Dataset Information

Abasy Atlas: a comprehensive inventory of systems, global network properties and systems-level elements across bacteria.

ABSTRACT: The availability of databases electronically encoding curated regulatory networks and of high-throughput technologies and methods to discover regulatory interactions provides an invaluable source of data to understand the principles underpinning the organization and evolution of these networks responsible for cellular regulation. Nevertheless, data on these sources never goes beyond the regulon level despite the fact that regulatory networks are complex hierarchical-modular structures still challenging our understanding. This brings the necessity for an inventory of systems across a large range of organisms, a key step to rendering feasible comparative systems biology approaches. In this work, we take the first step towards a global understanding of the regulatory networks organization by making a cartography of the functional architectures of diverse bacteria. Abasy ( A: cross- BA: cteria SY: stems) Atlas provides a comprehensive inventory of annotated functional systems, global network properties and systems-level elements (global regulators, modular genes shaping functional systems, basal machinery genes and intermodular genes) predicted by the natural decomposition approach for reconstructed and meta-curated regulatory networks across a large range of bacteria, including pathogenically and biotechnologically relevant organisms. The meta-curation of regulatory datasets provides the most complete and reliable set of regulatory interactions currently available, which can even be projected into subsets by considering the force or weight of evidence supporting them or the systems that they belong to. Besides, Abasy Atlas provides data enabling large-scale comparative systems biology studies aimed at understanding the common principles and particular lifestyle adaptions of systems across bacteria. Abasy Atlas contains systems and system-level elements for 50 regulatory networks comprising 78 649 regulatory interactions covering 42 bacteria in nine taxa, containing 3708 regulons and 1776 systems. All this brings together a large corpus of data that will surely inspire studies to generate hypothesis regarding the principles governing the evolution and organization of systems and the functional architectures controlling them.Database URL: http://abasy.ccg.unam.mx.

SUBMITTER: Ibarra-Arellano MA

PROVIDER: S-EPMC4885605 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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Abasy Atlas: a comprehensive inventory of systems, global network properties and systems-level elements across bacteria.

Ibarra-Arellano Miguel A MA Campos-González Adrián I AI Treviño-Quintanilla Luis G LG Tauch Andreas A Freyre-González Julio A JA

Database : the journal of biological databases and curation 20160530

The availability of databases electronically encoding curated regulatory networks and of high-throughput technologies and methods to discover regulatory interactions provides an invaluable source of data to understand the principles underpinning the organization and evolution of these networks responsible for cellular regulation. Nevertheless, data on these sources never goes beyond the regulon level despite the fact that regulatory networks are complex hierarchical-modular structures still chal ...[more]

PMID: 27242034

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Project description:The future of the food system on the planet is increasingly facing uncertainties that are attributable to population growth and a surge in demand for nutritious food. Traditional agricultural practices are poised to place strain on production, as well as natural resources and ecosystem services provided, particularly under a changing climate. Given their remarkable attributes, including a low environmental footprint, high food conversion ratio, rapid growth and nutritional values, edible insects can play a vital role in the global food system. Nonetheless, substantial knowledge gaps persist regarding their diversity, global distribution, and shared characteristics across regions, potentially impeding effective scaling and access to edible insects. Therefore, we compiled and analysed the fragmented database on edible insects and identified potential drivers that elucidate insect consumption, globally, focusing on promoting a sustainable food system. We collated data from various sources, including the literature for a list of edible insect species, the Global Biodiversity Information Facility and iNaturalist for the geographical presence of edible insects, the Copernicus Land Service library for Global Land Cover, and FAOSTAT for population, income, and nutritional security parameters. Subsequently, we performed a series of analytics at the country, regional and continental levels. Our study identifies 2205 insect species, consumed across 128 countries globally. Among continents, Asia has the highest number of edible insects (932 species), followed by North America (mainly Mexico) and Africa. The countries with the highest consumption of insects are Mexico (450 species), Thailand (272 species), India (262 species), DRC (255 species), China (235 species), Brazil (140 species), Japan (123 species), and Cameroon (100 species). Our study also revealed some common and specific practices related to edible insect access and utilisation among countries and regions. Although insect consumption is often rooted in cultural practices, it exhibits correlations with land cover, the geographical presence of potentially edible insects, the size of a country's population, and income levels. The practice of eating insects is linked to the culture of people in Africa, Asia, and Latin America, while increased consciousness and the need for food sustainability are driving most of the European countries to evaluate eating insects. Therefore, edible insects are becoming an increasingly significant part of the future of planetary food systems. Therefore, more proactive efforts are required to promote them for their effective contribution to achieving sustainable food production.

Dataset Information

Abasy Atlas: a comprehensive inventory of systems, global network properties and systems-level elements across bacteria.

Publications

Abasy Atlas: a comprehensive inventory of systems, global network properties and systems-level elements across bacteria.

Similar Datasets

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