WebGestalt 2019 is an updated version of the gene set analysis tool that supports 12 organisms, 342 gene identifiers, and 155 functional categories. It includes user-uploaded functional databases and provides phosphosite set analysis to identify important kinases from phosphoproteomics data. The tool has been completely redesigned for improved user-friendliness and offers multiple types of interactive and publication-ready figures. Two methods have been implemented to reduce redundancy between enriched gene sets. A web API allows other applications to access data programmatically from the WebGestalt server or pass data for analysis. The core computation has been wrapped into an R package called WebGestaltR, enabling users to perform analysis locally or in third-party workflows. WebGestalt can be freely accessed at http://www.webgestalt.org. WebGestalt supports 342 ID types from 12 organisms and includes 155,175 functional categories from public databases and computational analyses. It now supports phosphosite-level analysis, which is crucial for phosphoproteomics data interpretation. The tool has been enhanced with new visualizations, including bar charts, volcano plots, and DAGs, which help users understand enrichment results. The output report has been improved to include more information and allow sorting by scores and statistics. The tool also provides a web API for programmatic access to data and job submission forms. WebGestalt 2019 includes a new R package, WebGestaltR, which enables batch processing and integration with other computation pipelines. The package supports three methods: Over Representation Analysis (ORA), Gene Set Enrichment Analysis (GSEA), and Network Topology-based Analysis (NTA). The tool also provides RESTful APIs for accessing data and job submission forms. The system has been redesigned to focus on handling user submissions and serving results, with enhanced functionality for interaction with underlying data and job submission forms. The tool is now more accessible to users with programming skills and can be used for a wide range of applications. WebGestalt 2019 presents an update with expanded functionalities, revamped UIs, a new R package, and web APIs. It addresses the emerging need for tools to analyze phosphoproteomics data and provides a unique -omics enrichment tool. The tool has been validated and is freely accessible at http://www.webgestalt.org.WebGestalt 2019 is an updated version of the gene set analysis tool that supports 12 organisms, 342 gene identifiers, and 155 functional categories. It includes user-uploaded functional databases and provides phosphosite set analysis to identify important kinases from phosphoproteomics data. The tool has been completely redesigned for improved user-friendliness and offers multiple types of interactive and publication-ready figures. Two methods have been implemented to reduce redundancy between enriched gene sets. A web API allows other applications to access data programmatically from the WebGestalt server or pass data for analysis. The core computation has been wrapped into an R package called WebGestaltR, enabling users to perform analysis locally or in third-party workflows. WebGestalt can be freely accessed at http://www.webgestalt.org. WebGestalt supports 342 ID types from 12 organisms and includes 155,175 functional categories from public databases and computational analyses. It now supports phosphosite-level analysis, which is crucial for phosphoproteomics data interpretation. The tool has been enhanced with new visualizations, including bar charts, volcano plots, and DAGs, which help users understand enrichment results. The output report has been improved to include more information and allow sorting by scores and statistics. The tool also provides a web API for programmatic access to data and job submission forms. WebGestalt 2019 includes a new R package, WebGestaltR, which enables batch processing and integration with other computation pipelines. The package supports three methods: Over Representation Analysis (ORA), Gene Set Enrichment Analysis (GSEA), and Network Topology-based Analysis (NTA). The tool also provides RESTful APIs for accessing data and job submission forms. The system has been redesigned to focus on handling user submissions and serving results, with enhanced functionality for interaction with underlying data and job submission forms. The tool is now more accessible to users with programming skills and can be used for a wide range of applications. WebGestalt 2019 presents an update with expanded functionalities, revamped UIs, a new R package, and web APIs. It addresses the emerging need for tools to analyze phosphoproteomics data and provides a unique -omics enrichment tool. The tool has been validated and is freely accessible at http://www.webgestalt.org.