Computational protocol: ONS: an ontology for a standardized description of interventions and observational studies in nutrition

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[…] Terms to be included in the ONS were collected among partners of the ENPADASI consortium, as well as from templates for data and metadata upload into the DASH-IN databases. In compliance with the OBO Foundry principles [], the ONS has been developed to be as follows: (i) Interoperable with other ontologies, as it has been formalized using the latest OWL 2 Web Ontology Language [] and RDF specifications [] and edited using Protégé []; the hermit reasoner (http://hermit-reasoner.com/) was used for consistency checking. (ii) Accessible, under the Creative Commons license (CC BY 4.0), published on GitHub (https://github.com/enpadasi/Ontology-for-Nutritional-Studies) and at NCBO BioPortal (http://bioportal.bioontology.org/ontologies/ONS). (iii) Orthogonal to other ontologies by reusing existing terms. Besides assuring compliance with the OBO Foundry principles, we also ensured that the ONS followed the increasingly established FAIR principles []. As such, the ONS is also published in the FAIRsharing database (https://fairsharing.org/bsg-s001068).To enhance interoperability with other ontologies, the ONS builds on a subset of the Ontology for Biomedical Investigations (OBI) []. The subset was created using the ONTODOG tool [] and is composed of all terms relevant to nutritional investigations and extended also in accordance with the bioinformatics infrastructure of ENPADASI. Moreover, this assured the adoption of a well-defined and widely adopted structure for the top and mid-level classes and principally the adherence to the Basic Formal Ontology (BFO) [] as upper ontology.Additional relevant ontologies were used orthogonally in the ONS as discussed in the results. To ensure and enhance orthogonality, all terms were first searched using the ONTOBEE [] web service and catalogued with their URIs. ONTOFOX [] was then used to import all terms with related annotations and axioms (option includeAllAnnotations). Newly defined terms, specific to the ONS, have been labeled with “ONS_” followed by a 7-digit number. Terms related to food description were also included by importing a subset of terms from the FOODON ontology []. All intermediate files of this development process (i.e., template files used for web services or imported ontologies) were stored on GitHub repository. Additional file  contains instruction on how to browse, download, and contribute to ONS. The same instruction is also present online at the wiki page of the GitHub repository (https://github.com/enpadasi/Ontology-for-Nutritional-Studies/wiki). In this development process, terms from a number of different ontologies were imported. Table  reports a summary of the classes that were imported in the ONS (excluding individuals) and their ontology of origin. […]

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