The Type 2 Diabetes Knowledge Portal: an open access genetic resource dedicated to type 2 diabetes and related traits

Associations between human genetic variation and clinical phenotypes have become a foundation of biomedical research. Most repositories of these data seek to be disease-agnostic and therefore lack disease-focused views. The Type 2 Diabetes Knowledge Portal (T2DKP) is a public resource of genetic datasets and genomic annotations dedicated to type 2 diabetes (T2D) and related traits. Here, we seek to make the T2DKP more accessible to prospective users and more useful to existing users. First, we evaluate the T2DKP's comprehensiveness by comparing its datasets with those of other repositories. Second, we describe how researchers unfamiliar with human genetic data can begin using and correctly interpreting them via the T2DKP. Third, we describe how existing users can extend their current workflows to use the full suite of tools offered by the T2DKP. We finally discuss the lessons offered by the T2DKP toward the goal of democratizing access to complex disease genetic results

knowledge Modeling Semantic Web SBML

Abstract A large and growing network (‘‘cloud’’) of interlinked terms and records of items of Systems Biology knowledge is available from the web. These items include pathways, reactions, substances, literature references, organisms, and anatomy, all described in different data sets. Here, we discuss how the knowledge from the cloud can be molded into representations (views) useful for data visualization and modeling. We discuss methods to create and use various views relevant for visualization, modeling, and model annotations, while hiding irrelevant details without unacceptable loss or distortion. We show that views are compatible with understanding substances and processes as sets of microscopic compounds and events respectively, which allows the representation of specializations and generalizations as subsets and supersets respectively. We explain how these methods can be implemented based on the bridging ontology System

Critical Point of a Weakly Interacting Two-Dimensional Bose Gas

We study the Berezinskii-Kosterlitz-Thouless transition in a weakly interacting 2D quantum Bose gas using the concept of universality and numerical simulations of the classical |ψ|4 model on a lattice. The critical density and chemical potential are given by relations nc = (mT/2πħ2)ln(ξħ2/mU) and μc = (mTU/πħ2)ln(ξμħ2/mU), where T is the temperature, m is the mass, and U is the effective interaction. The dimensionless constant ξ = 380±3 is very large and thus any quantitative analysis of the experimental data crucially depends on its value. For ξμ our result is ξμ = 13.2±0.4. We also report the study of the quasicondensate correlations at the critical point

Weakly Interacting Bose Gas in the Vicinity of the Critical Point

We consider a three-dimensional weakly interacting Bose gas in the fluctuation region (and its vicinity) of the normal-superfluid phase transition point. We establish relations between basic thermodynamic functions: density, n(T, ì), superfluid density ns(T, ì), and condensate density, ncnd(T, ì). Being universal for all weakly interacting |ø|4 systems, these relations are obtained from Monte Carlo simulations of the classical |ø|4 model on a lattice. Comparing with the mean-field results yields a quantitative estimate of the fluctuation region size. Away from the fluctuation region, on the superfluid side, all the data perfectly agree with the predictions of the quasicondensate mean field theory.—This demonstrates that the only effect of the leading above-the-mean-field corrections in the condensate based treatments is to replace the condensate density with the quasicondensate one in all local thermodynamic relations. Surprisingly, we find that a significant fraction of the density profile of a loosely trapped atomic gas might correspond to the fluctuation region