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Neuroimaging data is raw material for cognitive neuroscience experiments, leading to scientific knowledge about human neurological and psychological disease, language, perception, attention and ultimately, cognition. The structure of the variables used in the experimental design defines the structure of the data gathered in the experiments; this in turn structures the interpretative assertions that may be presented as experimental conclusions. Representing these assertions and the experimental data which support them in a computable way means that they could be used in logical reasoning environments, i.e. for automated meta-analyses, or linking hypotheses and results across different levels of neuroscientific experiments. Therefore, a crucial first step in being able to represent neuroimaging results in a clear, computable way is to develop representations for the scientific variables involved in neuroimaging experiments. These representations should be expressive, computable, valid, extensible, and easy-to-use. They should also leverage existing semantic standards to interoperate easily with other systems. We present an ontology design pattern called the Ontology of Experimental Variables and Values (OoEVV). This is designed to provide a lightweight framework to capture mathematical properties of data, with appropriate 'hooks' to permit linkage to other ontology-driven projects (such as the Ontology of Biomedical Investigations, OBI). We instantiate the OoEVV system with a small number of functional Magnetic Resonance Imaging datasets, to demonstrate the system's ability to describe the variables of a neuroimaging experiment. OoEVV is designed to be compatible with the XCEDE neuroimaging data standard for data collection terminology, and with the Cognitive Paradigm Ontology (CogPO) for specific reasoning elements of neuroimaging experimental designs.
Pubmed ID: 23684873 RIS Download
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Open repository of biomedical ontologies that provides access via Web browsers and Web services to ontologies. It supports ontologies in OBO format, OWL, RDF, Rich Release Format (RRF), Protege frames, and LexGrid XML. Functionality includes the ability to browse, search and visualize ontologies as well as to comment on, and create mappings for ontologies. Any registered user can submit an ontology. The NCBO Annotator and NCBO Resource Index can also be accessed via BioPortal. Additional features: * Add Reviews: rate the ontology according to several criteria and describe your experience using the ontology. * Add Mappings: submit point-to-point mappings or upload bulk mappings created with external tools. Notification of new Mappings is RSS-enabled and Mappings can be browsed via BioPortal and accessed via Web services. * NCBO Annotator: Tool that tags free text with ontology terms. NCBO uses the Annotator to generate ontology annotations, creating an ontology index of these resources accessible via the NCBO Resource Index. The Annotator can be accessed through BioPortal or directly as a Web service. The annotation workflow is based on syntactic concept recognition (using the preferred name and synonyms for terms) and on a set of semantic expansion algorithms that leverage the ontology structure (e.g., is_a relations). * NCBO Resource Index: The NCBO Resource Index is a system for ontology based annotation and indexing of biomedical data; the key functionality of this system is to enable users to locate biomedical data linked via ontology terms. A set of annotations is generated automatically, using the NCBO Annotator, and presented in BioPortal. This service uses a concept recognizer (developed by the National Center for Integrative Biomedical Informatics, University of Michigan) to produce a set of annotations and expand them using ontology is_a relations. * Web services: Documentation on all Web services and example code is available at: BioPortal Web services.
View all literature mentionsSoftware repository for comparing structural (MRI) and functional neuroimaging (fMRI, PET, EEG, MEG) software tools and resources. NITRC collects and points to standardized information about structural or functional neuroimaging tool or resource.
View all literature mentionsPlatform for large-scale, automated synthesis of functional magnetic resonance imaging (fMRI) data extracted from published articles. It''s a website wrapped around a set of open-source Python and JavaScript packages. Neurosynth lets you run crude but useful analyses of fMRI data on a very large scale. You can: * Interactively visualize the results of over 3,000 term-based meta-analyses * Select specific locations in the human brain and view associated terms * Browse through the nearly 10,000 studies in the database Their ultimate goal is to enable dynamic real-time analysis, so that you''ll be able to select foci, tables, or entire studies for analysis and run a full-blown meta-analysis without leaving your browser. You''ll also be able to do things like upload entirely new images and obtain probabilistic estimates of the cognitive states most likely to be associated with the image.
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