title: A protocol for the update of references to scientific literature in biological databases.
abstract: Entries in biological databases are usually linked to scientific references. To generate those links and to keep them up-to-date, database maintainers have to continuously scan the scientific literature to select references that are relevant for each single database entry. The continuous growth of both the corpus of scientific literature and the size of biological databases makes this task very hard. We present a protocol intended to assist the updating of an existing set of literature (abstract) links from a single database entry with new references. It consists of taking the set of MEDLINE neighbour references of the existing linked abstracts and evaluating their relevance according to the existing set of abstracts. To test the applicability of the algorithm, we did a simple benchmark of the system using the references associated with the entries of a protein domain database. Human experts found the references that the algorithm scored highly were more relevant to the database entry than those scored lowly, suggesting that the algorithm was useful.
authors.affiliation: European Molecular Biology Laboratory, Heidelberg, Germany. cperez-iratxeta@ohri.ca
authors.forename: Carolina
authors.initials: C
authors.lastname: Perez-Iratxeta
authors.forename: Nagore
authors.initials: N
authors.lastname: Astola
authors.forename: Francesca D
authors.initials: FD
authors.lastname: Ciccarelli
authors.forename: Parantu K
authors.initials: PK
authors.lastname: Sha
authors.forename: Peer
authors.initials: P
authors.lastname: Bork
authors.forename: Miguel A
authors.initials: MA
authors.lastname: Andrade
mesh_terms: D000043:Abstracting and Indexing / Q000379:methods*; D000465:Algorithms; D003628:Database Management Systems; D016208:Databases, Factual; D004282:Documentation; D005240:Feasibility Studies; D016247:Information Storage and Retrieval / Q000379:methods*; D016239:MEDLINE; D009323:Natural Language Processing; D010506:Periodicals as Topic; D009626:Terminology as Topic