The Planteome project

Laurel Cooper; Austin Meier; Justin L. Elser; Justin Preece; Xu Xu; Ryan S. Kitchen; Botong Qu; Eugene Zhang; Sinisa Todorovic; Pankaj Jaiswal; Barry Smith; Marie Angélique Laporte; Elizabeth Arnaud; Georgios Gkoutos; Seth Carbon; Chris Mungall; John Doonan

The Planteome project

Laurel Cooper, Austin Meier, Justin L. Elser, Justin Preece, Xu Xu, Ryan S. Kitchen, Botong Qu, Eugene Zhang, Sinisa Todorovic, Pankaj Jaiswal, Barry Smith, Marie Angélique Laporte, Elizabeth Arnaud, Georgios Gkoutos, Seth Carbon, Chris Mungall, John Doonan

Cancer and Genomic Sciences

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Abstract

The Planteome project is a centralized online plant informatics portal which provides semantic integration of widely diverse datasets with the goal of plant improvement. Traditional plant breeding methods for crop improvement may be combined with next-generation analysis methods and automated scoring of traits and phenotypes to develop improved varieties. The Planteome project (www.planteome.org) develops and hosts a suite of reference ontologies for plants associated with a growing corpus of genomics data. Data annotations linking phenotypes and germplasm to genomics resources are achieved by data transformation and mapping species-specific controlled vocabularies to the reference ontologies. Analysis and annotation tools are being developed to facilitate studies of plant traits, phenotypes, diseases, gene function and expression and genetic diversity data across a wide range of plant species. The project database and the online resources provide researchers tools to search and browse and access remotely via APIs for semantic integration in annotation tools and data repositories providing resources for plant biology, breeding, genomics and genetics.

Original language	English
Title of host publication	ICBO-BioCreative 2016 Food, Nutrition, Health and Environment for the 9 Billion
Subtitle of host publication	Proceedings of the Joint International Conference on Biological Ontology and BioCreative
Editors	Pankaj Jaiswal, Robert Hoehndorf, Cecilia Arighi, Austin Meier
Publisher	CEUR
Volume	1747
Publication status	Published - 30 Nov 2016
Event	International Conference on Biological Ontology, 7th: ICBO2016 - Oregon State University, Corvallis, OR, United States Duration: 1 Aug 2016 → 4 Aug 2016

Publication series

Name	CEUR Workshop Proceedings
Volume	1747
ISSN (Print)	1613-0073

Conference

Conference	International Conference on Biological Ontology, 7th
Country/Territory	United States
City	Corvallis, OR
Period	1/08/16 → 4/08/16

Keywords

Data integration
Ontology
Plants
Semantic
Traits phenotype

ASJC Scopus subject areas

General Computer Science

Access to Document

http://ceur-ws.org/Vol-1747/IT406-IP35_ICBO2016.pdf

Cite this

Cooper, L., Meier, A., Elser, J. L., Preece, J., Xu, X., Kitchen, R. S., Qu, B., Zhang, E., Todorovic, S., Jaiswal, P., Smith, B., Laporte, M. A., Arnaud, E., Gkoutos, G., Carbon, S., Mungall, C., & Doonan, J. (2016). The Planteome project. In P. Jaiswal, R. Hoehndorf, C. Arighi, & A. Meier (Eds.), ICBO-BioCreative 2016 Food, Nutrition, Health and Environment for the 9 Billion: Proceedings of the Joint International Conference on Biological Ontology and BioCreative (Vol. 1747). (CEUR Workshop Proceedings; Vol. 1747). CEUR. http://ceur-ws.org/Vol-1747/IT406-IP35_ICBO2016.pdf

Cooper, Laurel ; Meier, Austin ; Elser, Justin L. et al. / The Planteome project. ICBO-BioCreative 2016 Food, Nutrition, Health and Environment for the 9 Billion: Proceedings of the Joint International Conference on Biological Ontology and BioCreative. editor / Pankaj Jaiswal ; Robert Hoehndorf ; Cecilia Arighi ; Austin Meier. Vol. 1747 CEUR, 2016. (CEUR Workshop Proceedings).

@inproceedings{b1a417ebda6c42eba4b314dfa6b22bbc,

title = "The Planteome project",

abstract = "The Planteome project is a centralized online plant informatics portal which provides semantic integration of widely diverse datasets with the goal of plant improvement. Traditional plant breeding methods for crop improvement may be combined with next-generation analysis methods and automated scoring of traits and phenotypes to develop improved varieties. The Planteome project (www.planteome.org) develops and hosts a suite of reference ontologies for plants associated with a growing corpus of genomics data. Data annotations linking phenotypes and germplasm to genomics resources are achieved by data transformation and mapping species-specific controlled vocabularies to the reference ontologies. Analysis and annotation tools are being developed to facilitate studies of plant traits, phenotypes, diseases, gene function and expression and genetic diversity data across a wide range of plant species. The project database and the online resources provide researchers tools to search and browse and access remotely via APIs for semantic integration in annotation tools and data repositories providing resources for plant biology, breeding, genomics and genetics.",

keywords = "Data integration, Ontology, Plants, Semantic, Traits phenotype",

author = "Laurel Cooper and Austin Meier and Elser, {Justin L.} and Justin Preece and Xu Xu and Kitchen, {Ryan S.} and Botong Qu and Eugene Zhang and Sinisa Todorovic and Pankaj Jaiswal and Barry Smith and Laporte, {Marie Ang{\'e}lique} and Elizabeth Arnaud and Georgios Gkoutos and Seth Carbon and Chris Mungall and John Doonan",

year = "2016",

month = nov,

day = "30",

language = "English",

volume = "1747",

series = "CEUR Workshop Proceedings",

publisher = "CEUR",

editor = "Pankaj Jaiswal and Robert Hoehndorf and Cecilia Arighi and Austin Meier",

booktitle = "ICBO-BioCreative 2016 Food, Nutrition, Health and Environment for the 9 Billion",

note = "International Conference on Biological Ontology, 7th : ICBO2016 ; Conference date: 01-08-2016 Through 04-08-2016",

}

Cooper, L, Meier, A, Elser, JL, Preece, J, Xu, X, Kitchen, RS, Qu, B, Zhang, E, Todorovic, S, Jaiswal, P, Smith, B, Laporte, MA, Arnaud, E, Gkoutos, G, Carbon, S, Mungall, C & Doonan, J 2016, The Planteome project. in P Jaiswal, R Hoehndorf, C Arighi & A Meier (eds), ICBO-BioCreative 2016 Food, Nutrition, Health and Environment for the 9 Billion: Proceedings of the Joint International Conference on Biological Ontology and BioCreative. vol. 1747, CEUR Workshop Proceedings, vol. 1747, CEUR, International Conference on Biological Ontology, 7th, Corvallis, OR, United States, 1/08/16. <http://ceur-ws.org/Vol-1747/IT406-IP35_ICBO2016.pdf>

The Planteome project. / Cooper, Laurel; Meier, Austin; Elser, Justin L. et al.
ICBO-BioCreative 2016 Food, Nutrition, Health and Environment for the 9 Billion: Proceedings of the Joint International Conference on Biological Ontology and BioCreative. ed. / Pankaj Jaiswal; Robert Hoehndorf; Cecilia Arighi; Austin Meier. Vol. 1747 CEUR, 2016. (CEUR Workshop Proceedings; Vol. 1747).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

TY - GEN

T1 - The Planteome project

AU - Cooper, Laurel

AU - Meier, Austin

AU - Elser, Justin L.

AU - Preece, Justin

AU - Xu, Xu

AU - Kitchen, Ryan S.

AU - Qu, Botong

AU - Zhang, Eugene

AU - Todorovic, Sinisa

AU - Jaiswal, Pankaj

AU - Smith, Barry

AU - Laporte, Marie Angélique

AU - Arnaud, Elizabeth

AU - Gkoutos, Georgios

AU - Carbon, Seth

AU - Mungall, Chris

AU - Doonan, John

PY - 2016/11/30

Y1 - 2016/11/30

N2 - The Planteome project is a centralized online plant informatics portal which provides semantic integration of widely diverse datasets with the goal of plant improvement. Traditional plant breeding methods for crop improvement may be combined with next-generation analysis methods and automated scoring of traits and phenotypes to develop improved varieties. The Planteome project (www.planteome.org) develops and hosts a suite of reference ontologies for plants associated with a growing corpus of genomics data. Data annotations linking phenotypes and germplasm to genomics resources are achieved by data transformation and mapping species-specific controlled vocabularies to the reference ontologies. Analysis and annotation tools are being developed to facilitate studies of plant traits, phenotypes, diseases, gene function and expression and genetic diversity data across a wide range of plant species. The project database and the online resources provide researchers tools to search and browse and access remotely via APIs for semantic integration in annotation tools and data repositories providing resources for plant biology, breeding, genomics and genetics.

AB - The Planteome project is a centralized online plant informatics portal which provides semantic integration of widely diverse datasets with the goal of plant improvement. Traditional plant breeding methods for crop improvement may be combined with next-generation analysis methods and automated scoring of traits and phenotypes to develop improved varieties. The Planteome project (www.planteome.org) develops and hosts a suite of reference ontologies for plants associated with a growing corpus of genomics data. Data annotations linking phenotypes and germplasm to genomics resources are achieved by data transformation and mapping species-specific controlled vocabularies to the reference ontologies. Analysis and annotation tools are being developed to facilitate studies of plant traits, phenotypes, diseases, gene function and expression and genetic diversity data across a wide range of plant species. The project database and the online resources provide researchers tools to search and browse and access remotely via APIs for semantic integration in annotation tools and data repositories providing resources for plant biology, breeding, genomics and genetics.

KW - Data integration

KW - Ontology

KW - Plants

KW - Semantic

KW - Traits phenotype

M3 - Conference contribution

AN - SCOPUS:85018723597

VL - 1747

T3 - CEUR Workshop Proceedings

BT - ICBO-BioCreative 2016 Food, Nutrition, Health and Environment for the 9 Billion

A2 - Jaiswal, Pankaj

A2 - Hoehndorf, Robert

A2 - Arighi, Cecilia

A2 - Meier, Austin

PB - CEUR

T2 - International Conference on Biological Ontology, 7th

Y2 - 1 August 2016 through 4 August 2016

ER -

The Planteome project

Abstract

Publication series

Conference

Keywords

ASJC Scopus subject areas

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