The Biomedical Systems and Services Laboratory is dedicated to investigate the development and application of conceptual models (including ontologies) to the development and integration of biomedical systems and services. In the biomedical area, we have a particular interest in the functional genomics domain.

Gene expression is the biological process in which the information stored in a gene is converted into protein or RNA. Once expression data is available, biologists are faced with the task of extracting (new) knowledge associated to the underlying biological phenomenon. Thus, the objectives of functional genomics include the definition of the functional roles of different genes and associated processes, the study of the interactions between gene and gene products, the study of gene expression variations in different cell types and under different conditions, among others. In order to carry out this task, biologists perform a sequence of analysis activities on the available gene expression data. In general these activities are carried out using separate tools, which hinder effective research.

LSSB’s current research topics include:

  • ontology development for the functional genomics domain (concepts, methodology and supporting tools);
  • gene expression service development (concepts, techniques and methodology;
  • semantic web services development and composition;
  • model-driven development and engineering.

Selected Publications

Waldemarin, R.C.; de Farias, C.R.G. OBO to UML: Support for the development of conceptual models in the biomedical domain. Journal of Biomedical Informatics 80: 14-25, 2018. DOI: 10.1016/j.jbi.2018.02.015.

Guardia, G.D.A.; Pires, Luís Ferreira; da Silva, E.G.; de Farias, C.R.G. SemanticSCo: A Platform to Support the Semantic Composition of Services for Gene Expression Analysis. Journal of Biomedical Informatics 66: 116–28, 2017. DOI: 10.1016/j.jbi.2016.12.014.

Guardia, G.D.A. ; Pires, L.F.; Vêncio, R.Z.N.; Malmegrim, K.C.R.; de Farias, C.R.G. A Methodology for the Development of RESTful Semantic Web Services for Gene Expression Analysis. PLoS ONE, v. 10, n. 7, p. e0134011, 2015. DOI: 10.1371/journal.pone.0134011

Miyazaki, F.A.; Guardia, G.D.A.; Vêncio, R.Z.N.; de Farias, C.R.G. Semantic Integration of Gene Expression Analysis Tools and Data Sources using Software Connectors. BMC Genomics, v. 14, p. S2, 2013.

Trepode, N. W. and de Farias, C. R. G. and Barrera, J. A pattern-oriented specification of gene network inference processes. Computers in Biology and Medicine, v. 43, p. 1415-1427, 2013.

Guardia, G. D. A. ; Vêncio, R. Z. N. ; de Farias, C. R. G. A UML Profile for the OBO Relation Ontology. BMC Genomics, v. 13, p. S3, 2012.