Post-composing ontology terms for effcient phenotyping in plant breeding

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cg.authorship.typesCGIAR and developing country instituteen
cg.contributor.affiliationBoyce Thompson Instituteen
cg.contributor.affiliationTexas A&M Agrilife Research Centeren
cg.contributor.affiliationInternational Institute of Tropical Agricultureen
cg.contributor.affiliationNational Agricultural Research Laboratories, Ugandaen
cg.contributor.affiliationCentre de Coopération Internationale en Recherche Agronomique pour le Développementen
cg.contributor.affiliationOregon State Universityen
cg.contributor.affiliationBioversity Internationalen
cg.contributor.crpRoots, Tubers and Bananas
cg.contributor.donorBill & Melinda Gates Foundationen
cg.contributor.donorCGIAR Trust Funden
cg.contributor.donorBioversity Centro Internacional de Agricultura Tropical Allianceen
cg.contributor.donorNational Science Foundationen
cg.contributor.donorUnited States Department of Agriculture—Agriculture Research Serviceen
cg.contributor.initiativeAccelerated Breeding
cg.creator.identifierNaama Menda: 0000-0002-9117-8116en
cg.creator.identifierAFOLABI AGBONA: 0000-0002-9756-5432en
cg.creator.identifierPaterne AGRE: 0000-0003-1231-2530en
cg.creator.identifierPrasad Peteti: 0000-0002-6013-8947en
cg.creator.identifierMeghar Karima: 0000-0002-7732-9184en
cg.creator.identifierThierry Tran: 0000-0002-9557-3340en
cg.creator.identifierDominique Dufour: 0000-0002-6046-0741en
cg.creator.identifierLaurel Cooper: 0000-0002-6379-8932en
cg.creator.identifierMarie-Angélique Laporte: 0000-0002-8461-9745en
cg.creator.identifierElizabeth Arnaud: 0000-0002-6020-5919en
cg.creator.identifierLukas Mueller: 0000-0001-8640-1750en
cg.howPublishedFormally Publisheden
cg.identifier.doihttps://doi.org/10.1093/database/baaf020en
cg.identifier.iitathemeBIOTECH & PLANT BREEDINGen
cg.isijournalISI Journalen
cg.issn1758-0463en
cg.journalDatabase-The Journal of Biological Databases and Curationen
cg.reviewStatusPeer Reviewen
cg.subject.actionAreaGenetic Innovation
cg.subject.iitaAGRONOMYen
cg.subject.iitaPLANT BREEDINGen
cg.subject.iitaRESEARCH METHODen
cg.subject.impactAreaNutrition, health and food security
cg.subject.impactPlatformNutrition, Health and Food Security
cg.subject.sdgSDG 2 - Zero hungeren
cg.volume2025en
dc.contributor.authorMenda, N.en
dc.contributor.authorEllerbrock, B.J.en
dc.contributor.authorSimoes, C.C.en
dc.contributor.authorKaraikal, S.K.en
dc.contributor.authorNyaga, C.en
dc.contributor.authorFlores-Gonzalez, M.en
dc.contributor.authorTecle, I.Y.en
dc.contributor.authorLyon, D.en
dc.contributor.authorAgbona, A.en
dc.contributor.authorAgre, A.P.en
dc.contributor.authorPeteti, P.en
dc.contributor.authorAkech, V.en
dc.contributor.authorAsiimwe, A.en
dc.contributor.authorFauvelle, E.en
dc.contributor.authorMeghar, K.en
dc.contributor.authorTran, T.en
dc.contributor.authorDufour, D.en
dc.contributor.authorCooper, L.en
dc.contributor.authorLaporte, M.A.en
dc.contributor.authorArnaud, E.en
dc.contributor.authorMueller, L.en
dc.date.accessioned2025-04-07T12:53:31Zen
dc.date.available2025-04-07T12:53:31Zen
dc.identifier.urihttps://hdl.handle.net/10568/174021
dc.titlePost-composing ontology terms for effcient 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 Access
dcterms.audienceScientistsen
dcterms.available2025-03-21en
dcterms.bibliographicCitationMenda, N., Ellerbrock, B.J., Simoes, C.C., Karaikal, S.K., Nyaga, C., Flores-Gonzalez, M., ... & Mueller, L. (2025). Post-composing ontology terms for efficient phenotyping in plant breeding. Database, 2025, 1-12.en
dcterms.descriptionOpen Access Journalen
dcterms.extent1-12en
dcterms.issued2025en
dcterms.languageen
dcterms.licenseCC-BY-4.0
dcterms.subjectontologyen
dcterms.subjectplant breedingen
dcterms.subjectdatabasesen
dcterms.subjectphenotypesen
dcterms.subjectdataen
dcterms.typeJournal Article

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