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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 06:49]
schuemie [Importing Source Codes into Usagi]
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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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 Finally you can set some restrictions for Usagi when mapping. ​ For example, in Figure 3, the user is mapping the source codes only to concepts in the Condition domain. By default, Usagi only maps to Standard Concepts, but if the the option '​Filter standard concepts'​ is turned off, Usagi will also consider Classification Concepts. Hover your mouse over the different filters for additional information about the filter. Finally you can set some restrictions for Usagi when mapping. ​ For example, in Figure 3, the user is mapping the source codes only to concepts in the Condition domain. By default, Usagi only maps to Standard Concepts, but if the the option '​Filter standard concepts'​ is turned off, Usagi will also consider Classification Concepts. Hover your mouse over the different filters for additional information about the filter.
  
-One special filter is //Filter by automatically selected concepts//​. ​ If there is information that you can use to restrict the search, you can do so by providing a list of CONCEPT_IDs in the column indicated in the //Auto concept ID column// (semicolon-delimited). ​ For example, in the case of drugs there might be a mapping available to ATC codes. ​ Even though an ATC code does not uniquely identify a single RxNorm drug code, it does help limit the search space to only those concepts that fall under the ATC code in the Vocabulary.  ​By providing this list of CONCEPT_IDs in the //Auto concept ID column//and turning ​on //Filter by automatically ​selected concepts//, Usagi will make use of this information. ​ In the example above, we used a partial mapping derived from UMLS to restrict Usagi to this mapping when available.+One special filter is //Filter by automatically selected concepts ​/ ATC code//.  If there is information that you can use to restrict the search, you can do so by providing a list of CONCEPT_IDs ​or an ATC code in the column indicated in the //Auto concept ID column// (semicolon-delimited). ​ For example, in the case of drugs there might already ​be ATC codes assigned to each drug. Even though an ATC code does not uniquely identify a single RxNorm drug code, it does help limit the search space to only those concepts that fall under the ATC code in the Vocabulary. ​To use the ATC code, follow these steps: 
 + 
 +  - In the Column mapping section, switch from 'Auto concept ID column' to 'ATC column'​ 
 +  - In the Column mapping sectionselect the column containing the ATC code as 'ATC column'​.  
 +  - Turn on the 'Filter by user selected concepts / ATC code' on in the Filters section. 
 + 
 +You can also use other sources ​of information ​than the ATC code to restrict as well.  In the example ​shown in the figure ​above, we used a partial mapping derived from UMLS to restrict ​the Usagi searh. In that case we will need to use 'Auto concept ID column'​.
  
 {{ :​documentation:​software:​usagiimport3.png?​direct |}} {{ :​documentation:​software:​usagiimport3.png?​direct |}}
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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