Computational pathology provides accurate tools for defining the intra-tumoral ecological spatial context, having substantial implications for cancer research and medicine. However, the large-scale implementation of computational pathology has been hindered by the lack of a common information standard to represent various histopathological features. Here we propose Histopathology Markup Language (HistoML) Level 1 and Histopathology Ontology for comprehensively and precisely representing various histopathological features, including histopathological phenotypes, their individual components at multiple levels of detail, in a machine-understandable format. We pilot HistoML in representing histopathological features of several neoplastic diseases and exemplify computational analyses on the representations. The example representation files, the source code of the uses cases, Histopathology Ontology, as well as the ontology specification and documentation of HistoML are available in this repository.
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