=Paper=
{{Paper
|id=Vol-2807/abstractT
|storemode=property
|title=The Plant Trait Ontology Links Wheat Traits for
Crop Improvement and Genomics (short paper)
|pdfUrl=https://ceur-ws.org/Vol-2807/abstractT.pdf
|volume=Vol-2807
|authors=Laurel Cooper,Marie-Angélique Laporte,Justin Elser,Victoria Carollo Blake,Taner Z. Sen,Chris Mungall,Elizabeth Arnaud,Pankaj Jaiswal
|dblpUrl=https://dblp.org/rec/conf/icbo/CooperLEBSMAJ20
}}
==The Plant Trait Ontology Links Wheat Traits for
Crop Improvement and Genomics (short paper)==
https://ceur-ws.org/Vol-2807/abstractT.pdf
The Plant Trait Ontology Links Wheat Traits for
Crop Improvement and Genomics
Laurel COOPERa,c , Marie-Angélique LAPORTEb, Justin ELSERa, Victoria Carollo
BLAKE c, Taner Z. SEN c, Chris MUNGALL d, Elizabeth ARNAUDb, Pankaj
JAISWALa.
a
Planteome Database, Oregon State University, Corvallis, OR, USA
b
Alliance Bioversity International-CIAT, Montpellier, France
c
GrainGenes Database, USDA-ARS-WRRC, Albany, CA, USA
d
Lawrence Berkeley National Laboratory, Berkeley, USA
Keywords. plant traits, phenotypes, ontology, design patterns, Triticum aesitvum
Global population growth and climate change result in the need to develop new and
better-adapted wheat varieties. Three integrated resources, the Plant Trait Ontology
(TO), the Crop Ontology (CO) and the GrainGenes1 database provide researchers and
plant breeders interconnected tools and resources to utilize the large amounts of genetic
and genomic data that are available for plant genomics and crop improvement. The TO
[1–3] is a reference-level ontology for plant traits, and is a key part of the Planteome
Project2 [4]. In the current Planteome Release Version 4.0, the TO consists of more than
1500 plant traits organized into nine upper-level categories: biochemical, biological
process, plant growth and development, plant morphology, plant quality, plant vigor,
plant stress and yield. As part of the Planteome, the TO is integrated with the Plant
Ontology [5,6], and is used to annotate, or link to plant genomics and genetics data
objects (e.g. germplasm, QTLs, genes, and proteins) from a wide variety of plant taxa,
including important world crops and model plant species. In this Release, there are more
than four million annotations linking TO terms to about 165,000 data objects in the
Planteome database. Users are encouraged to submit requests for new TO terms or
comments through the TO GitHub Issue Tracker 3.
The Planteome project has partnered with the CO 4 [7] to incorporate crop- and clade-
specific traits of interest to plant breeders into the Planteome database. Terms from
eleven CO trait dictionaries (banana, cassava, lentil, maize, pigeon pea, potato, rice,
sorghum, soybean, wheat and yam) have been mapped to the equivalent reference traits
in the TO in a semi-automated way, based on common design patterns [8], followed by
manual curation and quality checks. This integration of traits across species based on the
TO hierarchy allows users, for instance, to search for, or sort traits by plant structure or
by trait category and facilitates cross-species queries and data discovery.
The CO Wheat Trait Dictionary, developed along with CIMMYT 5 and the Triticeae
Toolbox Database 6 , consists of traits of interest to the international wheat breeding
1
https://wheat.pw.usda.gov/
2
http://planteome.org/
3
https://github.com/Planteome/plant-trait-ontology/issues
4
https://www.cropontology.org/
5
https://www.cimmyt.org/
6
http://triticeaetoolbox.org/
Copyright © 2020 for this paper by its authors. Use permitted under Creative Commons License Attribution 4.0 International (CC BY 4.0).
community, with methods and scales of measurement. It is incorporated into the
Breeders Field Book7 allowing scientists to record crop phenotype observations in the
field. Of the 316 traits in the Wheat Trait Dictionary, approximately 50 are mapped to
an exact matching class in the TO, while the others are mapped to a more general class.
The GrainGenes database [9] is an integrated relational database and internet resource
for the international small grains community which provides curated genetic and
genomic information about Triticeae species (mainly wheat, barley, rye and their wild
relatives), and Avena species (mainly oat), with a diversity of data types including
genome browsers, comparative linkage maps, sequence polymorphisms, and QTLs. To
improve data standardization and interoperability, 246 traits in the GrainGenes database
have been mapped to date to 155 unique TO terms, and 72 traits mapped to 42 unique
wheat CO terms, all of which link back to the Planteome database.
As new wheat traits are characterized to adapt to increased demands for food and changes
in the climate, these three integrated resources provide researchers and plant breeders
tools to utilize the large amounts of genetic and genomic data that are available for crop
improvement.
FUNDING: This work is supported by the NSF award IOS:1340112, the CGIAR Big Data Initiative, and
USDA-ARS Agreements #58-2030-9-043 and #58-8062-8-008.
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