Index Catalog // ScholarsArchive@OSU

Why pest plant control and native plant establishment failed : a restoration autopsy

Creator:: Wilson, Mark V., Ingersoll, Cheryl A., Clark, Deborah Louise, 1950-, and Wilson, Mark G.
Abstract:: Explaining restoration failure can be as important as touting success. We used a series of studies to understand the failure of techniques commonly used to restore wetland prairies in the Willamette Valley of western Oregon. Burning, fallowing, and solarization (covering tilled plots with plastic sheeting to heat the soil) had...
Resource Type:: Article

Phylogeny and Biogeography of Primula sect. Parryi (Primulaceae)

Creator:: Kelso, Sylvia, Beardsley, Paul M., and Weitemier, Kevin
Abstract:: Primula sect. Parryi comprises five species endemic to western North America: P. parryi, P. angustifolia, P. rusbyi, P. capillaris, and P. cusickiana with four varieties. This section, derived from a clade with representatives in Asia and Europe, exemplifies a phytogeographic pattern in which a widespread species is accompanied by multiple...
Resource Type:: Article

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

The Gene Ontology in 2010: extensions and refinements

Creator:: Gene Ontology Consortium, Berardini, Tanya Z., Li, Donghui, Huala, Eva, Bridges, Susan, Burgess, Shane, McCarthy, Fiona, Carbon, Seth, Lewis, Suzanna E., Mungall, Christopher J., Abdulla, Amina, Wood, Valerie, Feltrin, Erika, Valle, Giorgio, Chisholm, Rex L., Fey, Petra, Gaudet, Pascale, Kibbe, Warren, Basu, Siddhartha, Bushmanova, Yulia, Eilbeck, Karen, Siegele, Deborah A., McIntosh, Brenley, Renfro, Daniel, Zweifel, Adrienne, Hu, James C., Harris, Midori A., Deegan, Jennifer I., Ireland, Amelia, Lomax, Jane, Jaiswal, Pankaj, Chibucos, Marcus, Gwinn-Giglio, Michelle, Wortman, Jennifer, Hannick, Linda, Madupu, Ramana, Botstein, David, Dolinski, Kara, Livstone, Michael S., Oughtred, Rose, Blake, Judith A., Bult, Carol, Diehl, Alexander D., Dolan, Mary, Drabkin, Harold, Eppig, Janan T., Hill, David P., Ni, Li, Ringwald, Martin, Sitnikov, Dmitry, Collmer, Candace, Torto-Alalibo, Trudy, Laulederkind, Stan, Shimoyama, Mary, Twigger, Simon, D'Eustachio, Peter, Matthews, Lisa, Balakrishnan, Rama, Binkley, Gail, Cherry, J. Michael, Christie, Karen R., Costanzo, Maria C., Engel, Stacia R., Fisk, Dianna G., Hirschman, Jodi E., Hitz, Benjamin C., Hong, Eurie L., Krieger, Cynthia J., Miyasato, Stuart R., Nash, Robert S., Park, Julie, Skrzypek, Marek S., Weng, Shuai, Wong, Edith D., Aslett, Martin, Chan, Juancarlos, Kishore, Ranjana, Sternberg, Paul, Van Auken, Kimberly, Khodiyar, Varsha K., Lovering, Ruth C., and Talmud, Philippa J.
Abstract:: The Gene Ontology (GO) Consortium (http://www.geneontology.org) (GOC) continues to develop, maintain and use a set of structured, controlled vocabularies for the annotation of genes, gene products and sequences. The GO ontologies are expanding both in content and in structure. Several new relationship types have been introduced and used, along with...
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 Structure Ontology, a Unified Vocabulary of Anatomy and Morphology of a Flowering Plant

Creator:: Ilic, Katica, Kellogg, Elizabeth A., Jaiswal, Pankaj, Zapata, Felipe, Stevens, Peter F., Vincent, Leszek P., Avraham, Shulamit, Reiser, Leonore, Pujar, Anuradha, Sachs, Martin M., Whitman, Noah T., McCouch, Susan R., Schaeffer, Mary L., Ware, Doreen H., Stein, Lincoln D., and Rhee, Seung Y.
Abstract:: Formal description of plant phenotypes and standardized annotation of gene expression and protein localization data require uniform terminology that accurately describes plant anatomy and morphology. This facilitates cross species comparative studies and quantitative comparison of phenotypes and expression patterns. A major drawback is variable terminology that is used to describe...
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

The Generation Challenge Programme Platform: Semantic Standards and Workbench for Crop Science

Creator:: Bruskiewich, Richard, Senger, Martin, Davenport, Guy, Ruiz, Manuel, Rouard, Mathieu, Hazekamp, Tom, Takeya, Masaru, Doi, Koji, Satoh, Kouji, Costa, Marcos, Simon, Reinhard, Balaji, Jayashree, Akintunde, Akinnola, Mauleon, Ramil, Wanchana, Samart, Shah, Trushar, Anacleto, Mylah, Portugal, Arllet, Ulat, Victor Jun, Thongjuea, Supat, Braak, Kyle, Ritter, Sebastian, Dereeper, Alexis, Skofic, Milko, Rojas, Edwin, Martins, Natalia, Pappas, Georgios, Alamban, Ryan, Almodiel, Roque, Barboza, Lord Hendrix, Detras, Jeffrey, Manansala, Kevin, Mendoza, Michael Jonathan, Morales, Jeffrey, Peralta, Barry, Valerio, Rowena, Zhang, Yi, Gregorio, Sergio, Hermocilla, Joseph, Echavez, Michael, Yap, Jan Michael, Farmer, Andrew, Schiltz, Gary, Lee, Jennifer, Casstevens, Terry, Jaiswal, Pankaj, Meintjes, Ayton, Wilkinson, Mark, Good, Benjamin, Wagner, James, Morris, Jane, Marshall, David, Collins, Anthony, Kikuchi, Shoshi, Metz, Thomas, McLaren, Graham, and van Hintum, Theo
Abstract:: The Generation Challenge programme (GCP) is a global crop research consortium directed toward crop improvement through the application of comparative biology and genetic resources characterization to plant breeding. A key consortium research activity is the development of a GCP crop bioinformatics platform to support GCP research. This platform includes the...
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

ScholarsArchive@OSU

Why pest plant control and native plant establishment failed : a restoration autopsy

Phylogeny and Biogeography of Primula sect. Parryi (Primulaceae)

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

The Gene Ontology in 2010: extensions and refinements

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 Structure Ontology, a Unified Vocabulary of Anatomy and Morphology of a Flowering Plant

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

The Generation Challenge Programme Platform: Semantic Standards and Workbench for Crop Science

Gramene: a growing plant comparative genomics resource

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