title: Database constraints applied to metabolic pathway reconstruction tools.
abstract: Our group developed two biological applications, Biblio-MetReS and Homol-MetReS, accessing the same database of organisms with annotated genes. Biblio-MetReS is a data-mining application that facilitates the reconstruction of molecular networks based on automated text-mining analysis of published scientific literature. Homol-MetReS allows functional (re)annotation of proteomes, to properly identify both the individual proteins involved in the process(es) of interest and their function. It also enables the sets of proteins involved in the process(es) in different organisms to be compared directly. The efficiency of these biological applications is directly related to the design of the shared database. We classified and analyzed the different kinds of access to the database. Based on this study, we tried to adjust and tune the configurable parameters of the database server to reach the best performance of the communication data link to/from the database system. Different database technologies were analyzed. We started the study with a public relational SQL database, MySQL. Then, the same database was implemented by a MapReduce-based database named HBase. The results indicated that the standard configuration of MySQL gives an acceptable performance for low or medium size databases. Nevertheless, tuning database parameters can greatly improve the performance and lead to very competitive runtimes.
authors.affiliation: Computer Science Department & INSPIRES, University of Lleida, Jaume II 69, 25001 Lleida, Spain.
authors.forename: Jordi
authors.initials: J
authors.lastname: Vilaplana
authors.affiliation: Computer Science Department & INSPIRES, University of Lleida, Jaume II 69, 25001 Lleida, Spain.
authors.forename: Francesc
authors.initials: F
authors.lastname: Solsona
authors.affiliation: Computer Science Department & INSPIRES, University of Lleida, Jaume II 69, 25001 Lleida, Spain.
authors.forename: Ivan
authors.initials: I
authors.lastname: Teixido
authors.affiliation: CEBAL, IPBeja Campus, 7800 Beja, Portugal.
authors.forename: Anabel
authors.initials: A
authors.lastname: Usié
authors.affiliation: Department of Basic Medical Sciences & IRBLleida, Edifici Recerca Biomedica I, Universitat de Lleida, Avenida Rovira Roure 80, 25198 Lleida, Spain.
authors.forename: Hiren
authors.initials: H
authors.lastname: Karathia
authors.affiliation: Department of Basic Medical Sciences & IRBLleida, Edifici Recerca Biomedica I, Universitat de Lleida, Avenida Rovira Roure 80, 25198 Lleida, Spain.
authors.forename: Rui
authors.initials: R
authors.lastname: Alves
authors.affiliation: Computer Science Department & INSPIRES, University of Lleida, Jaume II 69, 25001 Lleida, Spain.
authors.forename: Jordi
authors.initials: J
authors.lastname: Mateo
mesh_terms: D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D053858:Metabolic Networks and Pathways; D008954:Models, Biological; D012984:Software