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SynDB: a Synapse protein DataBase based on synapse ontology.

Wuxue Zhang1, Yong Zhang, Hui Zheng

  • 1Center for Bioinformatics, National Laboratory of Protein Engineering and Plant Genetic Engineering College of Life Sciences, Peking University, Beijing 100871, P.R. China.

Nucleic Acids Research
|November 14, 2006
PubMed
Summary

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Researchers created Synapse Ontology (SynO) and Synapse protein DataBase (SynDB) to comprehensively catalog synapse proteins and their functions, aiding neurobiology research.

Area of Science:

  • Neurobiology
  • Bioinformatics
  • Proteomics

Background:

  • Synapses are crucial for neurobiological processes, mediating nerve impulse transmission.
  • Understanding synaptic molecules is essential for comprehending brain function.

Purpose of the Study:

  • To develop a comprehensive resource for synaptic proteins and their associated data.
  • To create a structured ontology for describing synaptic components and functions.

Main Methods:

  • Developed Synapse Ontology (SynO) with 177 terms and hierarchical structure.
  • Collected and curated 14,000 non-redundant synapse-related proteins using automated and manual methods.
  • Annotated proteins with sequence, structure, function, pathways, and disease associations.

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Main Results:

  • Created Synapse protein DataBase (SynDB) to store and present curated protein data.
  • SynDB includes 14,000 proteins, with 3000 human proteins, extensively annotated.
  • SynDB offers multiple browsing and searching functionalities, including by SynO and sequence similarity.

Conclusions:

  • SynDB is the most comprehensive database to date for synaptic proteins.
  • The SynO and SynDB resources facilitate in-depth study of synaptic structures and functions.
  • This work provides a valuable tool for neurobiological research and disease association studies.