Brede Tools and Federating Online Neuroinformatics Databases

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ORIGINAL ARTICLE

Brede Tools and Federating Online Neuroinformatics Databases ˚ Finn Arup Nielsen

© Springer Science+Business Media New York 2013

Abstract As open science neuroinformatics databases the Brede Database and Brede Wiki seek to make distribution and federation of their content as easy and transparent as possible. The databases rely on simple formats and allow other online tools to reuse their content. This paper describes the possible interconnections on different levels between the Brede tools and other databases. Keywords Database · Wiki · Semantic web · Open science · Meta-analysis · Data federation

Introduction The concept open science entails the free access to data and methods. In neuroinformatics open science would allow federation of databases, so researchers can make queries across data sets and ontologies. Open science represents the first step enabling data sharing. As the next step we would like to query across the different databases, and in a further step we would like to use the data across multiple databases in statistical computations so meta-analytic consensus emerge. For neuroinformatics these last two steps are hindered by the plethora of different data formats, brain atlases and terminology and the division of data between several databases, — making even the discovery of relevant resources difficult. We would like the databases to expose their data in both human-readable and machine-readable format. With a machine-readable format neuroinformaticians can work with data en masse and ˚ Nielsen () F. A. DTU Compute, Technical University of Denmark, Kongens Lyngby, Denmark e-mail: [email protected]

merge the data across databases. However, even with open science data in a machine-readable format one still has to match and link heterogenous data in different formats. This is where integrative neuroinformatics tools come into play. For information retrieval these tools should have an understanding of concepts rather than just keywords (Gupta et al. 2008). Several tools have been described for integrating or federating neuroscience databases (Gupta et al. 2008; Ashish et al. 2010; Cheung et al. 2009). One of the major database federation efforts is Neuroscience Information Framework (NIF) that uses the Neuroscience Information Framework standardized (NIFSTD) ontology (Bug et al. 2008). With this ontology NIF performs term expansion from a user query. The expanded query is translated to queries for the different source databases and through a data mediator the queries are sent to these external databases and aggregated. The system relies on tools, e.g., for registering the schema of the external database and for full text search. The complete system may search on web pages, databases, Extensible Markup Language (XML) and other documents. One way of database federation is by the so-called Semantic Web. First prominently described by Berners-Lee et al. (2001) its community has now established a number of technologies around the concept, e.g., triple stores, Resource Description Framework (R