Planteome 2024 Update: Reference Ontologiesãnd Kno wledg ebase f or Plant Biology

Abstract

The Planteome project ( https:// planteome.org/ ) providesã suite of referenceãnd crop-specific ontologiesãndãn integrated knowledgebase of plant genomics data. The plant genomics data in the Planteome has been obtained through manualãndãutomated curationãnd sourced from more than 40 partner databasesãnd resources. Here, we report on updates to the Planteome reference ontologies, namely, the Plant Ontology (PO), Trait Ontology (TO), the Plant Experimental Conditions Ontology (PECO),ãnd integration of species / crop-specific vocabularies from our partners, the Crop Ontology (CO) into the TO ontology graph. Currently, 11 CO vocabulariesãre integrated into the Planteome with theãddition of yam, sorghum,ãnd potato since 2018. Inãddition, the size of theãnnotãtion datãbase has increased by 34%,ãnd the number of bioentities (genes, proteins, etc.) from 125 plant taxa has increased by 72%. We de v eloped ne w tools to facilitate user requestsãnd improvements to the CO v ocabularies,ãnd toãllo w fãst searchingãnd bro wsing of PO termsãnd definitions. T hese enhancementsãnd future changes toãutomate the TO-CO mappingsãnd knowledge discovery tools ensure that the Planteome will continue to beã valuable resource for plant biology.