title: Terminologies for text-mining; an experiment in the lipoprotein metabolism domain.
abstract: BACKGROUND
  The engineering of ontologies, especially with a view to a text-mining use, is still a new research field. There does not yet exist a well-defined theory and technology for ontology construction. Many of the ontology design steps remain manual and are based on personal experience and intuition. However, there exist a few efforts on automatic construction of ontologies in the form of extracted lists of terms and relations between them.
  
  
  RESULTS
  We share experience acquired during the manual development of a lipoprotein metabolism ontology (LMO) to be used for text-mining. We compare the manually created ontology terms with the automatically derived terminology from four different automatic term recognition (ATR) methods. The top 50 predicted terms contain up to 89% relevant terms. For the top 1000 terms the best method still generates 51% relevant terms. In a corpus of 3066 documents 53% of LMO terms are contained and 38% can be generated with one of the methods.
  
  
  CONCLUSIONS
  Given high precision, automatic methods can help decrease development time and provide significant support for the identification of domain-specific vocabulary. The coverage of the domain vocabulary depends strongly on the underlying documents. Ontology development for text mining should be performed in a semi-automatic way; taking ATR results as input and following the guidelines we described.
  
  
  BACKGROUND
  The TFIDF term recognition is available as Web Service, described at http://gopubmed4.biotec.tu-dresden.de/IdavollWebService/services/CandidateTermGeneratorService?wsdl.
authors.affiliation: Biotechnology Center, Technische Universität Dresden, Dresden, D-01062, Germany. dimitra.alexopoulou@biotec.tu-dresden.de
authors.forename: Dimitra
authors.initials: D
authors.lastname: Alexopoulou
authors.forename: Thomas
authors.initials: T
authors.lastname: Wächter
authors.forename: Laura
authors.initials: L
authors.lastname: Pickersgill
authors.forename: Cecilia
authors.initials: C
authors.lastname: Eyre
authors.forename: Michael
authors.initials: M
authors.lastname: Schroeder
mesh_terms: D000465:Algorithms; D003628:Database Management Systems; D016208:Databases, Factual; D008074:Lipoproteins / Q000145:classification* / Q000378:metabolism*; D009323:Natural Language Processing; D010506:Periodicals as Topic; D012660:Semantics; D012984:Software; D009626:Terminology as Topic
chemical_list: D008074:Lipoproteins