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A Web Tool for Generating High Quality Machine-readable Biological Pathways
08:01

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

Application of XML database technology to biological pathway datasets.

Keyuan Jiang1, Christopher Nash

  • 1Dept. of Comput. Inf. Technol., Purdue Univ. Calumet, Hammond, IN 46323, USA. jiang@calumet.purdue.edu

Conference Proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference
|October 20, 2007
PubMed
Summary

Researchers created a new XML database and XQuery system to efficiently store and query biological pathway data. This system addresses challenges in aggregating BioPAX datasets, improving access for biomedical research.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Systems Biology

Background:

  • Biological systems generate vast amounts of pathway data across numerous databases.
  • The BioPAX standard facilitates data availability using XML, but lacks standardized storage.
  • Current limitations hinder efficient querying and aggregation of BioPAX-compliant biological pathway data.

Purpose of the Study:

  • To develop a standardized storage mechanism for biological pathway data.
  • To enable efficient querying and aggregation of BioPAX-compliant datasets.
  • To provide a generic, centralized data store for biomedical research needs.

Main Methods:

  • Leveraged existing XML technologies, specifically XML databases and XQuery.
  • Developed a SOAP-based Web service for online data access.
  • Implemented direct HTTP request methods for public data consumption.

Main Results:

  • Established a centralized storage solution for biological pathway data.
  • Enabled efficient querying and aggregation of BioPAX datasets.
  • Facilitated public access to curated biological pathway information.

Conclusions:

  • The developed XML database and XQuery system effectively address challenges in managing biological pathway data.
  • This approach provides a robust and accessible platform for biomedical research.
  • Enhanced data accessibility through web services promotes broader scientific collaboration and discovery.