documentation:oncology:meeting_notes_2017_apr_04
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documentation:oncology:meeting_notes_2017_apr_04 [2017/04/10 02:26] rimma_belenkaya created |
documentation:oncology:meeting_notes_2017_apr_04 [2017/04/10 03:36] (current) rimma_belenkaya1 |
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| **The group agreed to explore the onco domains in the following order:** | **The group agreed to explore the onco domains in the following order:** | ||
| - | 1. Diagnosis | + | - Diagnosis |
| - | 2. Treatment | + | - Treatment |
| - | 3. Outcomes survival | + | - Outcomes survival |
| - | 4. Molecular biomarkers | + | - Molecular biomarkers |
| - | 5. Pathology reports | + | - Pathology reports |
| - | 6. Imaging | + | - Imaging |
| - | 7. Performance status | + | - Performance status |
| **Existing standards** | **Existing standards** | ||
| Line 14: | Line 14: | ||
| **Exploratory data set** | **Exploratory data set** | ||
| + | |||
| · Christian would try putting together a working data set | · Christian would try putting together a working data set | ||
| **ICD-O-3 overview** | **ICD-O-3 overview** | ||
| - | · Mike outlined the ICD-O-3 that granularly captures the anatomic and morphological/behavior that can be mapped to the condition_occurence in the OMOP CDM model. | ||
| + | [[https://drive.google.com/file/d/0Bzcc8twUxevJcVpybm8zX2dUZWs/view?usp=sharing.| Michael Gurley's ICD-O-3 Presentation and proposal for CDM cancer diagnosis modeling ]] | ||
| - | · Iker suggested that the ICD-O-3 could be mapped to SNOMED and agreed to provide some links to the group. | + | * ICD-O-3 provides most granular representation of cancer diagnosis including anatomic side and morphological/behavior. |
| + | * Diagnosis can be represented in condition_occurence | ||
| + | |||
| + | |||
| + | **ICD-O-3 Mapping** | ||
| + | |||
| + | * Iker suggested that NCI Metatethaurus provides mapping of ICD-O-3 to SNOMED and some other vocabularies | ||
| + | |||
| + | * Memorial Sloan Kettering (MSK) Oncotree mapping | ||
| + | |||
| + | At MSK we maintain a cancer tumor terminology called oncotree (which is publicly available) | ||
| + | http://oncotree.mskcc.org/oncotree/ | ||
| + | |||
| + | We also have a public API that maps ICDO site and histology combinations to Oncotree concepts, which at the same time are mapped to NCI Thesaurus and UMLS, see | ||
| + | http://oncotree.mskcc.org/oncotree-mappings/ | ||
| + | |||
| + | An example for that API would be | ||
| + | http://oncotree.mskcc.org/oncotree-mappings/crosswalk?vocabularyId=ICDO&conceptId=&histologyCode=8490/3&siteCode=C16.1 | ||
documentation/oncology/meeting_notes_2017_apr_04.1491791203.txt.gz · Last modified: 2017/04/10 02:26 by rimma_belenkaya
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