Considerations to improve functional annotations in biological databases.
Despite the great effort to design efficient systems allowing the electronic indexation of information concerning genes, proteins, structures, and interactions published daily in scientific journals, some problems are still observed in specific tasks such as functional annotation. The annotation of function is a critical issue for bioinformatic routines, such as for instance, in functional genomics and the further prediction of unknown protein function, which are highly dependent of the quality of existing annotations. Some information management systems evolve to efficiently incorporate information from large-scale projects, but often, annotation of single records from the literature is difficult and slow. In this short report, functional characterizations of a representative sample of the entire set of uncharacterized proteins from Escherichia coli K12 was compiled from Swiss-Prot, PubMed, and EcoCyc and demonstrate a functional annotation deficit in biological databases. Some issues are postulated as causes of the lack of annotation, and different solutions are evaluated and proposed to avoid them. The hope is that as a consequence of these observations, there will be new impetus to improve the speed and quality of functional annotation and ultimately provide updated, reliable information to the scientific community.
Benítez-Páez
Alfonso
A
Bioinformatic Analysis Group (GABi), Centro de Investigación y Desarrollo en Biotecnología (CIDBIO), Bogotá D.C., Colombia, USA. abenitez@cidbio.org
D003628:Database Management Systems; D016208:Databases, Factual; D004926:Escherichia coli / Q000737:chemistry / Q000235:genetics; D029968:Escherichia coli Proteins / Q000235:genetics; D016247:Information Storage and Retrieval; D039781:PubMed
D029968:Escherichia coli Proteins