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Related Experiment Video

Updated: Jun 18, 2026

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

SMPDB: The Small Molecule Pathway Database.

Alex Frolkis1, Craig Knox, Emilia Lim

  • 1Department of Computing Science, University of Alberta, Edmonton, AB, Canada.

Nucleic Acids Research
|December 2, 2009
PubMed
Summary
This summary is machine-generated.

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The Small Molecule Pathway Database (SMPDB) offers over 350 human small-molecule pathways, with over 280 unique to the resource. This visual database aids in pathway discovery for systems biology and clinical research.

Area of Science:

  • Biochemistry
  • Systems Biology
  • Bioinformatics

Background:

  • Small-molecule pathways are crucial for understanding cellular functions and disease mechanisms.
  • Existing pathway databases often lack comprehensive coverage of human-specific metabolic and signaling pathways.

Purpose of the Study:

  • To introduce the Small Molecule Pathway Database (SMPDB) as a novel resource for exploring human small-molecule pathways.
  • To support pathway elucidation and discovery in fields like metabolomics, transcriptomics, proteomics, and systems biology.

Main Methods:

  • Development of an interactive, visual database integrating over 350 human small-molecule pathways.
  • Hyperlinking of pathway components (metabolites, proteins) to external databases (HMDB, DrugBank, UniProt).
  • Implementation of advanced search functionalities and data visualization tools for user queries and data analysis.

Related Experiment Videos

Last Updated: Jun 18, 2026

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

Main Results:

  • SMPDB contains >350 human small-molecule pathways, with >280 not found in other databases.
  • Detailed pathway diagrams include organelle localization, protein cofactors, and chemical/protein structures.
  • The database supports queries using various identifiers and allows visualization of concentration data.

Conclusions:

  • SMPDB is a unique and comprehensive resource for human small-molecule pathways.
  • The database facilitates pathway discovery and research in clinical metabolomics and systems biology.
  • Downloadable data and interactive features enhance its utility for researchers.