Literature DB >> 19505888

Approaches to neuroscience data integration.

Kei-Hoi Cheung1, Ernest Lim, Matthias Samwald, Huajun Chen, Luis Marenco, Matthew E Holford, Thomas M Morse, Pradeep Mutalik, Gordon M Shepherd, Perry L Miller.   

Abstract

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.

Mesh:

Year:  2009        PMID: 19505888      PMCID: PMC2691938          DOI: 10.1093/bib/bbp029

Source DB:  PubMed          Journal:  Brief Bioinform        ISSN: 1467-5463            Impact factor:   11.622


  16 in total

1.  Achieving evolvable Web-database bioscience applications using the EAV/CR framework: recent advances.

Authors:  Luis Marenco; Nicholas Tosches; Chiquito Crasto; Gordon Shepherd; Perry L Miller; Prakash M Nadkarni
Journal:  J Am Med Inform Assoc       Date:  2003-06-04       Impact factor: 4.497

2.  The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration.

Authors:  Barry Smith; Michael Ashburner; Cornelius Rosse; Jonathan Bard; William Bug; Werner Ceusters; Louis J Goldberg; Karen Eilbeck; Amelia Ireland; Christopher J Mungall; Neocles Leontis; Philippe Rocca-Serra; Alan Ruttenberg; Susanna-Assunta Sansone; Richard H Scheuermann; Nigam Shah; Patricia L Whetzel; Suzanna Lewis
Journal:  Nat Biotechnol       Date:  2007-11       Impact factor: 54.908

3.  The cell centered database project: an update on building community resources for managing and sharing 3D imaging data.

Authors:  Maryann E Martone; Joshua Tran; Willy W Wong; Joy Sargis; Lisa Fong; Stephen Larson; Stephan P Lamont; Amarnath Gupta; Mark H Ellisman
Journal:  J Struct Biol       Date:  2007-10-16       Impact factor: 2.867

4.  SenseLab: new developments in disseminating neuroscience information.

Authors:  Chiquito J Crasto; Luis N Marenco; Nian Liu; Thomas M Morse; Kei-Hoi Cheung; Peter C Lai; Gautam Bahl; Peter Masiar; Hugo Y K Lam; Ernest Lim; Huajin Chen; Prakash Nadkarni; Michele Migliore; Perry L Miller; Gordon M Shepherd
Journal:  Brief Bioinform       Date:  2007-05-17       Impact factor: 11.622

5.  The SWAN biomedical discourse ontology.

Authors:  Paolo Ciccarese; Elizabeth Wu; Gwen Wong; Marco Ocana; June Kinoshita; Alan Ruttenberg; Tim Clark
Journal:  J Biomed Inform       Date:  2008-05-04       Impact factor: 6.317

Review 6.  Interoperability across neuroscience databases.

Authors:  Luis Marenco; Prakash Nadkarni; Maryann Martone; Amarnath Gupta
Journal:  Methods Mol Biol       Date:  2007

7.  The neuroscience information framework: a data and knowledge environment for neuroscience.

Authors:  Daniel Gardner; Huda Akil; Giorgio A Ascoli; Douglas M Bowden; William Bug; Duncan E Donohue; David H Goldberg; Bernice Grafstein; Jeffrey S Grethe; Amarnath Gupta; Maryam Halavi; David N Kennedy; Luis Marenco; Maryann E Martone; Perry L Miller; Hans-Michael Müller; Adrian Robert; Gordon M Shepherd; Paul W Sternberg; David C Van Essen; Robert W Williams
Journal:  Neuroinformatics       Date:  2008-10-23

8.  Alzforum and SWAN: the present and future of scientific web communities.

Authors:  Tim Clark; June Kinoshita
Journal:  Brief Bioinform       Date:  2007-05-17       Impact factor: 11.622

9.  BioGRID: a general repository for interaction datasets.

Authors:  Chris Stark; Bobby-Joe Breitkreutz; Teresa Reguly; Lorrie Boucher; Ashton Breitkreutz; Mike Tyers
Journal:  Nucleic Acids Res       Date:  2006-01-01       Impact factor: 16.971

10.  ChEBI: a database and ontology for chemical entities of biological interest.

Authors:  Kirill Degtyarenko; Paula de Matos; Marcus Ennis; Janna Hastings; Martin Zbinden; Alan McNaught; Rafael Alcántara; Michael Darsow; Mickaël Guedj; Michael Ashburner
Journal:  Nucleic Acids Res       Date:  2007-10-11       Impact factor: 16.971

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  4 in total

1.  Brede tools and federating online neuroinformatics databases.

Authors:  Finn Årup Nielsen
Journal:  Neuroinformatics       Date:  2014-01

2.  Semantic SenseLab: Implementing the vision of the Semantic Web in neuroscience.

Authors:  Matthias Samwald; Huajun Chen; Alan Ruttenberg; Ernest Lim; Luis Marenco; Perry Miller; Gordon Shepherd; Kei-Hoi Cheung
Journal:  Artif Intell Med       Date:  2009-12-16       Impact factor: 5.326

3.  NeuroLex.org: an online framework for neuroscience knowledge.

Authors:  Stephen D Larson; Maryann E Martone
Journal:  Front Neuroinform       Date:  2013-08-30       Impact factor: 4.081

Review 4.  Why Study the History of Neuroscience?

Authors:  Richard E Brown
Journal:  Front Behav Neurosci       Date:  2019-05-22       Impact factor: 3.558

  4 in total

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