documentation:software:usagi
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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: 2021/04/09 18:56 by maximmoinat
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