The Harmonizome is a comprehensive collection of processed datasets that serve to integrate and mine knowledge about genes and proteins. It aggregates data from over 70 major online resources, extracting and organizing information into approximately 72 million functional associations between genes/proteins and their attributes, such as physical relationships, expression patterns, genetic associations, and drug response changes. These associations are stored in a relational database along with rich metadata. The Harmonizome provides a web portal with a graphical user interface, web service, and mobile app for querying, browsing, and downloading data. It also includes tools for visualizing gene-gene and attribute-attribute similarity networks, and for identifying unexpected relationships between datasets. The resource enables researchers to discover novel biological relationships and form data-driven hypotheses for experimental validation. The Harmonizome includes advanced search functionality, allowing users to search for genes, datasets, or attributes. It also provides a global summary visualization of gene knowledge across all datasets, known as the Harmonogram, which displays gene associations with datasets. The resource also includes interactive heat maps and hierarchical clustering for exploring data. The Harmonizome has been used to identify unexpected relationships, such as those between kinase perturbations and disease signatures, and to predict novel substrates for kinases, endogenous ligands for G-protein coupled receptors, and mouse phenotypes for knockout genes. The Harmonizome mobile app provides a user-friendly interface for exploring gene properties and functions. It is available on both Android and iOS platforms. The resource also includes machine learning case studies, such as predicting ion channels from uncharacterized transmembrane proteins, predicting mouse phenotypes for single gene knockouts, and predicting endogenous ligands for G-protein coupled receptors and kinase substrates. These studies demonstrate the utility of the Harmonizome in generating novel hypotheses for experimental validation. The Harmonizome is a valuable resource for researchers in the field of genomics and proteomics, providing a comprehensive collection of processed datasets that can be used to integrate and mine knowledge about genes and proteins. It enables the discovery of novel biological relationships and the generation of data-driven hypotheses for further experimental validation. The resource is freely available and continuously maintained and expanded.The Harmonizome is a comprehensive collection of processed datasets that serve to integrate and mine knowledge about genes and proteins. It aggregates data from over 70 major online resources, extracting and organizing information into approximately 72 million functional associations between genes/proteins and their attributes, such as physical relationships, expression patterns, genetic associations, and drug response changes. These associations are stored in a relational database along with rich metadata. The Harmonizome provides a web portal with a graphical user interface, web service, and mobile app for querying, browsing, and downloading data. It also includes tools for visualizing gene-gene and attribute-attribute similarity networks, and for identifying unexpected relationships between datasets. The resource enables researchers to discover novel biological relationships and form data-driven hypotheses for experimental validation. The Harmonizome includes advanced search functionality, allowing users to search for genes, datasets, or attributes. It also provides a global summary visualization of gene knowledge across all datasets, known as the Harmonogram, which displays gene associations with datasets. The resource also includes interactive heat maps and hierarchical clustering for exploring data. The Harmonizome has been used to identify unexpected relationships, such as those between kinase perturbations and disease signatures, and to predict novel substrates for kinases, endogenous ligands for G-protein coupled receptors, and mouse phenotypes for knockout genes. The Harmonizome mobile app provides a user-friendly interface for exploring gene properties and functions. It is available on both Android and iOS platforms. The resource also includes machine learning case studies, such as predicting ion channels from uncharacterized transmembrane proteins, predicting mouse phenotypes for single gene knockouts, and predicting endogenous ligands for G-protein coupled receptors and kinase substrates. These studies demonstrate the utility of the Harmonizome in generating novel hypotheses for experimental validation. The Harmonizome is a valuable resource for researchers in the field of genomics and proteomics, providing a comprehensive collection of processed datasets that can be used to integrate and mine knowledge about genes and proteins. It enables the discovery of novel biological relationships and the generation of data-driven hypotheses for further experimental validation. The resource is freely available and continuously maintained and expanded.