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| - | ====== Usagi ====== | ||
| - | {{ :documentation:usagi_logo.png |}} | ||
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| - | ===== Introduction ===== | ||
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| - | Usagi is a software tool created by the Observational Health Data Sciences and Informatics (OHDSI) team and is used to help in the process of mapping codes from a source system into terminologies, preferably standard ones, stored in the Observational Medical Outcomes Partnership (OMOP) Vocabulary ([[http://www.ohdsi.org/data-standardization/vocabulary-resources/]]). The word Usagi is Japanese for rabbit and was named after the first mapping exercise it was used for; mapping source codes used in a Japanese dataset into OMOP Vocabulary concepts. | ||
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| - | Mapping source codes into the OMOP Vocabulary is valuable for two main reasons: | ||
| - | - When converting a raw dataset into the OMOP Common Data Model (CDM) (http://www.ohdsi.org/data-standardization/the-common-data-model/), translating source specific codes into standard concepts (i.e. RxNorm or SNOMED) translates the source data into a “common language” other CDMs follow. | ||
| - | - Having source codes tied into the OMOP Vocabulary concepts allow a researcher to leverage the power of finding relevant source codes leveraging classification terminologies in the OMOP Vocabulary (e.g. find all antipsychotic medications or find all condition codes related to heart failure). | ||
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| - | ==== Scope and purpose ==== | ||
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| - | 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 Unified Medical Language System (UMLS) to find 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. | ||
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| - | 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. | ||
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| - | ==== Process Overview ==== | ||
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| - | The typical sequence for using this software is: | ||
| - | - Load codes from your sources system (“source codes”) that you would like to map to OMOP Vocabulary concepts. | ||
| - | - Usagi will run term similarity approach to map source codes to OMOP Vocabulary concepts. | ||
| - | - Leverage Usagi interface to check suggested mappings or create maps. Preferably an individual who has experience with the coding system and medical terminology should be used for this review. | ||
| - | - Export final map generated by Usagi into the OMOP Vocabulary’s SOURCE_TO_CONCEPT_MAP. | ||
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| - | ===== Installation and support ===== | ||
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| - | All source code and installation instructions are available on Usagi’s GitHub site: | ||
| - | [[https://github.com/OHDSI/Usagi]] | ||
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| - | Any bugs/issues/enhancements should be posted to the GitHub repository: | ||
| - | [[https://github.com/OHDSI/Usagi/issues]] | ||
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| - | Any questions/comments/feedback/discussion can be posted on the OHDSI Developer Forum: [[http://forums.ohdsi.org/c/developers]] | ||
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| - | ===== Using the Application Functions ===== | ||
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| - | ==== Importing Source Codes into Usagi ==== | ||
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| - | TBD | ||
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| - | ==== Reviewing Source Code to OMOP Vocabulary Concept Maps ==== | ||
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| - | TBD | ||
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| - | === Approving a Suggested Mapping === | ||
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| - | TBD | ||
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| - | === Searching for a New Mapping === | ||
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| - | TBD | ||
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| - | === Auto Mapped === | ||
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| - | TBD | ||
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| - | ==== Export the Usagi Map Created ==== | ||
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| - | TBD | ||
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| - | ==== Menu Options ==== | ||
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| - | TBD | ||
documentation/usagi.1418832326.txt.gz · Last modified: 2014/12/17 16:05 by ericavoss
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