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. 2024 Mar 4;15(1):1.
doi: 10.1186/s13326-024-00302-5.

Enriching the FIDEO ontology with food-drug interactions from online knowledge sources

Rabia Azzi #  1   2 , Georgeta Bordea #  1   3 , Romain Griffier  1   2 , Jean Noël Nikiema  4 , Fleur Mougin  5
Affiliations

Enriching the FIDEO ontology with food-drug interactions from online knowledge sources

Rabia Azzi et al. J Biomed Semantics. .

Abstract

The increasing number of articles on adverse interactions that may occur when specific foods are consumed with certain drugs makes it difficult to keep up with the latest findings. Conflicting information is available in the scientific literature and specialized knowledge bases because interactions are described in an unstructured or semi-structured format. The FIDEO ontology aims to integrate and represent information about food-drug interactions in a structured way. This article reports on the new version of this ontology in which more than 1700 interactions are integrated from two online resources: DrugBank and Hedrine. These food-drug interactions have been represented in FIDEO in the form of precompiled concepts, each of which specifies both the food and the drug involved. Additionally, competency questions that can be answered are reviewed, and avenues for further enrichment are discussed.

Keywords: Adverse drug effects; Biomedical ontology; FAIR principles; Food-drug interactions.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
a Organization of high-level concepts related to the food-drug interaction process in FIDEO, and b) Illustrative example of this framework with a food-drug interaction between garlic and warfarin described in DrugBank at the following URL: https://go.drugbank.com/drugs/DB00682. The ontologies from which the corresponding concepts and the relations existing between them originate, as well as the hierarchy to which these concepts belong are specified in the legend on the right of the figure
Fig. 2
Fig. 2
Complete FIDEO enrichment process. Knowledge was extracted from DrugBank and Hedrine, OLS was used to identify drugs, foods and herbs in existing ontologies and ROBOT to define patterns for creating logical definitions for concepts to be included in FIDEO
Fig. 3
Fig. 3
Integration of drugs and foods in FIDEO: a drugs are organized according to the ATC hierarchy (or as a “not elsewhere classified drug” for drugs not described in ATC), and b) foods are subclasses of the FoodOn concept “food product”
Fig. 4
Fig. 4
Extract from the ROBOT file containing as many rows as concepts and relations in FIDEO for which the following characteristics are available in the five columns: 1) their identifier in the ontology from which they are derived, 2) their label, 3) their parent concept(s) or relation(s) in FIDEO, 4) their type (owl:Class or owl:ObjectProperty), and 5) the logical definition(s) of defined concepts. Note that the concept “FDI garlic food product–warfarin” does not have a parent concept specified in column 3 because its logical definition already states that it is a child of the “food drug interaction” concept
Fig. 5
Fig. 5
a SPARQL query over FIDEO to search for foods interacting with the drug “warfarin”, b) the 17 foods described as interacting with this drug in DrugBank and/or Hedrine
See this image and copyright information in PMC

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