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--- documentation:software:usagi [2017/02/28 17:51]
schuemie
+++ documentation:software:usagi [2018/08/24 06:49]
schuemie [Importing Source Codes into Usagi]
@@ Line 15: / Line 15: @@
 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.
@@ Line 59: / Line 59: @@
 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 section, select 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'.
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