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Planteome 2024 Update: Reference Ontologies and Knowledgebase for Plant Biology

TitlePlanteome 2024 Update: Reference Ontologies and Knowledgebase for Plant Biology
Publication TypeJournal Article
Year of Publication2023
AuthorsCooper, L, Elser, J, Laporte, M-A, Arnaud, E, Jaiswal, P
JournalNucleic Acids Research
Date Published2023 Dec 06
ISSN1362-4962
Abstract

The Planteome project (https://planteome.org/) provides a suite of reference and crop-specific ontologies and an integrated knowledgebase of plant genomics data. The plant genomics data in the Planteome has been obtained through manual and automated curation and sourced from more than 40 partner databases and 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), and integration of species/crop-specific vocabularies from our partners, the Crop Ontology (CO) into the TO ontology graph. Currently, 11 CO vocabularies are integrated into the Planteome with the addition of yam, sorghum, and potato since 2018. In addition, the size of the annotation database has increased by 34%, and the number of bioentities (genes, proteins, etc.) from 125 plant taxa has increased by 72%. We developed new tools to facilitate user requests and improvements to the CO vocabularies, and to allow fast searching and browsing of PO terms and definitions. These enhancements and future changes to automate the TO-CO mappings and knowledge discovery tools ensure that the Planteome will continue to be a valuable resource for plant biology.

URLhttps://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkad1028/7459474#428834365
DOI10.1093/nar/gkad1028
Alternate JournalNucleic Acids Res
PubMed ID38055832
Grant List1340112 / / National Science Foundation /
/ / United States Department of Agriculture /
2029854 / / National Science Foundation /