WebGestalt 2019 is an updated version of the popular gene set analysis toolkit, featuring enhanced user interfaces and APIs. The tool now supports 12 organisms, 342 gene identifiers, and 155,175 functional categories, including user-uploaded databases. Key improvements include: 1. **Phosphoproteomics Data Interpretation**: New phosphosite set analysis to identify important kinases from phosphoproteomics data. 2. **Result Visualizations**: Redesigned result visualizations and user interfaces for better user-friendliness and publication readiness. 3. **Redundancy Reduction**: Implemented methods to reduce redundancy between enriched gene sets, making results more manageable. 4. **Web API**: A web API for programmatically accessing data from the WebGestalt server or passing data for analysis. 5. **R Package (WebGestaltR)**: Core computation wrapped into an R package for local analysis or integration into third-party workflows. 6. **Functional Annotations**: Updated functional annotations and ID mappings, including new databases like WikiPathways, CPTAC co-expression modules, CORUM, OMIM, and PhosphoSitePlus. The tool is freely accessible at http://www.webgestalt.org and has been cited in numerous papers since its last update. The improvements aim to enhance usability, accessibility, and the interpretability of functional enrichment analysis results.WebGestalt 2019 is an updated version of the popular gene set analysis toolkit, featuring enhanced user interfaces and APIs. The tool now supports 12 organisms, 342 gene identifiers, and 155,175 functional categories, including user-uploaded databases. Key improvements include: 1. **Phosphoproteomics Data Interpretation**: New phosphosite set analysis to identify important kinases from phosphoproteomics data. 2. **Result Visualizations**: Redesigned result visualizations and user interfaces for better user-friendliness and publication readiness. 3. **Redundancy Reduction**: Implemented methods to reduce redundancy between enriched gene sets, making results more manageable. 4. **Web API**: A web API for programmatically accessing data from the WebGestalt server or passing data for analysis. 5. **R Package (WebGestaltR)**: Core computation wrapped into an R package for local analysis or integration into third-party workflows. 6. **Functional Annotations**: Updated functional annotations and ID mappings, including new databases like WikiPathways, CPTAC co-expression modules, CORUM, OMIM, and PhosphoSitePlus. The tool is freely accessible at http://www.webgestalt.org and has been cited in numerous papers since its last update. The improvements aim to enhance usability, accessibility, and the interpretability of functional enrichment analysis results.