The metadata mapping workflow in data ingestion pipeline of bioCADDIE (biomedical and healthCAre Data Discovery Index Ecosystem) allows the different biomedical resources to be described with a unified and coherent metadata model, DATS (DAta Tagging Suite). However, we encountered several challenges during the process due to the differences in how the metadata are structured and what information the metadata are designed to capture between various data repositories (i.e., source data repositories) and DATS. In this presentation we introduce the method used in the metadata mapping and the challenges we encountered during the process of mapping.