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Publications and Presentations

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Author Type [ Year

]

2011

R. L. Walls, “The Plant Ontology: an updated tool for all plant biologists”, International Botanical Congress (IBC2011). Melbourne, Australia, 2011.

2012

R. L. Walls, Athreya, B., Cooper, L., Elser, J., Gandolfo, M. A., Jaiswal, P., Mungall, C. J., Preece, J., Rensing, S., Smith, B., and Stevenson, D. W., “Ontologies as Integrative Tools for Plant Science”, American Journal of Botany, vol. 99, no. 8, pp. 1263-75, 2012.

R. L. Walls, “Mapping of glossary terms from the Flora of North America to the Plant Ontology enhances both resources”, in 3rd International Conference on Biomedical Ontology (ICBO 2012), Graz, Austria, 2012.

2010

R. L. Walls, “The Plant Ontology: a tool for structural, developmental, and molecular plant biologists”, Botany 2010. Providence, RI, 2010.

2011

R. L. Walls, “Using the Plant Ontology to Link Anatomical Structures to Gene Annotations in Physcomitrella patens”, Moss 2011. Black Forest, Germany, 2011.

R. L. Walls, “Using the Plant Ontology to improve the interoperability of genomic and phenomic data sets”, Plant Genomes & Biotechnology: from Genes to Networks. Cold Spring Harbor Laboratory, New York, 2011.

2010

R. L. Walls, “The Plant Ontology: A Common Reference Ontology for Plants”, Bio-Ontologies 2010: Semantic Applications in Life Sciences. Boston, MA, 2010.

2012

R. Walls, Smith, B., Elser, J., and Goldfain, A., “A plant disease extension of the Infectious Disease Ontology”, in International Conference on Biomedical Ontology (ICBO-2012), Graz, Austria, 2012, vol. 897.

K. Van Auken, Fey, P., Berardini, T. Z., Dodson, R., Cooper, L., Li, D., Chan, J., Li, Y., Basu, S., Muller, H. - M., Chisholm, R., Huala, E., and Sternberg, P. W., “Text mining in the biocuration workflow: applications for literature curation at WormBase, dictyBase and TAIR”, Database, vol. 2012, 2012.

2009

C. - W. Tung, “POC poster presentation”, Plant & Animal Genome Conference XVII. San Diego, CA, 2009.

C. - W. Tung, “Plant and Trait Ontology”, GCP Ontology Workshop. Rome, Italy, 2009.

C. - W. Tung, “POC poster presentation”, 3rd International Biocuration Conference. Berlin, Germany, 2009.

2011

V. Shulaev, Sargent, D. J., Crowhurst, R. N., Mockler, T. C., Folkerts, O., Delcher, A. L., Jaiswal, P., Mockaitis, K., Liston, A., Mane, S. P., Burns, P., Davis, T. M., Slovin, J. P., Bassil, N., Hellens, R. P., Evans, C., Harkins, T., Kodira, C., Desany, B., Crasta, O. R., Jensen, R. V., Allan, A. C., Michael, T. P., Setubal, J. C., Celton, J. - M., Rees, J. D. G., Williams, K. P., Holt, S. H., Rojas, J. J. R., Chatterjee, M., Liu, B., Silva, H., Meisel, L., Adato, A., Filichkin, S. A., Troggio, M., Viola, R., Ashman, T. - L., Wang, H., Dharmawardhana, P., Elser, J., Raja, R., Priest, H. D., Bryant, D. W., Fox, S. E., Givan, S. A., Wilhelm, L. J., Naithani, S., Christoffels, A., Salama, D. Y., Carter, J., Girona, E. L., Zdepski, A., Wang, W., Kerstetter, R. A., Schwab, W., Korban, S. S., Davik, J., Monfort, A., Denoyes-Rothan, B., Arus, P., Mittler, R., Flinn, B., Aharoni, A., Bennetzen, J. L., Salzberg, S. L., Dickerman, A. W., Velasco, R., Borodovsky, M., Veilleux, R. E., and Folta, K. M., “The genome of woodland strawberry (Fragaria vesca)”, Nat Genet, vol. 43, pp. 109 - 116, 2011.

2006

A. Pujar, Jaiswal, P., Kellogg, E. A., Ilic, K., Vincent, L., Avraham, S., Stevens, P., Zapata, F., Reiser, L., Rhee, S. Y., Sachs, M. M., Schaeffer, M., Stein, L., Ware, D., and McCouch, S., “Whole-plant growth stage ontology for angiosperms and its application in plant biology”, Plant Physiology, vol. 142, no. 2, pp. 414-28, 2006.

2011

J. Preece, “Planteome Annotation Wiki: A Semantic Web Application for the Community Curation of Plant Genotypes and Phenotype.”, in 4th International Workshop on Semantic Web Applications and Tools for Life Sciences, Univ. of London and the Wellcome Trust Collection Conference Center (London, UK), 2011.

2012

J. Preece, “The Plant Ontology: A Tool for Linking Plant Anatomy and Development to Genomics Across Plant Taxa”, Genome Informatics 2012. Robinson College, Cambridge, UK, 2012.

2010

J. Preece, “A Semantic Wiki for Genotype/Phenotype Annotation in Plant Species”, in NETTAB 2010 conference on Biological Wikis, Naples, Italy, 2010, pp. 109-112.

2013

J. Preece, “AISO: Annotation of Image Segments using Ontologies”, Plant and Animal Genome XXI Conference. San Diego, CA, 2013.

2011

J. Preece, “Planteome Annotation Wiki: A Semantic Application for the Community Curation of Plant Genotypes and Phenotypes”, in SWAT4LS 2011, London, UK, 2011, pp. 96-97.

2013

N. T. V. Lingutla, “Annotation of image segments with ontologies (AISO)”, Oregon State University, Corvallis, 2013.

2012

F. Lens, Cooper, L., Gandolfo, M. A., Groover, P., Jaiswal, P., Lachenbruch, R., Spicer, R., Staton, D., Stevenson, D. W., Walls, R. L., and Wegrzyn, J., “An extension of the Plant Ontology project supporting wood anatomy and development research”, IAWA Journal, vol. 33, pp. 113-117, 2012.

2013

P. Jaiswal, “A Resource for a Common Reference Ontology for Plants”, Plant and Animal Genome XXI Meeting. San Diego, CA, 2013.

2012

P. Jaiswal, “Annotating the Maize B73 Gene Expression Atlas in the Plant Ontology- A Tool for Plant Genomics.”, 54th Annual Maize Genetics Conference. Portland, OR, 2012.

2014

P. Jaiswal, “Plant Environmental Condition Ontology (EO)”, Fourth Annual Summit of the Phenotype Ontology Research Coordination Network. Phenotype Research Coordination Network, Biosphere2, Tucson, AZ, 2014.

2005

P. Jaiswal, Avraham, S., Ilic, K., Kellogg, E. A., McCouch, S., Pujar, A., Reiser, L., Rhee, S. Y., Sachs, M. M., Schaeffer, M., Stein, L., Stevens, P., Vincent, L., Ware, D., and Zapata, F., “Plant Ontology (PO): a Controlled Vocabulary of Plant Structures and Growth Stages”, Comparative and Functional Genomics, vol. 6, no. 7-8, pp. 388-97, 2005.

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