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. ou can get a list of all ICD-O 3 codes through the Progenetix API.

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.

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 web interface or also as direct API calls:

Preferred ICD-O API calls

http://progenetix.org/icdo3/?

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

http://progenetix.org/icdo3/?85002
http://progenetix.org/icdo3/85002
http://progenetix.org/icdo3/85002/
http://progenetix.org/icdo3/?8500%2F2/

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:

http://progenetix.org/icdo3/?icdmcode=&icdmtext=&json=

Options:

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

Alternative methods

http://progenetix.org/qmongo/?db=progenetix&collection=subsets&all=multvalues&afqfield=SUBSETTYPE&querytext=ICDM&exportk_m=SUBSETTEXT,SAMPLENO&sortby=SUBSETTEXT&counter=y

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

http://progenetix.org/qmongo/?db=progenetix&collection=icdo3morphologies&all=multvalues&afqfield=ICDMORPHOLOGYCODE&querytext=^8140&exportk_m=ICDMORPHOLOGYCODE,ICDMORPHOLOGY,SYNONYMS&sortby=ICDMORPHOLOGYCODE&counter=y

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


Michael Baudis, 2018-05-10