植物本体论（PO）：植物结构与生长阶段的受控词汇表。
Plant Ontology (PO): a Controlled Vocabulary of Plant Structures and Growth Stages.
作者信息
Jaiswal Pankaj, Avraham Shulamit, Ilic Katica, Kellogg Elizabeth A, McCouch Susan, Pujar Anuradha, Reiser Leonore, Rhee Seung Y, Sachs Martin M, Schaeffer Mary, Stein Lincoln, Stevens Peter, Vincent Leszek, Ware Doreen, Zapata Felipe
机构信息
Department of Plant Breeding 240 Emerson Hall Cornell University Ithaca NY 14853 USA.
出版信息
Comp Funct Genomics. 2005;6(7-8):388-97. doi: 10.1002/cfg.496.
Abstract
The Plant Ontology Consortium (POC) (www.plantontology.org) is a collaborative effort among several plant databases and experts in plant systematics, botany and genomics. A primary goal of the POC is to develop simple yet robust and extensible controlled vocabularies that accurately reflect the biology of plant structures and developmental stages. These provide a network of vocabularies linked by relationships (ontology) to facilitate queries that cut across datasets within a database or between multiple databases. The current version of the ontology integrates diverse vocabularies used to describe Arabidopsis, maize and rice (Oryza sp.) anatomy, morphology and growth stages. Using the ontology browser, over 3500 gene annotations from three species-specific databases, The Arabidopsis Information Resource (TAIR) for Arabidopsis, Gramene for rice and MaizeGDB for maize, can now be queried and retrieved.
相似文献
1
Plant Ontology (PO): a Controlled Vocabulary of Plant Structures and Growth Stages.植物本体论（PO）：植物结构与生长阶段的受控词汇表。
Comp Funct Genomics. 2005;6(7-8):388-97. doi: 10.1002/cfg.496.
2
The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations.植物本体数据库：一个用于植物结构和发育阶段控制词汇及注释的社区资源。
Nucleic Acids Res. 2008 Jan;36(Database issue):D449-54. doi: 10.1093/nar/gkm908.
3
The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant.植物结构本体论，一种开花植物解剖学和形态学的统一词汇表。
Plant Physiol. 2007 Feb;143(2):587-99. doi: 10.1104/pp.106.092825. Epub 2006 Dec 1.
4
Gramene: development and integration of trait and gene ontologies for rice.Gramene：水稻性状和基因本体的开发与整合
Comp Funct Genomics. 2002;3(2):132-6. doi: 10.1002/cfg.156.
5
Whole-plant growth stage ontology for angiosperms and its application in plant biology.被子植物全株生长阶段本体论及其在植物生物学中的应用。
Plant Physiol. 2006 Oct;142(2):414-28. doi: 10.1104/pp.106.085720. Epub 2006 Aug 11.
6
The Plant Ontology: A Tool for Plant Genomics.植物本体论：植物基因组学的一个工具。
Methods Mol Biol. 2016;1374:89-114. doi: 10.1007/978-1-4939-3167-5_5.
7
The Plant Ontology Consortium and plant ontologies.植物本体论联盟与植物本体论
Comp Funct Genomics. 2002;3(2):137-42. doi: 10.1002/cfg.154.
8
The plant ontology as a tool for comparative plant anatomy and genomic analyses.植物本体作为一种用于比较植物解剖学和基因组分析的工具。
Plant Cell Physiol. 2013 Feb;54(2):e1. doi: 10.1093/pcp/pcs163. Epub 2012 Dec 5.
9
Gramene, a tool for grass genomics.Gramene，一种用于禾本科植物基因组学的工具。
Plant Physiol. 2002 Dec;130(4):1606-13. doi: 10.1104/pp.015248.
10
Gramene 2021: harnessing the power of comparative genomics and pathways for plant research.Gramene 2021：利用比较基因组学和途径为植物研究提供支持。
Nucleic Acids Res. 2021 Jan 8;49(D1):D1452-D1463. doi: 10.1093/nar/gkaa979.
引用本文的文献
1
Exploring Saccharomycotina Yeast Ecology Through an Ecological Ontology Framework.通过生态本体论框架探索酿酒酵母的生态。
Yeast. 2024 Oct;41(10):615-628. doi: 10.1002/yea.3981. Epub 2024 Sep 18.
2
C3PO: a crop planning and production process ontology and knowledge graph.C3PO：一种作物规划与生产过程本体及知识图谱。
Front Artif Intell. 2023 Oct 16;6:1187090. doi: 10.3389/frai.2023.1187090. eCollection 2023.
3
Sainfoin ( spp.) crop ontology: supporting germplasm characterization and international research collaborations.红豆草（属）作物本体论：支持种质特征描述和国际研究合作。
Front Plant Sci. 2023 May 15;14:1177406. doi: 10.3389/fpls.2023.1177406. eCollection 2023.
4
Digitalization of potato breeding program: Improving data collection and management.马铃薯育种计划的数字化：改进数据收集与管理。
Heliyon. 2023 Jan 20;9(1):e12974. doi: 10.1016/j.heliyon.2023.e12974. eCollection 2023 Jan.
5
Toward a data infrastructure for the Plant Cell Atlas.迈向植物细胞图谱的数据基础设施。
Plant Physiol. 2023 Jan 2;191(1):35-46. doi: 10.1093/plphys/kiac468.
6
Genetic Diversity of Transcription Factor Genes in and Mining for Promising Haplotypes for Beneficial Agronomic Traits.转录因子基因的遗传多样性及有益农艺性状优良单倍型挖掘
Front Plant Sci. 2022 Jul 8;13:899292. doi: 10.3389/fpls.2022.899292. eCollection 2022.
7
Genetic and Genomic Resources for Soybean Breeding Research.大豆育种研究的遗传和基因组资源
Plants (Basel). 2022 Apr 27;11(9):1181. doi: 10.3390/plants11091181.
8
A COMPASS for VESPUCCI: A FAIR Way to Explore the Grapevine Transcriptomic Landscape.VESPUCCI的指南针：探索葡萄转录组景观的公平方式。
Front Plant Sci. 2022 Feb 24;13:815443. doi: 10.3389/fpls.2022.815443. eCollection 2022.
9
Opportunities and limits of controlled-environment plant phenotyping for climate response traits.受控环境植物表型分析在气候响应性状研究中的机遇与限制。
Theor Appl Genet. 2022 Jan;135(1):1-16. doi: 10.1007/s00122-021-03892-1. Epub 2021 Jul 24.
10
Challenges for FAIR-compliant description and comparison of crop phenotype data with standardized controlled vocabularies.符合 FAIR 原则的作物表型数据描述和标准化控制词汇比较面临的挑战。
Database (Oxford). 2021 May 15;2021. doi: 10.1093/database/baab028.
本文引用的文献
1
Obol: integrating language and meaning in bio-ontologies.奥博尔：在生物本体中整合语言与意义
Comp Funct Genomics. 2004;5(6-7):509-20. doi: 10.1002/cfg.435.
2
The Plant Ontology Consortium and plant ontologies.植物本体论联盟与植物本体论
Comp Funct Genomics. 2002;3(2):137-42. doi: 10.1002/cfg.154.
3
The map-based sequence of the rice genome.水稻基因组的基于图谱的序列。
Nature. 2005 Aug 11;436(7052):793-800. doi: 10.1038/nature03895.
4
It's all GO for plant scientists.这对植物科学家来说一切顺利。
Plant Physiol. 2005 Jul;138(3):1268-79. doi: 10.1104/pp.104.058529.
5
Biological ontologies in rice databases. An introduction to the activities in Gramene and Oryzabase.水稻数据库中的生物本体论。介绍Gramene和Oryzabase中的相关活动。
Plant Cell Physiol. 2005 Jan;46(1):63-8. doi: 10.1093/pcp/pci505. Epub 2005 Jan 19.
6
The Arabidopsis COW1 gene encodes a phosphatidylinositol transfer protein essential for root hair tip growth.拟南芥COW1基因编码一种对根毛顶端生长至关重要的磷脂酰肌醇转移蛋白。
Plant J. 2004 Dec;40(5):686-98. doi: 10.1111/j.1365-313X.2004.02245.x.
7
Functional annotation of the Arabidopsis genome using controlled vocabularies.使用受控词汇对拟南芥基因组进行功能注释。
Plant Physiol. 2004 Jun;135(2):745-55. doi: 10.1104/pp.104.040071. Epub 2004 Jun 1.
8
Ontologies in biology: design, applications and future challenges.生物学中的本体论：设计、应用及未来挑战。
Nat Rev Genet. 2004 Mar;5(3):213-22. doi: 10.1038/nrg1295.
9
MaizeGDB, the community database for maize genetics and genomics.玉米基因数据库（MaizeGDB），玉米遗传学和基因组学的社区数据库。
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D393-7. doi: 10.1093/nar/gkh011.
10
Zea mays ontology--a database of international terms.玉米本体论——一个国际术语数据库。
Trends Plant Sci. 2003 Nov;8(11):517-20. doi: 10.1016/j.tplants.2003.09.014.
Zotero 插件