ETL Instructions for Mapping ICDO to SNOMED

COMPLETE ICD-O SOURCE CODES

Cancer diagnoses are usually represented by a combination of ICD-O-3 histology and topography codes. To map this combination to SNOMED follow these steps:

Transform diagnosis SOURCE VALUE

Histology code. In the source, it is normally formatted like this: 8140/3, where 8140 is histology type and 3 is tumor behavior. If histology type and behavior are stored separately, concatenate them to get single histology code.
Topography code. In the source, it is normally formatted like this: C15.3. Be aware of the before the fourth character . If the source doesn't have the dot, insert it after the 3d character: C513 -> C15.3. If the source code contains only 3 characters, add '.9' to get code for "unspecified part of" subcathegory: C50 -> C50.9.
Source value. Concatenate histology code and topography code using hyphen: 8140/3-C51.3. This value will be stored in the CONDITION_OCCURRENCE.CONDITION_SOURCE_VALUE field.

Extract value of diagnosis SOURCE_CONCEPT_ID. Concept_ID for the combined histology/topography code is stored in the CONCEPT table. The following SQL shows how to extract its value for the above example:
```
SELECT CONCEPT_ID
FROM CONCEPT
WHERE CONCEPT_CODE = ‘8140/3-C15.3’ --Adenocarcinoma, NOS, of upper third of esophagus
AND VOCABULARY_ID = ‘ICDO3’
```
The resulting value 44501519 will be stored in the CONDITION_OCCURRENCE.CONDITION_SOURCE_CONCEPT_ID field and will be used in mapping to a standard SNOMED code or itself (next section).
Extract value of STANDARD CONCEPT ID Source concept ID of the combined histology/topography code is mapped to itself or a standard concept ID in the CONCEPT_RELATIONSHIP table. The following SQL shows how to extract its value for the above example:
```
SELECT CONCEPT_ID_2
FROM CONCEPT_RELATIONSHIP
WHERE CONCEPT_ID_1 = 44501519
AND RELATIONSHIP_ID = 'Maps to'
```
The resulting value [36715848] will be stored in the CONDITION_OCCURRENCE.CONDITION_CONCEPT_ID field and/or the EPISODE.EPISODE_OBJECT_CONCEPT_ID.

INCOMPLETE ICD-O SOURCE CODES

In some cases when the source data are incomplete, apply the following approach.

Tumor behavior is not known Use 1 (uncertain behavior) to making your code complete: 8070 -> 8070/1
Topography is unknown Use mappings from this file https://seer.cancer.gov/tools/conversion/ICD03toICD9CM-ICD10-ICD10CM.xls (last 3 tabs of this file) to obtain topography if you have ICD-10 code for this diagnosis. Note, if you have long ICD-10CM code, you need to cut it off to have only 5 symbols (including dot): C50.211 -> C50.2. In case when a patient has several cancer diagnoses, use ICD-10 from the date closest to the ICD-O histology date.
Either Topography or Histology is unretrievable Use string value 'NULL' (spelled out) instead of the code. For instance, neoplasm of endometrium without specified morphology will have code 'NULL-C54.1', and neuronevus without specified site can be coded as '8725/0-NULL'.