ICD-O 3 Coding

ICD coding of tumor samples

The Progenetix and arrayMap resources use 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.

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 [[http://apps.who.int/classifications/icd/adaptations/oncology/en/index.html][the WHO]]. The primary codes have been updated from the 2011 update document [[http://www.who.int/classifications/icd/updates/ICDO3Updates2011.pdf][ICDO3Updates2011.pdf]].

As of 2016-08-22, we now list the whole content of ICD-O 3 morphology codings, including those codes for which no sample data is available (yet). The data can be accessed through the [[http://www.progenetix.org/subsets/?subsettype=ICDM][web interface]] or also as direct API calls:

Preferred ICD-O API calls


The base link above (alias to http://www.progenetix.org/icdo3morphologies/?) will list all >1000 ICD-O 3 codes, in a tab-delimited text format (synonyms are here concatenated by “::”).

Direct ICD-O text retrieval:

With a valid ICD-O 3 code as single keyword, the corresponding text is returned. The code can be provided as


ICD code & text queries:

The ICD-O data can be queried using 2 parameters; also, ICD-O data can be accessed in JSON format. The (current) query structure is expressed here:



The icdmcode and icdmtext query attributes are connected through a Boolean “AND”.

Alternative methods


… will list all ICD-O 3 morphologies, as text, with the corresponding samplenumber in Progenetix (use db=arraymap for the arraymap numbers)


…will list all ICD entities starting with 814, in a tab delimited table

Michael Baudis, 2018-05-10

Michael Baudis, 2018-05-10