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Ferre, Arnaud,Ba, Mouhamadou,Bossy, Robert Korea Genome Organization 2019 Genomics & informatics Vol.17 No.2
Entity normalization, or entity linking in the general domain, is an information extraction task that aims to annotate/bind multiple words/expressions in raw text with semantic references, such as concepts of an ontology. An ontology consists minimally of a formally organized vocabulary or hierarchy of terms, which captures knowledge of a domain. Presently, machine-learning methods, often coupled with distributional representations, achieve good performance. However, these require large training datasets, which are not always available, especially for tasks in specialized domains. CONTES (CONcept-TErm System) is a supervised method that addresses entity normalization with ontology concepts using small training datasets. CONTES has some limitations, such as it does not scale well with very large ontologies, it tends to overgeneralize predictions, and it lacks valid representations for the out-of-vocabulary words. Here, we propose to assess different methods to reduce the dimensionality in the representation of the ontology. We also propose to calibrate parameters in order to make the predictions more accurate, and to address the problem of out-of-vocabulary words, with a specific method.
WTO, an ontology for wheat traits and phenotypes in scientific publications
Nedellec, Claire,Ibanescu, Liliana,Bossy, Robert,Sourdille, Pierre Korea Genome Organization 2020 Genomics & informatics Vol.18 No.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 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.
Forced transverse vibration of composite sandwich beam with magnetorheological elastomer core
Salah Aguib,Abdelkader Nour,Toufik Djedid,Georges Bossis,Nourddine Chikh 대한기계학회 2016 JOURNAL OF MECHANICAL SCIENCE AND TECHNOLOGY Vol.30 No.1
We studied, experimentally and numerically, the vibrational response of a magnetorheological elastomer sandwich beam, clampedfree,delimited by two skins aluminum 7075T6, first subjected to a variable magnetic field perpendicular to the skin of the beam, andsecond to a harmonic excitation by magnetic force applied at the free end. Our main objective was to predict the effect of the intensity ofthe current flowing through a coil on several dynamic factors. The maximum amplitude of resonance and the variation of the loss factoras a function of structural stiffness are adjusted simultaneously by the application of different magnetic fields. The results of bothmethods are compared.
Arnaud Ferré,Mouhamadou Ba,Robert Bossy 한국유전체학회 2019 Genomics & informatics Vol.17 No.2
Entity normalization, or entity linking in the general domain, is an information extraction task that aims to annotate/bind multiple words/expressions in raw text with semantic references, such as concepts of an ontology. An ontology consists minimally of a formally organized vocabulary or hierarchy of terms, which captures knowledge of a domain. Presently, machine-learning methods, often coupled with distributional representations, achieve good performance. However, these require large training datasets, which are not always available, especially for tasks in specialized domains. CONTES (CONcept-TErm System) is a supervised method that addresses entity normalization with ontology concepts using small training datasets. CONTES has some limitations, such as it does not scale well with very large ontologies, it tends to overgeneralize predictions, and it lacks valid representations for the out-of-vocabulary words. Here, we propose to assess different methods to reduce the dimensionality in the representation of the ontology. We also propose to calibrate parameters in order to make the predictions more accurate, and to address the problem of out-of-vocabulary words, with a specific method.
류예성,Kyoung Ah Kang,Mei Jing Piao,Meejung Ahn,이주미,Guillaume Bossis,현영민,박창욱,Jin Won Hyun 생화학분자생물학회 2019 Experimental and molecular medicine Vol.51 No.-
Ambient air particulate matter (PM) induces senescence in human skin cells. However, the underlying mechanisms remain largely unknown. We investigated how epigenetic regulatory mechanisms participate in cellular senescence induced by PM with a diameter <2.5 (PM2.5) in human keratinocytes and mouse skin tissues. PM2.5-treated cells exhibited characteristics of cellular senescence. PM2.5 induced a decrease in DNA methyltransferase (DNMT) expression and an increase in DNA demethylase (ten–eleven translocation; TET) expression, leading to hypomethylation of the p16INK4A promoter region. In addition, PM2.5 led to a decrease in polycomb EZH2 histone methyltransferase expression, whereas the expression of the epigenetic transcriptional activator MLL1 increased. Furthermore, binding of DNMT1, DNMT3B, and EZH2 to the promoter region of p16INK4A decreased in PM2.5-treated keratinocytes, whereas TET1 and MLL1 binding increased, leading to decreased histone H3 lysine 27 trimethylation (H3K27Me3) and increased H3K4Me3 in the promoter of p16INK4A. PM2.5-induced senescence involved aryl hydrocarbon receptor (AhR)-induced reactive oxygen species (ROS) production. ROS scavenging dampened PM2.5-induced cellular senescence through regulation of DNA and histone methylation. Altogether, our work shows that skin senescence induced by environmental PM2.5 occurs through ROS-dependent the epigenetic modification of senescence-associated gene expression. Our findings provide information for the design of preventive and therapeutic strategies against skin senescence, particularly in light of the increasing problem of PM2.5 exposure due to air pollution.