{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,7]],"date-time":"2026-01-07T08:06:21Z","timestamp":1767773181795,"version":"build-2065373602"},"reference-count":45,"publisher":"MDPI AG","issue":"13","license":[{"start":{"date-parts":[[2022,6,29]],"date-time":"2022-06-29T00:00:00Z","timestamp":1656460800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Italian Ministry of Agriculture, Food, and Forestry Policies (MiPAAF)","award":["DM 36954\/7303\/18","863059"],"award-info":[{"award-number":["DM 36954\/7303\/18","863059"]}]},{"DOI":"10.13039\/501100000780","name":"European Union","doi-asserted-by":"publisher","award":["DM 36954\/7303\/18","863059"],"award-info":[{"award-number":["DM 36954\/7303\/18","863059"]}],"id":[{"id":"10.13039\/501100000780","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Foods"],"abstract":"<jats:p>Food ontologies are acquiring a central role in human nutrition, providing a standardized terminology for a proper description of intervention and observational trials. In addition to bioactive molecules, several fermented foods, particularly dairy products, provide the host with live microorganisms, thus carrying potential \u201cgenetic\/functional\u201d nutrients. To date, a proper ontology to structure and formalize the concepts used to describe fermented foods is lacking. Here we describe a semantic representation of concepts revolving around what consuming fermented foods entails, both from a technological and health point of view, focusing actions on kefir and Parmigiano Reggiano, as representatives of fresh and ripened dairy products. We included concepts related to the connection of specific microbial taxa to the dairy fermentation process, demonstrating the potential of ontologies to formalize the various gene pathways involved in raw ingredient transformation, connect them to resulting metabolites, and finally to their consequences on the fermented product, including technological, health and sensory aspects. Our work marks an improvement in the ambition of creating a harmonized semantic model for integrating different aspects of modern nutritional science. Such a model, besides formalizing a multifaceted knowledge, will be pivotal for a rich annotation of data in public repositories, as a prerequisite to generalized meta-analysis.<\/jats:p>","DOI":"10.3390\/foods11131939","type":"journal-article","created":{"date-parts":[[2022,6,29]],"date-time":"2022-06-29T20:47:56Z","timestamp":1656535676000},"page":"1939","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Semantics of Dairy Fermented Foods: A Microbiologist\u2019s Perspective"],"prefix":"10.3390","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9125-4337","authenticated-orcid":false,"given":"Francesco","family":"Vitali","sequence":"first","affiliation":[{"name":"Institute of Agricultural Biology and Biotechnology (IBBA), National Research Council (CNR), Via Moruzzi 1, 56124 Pisa, Italy"},{"name":"Research Centre for Agriculture and Environment, CREA (Consiglio per la Ricerca in Agricoltura e l\u2019Analisi dell\u2019Economia Agraria), Via di Lanciola 12\/A, 50125 Florence, Italy"}]},{"given":"Paola","family":"Zinno","sequence":"additional","affiliation":[{"name":"Research Centre for Food and Nutrition, CREA (Consiglio per la Ricerca in Agricoltura e l\u2019Analisi dell\u2019Economia Agraria), Via Ardeatina 546, 00178 Rome, Italy"}]},{"given":"Emily","family":"Schifano","sequence":"additional","affiliation":[{"name":"Research Centre for Food and Nutrition, CREA (Consiglio per la Ricerca in Agricoltura e l\u2019Analisi dell\u2019Economia Agraria), Via Ardeatina 546, 00178 Rome, Italy"}]},{"given":"Agnese","family":"Gori","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0892-7164","authenticated-orcid":false,"given":"Ana","family":"Costa","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2222-6524","authenticated-orcid":false,"given":"Carlotta","family":"De Filippo","sequence":"additional","affiliation":[{"name":"Institute of Agricultural Biology and Biotechnology (IBBA), National Research Council (CNR), Via Moruzzi 1, 56124 Pisa, Italy"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7597-2590","authenticated-orcid":false,"given":"Barbara","family":"Korou\u0161i\u0107 Seljak","sequence":"additional","affiliation":[{"name":"Computer Systems Department, Jozef Stefan Institute, Jamova Cesta 39, 1000 Ljubljana, Slovenia"}]},{"given":"Pan\u010de","family":"Panov","sequence":"additional","affiliation":[{"name":"Department of Knowledge Technologies, Jozef Stefan Institute, Jamova Cesta 39, 1000 Ljubljana, Slovenia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7114-7726","authenticated-orcid":false,"given":"Chiara","family":"Devirgiliis","sequence":"additional","affiliation":[{"name":"Research Centre for Food and Nutrition, CREA (Consiglio per la Ricerca in Agricoltura e l\u2019Analisi dell\u2019Economia Agraria), Via Ardeatina 546, 00178 Rome, Italy"}]},{"given":"Duccio","family":"Cavalieri","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy"}]}],"member":"1968","published-online":{"date-parts":[[2022,6,29]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"2446","DOI":"10.1002\/fsn3.846","article-title":"Fermentation and germination improve nutritional value of cereals and legumes through activation of endogenous enzymes","volume":"6","author":"Nkhata","year":"2018","journal-title":"Food Sci. 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