Abstract
Semantic web technologies have proved their usefulness in facilitating the documentation, annotation and to a certain extent the reuse and reproducibility of scientific experiments in laboratories. While useful, existing solutions suffer from some limitations when it comes to supporting scientists. Indeed, it is up to him/her to identify which ontologies to use, which fragments of those ontologies are useful for his experiments and how to combine them. Furthermore, the behavior and constraints of the domain of interest to the scientist, e.g., constraints and business rules, are not captured and as such are decoupled from the ontologies. To overcome the above limitations, we propose in this paper a methodology and underlying ontologies and solutions with the view to facilitate for the scientist the task of creating an ontology that captures the specificities of the domain of interest by combining existing well-known ontologies. Moreover, we provide the scientist with the means of specifying behavioral constraints, such as integrity constraints and business rules, with the ontology specified. We showcase our solution using a real-world case study from the field of agronomy.
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Notes
- 1.
AFO Ontologies: https://www.allotrope.org/ontologies.
- 2.
FOAF Ontology : http://www.foaf-project.org.
- 3.
vCard Ontology: https://www.w3.org/TR/vcard-rdf/.
- 4.
- 5.
ENVO Ontology: https://bioportal.bioontology.org/ontologies/ENVO.
- 6.
OBO Foundry: http://www.obofoundry.org.
- 7.
Scientific Experiments Core Ontology: https://github.com/aloulen/SECO.
- 8.
CC BY 4.0: http://creativecommons.org/licenses/by/4.0/.
- 9.
PATO Ontology: http://www.obofoundry.org/ontology/pato.html.
- 10.
QUDT Ontologies: http://www.qudt.org/release2/qudt-catalog.html.
- 11.
Scientific Experiments Agronomy Ontology: https://github.com/aloulen/SECO_AGRO.
- 12.
AgiLab is a software development company that provides information systems (LIMS) for managing the activities of research and development laboratories in different domains of activity.
- 13.
eSciDoc : https://www.escidoc.org.
- 14.
OBI Ontology: http://obi-ontology.org.
- 15.
Allotrope Foundation : https://www.allotrope.org/about-us.
- 16.
OBO Foundry best practices: http://www.obofoundry.org/principles/fp-000-summary.html.
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Aloulen, Z., Belhajjame, K., Grigori, D., Acker, R. (2019). A Domain-Independent Ontology for Capturing Scientific Experiments. In: Kotzinos, D., Laurent, D., Spyratos, N., Tanaka, Y., Taniguchi, Ri. (eds) Information Search, Integration, and Personalization. ISIP 2018. Communications in Computer and Information Science, vol 1040. Springer, Cham. https://doi.org/10.1007/978-3-030-30284-9_4
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