SynDB: A synapse protein database based on synapse ontology

W Zhang; Y Zhang; H Zheng; C Zhang; W Xiong; J G Olyarchuk; M Walker; W Xu; Min Zhao; S Zhao; Z Zhou; L Wei

doi:10.1093/nar/gkl876

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SynDB: A synapse protein database based on synapse ontology

Journal article

Open access

Peer reviewed

SynDB: A synapse protein database based on synapse ontology

W Zhang, Y Zhang, H Zheng, C Zhang, W Xiong, J G Olyarchuk, M Walker, W Xu, Min Zhao, S Zhao, …

Nucleic Acids Research, Vol.35(Supplement 1), pp.D737-D741

2007

DOI: https://doi.org/10.1093/nar/gkl876

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Abstract

cell protein

amino acid sequence

automation

chromosomal localization

computer interface

computer program

disease association

genetic database

information retrieval

Internet

protein database

protein determination

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. © 2007 Oxford University Press.

Details

Title: SynDB: A synapse protein database based on synapse ontology
Authors: W Zhang (Author) - Peking University, China
Y Zhang (Author) - Peking University, China
H Zheng (Author) - Peking University, China
C Zhang (Author) - Southwestern Medical Centre, United States
W Xiong (Author) - Peking University, China
J G Olyarchuk (Author) - Southwestern Medical Centre, United States
M Walker (Author) - Stanford University School of Medicine, United States
W Xu (Author) - Stanford University School of Medicine, United States
Min Zhao (Author) - Peking University, China
S Zhao (Author) - Peking University, China
Z Zhou (Author) - Peking University, China
L Wei (Author) - Peking University, China
Publication details: Nucleic Acids Research, Vol.35(Supplement 1), pp.D737-D741
Publisher: Oxford University Press
Date published: 2007
DOI: 10.1093/nar/gkl876
ISSN: 0305-1048
Copyright note: Copyright © 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.
Organisation Unit: School of Science and Engineering - Legacy; University of the Sunshine Coast, Queensland; School of Science, Technology and Engineering; Centre for Bioinnovation
Language: English
Record Identifier: 99447760902621
Output Type: Journal article

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