ICD coding of tumor samples

  • You can get a list of all ICD-O 3 codes here.

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 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

  • nnnnn (81403)
  • nnnnn/ (81403/)
  • nnnn/n (8140/3)
  • nnnn%2Fn (8140%2F3) - only with leading "?"!

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:

  • icdmcode=81...0
    • will return all ICD codes starting with "81" and having a grade code of "0"

  • icdmtext=myx
    • will return all ICD codes with a "myx" anywhere in the text of the primary icdmorphology or any of the synonyms

  • json=T
    • will return the data as JSON

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

Topic revision: r6 - 30 Sep 2016, MichaelBaudis
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