Index Catalog // ScholarsArchive@OSU

Whole-Plant Growth Stage Ontology for Angiosperms and Its Application in Plant Biology

Creator:: Pujar, Anuradha, Jaiswal, Pankaj, Kellogg, Elizabeth A., Ilic, Katica, Vincent, Leszek, Avraham, Shulamit, Stevens, Peter, Zapata, Felipe, Reiser, Leonore, Rhee, Seung Y., Sachs, Martin M., Schaeffer, Mary, Stein, Lincoln, Ware, Doreen, and McCouch, Susan
Abstract:: Plant growth stages are identified as distinct morphological landmarks in a continuous developmental process. The terms describing these developmental stages record the morphological appearance of the plant at a specific point in its life cycle. The widely differing morphology of plant species consequently gave rise to heterogeneous vocabularies describing growth...
Resource Type:: Article

Gramene: Development and Integration of Trait and Gene Ontologies for Rice

Creator:: Jaiswal, Pankaj, Ware, Doreen, Ni, Junjian, Chang, Kuan, Zhao, Wei, Schmidt, Steven, Pan, Xiaokang, Clark, Kenneth, Teytelman, Leonid, Cartinhour, Samuel, Stein, Lincoln, and McCouch, Susan
Abstract:: Gramene (http://www.gramene.org/) is a comparative genome database for cereal crops and a community resource for rice. We are populating and curating Gramene with annotated rice (Oryza sativa) genomic sequence data and associated biological information including molecular markers, mutants, phenotypes, polymorphisms and Quantitative Trait Loci (QTL). In order to support queries...
Resource Type:: Article

Plant Ontology (PO): a controlled vocabulary of plant structures and growth stages

Creator:: Jaiswal, Pankaj, Avraham, Shulamit, Ilic, Katica, Kellog, Elizabeth, A., McCouch, Susan, Pujar, Anuradha, Reiser, Leonore, Rhee, Seung Y., Sachs, Martin M., Schaeffer, Mary, Stein, Lincoln, Stevens, Peter, Vincent, Leszek, Ware, Doreen, and Zapata, Felipe
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...
Resource Type:: Article

The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations

Creator:: Avraham, Shulamit, Tung, Chih-Wei, Ilic, Katica, Jaiswal, Pankaj, Kellogg, Elizabeth A., McCouch, Susan, Pujar, Anuradha, Reiser, Leonore, Rhee, Seung Y., Sachs, Martin M., Schaeffer, Mary, Stein, Lincoln, Stevens, Peter, Vincent, Leszek, Zapata, Felipe, and Ware, Doreen
Abstract:: The Plant Ontology Consortium (POC, http://www.plantontology.org) is a collaborative effort among model plant genome databases and plant researchers that aims to create, maintain and facilitate the use of a controlled vocabulary (ontology) for plants. The ontology allows users to ascribe attributes of plant structure (anatomy and morphology) and developmental stages...
Resource Type:: Article

Gramene: a growing plant comparative genomics resource

Creator:: Liang, Chengzhi, Jaiswal, Pankaj, Hebbard, Claire, Avraham, Shuly, Buckler, Edward S., Casstevens, Terry, Hurwitz, Bonnie, McCouch, Susan, Ni, Junjian, Pujar, Anuradha, Ravenscroft, Dean, Ren, Liya, Spooner, William, Tecle, Isaak, Thomason, Jim, Tung, Chih-wei, Wei, Xuehong, Yap, Immanuel, Youens-Clark, Ken, Ware, Doreen, and Stein, Lincoln
Abstract:: Gramene (www.gramene.org) is a curated resource for genetic, genomic and comparative genomics data for the major crop species, including rice, maize, wheat and many other plant (mainly grass) species. Gramene is an open-source project. All data and software are freely downloadable through the ftp site (ftp.gramene.org/pub/gramene) and available for use...
Resource Type:: Article

Gramene: a resource for comparative grass genomics

Creator:: Ware, Doreen, Jaiswal, Pankaj, Ni, Junjian, Pan, Xiaokang, Chang, Kuan, Clark, Kenneth, Teytelman, Leonid, Schmidt, Steve, Zhao, Wei, Cartinhour, Samuel, McCouch, Susan, and Stein, Lincoln
Abstract:: Gramene (http://www.gramene.org) is a comparative genome mapping database for grasses and a community resource for rice. Rice, in addition to being an economically important crop, is also a model monocot for understanding other agronomically important grass genomes. Gramene replaces the existing AceDB database ‘RiceGenes’ with a relational database based on...
Resource Type:: Article

Gramene: a bird's eye view of cereal genomes

Creator:: Jaiswal, Pankaj, Ni, Junjian, Yap, Immanuel, Ware, Doreen, Spooner, William, Youens-Clark, Ken, Canaran, Payan, Fogleman, Molly, Hebbard, Claire, Ren, Liya, Liang, Chengzhi, Zhao, Wei, Ratnapu, Kiran, Faga, Benjamin, Avraham, Shuly, Schmidt, Steven, Casstevens, Terry M., Buckler, Edward S., Stein, Lincoln, and McCouch, Susan
Abstract:: Rice, maize, sorghum, wheat, barley and the other major crop grasses from the family Poaceae (Gramineae) are mankind’s most important source of calories and contribute tens of billions of dollars annually to the world economy (FAO 1999, http://www.fao.org; USDA 1997, http://www.usda.gov). Continued improvement of Poaceae crops is necessary in order...
Resource Type:: Article

Gramene QTL database: development, content and applications

Creator:: Ni, Junjian, Pujar, Anuradha, Youens-Clark, Ken, Yap, Immanuel, Jaiswal, Pankaj, Tecle, Isaak, Tung, Chih-Wei, Ren, Liya, Spooner, William, Wei, Xuehong, Avraham, Shuly, Ware, Doreen, Stein, Lincoln, and McCouch, Susan
Abstract:: Gramene is a comparative information resource for plants that integrates data across diverse data domains. In this article, we describe the development of a quantitative trait loci (QTL) database and illustrate how it can be used to facilitate both the forward and reverse genetics research. The QTL database contains the...
Resource Type:: Article

A genome scale metabolic network for rice and accompanying analysis of tryptophan, auxin and serotonin biosynthesis regulation under biotic stress

Creator:: Dharmawardhana, Palitha, Ren, Liya, Amarasinghe, Vindhya, Monaco, Marcela, Thomason, Jim, Ravenscroft, Dean, McCouch, Susan, Ware, Doreen, and Jaiswal, Pankaj
Abstract:: Background: Functional annotations of large plant genome projects mostly provide information on gene function and gene families based on the presence of protein domains and gene homology, but not necessarily in association with gene expression or metabolic and regulatory networks. These additional annotations are necessary to understand the physiology, development...
Resource Type:: Article

Nomenclature report on rice WRKY’s - Conflict regarding gene names and its solution

Creator:: Shen, Qingxi J., Yu, Diqiu, Jeon, Jong-Seong, Piffanelli, Pietro, Abbruscato, Pamela, Guo, Ze-Jian, Zhang, Yuanji, Itoh, Takeshi, Lee, Sung S., Buell, C. Robin, Nagato, Yasuo, McCouch, Susan, Yano, Masahiro, Wang, Guo-liang, Jena, Kshirod K., Xiong, Lizhong, Meyers, Blake, Jaiswal, Pankaj, and Yamazaki, Yukiko
Abstract:: Background: Since whole genome sequences of rice were made publically accessible, the number of articles on new rice genes has increased remarkably. The Committee on Gene Symbolization, Nomenclature and Linkage (CGSNL) of the Rice Genetics Cooperative published the gene nomenclature system for rice and encouraged researchers to follow the rules...
Resource Type:: Article

ScholarsArchive@OSU

Whole-Plant Growth Stage Ontology for Angiosperms and Its Application in Plant Biology

Gramene: Development and Integration of Trait and Gene Ontologies for Rice

Plant Ontology (PO): a controlled vocabulary of plant structures and growth stages

The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations

Gramene: a growing plant comparative genomics resource

Gramene: a resource for comparative grass genomics

Gramene: a bird's eye view of cereal genomes

Gramene QTL database: development, content and applications

A genome scale metabolic network for rice and accompanying analysis of tryptophan, auxin and serotonin biosynthesis regulation under biotic stress

Nomenclature report on rice WRKY’s - Conflict regarding gene names and its solution

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