title: BioSurfDB: knowledge and algorithms to support biosurfactants and biodegradation studies.
abstract: Crude oil extraction, transportation and use provoke the contamination of countless ecosystems. Therefore, bioremediation through surfactants mobilization or biodegradation is an important subject, both economically and environmentally. Bioremediation research had a great boost with the recent advances in Metagenomics, as it enabled the sequencing of uncultured microorganisms providing new insights on surfactant-producing and/or oil-degrading bacteria. Many research studies are making available genomic data from unknown organisms obtained from metagenomics analysis of oil-contaminated environmental samples. These new datasets are presently demanding the development of new tools and data repositories tailored for the biological analysis in a context of bioremediation data analysis. This work presents BioSurfDB, www.biosurfdb.org, a curated relational information system integrating data from: (i) metagenomes; (ii) organisms; (iii) biodegradation relevant genes; proteins and their metabolic pathways; (iv) bioremediation experiments results, with specific pollutants treatment efficiencies by surfactant producing organisms; and (v) a biosurfactant-curated list, grouped by producing organism, surfactant name, class and reference. The main goal of this repository is to gather information on the characterization of biological compounds and mechanisms involved in biosurfactant production and/or biodegradation and make it available in a curated way and associated with a number of computational tools to support studies of genomic and metagenomic data.
authors.affiliation: INESC-ID/IST-Instituto de Engenharia de Sistemas e Computadores/Instituto Superior Técnico, Universidade de Lisboa, Rua Alves Redol 9, 1000-029 Lisboa, Portugal, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil and Laboratório Nacional de Computação Científica, Petrópolis, RJ, Brazil.
authors.forename: Jorge S
authors.initials: JS
authors.lastname: Oliveira
authors.affiliation: INESC-ID/IST-Instituto de Engenharia de Sistemas e Computadores/Instituto Superior Técnico, Universidade de Lisboa, Rua Alves Redol 9, 1000-029 Lisboa, Portugal, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil and Laboratório Nacional de Computação Científica, Petrópolis, RJ, Brazil.
authors.forename: Wydemberg
authors.initials: W
authors.lastname: Araújo
authors.affiliation: INESC-ID/IST-Instituto de Engenharia de Sistemas e Computadores/Instituto Superior Técnico, Universidade de Lisboa, Rua Alves Redol 9, 1000-029 Lisboa, Portugal, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil and Laboratório Nacional de Computação Científica, Petrópolis, RJ, Brazil.
authors.forename: Ana Isabela
authors.initials: AI
authors.lastname: Lopes Sales
authors.affiliation: INESC-ID/IST-Instituto de Engenharia de Sistemas e Computadores/Instituto Superior Técnico, Universidade de Lisboa, Rua Alves Redol 9, 1000-029 Lisboa, Portugal, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil and Laboratório Nacional de Computação Científica, Petrópolis, RJ, Brazil.
authors.forename: Alaine de
authors.initials: Ad
authors.lastname: Brito Guerra
authors.affiliation: INESC-ID/IST-Instituto de Engenharia de Sistemas e Computadores/Instituto Superior Técnico, Universidade de Lisboa, Rua Alves Redol 9, 1000-029 Lisboa, Portugal, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil and Laboratório Nacional de Computação Científica, Petrópolis, RJ, Brazil.
authors.forename: Sinara Carla da
authors.initials: SC
authors.lastname: Silva Araújo
authors.affiliation: INESC-ID/IST-Instituto de Engenharia de Sistemas e Computadores/Instituto Superior Técnico, Universidade de Lisboa, Rua Alves Redol 9, 1000-029 Lisboa, Portugal, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil and Laboratório Nacional de Computação Científica, Petrópolis, RJ, Brazil.
authors.forename: Ana Tereza Ribeiro
authors.initials: AT
authors.lastname: de Vasconcelos
authors.affiliation: INESC-ID/IST-Instituto de Engenharia de Sistemas e Computadores/Instituto Superior Técnico, Universidade de Lisboa, Rua Alves Redol 9, 1000-029 Lisboa, Portugal, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil and Laboratório Nacional de Computação Científica, Petrópolis, RJ, Brazil.
authors.forename: Lucymara F
authors.initials: LF
authors.lastname: Agnez-Lima
authors.affiliation: INESC-ID/IST-Instituto de Engenharia de Sistemas e Computadores/Instituto Superior Técnico, Universidade de Lisboa, Rua Alves Redol 9, 1000-029 Lisboa, Portugal, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil and Laboratório Nacional de Computação Científica, Petrópolis, RJ, Brazil ana.freitas@tecnico.ulisboa.pt.
authors.forename: Ana Teresa
authors.initials: AT
authors.lastname: Freitas
mesh_terms: D001673:Biodegradation, Environmental; D030541:Databases, Genetic; D054892:Metagenome; D056186:Metagenomics; D010578:Petroleum / Q000378:metabolism; D059392:Petroleum Pollution; D012988:Soil Microbiology; D013501:Surface-Active Agents
chemical_list: D010578:Petroleum; D013501:Surface-Active Agents
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