Post-composing ontology terms for efficient phenotyping in plant breeding

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cg.authorship.typesCGIAR and developing country instituteen
cg.authorship.typesCGIAR and advanced research instituteen
cg.contributor.affiliationInternational Institute of Tropical Agricultureen
cg.contributor.affiliationInternational Center for Tropical Agricultureen
cg.contributor.affiliationCentre de Coopération Internationale en Recherche Agronomique pour le Développementen
cg.contributor.affiliationNational Agricultural Research Organisationen
cg.contributor.affiliationCornell Universityen
cg.contributor.affiliationFrench National Research Institute for Sustainable Developmenten
cg.contributor.affiliationOregon State Universityen
cg.contributor.affiliationInstitut Agro Montpellieren
cg.contributor.affiliationLawrence Berkeley National Laboratoryen
cg.contributor.affiliationIthaca Collegeen
cg.contributor.affiliationClemson Universityen
cg.contributor.affiliationUMR QualiSuden
cg.contributor.affiliationBioversity Internationalen
cg.creator.identifierNaama Menda: 0000-0002-9117-8116en
cg.creator.identifierElizabeth Arnaud: 0000-0002-6020-5919en
cg.creator.identifierMarie-Angélique Laporte: 0000-0002-8461-9745en
cg.creator.identifierLaurel Cooper: 0000-0002-6379-8932en
cg.creator.identifierDominique Dufour: 0000-0002-7794-8671en
cg.creator.identifierThierry Tran: 0000-0002-9557-3340en
cg.creator.identifierMeghar Karima: 0000-0002-7732-9184en
cg.creator.identifierAmos Asiimwe: 0000-0001-8216-6810en
cg.creator.identifierViolet Akech: 0000-0003-2330-0682en
cg.creator.identifierPrasad Peteti: 0000-0002-6013-8947en
cg.creator.identifierPaterne AGRE: 0000-0003-1231-2530en
cg.creator.identifierAFOLABI AGBONA: 0000-0002-9756-5432en
cg.creator.identifierLyon, David: 0000-0002-1927-3565en
cg.creator.identifierTecle, Isaak Y: 0000-0002-8677-9793en
cg.creator.identifierFlores Gonzalez, Mirella: 0000-0002-7759-1617en
cg.creator.identifierLukas Mueller: 0000-0001-8640-1750en
cg.identifier.doihttps://doi.org/10.1093/database/baaf020en
cg.isijournalISI Journalen
cg.issn1758-0463en
cg.journalDatabaseen
cg.reviewStatusPeer Reviewen
cg.subject.actionAreaSystems Transformationen
cg.subject.alliancebiovciatAGRICULTUREen
cg.subject.alliancebiovciatCASSAVAen
cg.subject.alliancebiovciatPLANT BREEDINGen
cg.subject.alliancebiovciatSTANDARDSen
cg.subject.impactAreaNutrition, health and food securityen
cg.subject.sdgSDG 2 - Zero hungeren
cg.volume2025en
dc.contributor.authorMenda, Naamaen
dc.contributor.authorEllerbrock, Bryan J.en
dc.contributor.authorSimoes, Christiano C.en
dc.contributor.authorKaraikal, Srikanth Kumaren
dc.contributor.authorNyaga, Christineen
dc.contributor.authorFlores-Gonzalez, Mirellaen
dc.contributor.authorTecle, Isaak Y.en
dc.contributor.authorLyon, Daviden
dc.contributor.authorAgbona, Afolabien
dc.contributor.authorAgre, Paterne A.en
dc.contributor.authorPeteti, Prasaden
dc.contributor.authorAkech, Violeten
dc.contributor.authorAsiimwe, Amosen
dc.contributor.authorFauvelle, Eglantineen
dc.contributor.authorMeghar, Karimaen
dc.contributor.authorTran, Thierryen
dc.contributor.authorDufour, Dominiqueen
dc.contributor.authorCooper, Laurelen
dc.contributor.authorLaporte, Marie-Angeliqueen
dc.contributor.authorArnaud, Elizabethen
dc.contributor.authorMueller, Lukas Aen
dc.date.accessioned2025-04-02T09:51:02Zen
dc.date.available2025-04-02T09:51:02Zen
dc.identifier.urihttps://hdl.handle.net/10568/173982
dc.titlePost-composing ontology terms for efficient phenotyping in plant breedingen
dcterms.abstractOntologies are widely used in databases to standardize data, improving data quality, integration, and ease of comparison. Within ontologies tailored to diverse use cases, post-composing user-defined terms reconciles the demands for standardization on the one hand and flexibility on the other. In many instances of Breedbase, a digital ecosystem for plant breeding designed for genomic selection, the goal is to capture phenotypic data using highly curated and rigorous crop ontologies, while adapting to the specific requirements of plant breeders to record data quickly and efficiently. For example, post-composing enables users to tailor ontology terms to suit specific and granular use cases such as repeated measurements on different plant parts and special sample preparation techniques. To achieve this, we have implemented a post-composing tool based on orthogonal ontologies providing users with the ability to introduce additional levels of phenotyping granularity tailored to unique experimental designs. Post-composed terms are designed to be reused by all breeding programs within a Breedbase instance but are not exported to the crop reference ontologies. Breedbase users can post-compose terms across various categories, such as plant anatomy, treatments, temporal events, and breeding cycles, and, as a result, generate highly specific terms for more accurate phenotyping.en
dcterms.accessRightsOpen Accessen
dcterms.bibliographicCitationMenda, N.; Ellerbrock, B.J.; Simoes, C.C.; Karaikal, S.K.; Nyaga, C.; Flores-Gonzalez, M.; Tecle, I.Y.; Lyon, D.; Agbona, A.; Agre, P.A.; Peteti, P.; Akech, V.; Asiimwe, A.; Fauvelle, E.; Meghar, K.; Tran, T.; Dufour, D.; Cooper, L.; Laporte, M.; Arnaud, E.; Mueller, L.A. (2025) Post-composing ontology terms for efficient phenotyping in plant breeding. Database 2025: baaf020. ISSN: 1758-0463en
dcterms.extentbaaf020en
dcterms.issued2025-03-21en
dcterms.languageenen
dcterms.licenseCC-BY-4.0en
dcterms.publisherOxford University Pressen
dcterms.subjectcassavaen
dcterms.subjectdatabasesen
dcterms.subjectbreedingen
dcterms.subjectontologiesen
dcterms.subjectphenotypingen
dcterms.typeJournal Articleen

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