Obo foundry food ontology interconnectivity

Since its creation in 2016, the FoodOn ontology has become an interconnected partner in various academic and government inter-agency ontology work spanning agricultural and public health domains. This paper examines existing and potential data interoperability capabilities arising from FoodOn and partner food-related ontologies belonging to the encyclopedic Open Biological and Biomedical Ontology Foundry (OBO) vocabulary platform, and how research organizations and industry might utilize them for their own operations or for data exchange. Projects are seeking standardized vocabulary across all direct food supply activities ranging from agricultural production, harvesting, preparation, food processing, marketing, distribution and consumption, as well as indirectly, within health, economic, food security and sustainability analysis and reporting tools. To satisfy this demand and provide data requires establishing domain specific ontologies whose curators coordinate closely to produce recommended patterns for food system vocabulary

Adeno-Associated Viral Vector-Mediated Transgene Expression Is Independent of DNA Methylation in Primate Liver and Skeletal Muscle

Recombinant adeno-associated viral (rAAV) vectors can support long-term transgene expression in quiescent tissues. Intramuscular (IM) administration of a single-stranded AAV vector (ssAAV) in the nonhuman primate (NHP) results in a peak protein level at 2–3 months, followed by a decrease over several months before reaching a steady-state. To investigate transgene expression and vector genome persistence, we previously demonstrated that rAAV vector genomes associate with histones and form a chromatin structure in NHP skeletal muscle more than one year after injection. In the mammalian nucleus, chromatin remodeling via epigenetic modifications plays key role in transcriptional regulation. Among those, CpG hyper-methylation of promoters is a known hallmark of gene silencing. To assess the involvement of DNA methylation on the transgene expression, we injected NHP via the IM or the intravenous (IV) route with a recombinant ssAAV2/1 vector. The expression cassette contains the transgene under the transcriptional control of the constitutive Rous Sarcoma Virus promoter (RSVp). Total DNA isolated from NHP muscle and liver biopsies from 1 to 37 months post-injection was treated with sodium bisulfite and subsequently analyzed by pyrosequencing. No significant CpG methylation of the RSVp was found in rAAV virions or in vector DNA isolated from NHP transduced tissues. Direct de novo DNA methylation appears not to be involved in repressing transgene expression in NHP after gene transfer mediated by ssAAV vectors. The study presented here examines host/vector interactions and the impact on transgene expression in a clinically relevant model

Genome-Wide Association Study in BRCA1 Mutation Carriers Identifies Novel Loci Associated with Breast and Ovarian Cancer Risk

BRCA1-associated breast and ovarian cancer risks can be modified by common genetic variants. To identify further cancer risk-modifying loci, we performed a multi-stage GWAS of 11,705 BRCA1 carriers (of whom 5,920 were diagnosed with breast and 1,839 were diagnosed with ovarian cancer), with a further replication in an additional sample of 2,646 BRCA1 carriers. We identified a novel breast cancer risk modifier locus at 1q32 for BRCA1 carriers (rs2290854, P = 2.7×10-8, HR = 1.14, 95% CI: 1.09-1.20). In addition, we identified two novel ovarian cancer risk modifier loci: 17q21.31 (rs17631303, P = 1.4×10-8, HR = 1.27, 95% CI: 1.17-1.38) and 4q32.3 (rs4691139, P = 3.4×10-8, HR = 1.20, 95% CI: 1.17-1.38). The 4q32.3 locus was not associated with ovarian cancer risk in the general population or BRCA2 carriers, suggesting a BRCA1-specific associat

Des ontologies pour la science

Poster de présentation de quelques notions autour des ontologies et de la sémantique au service du chercheur

Construction of a Generic and Evolutive Wheel and Lexicon of Food Textures

International audienceIn the context of data management and processing, food science needs tools to organize the results of diverse studies to make the data reusable. In sensory analysis, there are no classification or wheel of textural attributes that can be used to interpret the results of sensory studies. Research from the literature and databases was used to elaborate a list of attributes related to texture. With the help of a group of experts in food texture, work on these attributes and the related concepts was conducted to classify them into several categories, including intensity levels. The classification was represented as a texture wheel, completed by a generic lexicon of definitions of texture concepts. The work can be useful as a reference in texture attributes related to foods, and thanks to implementation in a general ontology based on food processing and observation, it can help query and interpret texture-related results from sensory studies

First steps towards FAIRization of product-focused sensory data

International audienc

How to Manage Incompleteness of Nutritional Food Sources?: A solution using FoodOn as pivot ontology

International audienceIn order to correctly assess the nutritional quality of a raw or manufactured food product, the first step is to obtain the associated nutritional values. Food composition databases (FCDBs) managed at national level provide values for nutrients of foods. Unfortunately, values associated with some nutrients of interest may be lacking in the FCDB of the country in which the nutritional quality must be assessed and finding values associated with nutrients for similar foods in other FCDBs is a way to deal with incompleteness. An additional issue arises because the vocabulary used to denote a given food in a given FCDB is usually different from the one used in others. In this paper, the authors address the problem of retrieving the nutritional value of foods by querying different FCDBs through FoodOn used as pivot ontology. The article presents a new food source alignment method between two FCDBs. The method has been evaluated on the French and United States food nutritional evaluation. The proposed solution for the incompleteness management task has been assessed with a real use case

A new alignment method based on FoodOn as pivot ontology to integrate nutritional legacy data sources

International audienceIn order to correctly assess the nutritional quality of a meal or a manufactured food product in a given country, the first step is to assess the nutritional values for its ingredients. Food composition databases (FCDBs) available in a lot of countries and managed at national level provide values for energy and nutrients of food components. Unfortunately, values associated with some nutrients of interest may be lacking in the FCDB of the country in which the nutritional quality must be assessed. Finding values associated with nutrients for similar foods in other FCDBs is a way to deal with incompleteness. An additional issue arises because the vocabulary used to describe the ingredients of a meal or a recipe in a given FCDB is usually different from the one used in other ones. In this paper we address the problem of identifying the nutritional value of recipe's ingredients by querying different FCDBs through FoodOn as pivot ontology. We present a new alignment method between two distinct FCDBs, based on syntactic and semantic approaches, whose vocabulary is previously transformed into an ontology. Our method has been evaluated on Ciqual, the French food nutritional database, USDA, the United States food nutritional database and the FoodOn ontology. The incompleteness management task based on FoodOn as pivot ontology has been assessed with a real use-case concerning iron, Vitamin B12, Vitamin C nutrients