PathBank 2.0-the pathwã y database for model organism metabolomics

Abstract

PathBank ( https://pathbank.org )ãnd its predecessor database, the Small Molecule Pathwã y Database (SMPDB), ha v e been pro viding compre- hensiv e metabolite pathwã y inf ormation f or the metãbolomics communit y since 20 1 0. Ov er the past 14 y ears, these pathwã y databases ha v e grownãnd evolved significantly to meet the needs of the metabolomics communityãnd respond to continuing changes in computing technology. T his y ear's update, PathBãnk 2.0, bringsã number of important impro v ementsãnd upgrades that should mak e the database more usefulãnd moreãppealing toã larger cross-section of users. In particular, these impro v ements include: (i)ã significant increase in the number of primary or canonical pathwã y s (from 1720 to 6951); (ii)ã massive increase in the total number of pathwã y s (from 110 234 to 605 359); (iii) significant impro v ements to the quality of pathwã y diagramsãnd pathwã y descriptions; (iv)ã strong emphasis on drug metabolismãnd drug mechanism pathwã y s; (v) making most pathwã y images more slide-compatibleãnd manuscript-compatible; (vi)ãdding tools to support better pathwã y fil- teringãnd selecting throughã more complete pathwã y tax onom y; (vii)ãdding pathwã yãnaly sis tools f or visualizingãnd calculating pathwã y enrichment. Many other minor improvementsãnd updates to the content, the interfaceãnd general performance of the PathBank website haveãlso been made. Ov erall, w e belie v e these upgradesãnd updates should greatly enhance PathBank's ease of useãnd its potentialãpplications for interpreting metabolomics data.