A harmonised vocabulary for communicating and interchanging Biofilms experimental results

Ana Margarida Sousa 1 , Maria Olívia Pereira 1 , Nuno F. Azevedo 2 ,  and Anália Lourenço 1 , 3
  • 1 CEB- Centre of Biological Engineering, LIBRO – Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
  • 2 LEPABE Dep. of Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, s/n, 4200-465, Porto, Portugal
  • 3 ESEI – Escuela Superior de Ingeniería Informática, Edificio Politéecnico, Campus Universitario As Lagoas s/n, Universidad de Vigo, 32004, Ourense, Portugal


Biofilm studies are at the crossroads of Biology, Chemistry, Medicine, Material Science and Engineering, among other fields. Data harmonisation in Biofilms is therefore crucial to allow for researchers to collaborate, interchange, understand, and replicate studies at an inter-laboratory and inter-domain scale. The international Minimum Information About a Biofilms Experiment initiative has prepared a set of guidelines for documenting biofilms experiments and data, namely the minimum information checklist. This paper goes a step forward and describes a new ontology for the broad description of biofilm experiments and data. In such an interdisciplinary context we chose to rely on a common integration framework provided by a foundational ontology that facilitates the addition and extension of various sub-domain modules, and the consistent integration of terminology extracted from several existing ontologies, e.g. EXPO and ChEBI. The community is participating actively in the production of this resource, and it is already used by public biofilms-centred databases, such as BiofOmics, and bioinformatics tools, such as the Biofilms Experiment Workbench. This practical validation serves the purpose of disseminating the controlled vocabulary among researchers and identifying current limitations, glitches, and inconsistencies. Information branches will be added, extended or refactored according to user feedback and group discussions.

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Journal + Issues

The Journal of Integrative Bioinformatics is an international journal dedicated to methods and tools of computer science and electronic infrastructure applied to biotechnology. The journal covers mainly but not exclusively data/method integration, modeling, simulation and visualization in combination with applications of theoretical/computational tools and any other approach supporting an integrative view of complex biological systems.