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The Plant Trait Ontology Links Wheat Traits for Crop Improvement and Genomics (short paper)

Laurel Cooper, Marie-Angélique Laporte, Justin Elser, Victoria Carollo Blake, Taner Z. Sen, Chris Mungall, Elizabeth Arnaud, Pankaj Jaiswal
2020 International Conference on Biomedical Ontology  
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 Project 2 [4].  ...  amounts of genetic and genomic data that are available for crop improvement.  ... 
dblp:conf/icbo/CooperLEBSMAJ20 fatcat:enneevponfhdbbtgp47ddjaufu

WTO, an ontology for wheat traits and phenotypes in scientific publications

Claire Nédellec, Liliana Ibanescu, Robert Bossy, Pierre Sourdille
2020 Genomics & Informatics  
In this paper we propose the Wheat Trait Ontology (WTO) that is suitable for the extraction and management of scientific information from scientific papers, and its combination with data from genomic and  ...  Phenotyping is a major issue for wheat agriculture to meet the challenges of adaptation of wheat varieties to climate change and chemical input reduction in crop.  ...  The author work at the 6th Biomedical Linked Annotation Hackathon (BLAH6) was supported by the Database Center for Life Science (DBCLS).  ... 
doi:10.5808/gi.2020.18.2.e14 pmid:32634868 fatcat:kccvjrbqwnetfcfj6irx54gipq

Unlimited Thirst for Genome Sequencing, Data Interpretation, and Database Usage in Genomic Era: The Road towards Fast-Track Crop Plant Improvement

Arun Prabhu Dhanapal, Mahalingam Govindaraj
2015 Genetics Research International  
This paper reviews some basic terms and considerations in dealing with crop plant databases utilization in advancing genomic era.  ...  The major focus of this review is to provide knowledge on platforms and databases for genome-based investigations of agriculturally important crop plants.  ...  Plant Ontology Database-a resource for plant structure and developmental stages View, search, and query plant ontology terms The PlantsP Functional Genomics Database Search for information on plant kinases  ... 
doi:10.1155/2015/684321 pmid:25874133 pmcid:PMC4383144 fatcat:kl7tgs6zx5dy7cyy2tisqfmjxi

Gramene QTL database: development, content and applications

Junjian Ni, Anuradha Pujar, Ken Youens-Clark, Immanuel Yap, Pankaj Jaiswal, Isaak Tecle, Chih-Wei Tung, Liya Ren, William Spooner, Xuehong Wei, Shuly Avraham, Doreen Ware (+2 others)
2009 Database: The Journal of Biological Databases and Curation  
Acknowledgements We appreciate the numerous authors of QTL publications who have kindly shared information with us on QTL, markers and maps by way of personal communication. .........................  ...  alleles for crop improvement.  ...  Trait descriptions were mapped to controlled vocabularies including the Trait Ontology (TO), Plant Ontology (PO) and Plant Growth Stage Ontology (GSO) (10) (11) (12) .  ... 
doi:10.1093/database/bap005 pmid:20157478 pmcid:PMC2790302 fatcat:thesfvm7mbdefmpgm4qjtg7jva

Wheat Omics: Classical Breeding to New Breeding Technologies

Fahad Alotaibi, Saif Alharbi, Majed Alotaibi, Mobarak Al Mosallam, Mohamed Motawei, Abdullah Alrajhi
2020 Saudi Journal of Biological Sciences  
Wheat is an important cereal crop, and its significance is more due to compete for dietary products in the world.  ...  Many constraints facing by the wheat crop due to environmental hazardous, biotic, abiotic stress and heavy matters factors, as a result, decrease the yield.  ...  Over time, techniques for sexual hybridization have been used to grow and improved new crops i.e. triticale, a crop developed by the cross among rye and wheat plant in 1875 (Macintyre and Campbell, 1974  ... 
doi:10.1016/j.sjbs.2020.11.083 pmid:33613071 pmcid:PMC7878716 fatcat:oknjn7movbhc7hsv6w6w5d4ape

KnetMiner: a comprehensive approach for supporting evidence-based gene discovery and complex trait analysis across species

Keywan Hassani-Pak, Ajit Singh, Marco Brandizi, Joseph Hearnshaw, Jeremy D Parsons, Sandeep Amberkar, Andrew L Phillips, John H Doonan, Chris Rawlings
2021 Plant Biotechnology Journal  
Here we give an overview of the main approaches to using KnetMiner and we report plant-centric case studies for identifying genes, gene networks and trait relationships in Triticum aestivum (bread wheat  ...  KnetMiner is an integrated, intelligent, interactive gene and gene network discovery platform that supports scientists discover and understand the biological stories of complex traits and diseases across  ...  Acknowledgements This work was supported by the UKRI Biotechnology and Biological Sciences Research Council (BBSRC) through the Designing Future Wheat ISP (BB/P016855/1), DiseaseNetMiner TRDF (BB/N022874  ... 
doi:10.1111/pbi.13583 pmid:33750020 fatcat:xsjgscimlncdvolkd5c5wvnsrq

Information Extraction from Bibliography for Marker-Assisted Selection in Wheat [chapter]

Claire Nédellec, Robert Bossy, Dialekti Valsamou, Marion Ranoux, Wiktoria Golik, Pierre Sourdille
2014 Communications in Computer and Information Science  
Improvement of most animal and plant species of agronomical interest in the near future has become an international stake because of the increasing demand for feeding a growing world population and to  ...  The recent advent of genomic tools contributed to improve the discovery of linkage between molecular markers and genes that are involved in the control of traits of agronomical interest such as grain number  ...  This increase needs a significant improvement of the agronomical potential of the species through breeding. This is especially true for wheat, the most widely grown crop worldwide.  ... 
doi:10.1007/978-3-319-13674-5_28 fatcat:jiznl6qz2fdpzahwsk42yvgsmi

KnetMiner - Intelligent search and visualisation of connected data to explain complex traits and diseases [article]

Keywan Hassani-Pak, Ajit Singh, Marco Brandizi, Joseph Hearnshaw, Andrew L Phillips, John H Doonan, Christopher Rawlings
2020 biorxiv/medrxiv   pre-print
as genes, biological pathways, phenotypes and publications, providing leads for scientists who are investigating the molecular basis of a particular trait or disease.  ...  KnetMiner can be easily developed and deployed for any species with a sequenced genome to provide a sophisticated search over connected data.  ...  Acknowledgements This work was supported by the UKRI Biotechnology and Biological Sciences Research Council (BBSRC) through the Designing Future Wheat ISP (BB/P016855/1), DiseaseNetMiner TRDF (BB/N022874  ... 
doi:10.1101/2020.04.02.017004 fatcat:infoxkiv7fdchcivkmj4nnlpei

Breeding for Economically and Environmentally Sustainable Wheat Varieties: An Integrated Approach from Genomics to Selection

Etienne Paux, Stéphane Lafarge, François Balfourier, Jérémy Derory, Gilles Charmet, Michael Alaux, Geoffrey Perchet, Marion Bondoux, Frédéric Baret, Romain Barillot, Catherine Ravel, Pierre Sourdille (+2 others)
2022 Biology  
Improvement in varieties particularly relies on the detection of genomic regions involved in agronomical traits including tolerance to biotic (diseases and pests) and abiotic (drought, nutrient deficiency  ...  There is currently a strong societal demand for sustainability, quality, and safety in bread wheat production.  ...  Despite the recognition that genome sequencing is critical for crop improvement, the size (approx. 16 Gb, 5× the human genome and 40× that of rice), and complexity (three homoeologous A-, B-, and D-genomes  ... 
doi:10.3390/biology11010149 pmid:35053148 pmcid:PMC8773325 fatcat:ttdipej4mnd4lbflakfcy5pc3i

Unlocking Triticeae genomics to sustainably feed the future

K. Mochida, K. Shinozaki
2013 Plant and Cell Physiology  
In this review, we provide an update on genomic tools for use with Triticeae plants and Brachypodium and describe emerging approaches toward crop improvements in Triticeae.  ...  The tribe Triticeae includes the major crops wheat and barley.  ...  Acknowledgments The authors thank Tetsuya Sakurai, Takuhiro Yoshida of the RIKEN Center for Sustainable Resource Science for their data generation of cDNA mapping among Pooideae plants.  ... 
doi:10.1093/pcp/pct163 pmid:24204022 pmcid:PMC3856857 fatcat:uuepryp45rhk3etegnzb3sedka

The Ontologies Community of Practice: A CGIAR Initiative for Big Data in Agrifood Systems

Elizabeth Arnaud, Marie-Angélique Laporte, Soonho Kim, Céline Aubert, Sabina Leonelli, Berta Miro, Laurel Cooper, Pankaj Jaiswal, Gideon Kruseman, Rosemary Shrestha, Pier Luigi Buttigieg, Christopher J. Mungall (+26 others)
2020 Patterns  
In this paper, we discuss the added value of the Ontologies Community of Practice (CoP) of the CGIAR Platform for Big Data in Agriculture for harnessing relevant expertise in ontology development and identifying  ...  As recommended by the FAIR principles, data, labels, and metadata must use controlled vocabularies and ontologies that are popular in the knowledge domain and commonly used by the community.  ...  Ontologies for Plant Traits and Agronomy Data Crop breeding relies on collecting data on the desired traits for a new crop variety by testing it in multiple locations and diverse environments, linking  ... 
doi:10.1016/j.patter.2020.100105 pmid:33205138 pmcid:PMC7660444 fatcat:6efus64zwzgldov6gy5y2motyi

The improved assembly of 7DL chromosome provides insight into the structure and evolution of bread wheat

Kewei Feng, Licao Cui, Le Wang, Dai Shan, Wei Tong, Pingchuan Deng, Zhaogui Yan, Mengxing Wang, Haoshuang Zhan, Xiaotong Wu, Weiming He, Xianqiang Zhou (+16 others)
2019 Plant Biotechnology Journal  
of the evolution of wheat, and supports wheat crop improvement.  ...  Wheat is one of the most important staple crops worldwide and also an excellent model species for crop evolution and polyploidization studies.  ...  ., M.W. and H.Z. conducted the genome assembling and predicted gene structure and repeat sequences. X.N., K.F., D.E., D.S. and S.Z. wrote the manuscript.  ... 
doi:10.1111/pbi.13240 pmid:31471988 fatcat:x2nwx5gyyzbivcs5ah4qpvtxeu

Plant phenome to genome: a mini-review

Rudi Appels
2012 Functional Plant Biology  
Rapid advances in biotechnologies have provided a template for defining the genome–transcriptome–proteome in many plant species and these advances now highlight a particular challenge to link the molecular  ...  Selected examples are provided to review advances in defining environment–phenotype interactions, the genome–transcriptome–proteome in plants and translating research outputs more broadly to society.  ...  The detailed phenology of plants is also considered within the trait ontology (TO) consortium.  ... 
doi:10.1071/fpv39n7_fo pmid:32480805 fatcat:5lhmponkanebrfrtewv4clkuq4

Shifting the limits in wheat research and breeding using a fully annotated reference genome

Rudi Appels, Kellye Eversole, Catherine Feuillet, Beat Keller, Jane Rogers, Nils Stein, Curtis J. Pozniak, Nils Stein, Frédéric Choulet, Assaf Distelfeld, Kellye Eversole, Jesse Poland (+372 others)
2018 Science  
(B) All enriched Plant Trait Ontology (TO) terms for the gene families depicted in (A).  ...  ., The Plant Ontology as a tool for comparative plant anatomy and genomic 15 analyses. Plant and Cell Physiology 54, e1-e1 (2013). 117. E.  ... 
doi:10.1126/science.aar7191 pmid:30115783 fatcat:4reazthsfrg45a7yo2aj7u4y2i

Developing data interoperability using standards: A wheat community use case

Esther Dzale Yeumo, Michael Alaux, Elizabeth Arnaud, Sophie Aubin, Ute Baumann, Patrice Buche, Laurel Cooper, Hanna Ćwiek-Kupczyńska, Robert P. Davey, Richard Allan Fulss, Clement Jonquet, Marie-Angélique Laporte (+9 others)
2017 F1000Research  
In this article, we present a joint effort of the wheat research community, along with data and ontology experts, to develop wheat data interoperability guidelines.  ...  During a period of more than 18 months, the RDA Wheat Data Interoperability Working Group (WDI-WG) surveyed the wheat research community about the  ...  ) the Crop Ontology 6 , especially the Wheat Trait Ontology for phenotypes (http://agroportal.lirmm. fr/ontologies/CO_321); and (iii) the FAO-IPGRI Multi-Crop Passport Ontology (  ... 
doi:10.12688/f1000research.12234.2 pmid:29333241 pmcid:PMC5747345 fatcat:46lgnysdmncf7bbq64de6pw6ie
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