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A Web Tool for Generating High Quality Machine-readable Biological Pathways
Published on: February 8, 2017
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SMPDB 2.0: big improvements to the Small Molecule Pathway Database.
Timothy Jewison1, Yilu Su, Fatemeh Miri Disfany
1Department of Computing Science, University of Alberta, Edmonton, AB, Canada T6G 2E8, Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E8 and National Institute for Nanotechnology, 11421 Saskatchewan Drive, Edmonton, AB, Canada T6G 2M9.
Nucleic Acids Research
|November 9, 2013
Summary
The Small Molecule Pathway Database (SMPDB) offers over 600 human metabolic, drug action, and disease pathways, with 75% unique content. Recent upgrades enhance visualization and data integration for metabolic research.
Area of Science:
- Biochemistry
- Systems Biology
- Bioinformatics
Background:
- The Small Molecule Pathway Database (SMPDB) is a key resource for biological pathway data.
- Previous versions have provided valuable insights into human metabolism and drug action.
Purpose of the Study:
- To present a significantly upgraded and expanded version of the SMPDB.
- To improve data accessibility, visualization, and integration capabilities.
Main Methods:
- Database expansion with over 70% new pathways.
- Redrawing, standardization, and updating of all existing pathways.
- Development of PathWhiz for standardized pathway creation and BioPAX export.
- Enhancements to the visualization interface for improved user interaction.
Main Results:
- SMPDB now contains over 600 pathways, with 75% unique content.
- Pathways include detailed information on tissues, organs, metabolites, and protein structures.
- New features include transporter proteins and expanded physiological data.
- Improved visualization allows for easier browsing, selection, recoloring, and zooming.
Conclusions:
- The upgraded SMPDB is a more comprehensive and user-friendly resource for exploring human biological pathways.
- Its integration with other databases like HMDB and DrugBank increases its utility.
- SMPDB serves as a valuable tool for researchers in metabolism, drug action, and disease pathways.
