<b>PathoGraph: A Graph-Based M</b><b>ethod</b><b> for Standardized Representation of Pathology Knowledge</b>

This repository contains the open-source datasets and source code associated with the research project titled "PathoGraph: A Graph-Based Method for Standardized Representation of Pathology Knowledge", as described in our manuscript submitted to Nature Scientific Data. The materials are intended to promote transparency, reproducibility, and further research in the field of data and knowledge management.Contents:Language Specification: The file named "PathoML.owl" is the ontology specification of Pathology Markup Language.PathoGraph Representations: The XML files included in the folder "Representation_Examples" are exemplar PathoGraph representations including the ones representing HER2 immunophenotypes, the follicular pattern of papillary thyroid carcinoma, the histological subtyping process for a cervical slide, and the differential diagnosis for histolgical subtyping of lymphoma.Source Code: The files in the folder "Use_Case" are source codes of the two use cases, including the case of quantitative analysis of her2 expression and the one of automatic histologic subtyping.