title: Strategies to improve usability and preserve accuracy in biological sequence databases.
abstract: Biology is increasingly dependent on large-scale analysis, such as proteomics, creating a requirement for efficient bioinformatics. Bioinformatic predictions of biological functions rely upon correctly annotated database sequences, and the presence of inaccurately annotated or otherwise poorly described sequences introduces noise and bias to biological analyses. Accurate annotations are, for example, pivotal for correct identification of polypeptide fragments. However, standards for how sequence databases are organized and presented are currently insufficient. Here, we propose five strategies to address fundamental issues in the annotation of sequence databases: (i) to clearly separate experimentally verified and unverified sequence entries; (ii) to enable a system for tracing the origins of annotations; (iii) to separate entries with high-quality, informative annotation from less useful ones; (iv) to integrate automated quality-control software whenever such tools exist; and (v) to facilitate postsubmission editing of annotations and metadata associated with sequences. We believe that implementation of these strategies, for example as requirements for publication of database papers, would enable biology to better take advantage of large-scale data.
authors.affiliation: Department of Infectious Diseases, Institute of Biomedicine, the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden. johan.bengtsson-palme@microbiology.se.|Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden. johan.bengtsson-palme@microbiology.se.
authors.forename: Johan
authors.initials: J
authors.lastname: Bengtsson-Palme
authors.affiliation: Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden.|Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden.|Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
authors.forename: Fredrik
authors.initials: F
authors.lastname: Boulund
authors.affiliation: Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden.|Department of Computer Science and Engineering, Chalmers University of Technology, Gothenburg, Sweden.
authors.forename: Robert
authors.initials: R
authors.lastname: Edström
authors.affiliation: Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
authors.forename: Amir
authors.initials: A
authors.lastname: Feizi
authors.affiliation: Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden.|Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden.
authors.forename: Anna
authors.initials: A
authors.lastname: Johnning
authors.affiliation: Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden.
authors.forename: Viktor A
authors.initials: VA
authors.lastname: Jonsson
authors.affiliation: Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
authors.forename: Fredrik H
authors.initials: FH
authors.lastname: Karlsson
authors.affiliation: Department of Infectious Diseases, Institute of Biomedicine, the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.|Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden.
authors.forename: Chandan
authors.initials: C
authors.lastname: Pal
authors.affiliation: Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden.|Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden.
authors.forename: Mariana Buongermino
authors.initials: MB
authors.lastname: Pereira
authors.affiliation: Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden.
authors.forename: Anna
authors.initials: A
authors.lastname: Rehammar
authors.affiliation: Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden.|Bioinformatics Core Facility, University of Gothenburg, Gothenburg, Sweden.
authors.forename: José
authors.initials: J
authors.lastname: Sanchez
authors.affiliation: Department of Biology and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.
authors.forename: Kemal
authors.initials: K
authors.lastname: Sanli
authors.affiliation: Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
authors.forename: Kaisa
authors.initials: K
authors.lastname: Thorell
mesh_terms: D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D011786:Quality Control; D017421:Sequence Analysis; D012984:Software
keywords: Annotation; Bioinformatics; Databases; Functional prediction; Sequencing; Standards