Nucleic Acids Research Advance Access originally published online on November 10, 2006
Nucleic Acids Research 2007 35(Database issue):D737-D741; doi:10.1093/nar/gkl876
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Nucleic Acids Research, 2007, Vol. 35, Database issue D737-D741
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Articles |
SynDB: a Synapse protein DataBase based on synapse ontology
Center for Bioinformatics, National Laboratory of Protein Engineering and Plant Genetic Engineering College of Life Sciences, Peking University, Beijing 100871, P.R. China 1 Institute of Molecular Medicine, Peking University Beijing 100871, P.R. China 2 Center for Basic Neuroscience, UT Southwestern Medical Center Dallas, TX 75235, USA 3 Department of Medicine Stanford, CA 94305, USA 4 Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine Stanford, CA 94305, USA
*To whom correspondence should be addressed: Tel: +86 10 6276 4970; Fax: +86 10 6275 2438; Email: weilp{at}mail.cbi.pku.edu.cn
Received August 15, 2006. Revised October 6, 2006. Accepted October 6, 2006.
A synapse is the junction across which a nerve impulse passes from an axon terminal to a neuron, muscle cell or gland cell. The functions and building molecules of the synapse are essential to almost all neurobiological processes. To describe synaptic structures and functions, we have developed Synapse Ontology (SynO), a hierarchical representation that includes 177 terms with hundreds of synonyms and branches up to eight levels deep. associated 125 additional protein keywords and 109 InterPro domains with these SynO terms. Using a combination of automated keyword searches, domain searches and manual curation, we collected 14 000 non-redundant synapse-related proteins, including 3000 in human. We extensively annotated the proteins with information about sequence, structure, function, expression, pathways, interactions and disease associations and with hyperlinks to external databases. The data are stored and presented in the Synapse protein DataBase (SynDB, http://syndb.cbi.pku.edu.cn). SynDB can be interactively browsed by SynO, Gene Ontology (GO), domain families, species, chromosomal locations or Tribe-MCL clusters. It can also be searched by text (including Boolean operators) or by sequence similarity. SynDB is the most comprehensive database to date for synaptic proteins.
*Correspondence may also be addressed to Zhuan Zhou. Tel: +86 10 6276 4986; Fax: +86 10 6275 3212; Email: zzhou{at}pku.edu.cn
The authors wish it to be known that, in their opinion, the first three authors should be regarded as joint First Authors
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