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1.  Approaches to neuroscience data integration 
Briefings in Bioinformatics  2009;10(4):345-353.
As the number of neuroscience databases increases, the need for neuroscience data integration grows. This paper reviews and compares several approaches, including the Neuroscience Database Gateway (NDG), Neuroscience Information Framework (NIF) and Entrez Neuron, which enable neuroscience database annotation and integration. These approaches cover a range of activities spanning from registry, discovery and integration of a wide variety of neuroscience data sources. They also provide different user interfaces for browsing, querying and displaying query results. In Entrez Neuron, for example, four different facets or tree views (neuron, neuronal property, gene and drug) are used to hierarchically organize concepts that can be used for querying a collection of ontologies. The facets are also used to define the structure of the query results.
PMCID: PMC2691938  PMID: 19505888
data integration; neuroinformatics; ontology; semantic web; user interface
3.  Bringing Web 2.0 to bioinformatics 
Briefings in Bioinformatics  2008;10(1):1-10.
Enabling deft data integration from numerous, voluminous and heterogeneous data sources is a major bioinformatic challenge. Several approaches have been proposed to address this challenge, including data warehousing and federated databasing. Yet despite the rise of these approaches, integration of data from multiple sources remains problematic and toilsome. These two approaches follow a user-to-computer communication model for data exchange, and do not facilitate a broader concept of data sharing or collaboration among users. In this report, we discuss the potential of Web 2.0 technologies to transcend this model and enhance bioinformatics research. We propose a Web 2.0-based Scientific Social Community (SSC) model for the implementation of these technologies. By establishing a social, collective and collaborative platform for data creation, sharing and integration, we promote a web services-based pipeline featuring web services for computer-to-computer data exchange as users add value. This pipeline aims to simplify data integration and creation, to realize automatic analysis, and to facilitate reuse and sharing of data. SSC can foster collaboration and harness collective intelligence to create and discover new knowledge. In addition to its research potential, we also describe its potential role as an e-learning platform in education. We discuss lessons from information technology, predict the next generation of Web (Web 3.0), and describe its potential impact on the future of bioinformatics studies.
PMCID: PMC2638627  PMID: 18842678
Web 2.0; bioinformatics; scientific social community; web service; pipelines
4.  SenseLab 
Briefings in bioinformatics  2007;8(3):150-162.
This article presents the latest developments in neuroscience information dissemination through the SenseLab suite of databases: NeuronDB, CellPropDB, ORDB, OdorDB, OdorMapDB, ModelDB and BrainPharm. These databases include information related to: (i) neuronal membrane properties and neuronal models, and (ii) genetics, genomics, proteomics and imaging studies of the olfactory system. We describe here: the new features for each database, the evolution of SenseLab’s unifying database architecture and instances of SenseLab database interoperation with other neuroscience online resources.
PMCID: PMC2756159  PMID: 17510162
neuroscience; databases; SenseLab; neuroinformatics; Human Brain Project

Results 1-4 (4)