documentation:software:usagi
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documentation:software:usagi [2015/05/21 02:30] schuemie |
documentation:software:usagi [2017/02/28 12:42] schuemie [Importing Source Codes into Usagi] |
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| ==== Scope and purpose ==== | ==== Scope and purpose ==== | ||
| - | A source codes file 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 OMOP Vocabulary concepts (currently only OMOP Vocabulary V5). At a high level this term similarity approach works by 1) leveraging synonyms for concepts in the OMOP Vocabulary (i.e. if the concept in the OMOP Vocabulary is “Myocardial infarction” a synonym for that concept is “heart attack”) and 2) map source code descriptions (in English) to the OMOP Vocabulary concepts by using by using a term similarity score. 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 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 will only propose concepts that are marked as **standard concepts** in the OMOP Vocabulary. | + | Usagi will only propose concepts that are marked as **standard concepts** in the Vocabulary. |
| ==== Process Overview ==== | ==== Process Overview ==== | ||
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| ==== Importing Source Codes into Usagi ==== | ==== Importing Source Codes into Usagi ==== | ||
| - | Export source codes from source system into a CSV or Excel (.xlsx) file. This should at least have the columns SOURCE_CODE and SOURCE_CODE_DESCRIPTION however additional information about codes can be brought over as well (e.g. DOSE_UNIT). In addition to information about the source codes, the frequency of the code should also be brought over as FREQUENCY, this can help prioritize which codes should receive the most effort in mapping (i.e. you can have 1,000 source codes but only 100 are truly used within the system). If any source code information needs translating to English, use Google Translate to do that. Add the English translations to your file. | + | Export source codes from source system into a CSV or Excel (.xlsx) file. This should at least have columns containing the **source code** and an English **source code description**, however additional information about codes can be brought over as well (e.g. dose unit, or the description in the original language if translated). In addition to information about the source codes, the **frequency of the code** should preferably also be brought over, since this can help prioritize which codes should receive the most effort in mapping (e.g. you can have 1,000 source codes but only 100 are truly used within the system). If any source code information needs translating to English, use Google Translate to do that. |
| Note: source code extracts should be broken out by domain (i.e. drugs, procedures, conditions, observations) and not lumped into one large file. | Note: source code extracts should be broken out by domain (i.e. drugs, procedures, conditions, observations) and not lumped into one large file. | ||
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| Source codes are loaded into Usagi from the File --> Import codes menu. From here an “Import codes ...” will display as seen in Figure 1. | Source codes are loaded into Usagi from the File --> Import codes menu. From here an “Import codes ...” will display as seen in Figure 1. | ||
| - | {{ :documentation:loadingscreen1.png?direct |}} | + | {{ :documentation:software:usagiimport.png?direct |}} |
| **Figure 1: Usagi Source Code Input Screen** | **Figure 1: Usagi Source Code Input Screen** | ||
| - | In Figure 1, the source code terms were in Dutch and were also translated into English. Usagi will leverage the English translations to map to the standard vocabulary (SNOMED in this case). | + | In Figure 1, the source code terms were in Dutch and were also translated into English. Usagi will leverage the English translations to map to the standard vocabulary. |
| - | {{ :documentation:loadingscreen2.png?direct |}} | + | {{ :documentation:software:usagiimport2.png?direct |}} |
| **Figure 2: Telling Usagi how to Read Input File** | **Figure 2: Telling Usagi how to Read Input File** | ||
| Seen in Figure 2, the //Column mapping// section is where you define for Usagi how to use the imported CSV. If you mouse hover over the drop downs, a pop-up will appear defining each column. Usagi will not use the //Additional info column(s)// as information to associate source codes to Vocabulary concept codes; however this additional information may help the individual reviewing the source code mapping and should be included. | Seen in Figure 2, the //Column mapping// section is where you define for Usagi how to use the imported CSV. If you mouse hover over the drop downs, a pop-up will appear defining each column. Usagi will not use the //Additional info column(s)// as information to associate source codes to Vocabulary concept codes; however this additional information may help the individual reviewing the source code mapping and should be included. | ||
| - | Finally you can tell Usagi what OMOP Vocabulary terminologies you plan to map into. For example, in Figure 3, the user is mapping the source codes to the SNOMED standard terminology the OMOP Vocabulary. 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//. 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. | ||
| - | {{ :documentation:loadingscreen3.png?direct |}} | + | {{ :documentation:software:usagiimport3.png?direct |}} |
| - | **Figure 3: Defining OMOP Vocabulary Terminology Usagi Should Plan to Map to** | + | **Figure 3: Defining filter rules when mapping** |
| Once all your settings are finalized, click the "Import" button to import the file. The file import will take a few minutes as it is running the term similarity algorithm to map source codes. | Once all your settings are finalized, click the "Import" button to import the file. The file import will take a few minutes as it is running the term similarity algorithm to map source codes. | ||
documentation/software/usagi.txt · Last modified: 2021/04/09 18:56 by maximmoinat
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