The Progenetix resource utilizes standardized diagnostic coding systems, with a move towards hierarchical ontologies. As part of the coding process we have developed and provide several code mapping resources through repositories, the Progenetix website and APIs.
The Progenetix resource primarily used the coding schemas of the _International Classification of Diseases in Oncology__ (3rd edition; “ICD-O 3”), to classify all biosamples for which experimental data is available. Users can get a list of ICD-O 3 codes in the Progenetix format through Progenetix collations.
The mappings used here for the ICD morphology codings (mapped to ICDMORPHOLOGY and ICDMORPHOLOGYCODE) are derived from the original source file last accessed on 2016-08-18 from the WHO. The primary codes have been updated from the 2011 update document ICDO3Updates2011.pdf.
The organ sites of the original coding have been mapped to UBERON. The mappings are detailed in the related icdot2uberon project.