A multilayer ontology of instruments for neurological, behavioral and cognitive assessments.

Advances in neuroscience are underpinned by large, multicenter studies and a mass of heterogeneous datasets. When investigating the relationships between brain anatomy and brain functions under normal and pathological conditions, measurements obtained from a broad range of brain imaging techniques are correlated with the information on each subject's neurologic states, cognitive assessments and behavioral scores derived from questionnaires and tests. The development of ontologies in neuroscience appears to be a valuable way of gathering and handling properly these heterogeneous data - particularly through the use of federated architectures. We recently proposed a multilayer ontology for sharing brain images and regions of interest in neuroimaging. Here, we report on an extension of this ontology to the representation of instruments used to assess brain and cognitive functions and behavior in humans. This extension consists of a 'core' ontology that accounts for the properties shared by all instruments supplemented by 'domain' ontologies that conceptualize standard instruments. We also specify how this core ontology has been refined to build domain ontologies dedicated to widely used instruments and how various scores used in the neurosciences are represented. Lastly, we discuss our design choices, the ontology's limitations and planned extensions aimed at querying and reasoning across distributed data sources.

NeuroLOG: sharing neuroimaging data using an ontology-based federated approach.

This paper describes the design of the NeuroLOG middleware data management layer, which provides a platform to share heterogeneous and distributed neuroimaging data using a federated approach. The semantics of shared information is captured through a multi-layer application ontology and a derived Federated Schema used to align the heterogeneous database schemata from different legacy repositories. The system also provides a facility to translate the relational data into a semantic representation that can be queried using a semantic search engine thus enabling the exploitation of knowledge embedded in the ontology. This work shows the relevance of the distributed approach for neurosciences data management. Although more complex than a centralized approach, it is also more realistic when considering the federation of large data sets, and open strong perspectives to implement multi-centric neurosciences studies.

Grid-wide neuroimaging data federation in the context of the NeuroLOG project.

Grid technologies are appealing to deal with the challenges raised by computational neurosciences and support multi-centric brain studies. However, core grids middleware hardly cope with the complex neuroimaging data representation and multi-layer data federation needs. Moreover, legacy neuroscience environments need to be preserved and cannot be simply superseded by grid services. This paper describes the NeuroLOG platform design and implementation, shedding light on its Data Management Layer. It addresses the integration of brain image files, associated relational metadata and neuroscience semantic data in a heterogeneous distributed environment, integrating legacy data managers through a mediation layer.

Towards an ontology for sharing medical images and regions of interest in neuroimaging.

The goal of the NeuroBase project is to facilitate collaborative research in neuroimaging through a federated system based on semantic web technologies. The cornerstone and focus of this paper is the design of a common semantic model providing a unified view on all data and tools to be shared. For this purpose, we built a multi-layered and multi-components formal ontology. This paper presents two major contributions. The first is related to the general methodology we propose for building an application ontology based on consistent conceptualization choices provided by the DOLCE foundational ontology and core ontologies of domains that we reuse; the second concerns the domain ontology we designed for neuroimaging, which encompasses both the objective nature of image data and the subjective nature of image content, through annotations based on regions of interest made by agents (humans or computer programs). We report on realistic domain use-case queries referring to our application ontology.