Dataset Information

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

ABSTRACT: 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.

SUBMITTER: Nedellec C

PROVIDER: S-EPMC7362939 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature

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

Nédellec Claire C Ibanescu Liliana L Bossy Robert R Sourdille Pierre P

Genomics & informatics 20200616 2

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 i ...[more]

PMID: 32634868

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Project description:In addition to its primary regulatory role, the Office of Hematology and Oncology Products at the U.S. Food and Drug Administration (FDA) is engaged in many forms of scientific authorship. During the period of 2010 to 2018, FDA oncology staff contributed to 356 publications in the scientific literature. Here, we collaborated with analysts in the Office of Program Planning, Analysis, and Evaluation at the National Institute of General Medical Sciences, National Institutes of Health (NIH), to present a series of analyses aimed at quantifying the characteristics and potential impact of these contributions, as well as characterizing the areas of work addressed. We found that FDA oncology papers are enriched for high-impact publications and have about two times the number of citations as an average NIH-funded paper. Further impact of the publications was measured based on the presence of 65 publications that were cited by guidelines and 12 publications cited by publicly listed clinical trials. The results seen here are promising in determining the impact of FDA oncology publication work but prompt further investigation into longer-term impacts, such as the influence of this work on other regulatory activities at FDA. IMPLICATIONS FOR PRACTICE: This article describes the first comprehensive study of scientific publications produced by U.S. Food and Drug Administration (FDA) oncology staff. The analysis illustrates that staff are highly engaged in publishing in the scientific literature in addition to completing regulatory review work. Publications are generally in clinical medicine, consistent with the large number of medical oncologists working at the Office of Hematology and Oncology Products (OHOP). OHOP publications generally focus either on communicating important regulatory work (approval summaries) or highlighting regulatory science issues to encourage dialogue with the scientific community (commentaries, reviews, and expert working papers). The analysis also suggests that several FDA oncology publications may influence clinical guidelines, but further work is needed to evaluate impact.

Dataset Information

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

Publications

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

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