title: Identifying named entities from PubMed for enriching semantic categories.
abstract: BACKGROUND
  Controlled vocabularies such as the Unified Medical Language System (UMLS) and Medical Subject Headings (MeSH) are widely used for biomedical natural language processing (NLP) tasks. However, the standard terminology in such collections suffers from low usage in biomedical literature, e.g. only 13% of UMLS terms appear in MEDLINE.
  
  
  RESULTS
  We here propose an efficient and effective method for extracting noun phrases for biomedical semantic categories. The proposed approach utilizes simple linguistic patterns to select candidate noun phrases based on headwords, and a machine learning classifier is used to filter out noisy phrases. For experiments, three NLP rules were tested and manually evaluated by three annotators. Our approaches showed over 93% precision on average for the headwords, "gene", "protein", "disease", "cell" and "cells".
  
  
  CONCLUSIONS
  Although biomedical terms in knowledge-rich resources may define semantic categories, variations of the controlled terms in literature are still difficult to identify. The method proposed here is an effort to narrow the gap between controlled vocabularies and the entities used in text. Our extraction method cannot completely eliminate manual evaluation, however a simple and automated solution with high precision performance provides a convenient way for enriching semantic categories by incorporating terms obtained from the literature.
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, 20894, MD, USA. sun.kim@nih.gov.
authors.forename: Sun
authors.initials: S
authors.lastname: Kim
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, 20894, MD, USA. zhiyong.lu@nih.gov.
authors.forename: Zhiyong
authors.initials: Z
authors.lastname: Lu
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, 20894, MD, USA. wilbur@ncbi.nlm.nih.gov.
authors.forename: W John
authors.initials: WJ
authors.lastname: Wilbur
mesh_terms: D001185:Artificial Intelligence; D006801:Humans; D046650:Medical Subject Headings; D009323:Natural Language Processing; D039781:PubMed; D012660:Semantics; D017432:Unified Medical Language System; D018875:Vocabulary, Controlled