title: Can inferred provenance and its visualisation be used to detect erroneous annotation? A case study using UniProtKB.
abstract: A constant influx of new data poses a challenge in keeping the annotation in biological databases current. Most biological databases contain significant quantities of textual annotation, which often contains the richest source of knowledge. Many databases reuse existing knowledge; during the curation process annotations are often propagated between entries. However, this is often not made explicit. Therefore, it can be hard, potentially impossible, for a reader to identify where an annotation originated from. Within this work we attempt to identify annotation provenance and track its subsequent propagation. Specifically, we exploit annotation reuse within the UniProt Knowledgebase (UniProtKB), at the level of individual sentences. We describe a visualisation approach for the provenance and propagation of sentences in UniProtKB which enables a large-scale statistical analysis. Initially levels of sentence reuse within UniProtKB were analysed, showing that reuse is heavily prevalent, which enables the tracking of provenance and propagation. By analysing sentences throughout UniProtKB, a number of interesting propagation patterns were identified, covering over [Formula: see text] sentences. Over [Formula: see text] sentences remain in the database after they have been removed from the entries where they originally occurred. Analysing a subset of these sentences suggest that approximately [Formula: see text] are erroneous, whilst [Formula: see text] appear to be inconsistent. These results suggest that being able to visualise sentence propagation and provenance can aid in the determination of the accuracy and quality of textual annotation. Source code and supplementary data are available from the authors website at http://homepages.cs.ncl.ac.uk/m.j.bell1/sentence_analysis/.
authors.affiliation: School of Computing Science, Newcastle University, Newcastle upon Tyne, United Kingdom.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Bell
authors.forename: Matthew
authors.initials: M
authors.lastname: Collison
authors.forename: Phillip
authors.initials: P
authors.lastname: Lord
mesh_terms: D003196:Computer Graphics; D016001:Confidence Intervals; D030562:Databases, Protein; D016247:Information Storage and Retrieval; D058977:Molecular Sequence Annotation / Q000379:methods*; D012107:Research Design