MetaMap Lite in Excel: Biomedical Named-Entity Recognition for Non-Technical Users

摘要

We developed an easy-to-use tool for non-technical biomedical researchers to conduct Named-Entity Recognition (NER) on biomedical text, in a familiar spreadsheet environment. The system is a simple, offline, easy to install, end-user front-end to the new MetaMap Lite. Early adopters found it to be a quick starting-point to incorporate NER in their investigations. The application of Named Entity Recognition (NER) has become pervasive. Biomedical researchers, who may not have strong computer skills, often wish to apply NER methods and tools to extract information from text. MetaMap (https://metamap.nlm.nih.gov/) is one of the most popular tools for biomedical Named Entity Recognition (NER), more specifically for identifying terms from the Unified Medical Language System (UMLS) Metathesaurus in biomedical text. MetaMap Lite is a recent Java reimplementation of the original MetaMap. Running these tools on biomedical text and parsing their output generally requires some programming skills, which places them out of reach for non-technical users. Our objective is to make biomedical NER tools easier to use by non-technical users.