What is NER?
Named Entity Recognition, including entities such as proteins, genes, diseases, treatments, drugs, etc. in the biomedical domain
Biomedical Information Extraction is an exciting field at the crossroads of Natural Language Processing, Biology and Medicine. It encompasses a variety of different tasks that require application of state-of-the-art NLP techniques, such as NER and Relation Extraction. This paper provides an overview of the problems in the field and discusses some of the techniques used for solving them.
The explosion of available scientific articles in the Biomedical domain has led to the rise of Biomedical Information Extraction (BioIE). BioIE systems aim to extract information from a wide spectrum of articles including medical literature, biological literature, electronic health records, etc. that can be used by clinicians and researchers in the field. Often the outputs of BioIE systems are used to assist in the creation of databases, or to suggest new paths for research. For example, a ranked list of interacting proteins that are extracted from biomedical literature, but are not present in existing databases, can allow researchers to make informed decisions about which protein/gene to study further. Interactions between drugs are necessary for clinicians who simultaneously administer multiple drugs to their patients. A database of diseases, treatments and tests is beneficial for doctors consulting in complicated medical cases. The main problems in BioIE are similar to those in Information Extraction: This paper discusses, in each section, various methods that have been adopted to solve the listed problems. Each section also highlights the difficulty of Information Extraction tasks in the biomedical domain. This paper is intended as a primer to Biomedical Information Extraction for current NLP researchers. It aims to highlight the diversity of the various techniques from Information Extraction that have been applied in the Biomedical domain. The state of biomedical text mining is reviewed regularly. For more extensive surveys, consult BIBREF0 , BIBREF1 , BIBREF2 .