Index Catalog // ScholarsArchive@OSU

Ontologies as Integrative Tools for Plant Science

Creator:: Walls, Ramona L., Athreya, Balaji, Cooper, Laurel, Elser, Justin, Gandolfo, Maria A., Jaiswal, Pankaj, Mungall, Christopher J., Preece, Justin, Rensing, Stefan, Smith, Barry, and Stevenson, Dennis W.
Abstract:: Premise of the study: Bio-ontologies are essential tools for accessing and analyzing the rapidly growing pool of plant genomic and phenomic data. Ontologies provide structured vocabularies to support consistent aggregation of data and a semantic framework for automated analyses and reasoning. They are a key component of the semantic web....
Resource Type:: Article
Full Text:: such tools, by standardizing terminology, supporting data aggregation and re- trieval, and creating a

An Extension of the Plant Ontology Project Supporting Wood Anatomy and Development Research

Creator:: Lens, Frederic, Cooper, Laurel, Gandolfo, Maria Alejandra, Groover, Andrew, Jaiswal, Pankaj, Lachenbruch, Barbara, Spicer, Rachel, Staton, Margaret E., Stevenson, Dennis W., Walls, Ramona L., and Wegrzyn, Jill
Abstract:: A wealth of information on plant anatomy and morphology is available in the current and historical literature, and molecular biologists are producing massive amounts of transcriptome and genome data that can be used to gain better insights into the development, evolution, ecology, and physiological function of plant anatomical attributes. Integrating...
Resource Type:: Article
Full Text:: PlAnt ontology Project suPPorting wood AnAtomy And develoPment reseArch frederic lens1*, laurel

The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses

Creator:: Cooper, Laurel, Walls, Ramona L., Elser, Justin, Gandolfo, Maria A., Stevenson, Dennis W., Smith, Barry, Preece, Justin, Athreya, Balaji, Mungall, Christopher J., Rensing, Stefan, Hiss, Manuel, Lang, Daniel, Reski, Ralf, Berardini, Tanya Z., Li, Donghui, Huala, Eva, Schaeffer, Mary, Menda, Naama, Arnaud, Elizabeth, Shrestha, Rosemary, Yamazaki, Yukiko, and Jaiswal, Pankaj
Abstract:: The Plant Ontology (PO;http://www.plantontology.org/" is a publicly available, collaborative effort to develop and maintain a controlled, structured vocabulary ('ontology') of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and...
Resource Type:: Article
Full Text:: OP-PCPJ120087 1..23 The Plant Ontology as a Tool for Comparative

Text mining in the biocuration workflow: applications for literature curation at WormBase, dictyBase and TAIR

Creator:: Van Auken, Kimberly, Fey, Petra, Berardini, Tanya Z., Dodson, Robert, Cooper, Laurel, Li, Donghui, Chan, Juancarlos, Li, Yuling, Basu, Siddhartha, Muller, Hans-Michael, Chisholm, Rex, Huala, Eva, Sternberg, Paul W., and WormBase Consortium
Abstract:: WormBase, dictyBase and The Arabidopsis Information Resource (TAIR) are model organism databases containing information about Caenorhabditis elegans and other nematodes, the social amoeba Dictyostelium discoideum and related Dictyostelids and the flowering plant Arabidopsis thaliana, respectively. Each database curates multiple data types from the primary research literature. In this article, we...
Resource Type:: Article
Full Text:: Auken1,*, Petra Fey2, Tanya Z. Berardini3, Robert Dodson2, Laurel Cooper4, Donghui Li3, Juancarlos Chan1

Toward a flexible and accurate approach to null network sampling

Creator:: Bright, Zachary A.
Abstract:: Null networks are a type of random graph that is favored for the analysis of a wide variety of real-world networks, including gene-regulatory networks, food webs, and species co-occurrence matrices. As a hypothesis-generating tool, null networks are invaluable because they can reveal network motifs and unusual large-scale properties of networks...
Resource Type:: Masters Thesis
Full Text:: AN ABSTRACT OF THE THESIS OF Zachary A. Bright for the

Emerging semantics to link phenotype and environment

Creator:: Thessen, Anne E., Bunkers, Daniel E., Buttigieg, Pier Luigi, Cooper, Laurel D., Dahdul, Wasila M., Domisch, Sami, Franz, Nico M., Jaiswal, Pankaj, Lawrence-Dill, Carolyn J., Midford, Peter E., Mungall, Christopher J., Ramírez, Martín J., Specht, Chelsea D., Vogt, Lars, Aldo Vos, Rutger, Walls, Ramona L., White, Jeffrey W., Zhang, Guanyang, Deans, Andrew R., Huala, Eva, Lewis, Suzanna E., and Mabee, Paula M.
Abstract:: Understanding the interplay between environmental conditions and phenotypes is a fundamental goal of biology. Unfortunately, data that include observations on phenotype and environment are highly heterogeneous and thus difficult to find and integrate. One approach that is likely to improve the status quo involves the use of ontologies to standardize...
Resource Type:: Article
Full Text:: environment Emerging semantics to link phenotype and environment Thessen, A. E., Bunker, D. E., Buttigieg

Insights into the pathology and epidemiology of Phytophthora ramorum, causal agent of sudden oak death

Creator:: Daniels, Hazel A.
Abstract:: Sudden oak death is caused by the clonally reproducing generalist oomycete Phytophthora ramorum. The pathogen can infect more than 130 different plant hosts including Quercus spp., Larix kaempferi, and Notholithocarpus densiflorus, as well as common nursery genera such as Rhododendron and Camelia, where it causes symptoms ranging from bleeding cankers...
Resource Type:: Dissertation
Full Text:: asked regarding management, epidemiology, and pathology of the disease. The first chapter is a review

Science Takes Flight: Detection of Black Leg on Turnip Gray Mold on Hemp

Creator:: Bates, Taylor A.
Abstract:: Disease detection through traditional techniques such as scouting fields on foot, molecular assays, or morphological identification of plant pathogens is time consuming and costly. Disease diagnosis in the field can be extremely subjective, and largely depends on the experience and knowledge of pathogen identification and disease quantification. This thesis provides...
Resource Type:: Masters Thesis
Full Text:: AN ABSTRACT OF THE THESIS OF Taylor A. Bates for

An overview of the BioCreative 2012 Workshop Track III: interactive text mining task

Creator:: Arighi, Cecilia N., Carterette, Ben, Cohen, K. Bretonnel, Krallinger, Martin, Wilbur, W. John, Fey, Petra, Dodson, Robert, Cooper, Laurel, Van Slyke, Ceri E., Dahdul, Wasila, Mabee, Paula, Li, Donghui, Harris, Bethany, Gillespie, Marc, Jimenez, Silvia, Roberts, Phoebe, Matthews, Lisa, Becker, Kevin, Drabkin, Harold, Bello, Susan, Licata, Luana, Chatr-aryamontri, Andrew, Schaeffer, Mary L., Park, Julie, Haendel, Melissa, Van Auken, Kimberly, Li, Yuling, Chan, Juancarlos, Muller, Hans-Michael, Cui, Hong, Balhoff, James P., Wu, Johnny Chi-Yang, Lu, Zhiyong, Wei, Chih-Hsuan, Tudor, Catalina O., Raja, Kalpana, Subramani, Suresh, Natarajan, Jeyakumar, Cejuela, Juan Miguel, Dubey, Pratibha, and Wu, Cathy
Abstract:: In many databases, biocuration primarily involves literature curation, which usually involves retrieving relevant articles, extracting information that will translate into annotations and identifying new incoming literature. As the volume of biological literature increases, the use of text mining to assist in biocuration becomes increasingly relevant. A number of groups have...
Resource Type:: Article
Full Text:: . Bretonnel Cohen3, Martin Krallinger4, W. John Wilbur5, Petra Fey6, Robert Dodson6, Laurel Cooper7, Ceri E

The epidemiology of sudden oak death in Oregon forests

Creator:: Peterson, Ebba K.
Abstract:: The phytopathogen Phytophthora ramorum (Werres, DeCock & Man in't Veld), causal agent of Sudden Oak Death (SOD) of oaks (Quercus spp.) and tanoaks (Notholithocarpus densiflorus syn. Lithocarpus densiflorus), is established in coastal forests of the western United States. Since the discovery of SOD in the Douglas-fir / tanoak forests of...
Resource Type:: Dissertation
Full Text:: petioles………………………………... 110 A.4 Leaf lesions indicating potential infection on bay laurel………………. 110 A

ScholarsArchive@OSU

Ontologies as Integrative Tools for Plant Science

An Extension of the Plant Ontology Project Supporting Wood Anatomy and Development Research

The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses

Text mining in the biocuration workflow: applications for literature curation at WormBase, dictyBase and TAIR

Toward a flexible and accurate approach to null network sampling

Emerging semantics to link phenotype and environment

Insights into the pathology and epidemiology of Phytophthora ramorum, causal agent of sudden oak death

Science Takes Flight: Detection of Black Leg on Turnip Gray Mold on Hemp

An overview of the BioCreative 2012 Workshop Track III: interactive text mining task

The epidemiology of sudden oak death in Oregon forests

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