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documentation:software:usagi [2017/02/28 17:40]
schuemie [Reviewing Source Code to OMOP Vocabulary Concept Maps]
documentation:software:usagi [2018/08/24 06:42]
schuemie [Scope and purpose]
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 Source codes that needs mapping are loaded into the Usagi (if the codes are not in English additional translations columns are needed). ​ A term similarity approach is used to connect source codes to Vocabulary concepts. However these code connections need to be manually reviewed and Usagi provides an interface to facilitate that.  ​ Source codes that needs mapping are loaded into the Usagi (if the codes are not in English additional translations columns are needed). ​ A term similarity approach is used to connect source codes to Vocabulary concepts. However these code connections need to be manually reviewed and Usagi provides an interface to facilitate that.  ​
  
-Usagi currently does not currently ​translate non-English codes to English. ​ We suggest using Google Translate ([[https://​translate.google.com/​]]). ​ You can paste an entire column of non-English terms into Google Translate, and it will return that same column translated to English.+Usagi currently does not translate non-English codes to English. ​ We suggest using Google Translate ([[https://​translate.google.com/​]]). ​ You can paste an entire column of non-English terms into Google Translate, and it will return that same column translated to English.
  
 Usagi will only propose concepts that are marked as **standard concepts** in the Vocabulary. Usagi will only propose concepts that are marked as **standard concepts** in the Vocabulary.
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 After selecting the SOURCE_VOCABULARY_ID,​ you give your export CSV a name and save to location. ​ The export CSV structure is in that of the SOURCE_TO_CONCEPT_MAP table. ​ This mapping could be appended to the OMOP Vocabulary’s SOURCE_TO_CONCEPT_MAP table. ​ It would also make sense to append a single row to the VOCABULARY table defining the SOURCE_VOCABULARY_ID you defined in the step above. ​ Finally, it is important to note that only mappings with the “Approved” status will be exported into the CSV file; the mapping needs to be completed in USAGI in order to export it. After selecting the SOURCE_VOCABULARY_ID,​ you give your export CSV a name and save to location. ​ The export CSV structure is in that of the SOURCE_TO_CONCEPT_MAP table. ​ This mapping could be appended to the OMOP Vocabulary’s SOURCE_TO_CONCEPT_MAP table. ​ It would also make sense to append a single row to the VOCABULARY table defining the SOURCE_VOCABULARY_ID you defined in the step above. ​ Finally, it is important to note that only mappings with the “Approved” status will be exported into the CSV file; the mapping needs to be completed in USAGI in order to export it.
 +
 +==== Updating an Usagi mapping ====
 +
 +Often a mapping is not a one-time effort. As data is updated perhaps new source codes are added, and also the vocabulary is updated regularly, perhaps requiring an update of the mapping. ​
 +
 +When the set of source codes is updated the following steps can be followed to support the update:
 +
 +1. Import the new source code file
 +2. Choose //File// --> //Apply previous mapping//, and select the old Usagi mapping file
 +3. Identify codes that haven'​t inherited approved mappings from the old mapping, and map them as usual.
 +
 +When the vocabulary is updated, follow these steps:
 +1. Download the new vocabulary files from Athena
 +2. Rebuild the Usagi index (//Help// --> //Rebuild index//)
 +3. Open the mapping file
 +4. Identify codes that map to concepts that in the new vocabulary version no longer are Standard concepts, and find more appropriate target concepts. ​
  
 ==== Menu Options ==== ==== Menu Options ====
documentation/software/usagi.txt · Last modified: 2018/08/24 06:49 by schuemie