Dynamic publication model for neurophysiology databases.

We have implemented a pair of database projects, one serving cortical electrophysiology and the other invertebrate neurones and recordings. The design for each combines aspects of two proven schemes for information interchange. The journal article metaphor determined the type, scope, organization and quantity of data to comprise each submission. Sequence databases encouraged intuitive tools for data viewing, capture, and direct submission by authors. Neurophysiology required transcending these models with new datatypes. Time-series, histogram and bivariate datatypes, including illustration-like wrappers, were selected by their utility to the community of investigators. As interpretation of neurophysiological recordings depends on context supplied by metadata attributes, searches are via visual interfaces to sets of controlled-vocabulary metadata trees. Neurones, for example, can be specified by metadata describing functional and anatomical characteristics. Permanence is advanced by data model and data formats largely independent of contemporary technology or implementation, including Java and the XML standard. All user tools, including dynamic data viewers that serve as a virtual oscilloscope, are Java-based, free, multiplatform, and distributed by our application servers to any contemporary networked computer. Copyright is retained by submitters; viewer displays are dynamic and do not violate copyright of related journal figures. Panels of neurophysiologists view and test schemas and tools, enhancing community support.

[1]  E. F. CODD,et al.  A relational model of data for large shared data banks , 1970, CACM.

[2]  Donald D. Chamberlin,et al.  Implementation of a structured English query language , 1975, SIGMOD '75.

[3]  Peter P. Chen.  The entity-relationship model: toward a unified view of data , 1975, VLDB '75.

[4]  Peter P. Chen.  The Entity-Relationship Model: Towards a unified view of Data , 1976 .

[5]  Edward G. Jones,et al.  Connectivity of the Primate Sensory-Motor Cortex , 1986 .

[6]  Richard W. Hamming,et al.  Numerical methods for scientists and engineers (2nd ed.) , 1986 .

[7]  Michael Stonebraker,et al.  The POSTGRES Data Model , 1987, Research Foundations in Object-Oriented and Semantic Database Systems.

[8]  Matthew A. Wilson,et al.  GENESIS: A System for Simulating Neural Networks , 1988, NIPS.

[9]  M Hines,et al.  A program for simulation of nerve equations with branching geometries. , 1989, International journal of bio-medical computing.

[10]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[11]  Eugene W. Myers,et al.  Basic local alignment search tool. Journal of Molecular Biology , 1990 .

[12]  R. G. G. Cattell,et al.  Object Data Management: Object-Oriented and Extended Relational Database Systems (Revised Edition) , 1991 .

[13]  Constance M. Pechura,et al.  Committee on a National Neural Circuitry Database , 1991 .

[14]  Constance M. Pechura,et al.  Mapping the brain and its functions: integrating enabling technologies into neuroscience research , 1991 .

[15]  D. J. Felleman,et al.  Distributed hierarchical processing in the primate cerebral cortex. , 1991, Cerebral cortex.

[16]  M. F. Huerta,et al.  The human brain project: an international resource , 1993, Trends in Neurosciences.

[17]  D. Lindberg,et al.  The Unified Medical Language System , 1993, Methods of Information in Medicine.

[18]  Jean Clucas,et al.  Interactive Visualization of Computational Fluid Dynamics using Mosaic , 1994 .

[19]  Michael F. Schwartz,et al.  Integrating Complex Data Access Methods into the Mosaic/WWW Environment , 1994 .

[20]  Arthur W. Toga,et al.  A Probabilistic Atlas of the Human Brain: Theory and Rationale for Its Development The International Consortium for Brain Mapping (ICBM) , 1995, NeuroImage.

[21]  D Gardner,et al.  Physiology on the World-Wide Web. , 1995, The Physiologist.

[22]  G. Schuler,et al.  Entrez: molecular biology database and retrieval system. , 1996, Methods in enzymology.

[23]  Gapped BLAST and PSI-BLAST: A new , 1997 .

[24]  James F. Brinkley,et al.  A Structural Information Framework for Brain Mapping , 1997 .

[25]  Perry L. Miller,et al.  The Human Brain Project: neuroinformatics tools for integrating, searching and modeling multidisciplinary neuroscience data , 1998, Trends in Neurosciences.

[26]  J. Cimino.  Desiderata for Controlled Medical Vocabularies in the Twenty-First Century , 1998, Methods of Information in Medicine.

[27]  Robert Sikorski,et al.  XML Is Hatching , 1998, Science.

[28]  Hongfang Liu,et al.  Representing information in patient reports using natural language processing and the extensible markup language. , 1999, Journal of the American Medical Informatics Association : JAMIA.

[29]  M. Young,et al.  Computational analysis of functional connectivity between areas of primate cerebral cortex. , 2000, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[30]  Andreas D. Baxevanis,et al.  The Molecular Biology Database Collection: an online compilation of relevant database resources , 2000, Nucleic Acids Res..

[31]  김삼묘,et al.  “Bioinformatics” 특집을 내면서 , 2000 .

[32]  Daniel Gardner,et al.  Model Formulation: Common Data Model for Neuroscience Data and Data Model Exchange , 2001, J. Am. Medical Informatics Assoc..