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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