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The NIFSTD and BIRNLex Vocabularies: Building Comprehensive Ontologies for Neuroscience
TLDR
The structure of the NIFSTD, and its predecessor BIRNLex, is reported on, the principles followed in its construction and examples of its use within NIF are provided, to promote easy extension and modification.
Sensory maps in the olfactory cortex defined by long-range viral tracing of single neurons
TLDR
A pronounced reorganization of sensory maps in the cortex offers an anatomic substrate for expanded combinatorial integration of information from spatially distinct glomeruli and predicts an unanticipated role for diversification of otherwise similar output neurons.
NeuroLex.org: an online framework for neuroscience knowledge
TLDR
It is shown how the structuring of information about anatomical parts in the nervous system can be reused to answer multiple neuroscience questions, such as displaying all known GABAergic neurons aggregated in NeuroLex or displaying all brain regions that are known within NeuroLex to send axons into the cerebellar cortex.
Digital Atlasing and Standardization in the Mouse Brain
TLDR
A collaborative digital atlasing framework for coordinating mouse brain research that allows access to data, tools, and analyses from multiple sources is proposed.
Ontologies for Neuroscience: What are they and What are they Good for?
TLDR
The benefits and limits of ontologies as a solution for data integration problem of neuroscience are examined and several examples of their application to problems of image annotation, content-based retrieval of structural data, and integration of data across scales and researchers are provided.
A Formal Ontology of Subcellular Neuroanatomy
TLDR
The structure and content of a formal ontology whose scope is the subcellular anatomy of the nervous system (SAO), covering nerve cells, their parts, and interactions between these parts are described and many applications of this ontology to image annotation, content-based retrieval of structural data, and integration of shared data across scales and researchers are described.
OpenWorm: an open-science approach to modeling Caenorhabditis elegans
TLDR
The rationale is presented for creating the OpenWorm collaboration, the tools and resources developed thus far are outlined and the unique challenges associated with the project are discussed.
OpenWorm: overview and recent advances in integrative biological simulation of Caenorhabditis elegans
TLDR
An overview of the history and philosophy of OpenWorm is given, descriptions of the constituent sub-projects and corresponding open-science management practices are described, and current achievements of the project and future directions are discussed.
c302: a multiscale framework for modelling the nervous system of Caenorhabditis elegans
TLDR
A framework is developed that allows different instances of neuronal networks to be generated incorporating varying levels of anatomical and physiological detail, which can be investigated and refined independently or linked to other tools developed in the OpenWorm modelling toolchain.
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