title: GOChase-II: correcting semantic inconsistencies from Gene Ontology-based annotations for gene products.
abstract: BACKGROUND
  The Gene Ontology (GO) provides a controlled vocabulary for describing genes and gene products. In spite of the undoubted importance of GO, several drawbacks associated with GO and GO-based annotations have been introduced. We identified three types of semantic inconsistencies in GO-based annotations; semantically redundant, biological-domain inconsistent and taxonomy inconsistent annotations.
  
  
  METHODS
  To determine the semantic inconsistencies in GO annotation, we used the hierarchical structure of GO graph and tree structure of NCBI taxonomy. Twenty seven biological databases were collected for finding semantic inconsistent annotation.
  
  
  RESULTS
  The distributions and possible causes of the semantic inconsistencies were investigated using twenty seven biological databases with GO-based annotations. We found that some evidence codes of annotation were associated with the inconsistencies. The numbers of gene products and species in a database that are related to the complexity of database management are also in correlation with the inconsistencies. Consequently, numerous annotation errors arise and are propagated throughout biological databases and GO-based high-level analyses. GOChase-II is developed to detect and correct both syntactic and semantic errors in GO-based annotations.
  
  
  CONCLUSIONS
  We identified some inconsistencies in GO-based annotation and provided software, GOChase-II, for correcting these semantic inconsistencies in addition to the previous corrections for the syntactic errors by GOChase-I.
authors.affiliation: Seoul National University Biomedical Informatics, Div of Biomedical Informatics, Seoul National University College of medicine, Seoul 110799, Korea. kirarang@snu.ac.kr
authors.forename: Yu Rang
authors.initials: YR
authors.lastname: Park
authors.forename: Jihun
authors.initials: J
authors.lastname: Kim
authors.forename: Hye Won
authors.initials: HW
authors.lastname: Lee
authors.forename: Young Jo
authors.initials: YJ
authors.lastname: Yoon
authors.forename: Ju Han
authors.initials: JH
authors.lastname: Kim
mesh_terms: D019295:Computational Biology / Q000379:methods; D003628:Database Management Systems; D030541:Databases, Genetic; D058977:Molecular Sequence Annotation; D011506:Proteins / Q000737:chemistry / Q000145:classification; D012660:Semantics; D012984:Software; D018875:Vocabulary, Controlled
chemical_list: D011506:Proteins