WTO, an ontology for wheat traits and phenotypes in scientific publications
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 need to improve the reuse of observations and experimental data has led to the creation of reference ontologies to standardize descri...
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| Format: | Article |
| Language: | English |
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BioMed Central
2020-06-01
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| Series: | Genomics & Informatics |
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| Online Access: | http://genominfo.org/upload/pdf/gi-2020-18-2-e14.pdf |
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| author | Claire Nédellec Liliana Ibanescu Robert Bossy Pierre Sourdille |
| author_facet | Claire Nédellec Liliana Ibanescu Robert Bossy Pierre Sourdille |
| author_sort | Claire Nédellec |
| collection | DOAJ |
| description | 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 need to improve the reuse of observations and experimental data has led to the creation of reference ontologies to standardize descriptions of phenotypes and to facilitate their comparison. The scientific literature is largely under-exploited, although extremely rich in phenotype descriptions associated with cultivars and genetic information. 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 experimental databases. We describe the principles of WTO construction and show examples of WTO use for the extraction and management of phenotype descriptions obtained from scientific documents. |
| format | Article |
| id | doaj-art-43f4bb8e23dc4b658ae114f01c8c55c3 |
| institution | Kabale University |
| issn | 2234-0742 |
| language | English |
| publishDate | 2020-06-01 |
| publisher | BioMed Central |
| record_format | Article |
| series | Genomics & Informatics |
| spelling | doaj-art-43f4bb8e23dc4b658ae114f01c8c55c32025-02-02T04:29:36ZengBioMed CentralGenomics & Informatics2234-07422020-06-01182e1410.5808/GI.2020.18.2.e14611WTO, an ontology for wheat traits and phenotypes in scientific publicationsClaire Nédellec0Liliana Ibanescu1Robert Bossy2Pierre Sourdille3 Paris-Saclay University, INRAE, MaIAGE, F-78350 Jouy-en-Josas, France Paris-Saclay University, INRAE, UMR MIA-Paris, AgroParisTech, F-75005, Paris, France Paris-Saclay University, INRAE, MaIAGE, F-78350 Jouy-en-Josas, France University Clermont-Auvergne, INRAE, UMR 1095 GDEC, F-63000 Clermont-Ferrand, FrancePhenotyping 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 need to improve the reuse of observations and experimental data has led to the creation of reference ontologies to standardize descriptions of phenotypes and to facilitate their comparison. The scientific literature is largely under-exploited, although extremely rich in phenotype descriptions associated with cultivars and genetic information. 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 experimental databases. We describe the principles of WTO construction and show examples of WTO use for the extraction and management of phenotype descriptions obtained from scientific documents.http://genominfo.org/upload/pdf/gi-2020-18-2-e14.pdfontologytext miningwheat trait and phenotype |
| spellingShingle | Claire Nédellec Liliana Ibanescu Robert Bossy Pierre Sourdille WTO, an ontology for wheat traits and phenotypes in scientific publications Genomics & Informatics ontology text mining wheat trait and phenotype |
| title | WTO, an ontology for wheat traits and phenotypes in scientific publications |
| title_full | WTO, an ontology for wheat traits and phenotypes in scientific publications |
| title_fullStr | WTO, an ontology for wheat traits and phenotypes in scientific publications |
| title_full_unstemmed | WTO, an ontology for wheat traits and phenotypes in scientific publications |
| title_short | WTO, an ontology for wheat traits and phenotypes in scientific publications |
| title_sort | wto an ontology for wheat traits and phenotypes in scientific publications |
| topic | ontology text mining wheat trait and phenotype |
| url | http://genominfo.org/upload/pdf/gi-2020-18-2-e14.pdf |
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