J Am Med Inform Assoc - MedXN: an open source medication extraction and normalization tool for clinical text.

Tópicos

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Resumo

JECTIVE: We developed the Medication Extraction and Normalization (MedXN) system to extract comprehensive medication information and normalize it to the most appropriate RxNorm concept unique identifier (RxCUI) as specifically as possible.METHODS: Medication descriptions in clinical notes were decomposed into medication name and attributes, which were separately extracted using RxNorm dictionary lookup and regular expression. Then, each medication name and its attributes were combined together according to RxNorm convention to find the most appropriate RxNorm representation. To do this, we employed serialized hierarchical steps implemented in Apache's Unstructured Information Management Architecture. We also performed synonym expansion, removed false medications, and employed inference rules to improve the medication extraction and normalization performance.RESULTS: An evaluation on test data of 397 medication mentions showed F-measures of 0.975 for medication name and over 0.90 for most attributes. The RxCUI assignment produced F-measures of 0.932 for medication name and 0.864 for full medication information. Most false negative RxCUI assignments in full medication information are due to human assumption of missing attributes and medication names in the gold standard.CONCLUSIONS: The MedXN system (http://sourceforge.net/projects/ohnlp/files/MedXN/) was able to extract comprehensive medication information with high accuracy and demonstrated good normalization capability to RxCUI as long as explicit evidence existed. More sophisticated inference rules might result in further improvements to specific RxCUI assignments for incomplete medication descriptions.

Resumo Limpo

jectiv develop medic extract normal medxn system extract comprehens medic inform normal appropri rxnorm concept uniqu identifi rxcui specif possiblemethod medic descript clinic note decompos medic name attribut separ extract use rxnorm dictionari lookup regular express medic name attribut combin togeth accord rxnorm convent find appropri rxnorm represent employ serial hierarch step implement apach unstructur inform manag architectur also perform synonym expans remov fals medic employ infer rule improv medic extract normal performanceresult evalu test data medic mention show fmeasur medic name attribut rxcui assign produc fmeasur medic name full medic inform fals negat rxcui assign full medic inform due human assumpt miss attribut medic name gold standardconclus medxn system httpsourceforgenetprojectsohnlpfilesmedxn abl extract comprehens medic inform high accuraci demonstr good normal capabl rxcui long explicit evid exist sophist infer rule might result improv specif rxcui assign incomplet medic descript

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