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documentation:software:usagi [2017/02/28 17:27]
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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 When we apply these search criteria we find “254761-Cough” and feel this may be an appropriate Vocabulary concept to map to our Dutch code, in order to do that we can hit the “Replace concept”, which you will see the Selected Source Code section update, followed by the “Approved” button. ​ There is also an “Add concept” button, this allows for multiple standardized Vocabulary concepts to map to one source code (e.g. some source codes may bundle multiple diseases together while the standardized vocabulary may not). When we apply these search criteria we find “254761-Cough” and feel this may be an appropriate Vocabulary concept to map to our Dutch code, in order to do that we can hit the “Replace concept”, which you will see the Selected Source Code section update, followed by the “Approved” button. ​ There is also an “Add concept” button, this allows for multiple standardized Vocabulary concepts to map to one source code (e.g. some source codes may bundle multiple diseases together while the standardized vocabulary may not).
 +
 +=== Concept information ===
 +
 +When looking for appropriate concepts to map to, it is important to consider the '​social life' of a concept. The meaning of a concept might depend partially on its place in the hierarchy, and sometimes there are '​orphan concepts'​ in the vocabulary with few or no hierarchical relationships,​ which would be ill-suited as target concepts. Usagi will often report the number of parents and children a concept has, and it also possible to show more information by pressing ALT + C, or selecting //view// --> //Concept information//​ in the top menu bar. 
 +
 +{{ :​documentation:​software:​conceptinformation.png?​direct |}}
 +**Figure 7:  Concept information panel**
 +
 +Figure 7 shows the concept information panel. It shows general information about a concept, as well as its parents, children, and other source codes that map to the concept. Users can use this panel to navigate the hierarchy and potentially choose a different target concept.
  
 === Auto Mapped === === Auto Mapped ===
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 When you import your source codes there is an option to add information about “Auto concept ID column”. ​ If there is information already known that will allow you to map your source data to a CONCEPT_ID, you can include that in the file you upload into Usagi. ​ Once loaded, the Overview Table will list these codes with a status of “Auto mapped to 1” if only one CONCEPT_ID was provided, or just “Auto mapped” if there were more.  You still will be required to approve these auto mappings using the “Approve” button, or if you really trust the underlying information,​ you can sort by status, select all codes with status ‘Auto mapped to 1”, and click //Edit --> Approve selected//. When you import your source codes there is an option to add information about “Auto concept ID column”. ​ If there is information already known that will allow you to map your source data to a CONCEPT_ID, you can include that in the file you upload into Usagi. ​ Once loaded, the Overview Table will list these codes with a status of “Auto mapped to 1” if only one CONCEPT_ID was provided, or just “Auto mapped” if there were more.  You still will be required to approve these auto mappings using the “Approve” button, or if you really trust the underlying information,​ you can sort by status, select all codes with status ‘Auto mapped to 1”, and click //Edit --> Approve selected//.
  
 +Continue to move through this process, code by code, until all codes have been checked. ​ In the list of source codes at the top of the screen, by selecting the column heading you can sort the codes. ​ Often we suggest going from the highest frequency codes to the lowest. In the bottom left of the screen you can see the number of codes that have approved mappings, and how many code occurrences that corresponds to. 
  
-Continue ​to move through this processcode by code, until all codes have been checked. ​ In the list of source codes at the top of the screen, by selecting the column heading you can sort the codes. ​ Often we suggest going from the highest frequency codes to the lowest (often you will find the two set of codes cover most of the data)   +It is possible ​to add comments to mappingswhich could be used to document why a particular mapping decision was made.
  
 Best Practices: Best Practices:
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   * By clicking on a column name you can sort the columns in the Overview Table. ​ It may be valuable to sort on “Match Score”; reviewing codes that Usagi is most confident on first may quickly knock out a significant chunk of codes. ​ Also sorting on “Frequency” is valuable, spending more effort on frequent codes versus non-frequent is important.   * By clicking on a column name you can sort the columns in the Overview Table. ​ It may be valuable to sort on “Match Score”; reviewing codes that Usagi is most confident on first may quickly knock out a significant chunk of codes. ​ Also sorting on “Frequency” is valuable, spending more effort on frequent codes versus non-frequent is important.
   * It is okay to map some codes to CONCEPT_ID = 0, some codes may not be worth it to find a good map and others may just lack a proper map.   * It is okay to map some codes to CONCEPT_ID = 0, some codes may not be worth it to find a good map and others may just lack a proper map.
 +  * It is important to consider the context of a concept, specifically its parents and children.
  
 ==== Export the Usagi Map Created ==== ==== Export the Usagi Map Created ====
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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