experimental metadata, and (5) creating new XML specifications for models.

Affiliation(s): (4) Department of Mathematics and Statistics and School of Life Sciences, Arizona State University, Tempe, AZ
(5) Textensor Limited, Edinburgh, Scotland, UK

Book Title: Neuroinformatics

Series: Methods in Molecular Biology | Volume: 401 | Pub. Date: Nov-29-2007 | Page Range: 53-66 | DOI: 10.1007/978-1-59745-520-6_4

Subject: Neuroscience

Key Words: XML - MorphML - NeuroML - neuronal morphology - neuroinformatics

References

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