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Trait ontology analysis based on association mapping studies bridges the gap between crop genomics and Phenomics

Qingchun Pan, Junfeng Wei, Feng Guo, Suiyong Huang, Yong Gong, Hao Liu, Jianxiao Liu, Lin Li
2019 BMC Genomics  
Trait ontology (TO) analysis is a powerful system for functional annotation and enrichment analysis of genes.  ...  A comparison of Gene Ontology (GO) vs. TO analysis demonstrated that the TAS-derived TO system is an efficient alternative tool for gene functional annotation and enrichment analysis.  ...  Availability of data and materials All of the data and code can be downloaded at https://github.com/ panqingchun/Trait-Ontology (Public, free resource website).  ... 
doi:10.1186/s12864-019-5812-0 fatcat:7f7fxqm2azb4rnmnsgwotlg4c4

Biological Ontologies in Rice Databases. An Introduction to the Activities in Gramene and Oryzabase

Yukiko Yamazaki, Pankaj Jaiswal
2005 Plant and Cell Physiology  
Since each term is strictly defined and identified with an ID number, a set of data represented in biological ontology is easily accessible to automated information processing, even if the data sets are  ...  A concept, ontology, has been introduced in biology to support and encourage researchers to share and reuse information among biological databases.  ...  David Mathews of Cornell University for critical reading of the manuscript. Reviewers of the paper provided helpful advice.  ... 
doi:10.1093/pcp/pci505 pmid:15659431 fatcat:umxcazu6vbadrhfkjy6h6ujesm

RoBuST: an integrated genomics resource for the root and bulb crop families Apiaceae and Alliaceae

Ashwini Bhasi, Doug Senalik, Philipp W Simon, Brajendra Kumar, Vinu Manikandan, Philge Philip, Periannan Senapathy
2010 BMC Plant Biology  
ESTs and 11,438 regulatory sequence elements from Apiaceae and Alliaceae plant families; (2) graphical tools for visualization and analysis of sequence data; (3) access to traits, biosynthetic pathways  ...  , genetic linkage maps and molecular taxonomy data associated with Alliaceae and Apiaceae plants; and (4) comprehensive plant splice signal repository of 659,369 splice signals collected from 6015 plant  ...  Implementing Ontologies We submitted seventeen new carrot and garlic trait terms to Trait Ontology (TO), which is part of the Plant Ontology Consortium [15] .  ... 
doi:10.1186/1471-2229-10-161 pmid:20691054 pmcid:PMC3017783 fatcat:jto24dbjevfpdeanjtm34c4dga

Gramene: Development and Integration of Trait and Gene Ontologies for Rice

Pankaj Jaiswal, Doreen Ware, Junjian Ni, Kuan Chang, Wei Zhao, Steven Schmidt, Xiaokang Pan, Kenneth Clark, Leonid Teytelman, Samuel Cartinhour, Lincoln Stein, Susan McCouch
2002 Comparative and Functional Genomics  
The specific goal of Gramene is, first to provide a Trait Ontology (TO) that can be used across the cereal crops to facilitate phenotypic comparisons both within and between the genera.  ...  Second, a vocabulary for plant anatomy terms, the Plant Ontology (PO) will facilitate the curation of morphological and anatomical feature information with respect to expression, localization of genes  ...  (MaizeDB) for their help on development of the Trait Ontology.  ... 
doi:10.1002/cfg.156 pmid:18628886 pmcid:PMC2447246 fatcat:aclyisvbkzbtdacja4sn7kzuwq

Improving the interoperability of biomedical ontologies with compound alignments

Daniela Oliveira, Catia Pesquita
2018 Journal of Biomedical Semantics  
The algorithms were also applied to the potential extension of logical definitions of the OBO and the matching of several plant-related ontologies.  ...  Results: We have developed ontology matching algorithms that are able to find compound mappings between multiple biomedical ontologies, in the form of ternary mappings, finding for instance that "aortic  ...  We would also like to thank Marie-Angélique Laporte from the Max Planck Institute for Biogeochemistry for providing us with the challenge of aligning plant ontologies.  ... 
doi:10.1186/s13326-017-0171-8 pmid:29316968 pmcid:PMC5761129 fatcat:krulwajynvbk7ohb3swxnji3hq

Computable visually observed phenotype ontological framework for plants

Jaturon Harnsomburana, Jason M Green, Adrian S Barb, Mary Schaeffer, Leszek Vincent, Chi-Ren Shyu
2011 BMC Bioinformatics  
This is accomplished by means of a robust and accurate semantic mapping module that automatically maps high-level semantics to low-level measurements computed from phenotype imagery.  ...  This work provides a novel quantitative view of descriptions of plant phenotypes that leverages existing bio-ontologies and utilizes a computational approach to capture and represent domain knowledge in  ...  Acknowledgements The authors would like to thank Peter Balint-Kurti for SLB images and scoring descriptions, Toni Kazic for les mimic mutant images, SGN for making tomato fruit images and semantics available  ... 
doi:10.1186/1471-2105-12-260 pmid:21702966 pmcid:PMC3149582 fatcat:4bywgg25cjeqxcn44k6ddkf4um

Bioinformatics Tools for Crop Research and Breeding [chapter]

B Jayashree, Dave Hoisington
2009 Molecular Techniques in Crop Improvement  
Plant breeders are now realizing the importance of innovative approaches that include the use of a range of molecular methods and their outputs, and the possibilities of transferring this information from  ...  For effective and efficient improvement, a range of activities from molecular biology to genetics to indirect selection must now be involved.  ...  For genomics to be applied to plant breeding, there is need for high throughput techniques, cost effective protocols, precise determination of quantitative trait expression, besides bioinformatics platforms  ... 
doi:10.1007/978-90-481-2967-6_4 fatcat:aua2644ikrez5hmuemxybom4lq

XMap: results for OAEI 2018

Warith Eddine Djeddi, Sadok Ben Yahia, Mohamed Tarek Khadir
2018 International Semantic Web Conference  
Our strategies aim to provide a set of requirements that foster the using of a domain-specific thesaurus for the alignment of specialized ontologies.  ...  XMap aims to tackle the issue of matching large scale ontologies by involving particular parallel matching on multiple cores or machines.  ...  Phenotype Ontology (FLOPO) and the Plant Trait Ontology (PTO).  ... 
dblp:conf/semweb/DjeddiYK18 fatcat:f2fqswrlmfbatbjdcnsdb7zigu

Knowledge Discovery in Biological Databases for Revealing Candidate Genes Linked to Complex Phenotypes

Keywan Hassani-Pak, Christopher Rawlings
2017 Journal of Integrative Bioinformatics  
AbstractGenetics and "omics" studies designed to uncover genotype to phenotype relationships often identify large numbers of potential candidate genes, among which the causal genes are hidden.  ...  Computational tools are needed for the integration and evaluation of heterogeneous information in order to prioritise candidate genes and components of interaction networks that, if perturbed through potential  ...  For example, available ontologies for plants and crops include the Plant Ontology (www.plantontology.org), the Crop Ontology (www.cropontology.org), the Plant Trait Ontology (www.planteome.org) and the  ... 
doi:10.1515/jib-2016-0002 pmid:28609292 pmcid:PMC6042805 fatcat:5n6hsndt5fecpkolgctalg4oca

BigDataGrapes D3.1 - Data Modelling and Linking Components

Vladimir Alexiev
2018 Zenodo  
we have taken to engage with the AgroBio communities to improve the quality of these ontologies.  ...  resources related to the task. • Chapter 2 Relevant AgroBio Ontologies outlines the vast number of potentially relevant ontologies and the terms included in them.  ...  measured • Trait = entity + quality: what quality of which entity • Method: what exactly are we measuring (e.g. height to youngest growing leaf or total plant height) and how (instrument, technique, etc  ... 
doi:10.5281/zenodo.1482757 fatcat:fozv63mxjrbrhnfpjljg6hymue

Integrating genome annotation and QTL position to identify candidate genes for productivity, architecture and water-use efficiency in Populus spp

Romain Monclus, Jean-Charles Leplé, Catherine Bastien, Pierre-François Bert, Marc Villar, Nicolas Marron, Franck Brignolas, Véronique Jorge
2012 BMC Plant Biology  
Integrating genome annotation and QTL position to identify candidate genes for productivity, architecture and water-use efficiency in Populus spp.  ...  on the anchoring of genetic maps on the genome and the gene ontology information linked to genome annotation.  ...  Trait names were explained in Material and Methods Figure 3 3 Comparison of enrichment analyses of GO terms using TW or MGAS methods.  ... 
doi:10.1186/1471-2229-12-173 pmid:23013168 pmcid:PMC3520807 fatcat:bslgea2trjhvplnq2ke3ljibcu

QTLTableMiner++: semantic mining of QTL tables in scientific articles

Gurnoor Singh, Arnold Kuzniar, Erik M. van Mulligen, Anand Gavai, Christian W. Bachem, Richard G.F. Visser, Richard Finkers
2018 BMC Bioinformatics  
Crop Ontology, Plant Ontology and Trait Ontology) using the Apache Solr search platform and the results are stored in a relational database and a text file.  ...  Traditional text mining techniques aim to extract information from unstructured text rather than from tables.  ...  In particular, the Solanaceae Phenotype Ontology (SPTO) [17, 18] , Plant Ontology (PO) [19, 20] , Phenotypic Quality Ontology (PATO) [21, 22] and Trait Ontology (TO) [23] were used to identify plant-specific  ... 
doi:10.1186/s12859-018-2165-7 pmid:29801439 pmcid:PMC5970438 fatcat:3a4lgrifobdiro5bqfzemfmpkm

Enrichment of the phenotypic and genotypic Data Warehouse analysis using Question Answering systems to facilitate the decision making process in cereal breeding programs

Jesús Peral, Antonio Ferrández, Elisa De Gregorio, Juan Trujillo, Alejandro Maté, Luis José Ferrández
2015 Ecological Informatics  
We thank Domenico Beneventano and his research group for the cession of the CEREALAB database for academic purposes.  ...  ACKNOWLEDGEMENTS This paper has been partially supported by the MESOLAP (TIN2010-14860) and GEODAS-BI (TIN2012-37493-C03-03) projects from the Spanish Ministry of Education and Competitivity.  ...  Finally, a semiautomatic mapping process is carried out in order to detect connections between the QA and DW ontologies) (seeFigure 5): Mapping between subsets of QA ontology and DW ontology Figure 6  ... 
doi:10.1016/j.ecoinf.2014.05.003 fatcat:sngczta6vrdvha3zyibjultdaq

Refining bulk segregant analyses: ontology-mediated discovery of flowering time genes in Brassica oleracea

Rutger A. Vos, Catharina A. M. van der Veen-van Wijk, M. Eric Schranz, Klaas Vrieling, Peter G. L. Klinkhamer, Frederic Lens
2022 Plant Methods  
Results Here we develop a Gene Ontology-mediated approach to zoom in on specific genes located inside QTLs identified by BSA as implicated in a continuous trait.  ...  Conclusions Our method is potentially applicable to the study of other complex traits and we therefore make our workflows available as open-source code and a reusable Docker container.  ...  Acknowledgements The authors are grateful to Sarah-Veronica Schießl-Weidenweber for the insightful exchanges we had about her previous work on flowering time in B. oleracea and for the background data  ... 
doi:10.1186/s13007-022-00921-y pmid:35780674 pmcid:PMC9252076 fatcat:gfjmzc3bfrf4ndzr5d4uulqfe4

The Plant Phenology Ontology: A New Informatics Resource for Large-Scale Integration of Plant Phenology Data

Brian J. Stucky, Rob Guralnick, John Deck, Ellen G. Denny, Kjell Bolmgren, Ramona Walls
2018 Frontiers in Plant Science  
To address this problem, we have developed the Plant Phenology Ontology (PPO).  ...  Here, we describe the PPO, and we also report preliminary results of using the PPO and a new data processing pipeline to build a large dataset of phenology information from North America and Europe.  ...  ACKNOWLEDGMENTS We thank the participants of workshops sponsored by NEON, USGS, and iDigBio for their contributions to this project.  ... 
doi:10.3389/fpls.2018.00517 pmid:29765382 pmcid:PMC5938398 fatcat:l4vhdhctkvfzbmefrjny3kmr2a
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