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. 2024 Jan 5;52(D1):D654-D662.
doi: 10.1093/nar/gkad1041.

PathBank 2.0-the pathway database for model organism metabolomics

David S Wishart  1   2   3   4 , Ray Kruger  1 , Aadhavya Sivakumaran  1 , Karxena Harford  1 , Selena Sanford  1 , Rahil Doshi  1 , Nitya Kehrtarpal  1 , Omolola Fatokun  1 , Daphnee Doucet  1 , Ashley Zubkowski  1 , Hayley Jackson  1 , Gina Sykes  1 , Miguel Ramirez-Gaona  5 , Ana Marcu  1 , Carin Li  1 , Kristen Yee  1 , Christiana Garros  1 , Dorsa Yahya Rayat  1 , Jeanne Coleongco  1 , Tharuni Nandyala  1 , Vasuk Gautam  1 , Eponine Oler  1
Affiliations

PathBank 2.0-the pathway database for model organism metabolomics

David S Wishart et al. Nucleic Acids Res. .

Erratum in

Abstract

PathBank (https://pathbank.org) and its predecessor database, the Small Molecule Pathway Database (SMPDB), have been providing comprehensive metabolite pathway information for the metabolomics community since 2010. Over the past 14 years, these pathway databases have grown and evolved significantly to meet the needs of the metabolomics community and respond to continuing changes in computing technology. This year's update, PathBank 2.0, brings a number of important improvements and upgrades that should make the database more useful and more appealing to a larger cross-section of users. In particular, these improvements include: (i) a significant increase in the number of primary or canonical pathways (from 1720 to 6951); (ii) a massive increase in the total number of pathways (from 110 234 to 605 359); (iii) significant improvements to the quality of pathway diagrams and pathway descriptions; (iv) a strong emphasis on drug metabolism and drug mechanism pathways; (v) making most pathway images more slide-compatible and manuscript-compatible; (vi) adding tools to support better pathway filtering and selecting through a more complete pathway taxonomy; (vii) adding pathway analysis tools for visualizing and calculating pathway enrichment. Many other minor improvements and updates to the content, the interface and general performance of the PathBank website have also been made. Overall, we believe these upgrades and updates should greatly enhance PathBank's ease of use and its potential applications for interpreting metabolomics data.

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Figures

Graphical Abstract
Graphical Abstract
Figure 1.
Figure 1.
(A) The drug action (mechanism of action or MOA) and (B) drug metabolism (absorption, distribution, metabolism and excretion or ADME) pathway for the drug Abciximab.
Figure 2.
Figure 2.
Pathway illustrating how the COVID-19 virus can cause viral sepsis. This showcases the additional icons and images that have been added to improve the content and quality of PathBank pathways.
Figure 3.
Figure 3.
Screenshots illustrating how to use Pathway Enrichment Analysis (PEA). (A) View of the PEA search screen with example data entered. (B) A Pathway Impact plot of the results from the PEA. The Pathway Impact plot is interactive and when individual dots are hovered over, pathway information is provided. (C) Shown is the results table which gives more pathway information.
See this image and copyright information in PMC

References

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