A harmonised vocabulary for communicating and interchanging Biofilms experimental results
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-do...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
| Published: |
De Gruyter
2014-12-01
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| Series: | Journal of Integrative Bioinformatics |
| Online Access: | https://doi.org/10.1515/jib-2014-249 |
| _version_ | 1818587258474725376 |
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| author | Sousa Ana Margarida Pereira Maria Olívia Azevedo Nuno F. Lourenço Anália |
| author_facet | Sousa Ana Margarida Pereira Maria Olívia Azevedo Nuno F. Lourenço Anália |
| author_sort | Sousa Ana Margarida |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-16T09:06:00Z |
| format | Article |
| id | doaj.art-8361c834d4ac42b2b310366f5ba3bfa9 |
| institution | Directory Open Access Journal |
| issn | 1613-4516 |
| language | English |
| last_indexed | 2024-12-16T09:06:00Z |
| publishDate | 2014-12-01 |
| publisher | De Gruyter |
| record_format | Article |
| series | Journal of Integrative Bioinformatics |
| spelling | doaj.art-8361c834d4ac42b2b310366f5ba3bfa92022-12-21T22:37:03ZengDe GruyterJournal of Integrative Bioinformatics1613-45162014-12-01113324710.1515/jib-2014-249jib-2014-249A harmonised vocabulary for communicating and interchanging Biofilms experimental resultsSousa Ana Margarida0Pereira Maria Olívia1Azevedo Nuno F.2Lourenço Anália3CEB- Centre of Biological Engineering, LIBRO – Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057Braga, PortugalCEB- Centre of Biological Engineering, LIBRO – Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057Braga, PortugalLEPABE Dep. of Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, s/n, 4200-465Porto, PortugalESEI – Escuela Superior de Ingeniería Informática, Edificio Politéecnico, Campus Universitario As Lagoas s/n, Universidad de Vigo, 32004OurensePortugalBiofilm 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.https://doi.org/10.1515/jib-2014-249 |
| spellingShingle | Sousa Ana Margarida Pereira Maria Olívia Azevedo Nuno F. Lourenço Anália A harmonised vocabulary for communicating and interchanging Biofilms experimental results Journal of Integrative Bioinformatics |
| title | A harmonised vocabulary for communicating and interchanging Biofilms experimental results |
| title_full | A harmonised vocabulary for communicating and interchanging Biofilms experimental results |
| title_fullStr | A harmonised vocabulary for communicating and interchanging Biofilms experimental results |
| title_full_unstemmed | A harmonised vocabulary for communicating and interchanging Biofilms experimental results |
| title_short | A harmonised vocabulary for communicating and interchanging Biofilms experimental results |
| title_sort | harmonised vocabulary for communicating and interchanging biofilms experimental results |
| url | https://doi.org/10.1515/jib-2014-249 |
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