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Jaiswal, Pankaj
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2018
L. Harper
,
Campbell, J.
,
Cannon, E. K. S.
,
Jung, S.
,
Poelchau, M.
,
Walls, R.
,
Andorf, C.
,
Arnaud, E.
,
Berardini, T. Z.
,
Birkett, C.
,
Cannon, S.
,
Carson, J.
,
Condon, B.
,
Cooper, L.
,
Dunn, N.
,
Elsik, C. G.
,
Farmer, A.
,
Ficklin, S. P.
,
Grant, D.
,
Grau, E.
,
Herndon, N.
,
Hu, Z. - L.
,
Humann, J.
,
Jaiswal, P.
,
Jonquet, C.
,
Laporte, M. - A.
,
Larmande, P.
,
Lazo, G.
,
McCarthy, F.
,
Menda, N.
,
Mungall, C. J.
,
Munoz-Torres, M. C.
,
Naithani, S.
,
Nelson, R.
,
Nesdill, D.
,
Park, C.
,
Reecy, J.
,
Reiser, L.
,
Sanderson, L. - A.
,
Sen, T. Z.
,
Staton, M.
,
Subramaniam, S.
,
Tello-Ruiz, M. K.
,
Unda, V.
,
Unni, D.
,
Wang, L.
,
Ware, D.
,
Wegrzyn, J.
,
Williams, J.
,
Woodhouse, M.
,
Yu, J.
, and
Main, D.
,
“
AgBioData Consortium Recommendations for Sustainable Genomics and Genetics Databases for Agriculture
”
,
Database
, vol. 2018, no. 1, 2018.
I. Braun
,
Balhoff, J.
,
Berardini, T. Z.
,
Cooper, L. D.
,
Gkoutos, G.
,
Harper, L.
,
Huala, E.
,
Jaiswal, P.
,
Kazic, T.
,
Lapp, H.
,
Macklin, J. A.
,
Specht, C. D.
,
Vision, T. J.
,
Walls, R. L.
, and
Lawerence-Dill, C. J.
,
“
'Computable' phenotypes enable comparative and predictive phenomics among plant species across domains of life
”
, in
Application of Semantic Technologies in Biodiversity Science
, vol. 33,
A. E. Thessen
, Ed.
Berlin: OS Press/AKA Verlag, 2018, pp. 187-205.
L. Endara
,
Burleigh, G.
,
Cooper, L.
,
Jaiswal, P.
,
Laporte, M. - A.
, and
Cui, H.
,
“
A Natural Language Processing Pipeline to extract phenotypic data from formal taxonomic descriptions with a Focus on Flagellate Plants
”
, in
ICBO 2018
, Corvallis, OR, 2018.
A. Meier
,
Laporte, M. - A.
,
Elser, J.
,
Cooper, L.
,
Preece, J.
,
Jaiswal, P.
, and
Poelen, J.
,
“
OOPS: The Ontology of Plant Stress, A semi-automated standardization methodology
”
, in
ICBO 2018
, Corvallis, OR, 2018.
D. Trigkakis
,
Preece, J.
,
Meier, A.
,
Elser, J.
,
Kvilekval, K.
,
Fedorov, D.
,
Manjunath, B. S.
,
Jaiswal, P.
, and
Todorovic, S.
,
“
Planteome & BisQue: Automating Image Annotation with Ontologies using Deep-Learning Networks
”
, in
9th International Conference on Biological Ontology (ICBO 2018)
, Corvallis, OR, 2018.
L. Cooper
,
Meier, A.
,
Laporte, M. - A.
,
Elser, J. L.
,
Mungall, C.
,
Sinn, B. T.
,
Cavaliere, D.
,
Dunn, N. A.
,
Smith, B.
,
Qu, B.
,
Preece, J.
,
Zhang, E.
,
Todorovic, S.
,
Gkoutos, G.
,
Doonan, J.
,
Stevenson, D. W.
,
Arnaud, E.
, and
Jaiswal, P.
,
“
The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics
”
,
Nucleic Acids Research
, 2018.
L. Cooper
and
Jaiswal, P.
,
“
The Planteome Project- Reference Ontologies for Data Integration
”
. 2018.
2017
B. Qu
,
Kumar, P.
,
Zhang, E.
,
Jaiswal, P.
,
Cooper, L. D.
,
Elser, J.
, and
Zhang, Y.
,
“
Interactive design and visualization of N-ary relationships
”
, in
SIGGRAPH Asia 2017 Symposium on Visualization
, Bangkok, Thailand, 2017.
2016
A. Meier
,
Cooper, L.
,
Laporte, M. A. -
,
Elser, J.
, and
Jaiswal, P.
,
“
Annotating germplasm to Planteome reference ontologies
”
, in
ICBO-BioCreative 2016 Food, Nutrition, Health and Environment for the 9 Billion
, Corvallis, Oregon, USA, 2016.
M. - A. Laporte
,
Valette, Léo
,
Cooper, L.
,
Mungall, C.
,
Meier, A.
,
Jaiswal, P.
, and
Arnaud, E.
,
“
Comparison of ontology mapping techniques to map plant trait ontologies
”
, in
ICBO-BioCreative 2016 Food, Nutrition, Health and Environment for the 9 Billion
, Corvallis, Oregon, USA, 2016.
L. D. Cooper
and
Jaiswal, P.
,
“
The Plant Ontology: A Tool for Plant Genomics
”
, in
Plant Bioinformatics: Methods and Protocols
, vol. 1374,
D. Edwards
, Ed.
2016.
P. Jaiswal
,
Cooper, L.
,
Elser, J.
,
Meier, A.
, and
et al,
“
Planteome: A Resource for Common Reference Ontologies and Applications for Plant Biology
”
. 2016.
B. Qu
,
Diefenbaugh, J.
,
Elser, J.
,
Carbon, S.
,
Mungall, C.
,
Zhang, E.
, and
Jaiswal, P.
,
“
Planteome Gene Annotation Enrichment Analysis
”
, in
ICBO-BioCreative 2016 Food, Nutrition, Health and Environment for the 9 Billion
, Corvallis, Oregon, USA, 2016.
L. Cooper
,
Meier, A.
,
Elser, J. L.
,
Laporte, M. - A.
,
Preece, J.
,
Carbon, S.
,
Xu, X.
,
Kitchen, R. S.
,
Qu, B.
,
Zhang, E.
,
Todorovic, S.
,
Smith, B.
,
Gkoutos, G.
,
Doonan, J.
,
Stevenson, D. W.
,
Arnaud, E.
,
Mungall, C.
, and
Jaiswal, P.
,
“
The Planteome Project
”
, in
ICBO-BioCreative 2016 Food, Nutrition, Health and Environment for the 9 Billion
, Corvallis, OR, 2016.
2015
A. E. Thessen
,
Bunker, D. E.
,
Buttigieg, P. L.
,
Cooper, L. D.
,
Dahdul, W. M.
,
Domisch, S.
,
Franz, N. M.
,
Jaiswal, P.
,
Lawrence-Dill, C. J.
,
Midford, P. E.
,
Mungall, C. J.
,
Ramírez, M. J.
,
Specht, C. D.
,
Vogt, L.
,
Vos, R. A.
,
Walls, R. L.
,
White, J. W.
,
Zhang, G.
,
Deans, A. R.
,
Huala, E.
,
Lewis, S. E.
, and
Mabee, P. M.
,
“
Emerging semantics to link phenotype and environment
”
,
PeerJ
, vol. 3, no. e1470, 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.
S. Lennon
,
Cooper, L.
,
Jaiswal, P.
,
Ougham, H.
, and
Stevenson, D. W.
,
“
New Phytologist and the Plant Ontology: Working Together to Enhance Journal Content
”
. 2015.
A. Oellrich
,
Walls, R. L.
,
Cannon, E. K. S.
,
Cannon, S. B.
,
Cooper, L.
,
Gardiner, J.
,
Gkoutos, G. V.
,
Harper, L.
,
He, M.
,
Hoehndorf, R.
,
Jaiswal, P.
,
Kalberer, S. R.
,
Lloyd, J. P.
,
Meinke, D.
,
Menda, N.
,
Moore, L.
,
Nelson, R. T.
,
Pujar, A.
,
Lawrence, C. J.
, and
Huala, E.
,
“
An ontology approach to comparative phenomics in plants.
”
,
Plant methods
, vol. 11, p. 10, 2015.
L. Cooper
,
“
Planteome Overview- DivSeek 2015
”
. 2015.
2014
N. Lingutla
,
Preece, J.
,
Todorovic, S.
,
Cooper, L.
,
Moore, L.
, and
Jaiswal, P.
,
“
AISO: Annotation of Image Segments with Ontologies
”
,
Journal of Biomedical Semantics
, vol. 5, p. 50, 2014.
L. Cooper
,
“
Common Reference Ontologies for Plant Biology (cROP): A Platform for Integrative Plant Genomics
”
. San Diego, CA, 2014.
P. Jaiswal
,
“
Plant Environmental Condition Ontology (EO)
”
. Phenotype Research Coordination Network, Biosphere2, Tucson, AZ, 2014.
2013
E. Huala
,
“
Development of a Unified Phenotype Dataset for Plants
”
. San Diego, CA, 2013.
L. Cooper
,
“
Development of the Reference Plant Trait Ontology: A Unified Resource for Plant Phenomics
”
. San Diego, CA, 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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