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PhecodeXVocabulary

This repo includes support files for phecodes, including:

  • Mapping files which specify the ICD codes that define a phecode
  • Information files which include descriptions of phecodes (e.g. phecode strings and phecode categories)

Here is a description of each file:

UPDATE!

We have released a new version of phecodeX. The original version described in our publication is called version 1.0 (we regret not specifying this version number in the publication).

The new version 1.1 includes several updates, including the addition of over 850 ICD10 codes added to the ICD10-CM coding system since 2023. It also corrects spelling errors, mapping errors, and other issues that have been brought to our attention.

We are still working on a WHO-compatible version for phecodeX 1.1. For now, please use the 1.0 files & stay tuned.

Information about phecodeX files

Note: Links in the document below point to the newest release (phecodeX version 1.1), except the WHO mapping codes which have not yet been released.

phecodeX information file

The phecodeX_info.csv file includes information related to each phecode, including the phecode string, category, and columns indicating sex-specificity and ICD-10 only status. The columns are as follows:

phecode         The phecode label (two letters, "_", and numeric phecode)
phecode_string  A descriptive label for phecode
category_num    A numeric value corresponding to the phecode category
category        A string indicating the phecode category
sex             A string with values "Both", "Female", or "Male."  
                Sex specific phecodes (e.g. Prostate cancer) are labeled accordingly
icd10_only      A Boolean value: 1 if the phecode is defined only by ICD-10 codes;
                0 if the phecode is defined by both ICD-9 and -10 codes
phecode_num     The unique numeric component of the phecode label.  Can be useful for                     sorting.

phecodeX to ICD unrolled map

This file includes the ICD-9 and -10 codes that define each phecodes. All codes are “unrolled” meaning that phecode ID_002.1 implies ID_002. This file is particularly useful for generating phecodes from ICD tables using join my mysql or merge in R. The columns are as follows:

phecode         The phecode label
ICD             The ICD code included in the phecode grouping
vocabulary_id   A string indicating the type of ICD code (ICD9CM or 
                ICD10CM)

Use phecodeX_unrolled_ICD_CM.csv for the clinical modification of ICD used in the United States. Use phecodeX_unrolled_ICD_WHO.csv WHO ICD-10 codes.

phecodeX to ICD descriptive map

A highly descriptive file that includes both phecode strings and ICD descriptions. This file is “flat” (i.e. not “unrolled”) such that child codes are not mapped to parents. This file is useful for examining which ICDs inform a particular phecode. The columns are as follows:

phecode         The phecode label
phecode_string  A descriptive label for phecode
category_num    A numeric value corresponding to the phecode category
category        A string indicating the phecode category
ICD             The ICD-9 or ICD-10 code
vocabulary_id   A string indicating the type of ICD code (ICD9CM, ICD10CM, or ICD10)
ICD_string      A string description of the ICD code
ICD_chapter     The chapter of the ICD code

Use phecodeX_ICD_CM_map_flat.csv for the clinical modification of ICD used in the United States. Use phecodeX_ICD_WHO_map_flat.csv WHO ICD-10 codes.

For files that are compatible with the R PheWAS package, along with example code, use this link. (Currently v1.0; never version coming soon!)