Index Catalog // ScholarsArchive@OSU

AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture

Creator:: Harper, Lisa, Campbell, Jacqueline, Cannon, Steve, Carson, James, Condon, Bradford, Cooper, Laurel, Dunn, Nathan, Elsik, Christine G., Farmer, Andrew, Ficklin, Stephen P., Grant, David, Grau, Emily, Cannon, Ethalinda K. S., Herndon, Nic, Hu, Zhi-Liang, Humann, Jodi, Jaiswal, Pankaj, Jonquet, Clement, Laporte, Marie-Angelique, Larmande, Pierre, Lazo, Gerard, McCarthy, Fiona, Menda, Naama, Jung, Sook, Mungall, Christopher J., Munoz-Torres, Monica C., Naithani, Sushma, Nelson, Rex, Nesdill, Daureen, Park, Carissa, Reecy, James, Reiser, Leonore, Sanderson, Lacey-Anne, Sen, Taner Z., Poelchau, Monica, Staton, Margaret, Subramaniam, Sabarinath, Tello-Ruiz, Marcela Karey, Unda, Victor, Unni, Deepak, Wang, Liya, Ware, Doreen, Wegrzyn, Jill, Williams, Jason, Woodhouse, Margaret, Walls, Ramona, Yu, Jing, Main, Doreen, Andorf, Carson, Arnaud, Elizabeth, Berardini, Tanya Z., and Birkett, Clayton
Abstract:: The future of agricultural research depends on data. The sheer volume of agricultural biological data being produced today makes excellent data management essential. Governmental agencies, publishers and science funders require datamanagement plans for publicly funded research. Furthermore, the value of data increases exponentially when they are properly stored, described, integrated...
Resource Type:: Article

Differential Expression of Genes Involved in Host Recognition, Attachment, and Degradation in the Mycoparasite Tolypocladium ophioglossoides

Creator:: Quandt, C. Alisha, Di, Yanming, Elser, Justin, Jaiswal, Pankaj, and Spatafora, Joseph W.
Abstract:: This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by the Genetics Society of America. The published article can be found at: https://doi.org/10.1534/g3.116.027045
Resource Type:: Article

FragariaCyc: A Metabolic Pathway Database for Woodland Strawberry Fragaria vesca

Creator:: Naithani, Sushma, Partipilo, Christina M., Raja, Rajani, Elser, Justin L., and Jaiswal, Pankaj
Abstract:: FragariaCyc is a strawberry-specific cellular metabolic network based on the annotated genome sequence of Fragaria vesca L. ssp. vesca, accession Hawaii 4. It was built on the Pathway-Tools platform using MetaCyc as the reference. The experimental evidences from published literature were used for supporting/editing existing entities and for the addition...
Resource Type:: Article

Expression Atlas update-an integrated database of gene and protein expression in humans, animals and plants

Creator:: Petryszak, Robert, Keays, Maria, Tang, Y. Amy, Fonseca, Nuno A., Barrera, Elisabet, Burdett, Tony, Füllgrabe, Anja, Muñoz-Pomer Fuentes, Alfonso, Jupp, Simon, Koskinen, Satu, Mannion, Oliver, Huerta, Laura, Megy, Karine, Snow, Catherine, Williams, Eleanor, Barzine, Mitra, Hastings, Emma, Weisser, Hendrik, Wright, James, Jaiswal, Pankaj, Huber, Wolfgang, Choudhary, Jyoti, Parkinson, Helen E., and Brazma, Alvis
Abstract:: Expression Atlas (http://www.ebi.ac.uk/gxa) provides information about gene and protein expression in animal and plant samples of different cell types, organism parts, developmental stages, diseases and other conditions. It consists of selected microarray and RNA-sequencing studies from ArrayExpress, which have been manually curated, annotated with ontology terms, checked for high quality...
Resource Type:: Article

Gramene 2016: comparative plant genomics and pathway resources

Creator:: Tello-Ruiz, Marcela K., Stein, Joshua, Wei, Sharon, Preece, Justin, Olson, Andrew, Naithani, Sushma, Amarasinghe, Vindhya, Dharmawardhana, Palitha, Jiao, Yinping, Mulvaney, Joseph, Kumari, Sunita, Chougule, Kapeel, Elser, Justin, Wang, Bo, Thomason, James, Bolser, Daniel M., Kerhornou, Arnaud, Walts, Brandon, Fonseca, Nuno A., Huerta, Laura, Keays, Maria, Tanga, Y. Amy, Parkinson, Helen, Fabregat, Antonio, McKay, Sheldon, Weiser, Joel, D'Eustachio, Peter, Stein, Lincoln, Petryszak, Robert, Kersey, Paul J., Jaiswal, Pankaj, and Ware, Doreen
Abstract:: Gramene (http://www.gramene.org) is an online resource for comparative functional genomics in crops and model plant species. Its two main frameworks are genomes (collaboration with Ensembl Plants) and pathways (The Plant Reactome and archival BioCyc databases). Since our last NAR update, the database website adopted a new Drupal management platform. The...
Resource Type:: Article

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

Quantitative Trait Loci Associated with the Tocochromanol (Vitamin E) Pathway in Barley

Creator:: Graebner, Ryan C., Wise, Mitchell, Cuesta-Marcos, Alfonso, Geniza, Matthew, Blake, Tom, Blake, Victoria C., Butler, Joshua, Chao, Shiaoman, Hole, David J., Horsley, Rich, Jaiswal, Pankaj, Obert, Don, Smith, Kevin P., Ullrich, Steven, and Hayes, Patrick M.
Abstract:: The Genome-Wide Association Studies approach was used to detect Quantitative Trait Loci associated with tocochromanol concentrations using a panel of 1,466 barley accessions. All major tocochromanol types- α-, β-, δ-, γ-tocopherol and tocotrienol- were assayed. We found 13 single nucleotide polymorphisms associated with the concentration of one or more of...
Resource Type:: Article

An ontology approach to comparative phenomics in plants

Creator:: Oellrich, Anika, Walls, Ramona L., Cannon, Ethalinda K. S., Cannon, Steven B., Cooper, Laurel, Gardiner, Jack, Gkoutos, Georgios V., Harper, Lisa, He, Mingze, Hoehndorf, Robert, Jaiswal, Pankaj, Kalberer, Scott R., Lloyd, John P., Meinke, David, Menda, Naama, Moore, Laura, Nelson, Rex T., Pujar, Anuradha, Lawrence, Carolyn J., and Huala, Eva
Abstract:: BACKGROUND: Plant phenotype datasets include many different types of data, formats, and terms from specialized vocabularies. Because these datasets were designed for different audiences, they frequently contain language and details tailored to investigators with different research objectives and backgrounds. Although phenotype comparisons across datasets have long been possible on a...
Resource Type:: Article

AISO: Annotation of Image Segments with Ontologies

Creator:: Lingutla, Nikhil Tej, Preece, Justin, Todorovic, Sinisa, Cooper, Laurel, Moore, Laura, and Jaiswal, Pankaj
Abstract:: BACKGROUND: Large quantities of digital images are now generated for biological collections, including those developed in projects premised on the high-throughput screening of genome-phenome experiments. These images often carry annotations on taxonomy and observable features, such as anatomical structures and phenotype variations often recorded in response to the environmental factors...
Resource Type:: Article

Finding Our Way through Phenotypes

Creator:: Deans, Andrew R., Lewis, Suzanna E., Huala, Eva, Anzaldo, Salvatore S., Ashburner, Michael, Balhoff, James P., Blackburn, David C., Blake, Judith A., Burleigh, J. Gordon, Chanet, Bruno, Cooper, Lauren D., Courtot, Mélanie, Csösz, Sándor, Cul, Hong, Dahdul, Wasila, Das, Sandip, Dececchi, T. Alexander, Dettal, Agnes, Diogo, Rui, Druzinsky, Robert E., Dumontier, Michel, Franz, Nico M., Friedrich, Frank, Gkoutos, George V., Haendel, Melissa, Harmon, Luke J., Hayamizu, Terry F., He, Yongqun, Hines, Heather M., Ibrahim, Nizar, Jackson, Laura M., Jaiswal, Pankaj, James-Zorn, Christina, Köhler, Sebastian, Lecointre, Guillaume, Lapp, Hilmar, Lawrence, Carolyn J., Le Novère, Nicolas, Lundberg, John G., Macklin, James, Mast, Austin R., Midford, Peter E., Mikó, István, Mungall, Christopher J., Oellrich, Anika, Osumi-Sutherland, David, Parkinson, Helen, Ramírez, Martín J., Richter, Stefan, Robinson, Peter N., Ruttenberg, Alan, Schulz, Katja S., Segerdell, Erik, Seltmann, Katja C., Sharkey, Michael J., Smith, Aaron D., Smith, Barry, Specht, Chelsea D., Squires, R. Burke, Thacker, Robert W., Thessen, Anne, Fernandez-Triana, Jose, Vihinen, Mauno, Vize, Peter D., Vogt, Lars, Wall, Christine E., Walls, Ramona L., Westerfeld, Monte, Wharton, Robert A., Wirkner, Christian S., Woolley, James B., Yoder, Matthew J., Zorn, Aaron M., and Mabee, Paula
Abstract:: Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across...
Resource Type:: Article

ScholarsArchive@OSU

AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture

Differential Expression of Genes Involved in Host Recognition, Attachment, and Degradation in the Mycoparasite Tolypocladium ophioglossoides

FragariaCyc: A Metabolic Pathway Database for Woodland Strawberry Fragaria vesca

Expression Atlas update-an integrated database of gene and protein expression in humans, animals and plants

Gramene 2016: comparative plant genomics and pathway resources

Emerging semantics to link phenotype and environment

Quantitative Trait Loci Associated with the Tocochromanol (Vitamin E) Pathway in Barley

An ontology approach to comparative phenomics in plants

AISO: Annotation of Image Segments with Ontologies

Finding Our Way through Phenotypes

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