{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,21]],"date-time":"2026-10-21T11:32:41Z","timestamp":1792582361531,"version":"4.5.0"},"reference-count":27,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2023,12,6]],"date-time":"2023-12-06T00:00:00Z","timestamp":1701820800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["1340112"],"award-info":[{"award-number":["1340112"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["2029854"],"award-info":[{"award-number":["2029854"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["1940330"],"award-info":[{"award-number":["1940330"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000199","name":"United States Department of Agriculture","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000199","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["2029854"],"award-info":[{"award-number":["2029854"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,1,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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.<\/jats:p>","DOI":"10.1093\/nar\/gkad1028","type":"journal-article","created":{"date-parts":[[2023,12,7]],"date-time":"2023-12-07T05:37:00Z","timestamp":1701927420000},"page":"D1548-D1555","source":"Crossref","is-referenced-by-count":39,"title":["Planteome 2024 Update: Reference Ontologies and Knowledgebase for Plant Biology"],"prefix":"10.1093","volume":"52","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6379-8932","authenticated-orcid":false,"given":"Laurel","family":"Cooper","sequence":"first","affiliation":[{"name":"Department of Botany and Plant Pathology, Oregon State University , Corvallis , OR\u00a0 97331 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0921-1982","authenticated-orcid":false,"given":"Justin","family":"Elser","sequence":"additional","affiliation":[{"name":"Department of Botany and Plant Pathology, Oregon State University , Corvallis , OR\u00a0 97331 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8461-9745","authenticated-orcid":false,"given":"Marie-Angelique","family":"Laporte","sequence":"additional","affiliation":[{"name":"Digital Inclusion, Biodiversity International , 34397\u00a0 Montpellier , France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6020-5919","authenticated-orcid":false,"given":"Elizabeth","family":"Arnaud","sequence":"additional","affiliation":[{"name":"Digital Inclusion, Biodiversity International , 34397\u00a0 Montpellier , France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1005-8383","authenticated-orcid":false,"given":"Pankaj","family":"Jaiswal","sequence":"additional","affiliation":[{"name":"Department of Botany and Plant Pathology, Oregon State University , Corvallis , OR\u00a0 97331 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2023,12,6]]},"reference":[{"key":"2024010511433444100_B1","doi-asserted-by":"crossref","first-page":"e1","DOI":"10.1093\/pcp\/pcs163","article-title":"The plant ontology as a tool for comparative plant anatomy and genomic analyses","volume":"54","author":"Cooper","year":"2013","journal-title":"Plant Cell Physiol."},{"key":"2024010511433444100_B2","doi-asserted-by":"crossref","first-page":"631","DOI":"10.3389\/fpls.2019.00631","article-title":"The Plant Ontology facilitates comparisons of plant development stages across species","volume":"10","author":"Walls","year":"2019","journal-title":"Front. Plant Sci."},{"key":"2024010511433444100_B3","first-page":"89","article-title":"The Plant Ontology: a Tool for Plant Genomics","volume-title":"Plant Bioinformatics, Methods in Molecular Biology","author":"Cooper","year":"2016"},{"key":"2024010511433444100_B4","first-page":"220","article-title":"Towards a reference Plant Trait Ontology for modeling knowledge of plant traits and phenotypes","volume-title":"Proceedings of the International Conference on Knowledge Engineering and Ontology Development","author":"Arnaud","year":"2012"},{"key":"2024010511433444100_B5","doi-asserted-by":"crossref","first-page":"D1168","DOI":"10.1093\/nar\/gkx1152","article-title":"The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics","volume":"46","author":"Cooper","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2024010511433444100_B6","doi-asserted-by":"crossref","first-page":"iyad031","DOI":"10.1093\/genetics\/iyad031","article-title":"The Gene Ontology knowledgebase in 2023","volume":"224","author":"The Gene Ontology Consortium","year":"2023","journal-title":"Genetics"},{"key":"2024010511433444100_B7","doi-asserted-by":"crossref","first-page":"D136","DOI":"10.1093\/nar\/gkr1178","article-title":"The NCBI Taxonomy database","volume":"40","author":"Federhen","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2024010511433444100_B8","doi-asserted-by":"crossref","first-page":"160018","DOI":"10.1038\/sdata.2016.18","article-title":"The FAIR Guiding Principles for scientific data management and stewardship","volume":"3","author":"Wilkinson","year":"2016","journal-title":"Sci. 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Biomed Semant."},{"key":"2024010511433444100_B10","doi-asserted-by":"crossref","first-page":"D1214","DOI":"10.1093\/nar\/gkv1031","article-title":"ChEBI in 2016: improved services and an expanding collection of metabolites","volume":"44","author":"Hastings","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"2024010511433444100_B11","doi-asserted-by":"crossref","first-page":"D712","DOI":"10.1093\/nar\/gkw1128","article-title":"The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species","volume":"45","author":"Mungall","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"2024010511433444100_B12","doi-asserted-by":"crossref","first-page":"D234","DOI":"10.1093\/nar\/gku1203","article-title":"InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic","volume":"43","author":"Sonnhammer","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"2024010511433444100_B13","doi-asserted-by":"crossref","first-page":"474","DOI":"10.1002\/dvg.22877","article-title":"The arabidopsis information resource: making and mining the \u201cgold standard\u201d annotated reference plant genome","volume":"53","author":"Berardini","year":"2015","journal-title":"Genesis"},{"key":"2024010511433444100_B14","doi-asserted-by":"crossref","first-page":"751","DOI":"10.1007\/s00122-018-3212-5","article-title":"The Sorghum QTL Atlas: a powerful tool for trait dissection, comparative genomics and crop improvement","volume":"132","author":"Mace","year":"2019","journal-title":"Theor. 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