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Year
]
2013
C. N. Arighi
,
Carterette, B.
,
Cohen, B. K.
,
Krallinger, M.
,
Wilbur, J. W.
,
Fey, P.
,
Dodson, R.
,
Cooper, L.
,
Van Slyke, C. E.
,
Dahdul, W.
,
Mabee, P.
,
Li, D.
,
Harris, B.
,
Gillespie, M.
,
Jimenez, S.
,
Roberts, P.
,
Matthews, L.
,
Becker, K.
,
Drabkin, H.
,
Bello, S.
,
Licata, L.
,
Chatr-aryamontri, A.
,
Schaeffer, M. L.
,
Park, J.
,
Haendel, M.
,
Van Auken, K.
,
Li, Y.
,
Chan, J.
,
Muller, H. - M.
,
Cui, H.
,
Balhoff, J. P.
,
Chi-Yang Wu, J.
,
Lu, Z.
,
Wei, C. - H.
,
Tudor, C. O.
,
Raja, K.
,
Subramani, S.
,
Natarajan, J.
,
Cejuela, J. M.
,
Dubey, P.
, and
Wu, C.
,
“
An overview of the BioCreative 2012 Workshop Track III: interactive text mining task
”
,
Database
, vol. 2013, 2013.
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E. Arnaud
,
“
The Species-Specific Crop Ontology (Generation Challenge Programme): Application and Integration into the Reference Plant Trait Ontology to Enable Data Mining on Phenotypes
”
,
Plant and Animal Genome XXI Conference
. San Diego, CA, 2013.
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2012
E. Arnaud
,
Cooper, L.
,
Shrestha, R.
,
Menda, N.
,
Nelson, R. T.
,
Matteis, L.
,
Skofic, M.
,
Bastow, R.
,
Jaiswal, P.
,
Mueller, L.
, and
McLaren, G.
,
“
Towards a Reference Plant Trait Ontology for Modeling Knowledge of Plant Traits and Phenotype
”
, in
International Conference on Knowledge Discovery and Information Retrieval (IC3K2012)
, Barcelona, Spain, 2012.
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2013
B. Atkinson
,
“
Plant Ontology, a controlled and structured plant vocabulary for all botanical disciplines
”
,
Botany 2013
. New Orleans, LA, 2013.
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2008
S. Avraham
,
Tung, C. - W.
,
Ilic, K.
,
Jaiswal, P.
,
Kellogg, E. A.
,
McCouch, S.
,
Pujar, A.
,
Reiser, L.
,
Rhee, S. Y.
,
Sachs, M. M.
,
Schaeffer, M.
,
Stein, L.
,
Stevens, P.
,
Vincent, L.
,
Zapata, F.
, and
Ware, D.
,
“
The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations
”
,
Nucleic Acids Research
, vol. 36, pp. D449-54, 2008.
DOI
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2002
P. O. Consortium
,
“
The Plant Ontology™ Consortium and Plant Ontologies
”
,
Comparative and Functional Genomics
, vol. 3, no. 2, pp. 137-142, 2002.
DOI
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2014
L. Cooper
,
“
Common Reference Ontologies for Plant Biology (cROP): A Platform for Integrative Plant Genomics
”
,
Plant and Animal Genome XXII Meeting
. San Diego, CA, 2014.
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L. Cooper
,
“
The Plant Ontology and the Trait Ontology: Resources for Plant Genomics
”
,
Workshop on Crop Ontology and Phenotyping Data Interoperability
. Montpellier, France, 2014.
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2012
L. Cooper
,
“
The Plant Ontology: A Tool for Linking Plant Anatomy and Development to Genomics Across Plant Taxa
”
,
Plant Biology 2012
. Austin, Tx, 2012.
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L. D. Cooper
,
“
Annotating the Maize B73 Gene Expression Atlas – A Plant Ontology Use Case for Genomics Data Curation
”
,
Biocuration 2012
. Washington DC, USA, 2012.
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L. D. Cooper
,
“
Annotating Gene Expression in
Physcomitrella patens
using the Plant Ontology: Facilitating Cross-Taxa Comparisons
”
,
Plant and Animal Genome XX Conference
. San Diego, CA, 2012.
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2013
L. Cooper
,
Walls, R. L.
,
Elser, J.
,
Gandolfo, M. A.
,
Stevenson, D. W.
,
Smith, B.
,
Preece, J.
,
Athreya, B.
,
Mungall, C. J.
,
Rensing, S.
,
Hiss, M.
,
Lang, D.
,
Reski, R.
,
Berardini, T. Z.
,
Li, D.
,
Huala, E.
,
Schaeffer, M.
,
Menda, N.
,
Arnaud, E.
,
Shrestha, R.
,
Yamazaki, Y.
, and
Jaiswal, P.
,
“
The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses
”
,
Plant & Cell Physiology
, vol. 54, no. 2, pp. 1-23, 2013.
PubMed
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2012
L. D. Cooper
,
“
The Plant Ontology: Linking Plant Anatomy and Development to Genomics Across Plant Taxa
”
,
Plant and Animal Genome XX Conference
. San Diego, CA, 2012.
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2010
L. Cooper
,
“
The Plant Ontology: A Database for Plant Genomics
”
,
Plant Biology 2010
. Quebec, Montreal, Canada, 2010.
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2012
L. D. Cooper
,
“
Expanding the Plant Ontology: Linking Plant Anatomy and Development to Genomics Across Plant Taxa
”
,
Plant and Animal Genome XX Conference
. San Diego, CA, 2012.
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L. D. Cooper
,
“
The Plant Ontology: Linking Genomic and Phenomic Data Across Plant Taxa
”
,
Plant and Animal Genome XX Conference
. San Diego, CA, 2012.
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2013
L. Cooper
,
“
Development of the Reference Plant Trait Ontology: A Unified Resource for Plant Phenomics
”
,
Plant and Animal Genome XXI Conference
. San Diego, CA, 2013.
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2015
A. R. Deans
,
Lewis, S. E.
,
Huala, E.
,
Anzaldo, S. S.
,
Ashburner, M.
,
Balhoff, J. P.
,
Blackburn, D. C.
,
Blake, J. A.
,
Burleigh, G. J.
,
Chanet, B.
,
Cooper, L. D.
,
Courtot, M.
,
Csösz, S.
,
Cui, H.
,
Dahdul, W.
,
Das, S.
,
Dececchi, A. T.
,
Dettai, A.
,
Diogo, R.
,
Druzinsky, R. E.
,
Dumontier, M.
,
Franz, N. M.
,
Friedrich, F.
,
Gkoutos, G. V.
,
Haendel, M.
,
Harmon, L. J.
,
Hayamizu, T. F.
,
He, Y.
,
Hines, H. M.
,
Ibrahim, N.
,
Jackson, L. M.
,
Jaiswal, P.
,
James-Zorn, C.
,
Köhler, S.
,
Lecointre, G.
,
Lapp, H.
,
Lawrence, C. J.
,
Le Novère, N.
,
Lundberg, J. G.
,
Macklin, J.
,
Mast, A. R.
,
Midford, P. E.
,
Mikó, I.
,
Mungall, C. J.
,
Oellrich, A.
,
Osumi-Sutherland, D.
,
Parkinson, H.
,
Ramírez, M. J.
,
Richter, S.
,
Robinson, P. N.
,
Ruttenberg, A.
,
Schulz, K. S.
,
Segerdell, E.
,
Seltmann, K. C.
,
Sharkey, M. J.
,
Smith, A. D.
,
Smith, B.
,
Specht, C. D.
,
Squires, B. R.
,
Thacker, R. W.
,
Thessen, A.
,
Fernandez-Triana, J.
,
Vihinen, M.
,
Vize, P. D.
,
Vogt, L.
,
Wall, C. E.
,
Walls, R. L.
,
Westerfeld, M.
,
Wharton, R. A.
,
Wirkner, C. S.
,
Woolley, J. B.
,
Yoder, M. J.
,
Zorn, A. M.
, and
Mabee, P.
,
“
Finding Our Way through Phenotypes
”
,
PLoS Biol
, vol. 13, p. e1002033, 2015.
DOI
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2010
J. L. Elser
,
“
Plant Ontology: Databases And Applications
”
,
Plant & Animal Genomes XVIII Conference
. San Diego, CA, 2010.
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J. L. Elser
,
“
Plant Ontology: Databases And Applications
”
,
Plant & Animal Genomes XVIII Conference
. San Diego, CA, 2010.
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2013
E. Huala
,
“
Development of a Unified Phenotype Dataset for Plants
”
,
Plant and Animal Genome 2013
. San Diego, CA, 2013.
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2008
K. Ilic
,
Rhee, S. Y.
,
Kellogg, E. A.
, and
Stevens, P. F.
,
“
Plant Structure Ontology (PSO) - A Morphological and Anatomical Ontology of Flowering Plants
”
, in
Anatomy Ontologies for Bioinformatics
, vol. 6,
A. Burger
,
Davidson, D.
, and
Baldock, R.
, Eds.
London: Springer, 2008, pp. 27-42.
DOI
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2007
K. Ilic
,
Kellogg, E. A.
,
Jaiswal, P.
,
Zapata, F.
,
Stevens, P. F.
,
Vincent, L. P.
,
Avraham, S.
,
Reiser, L.
,
Pujar, A.
,
Sachs, M. M.
,
Whitman, N. T.
,
McCouch, S. R.
,
Schaeffer, M. L.
,
Ware, D. H.
,
Stein, L. D.
, and
Rhee, S. Y.
,
“
The Plant Structure Ontology, a Unified Vocabulary of Anatomy and Morphology of a Flowering Plant
”
,
Plant Physiology
, vol. 143, no. 2, pp. 587-99, 2007.
PubMed
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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.
PubMed
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2013
P. Jaiswal
,
“
A Resource for a Common Reference Ontology for Plants
”
,
Plant and Animal Genome XXI Meeting
. San Diego, CA, 2013.
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