This paper presents a novel prototype for biomedical term normalization of electronic health record excerpts with the Unified Medical Language System (UMLS) Metathesaurus. Despite being multilingual and cross-lingual by design, we first focus on processing clinical text in Spanish because there is no existing tool for this language and for this specific purpose. The tool is based on Apache Lucene to index the Metathesaurus and generate mapping candidates from input text. It uses the IXA pipeline for basic language processing and resolves ambiguities with the UKB toolkit. It has been evaluated by measuring its agreement with MetaMap in two English-Spanish parallel corpora. In addition, we present a web-based interface for the tool.
@cite_17 @cite_8 proposed a Spanish MetaMap'' that combines machine translation techniques with the use of MetaMap. Unfortunately, they did not apply this system to any task, so performance scores cannot be reported.
@cite_8 @cite_17
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MetaMap is an online application that allows mapping text to UMLS Metathesaurus concepts, which is very useful interoperability among different languages and systems within the biomedical domain. MetaMap Transfer (MMTx) is a Java program that makes MetaMap available to biomedical researchers. Currently there is no Spanish version of MetaMap, which difficults the use of UMLS Metathesaurus to extract concepts from Spanish biomedical texts. Our ongoing research is mainly focused on using biomedical concepts for cross-lingual text classification and retrieval [3]. In this context the use of concepts instead of bag of words representation allows us to face text classification tasks abstracting from the language [4]. In this paper we evaluate the possibility of combining automatic translation techniques with the use of biomedical ontologies to produce an English text that can be processed by MMTx. The use of domain ontologies is becoming increasingly popular in Medical Natural Language Processing Systems. A wide variety of knowledge bases in multiple languages has been integrated into the Unified Medical Language System (UMLS) to create a huge knowledge source that can be accessed with diverse lexical tools. MetaMap (and its java version MMTx) is a tool that allows extracting medical concepts from free text, but currently there not exists a Spanish version. Our ongoing research is centered on the application of biomedical concepts to cross-lingual text classification, what makes it necessary to have a Spanish MMTx available. We have combined automatic translation techniques with biomedical ontologies and the existing English MMTx to produce a Spanish version of MMTx. We have evaluated different approaches and applied several types of evaluation according to different concept representations for text classification. Our results prove that the use of existing translation tools such as Google Translate produce translations with a high similarity to original texts in terms of extracted concepts.