Exposing WikiPathways as Linked Open Data

Biology has become a data intensive science. Discovery of new biological facts increasingly relies on the ability to find and match appropriate biological data. For instance for functional annotation of genes of interest or for identification of pathways affected by over-expressed genes. Functional and pathway information about genes and proteins is typically distributed over a variety of databases and the literature.

Pathways are a convenient, easy to interpret way to describe known biological interactions. WikiPathways provides community curated pathways. WikiPathways users integrate their knowledge with facts from the literature and biological databases. The curated pathway is then reviewed and possibly corrected or enriched. Different tools (e.g. Pathvisio and Cytoscape) support the integration of WikiPathways-knowledge for additional tasks, such as the integration with personal data sets. 

Data from WikiPathways is increasingly also used for advanced analysis where it is integrated or compared with other data, Currently, integration with data from different biological sources is mostly done manually. This can be a very time consuming task because the curator often first needs to find the available resources, needs to learn about their specific content and qualities and often spends a lot of time to technically combine the two. 

Semantic web and Linked Data technologies eliminate the barriers between database silos by relying on a set of standards and best practices for representing and describing data. The architecture of the semantic web relies on the architecture of the web itself for integrating and mapping universal resource identifiers (URI), coupled with basic inference mechanisms to enable matching concepts and properties across data sources. Semantic Web and Linked Data technologies are increasingly being successfully applied as integration engines for linking biological elements. 

Exposing WikiPathways content as Linked Open Data to the Semantic Web, enables rapid, semi-automated integration with a the growing amount of biological resources available from the linked open data cloud, it also allows really fast queries of WikiPathways itself. 

We have harmonised WikiPathways content according to a selected set of vocabularies (Biopax, CHEMBL, etc), common to resources already available as Linked Open Data. 
WikiPathways content is now available as Linked Open Data for dynamic querying through a SPARQL endpoint: http://semantics.bigcat.unimaas.nl:8000/sparql

POPEYE: A production rule-based model of multitask supervisory control (POPCORN)

Recent studies of relationships between subjective ratings of mental workload, performance, and human operator and task characteristics have indicated that these relationships are quite complex. In order to study the various relationships and place subjective mental workload within a theoretical framework, we developed a production system model for the performance component of the complex supervisory task called POPCORN. The production system model is represented by a hierarchial structure of goals and subgoals, and the information flow is controlled by a set of condition-action rules. The implementation of this production system, called POPEYE, generates computer simulated data under different task difficulty conditions which are comparable to those of human operators performing the task. This model is the performance aspect of an overall dynamic psychological model which we are developing to examine and quantify relationships between performance and psychological aspects in a complex environment

Optimal control of a dengue epidemic model with vaccination

We present a SIR+ASI epidemic model to describe the interaction between human and dengue fever mosquito populations. A control strategy in the form of vaccination, to decrease the number of infected individuals, is used. An optimal control approach is applied in order to find the best way to fight the disease.Comment: This is a preprint of a paper accepted for presentation at ICNAAM 2011, Halkidiki, Greece, 19-25 September 2011, and to appear in AIP Conference Proceedings, volume 138

Modeling and Optimal Control Applied to a Vector Borne Disease

A model with six mutually-exclusive compartments related to Dengue disease is presented. In this model there are three vector control tools: insecticides (larvicide and adulticide) and mechanical control. The problem is studied using an Optimal Control (OC) approach. The human data for the model is based on the Cape Verde Dengue outbreak. Some control measures are simulated and their consequences analyzed

Insecticide control in a Dengue epidemics model

A model for the transmission of dengue disease is presented. It consists of eight mutually-exclusive compartments representing the human and vector dynamics. It also includes a control parameter (insecticide) in order to fight the mosquitoes. The main goal of this work is to investigate the best way to apply the control in order to effectively reduce the number of infected humans and mosquitoes. A case study, using data of the outbreak that occurred in 2009 in Cape Verde, is presented.Comment: Accepted 28/07/2010 in the special session "Numerical Optimization" of the 8th International Conference of Numerical Analysis and Applied Mathematics (ICNAAM 2010), Rhodes, Greece, 19-25 September 201

Quantitative and Qualitative Analysis on Sex and Gender in Preparatory Material for National Medical Examination in Germany and the United States

Background: Sex- and gender-based medicine (SGBM) should be a mandatory part of medical education. We compared the quantity and quality of sex- and gender-related content of e-learning materials commonly used by German and American medical students while preparing for national medical examinations. Methods: Quantitative, line-by-line analysis of the preparatory materials AMBOSS 2017 and USMLE Step 1 Lecture Notes (2017) by KAPLAN MEDICAL was performed between April and October 2017. Subjects were allocated to one of the three main fields: clinical subjects, behavioral and social science, and pharmacology. Qualitative analysis comprised binary categorization into sex- and gender-based aspects and qualification with respect to the presence of a pathophysiological explanation for the sex or gender difference. Results: In relation to the total content of AMBOSS and KAPLAN, the sex- and gender-based share of the clinical subjects content was 26.8% (±8.2) in AMBOSS and 21.1% (±10.2) in KAPLAN. The number of sex- and gender-based aspects in the behavioral and social science learning material differed significantly for AMBOSS and KAPLAN (4.4% ± 3.1% vs 10.7% ± 7.5%; P = .044). Most of the sex- and gender-related content covered sex differences. Most learning cards and texts did not include a detailed pathophysiological explanation for sex- or gender-based aspects. The knowledge provided in the preparatory documents represents only a small part of facts that are already known about sex and gender differences. Conclusions: The preparatory materials focused almost exclusively on biological sex differences and the sociocultural dimension in particular is underrepresented. A lot more evidence-based facts are known and should be integrated into the materials to reflect the importance of SGBM as an integral component of patient-centered medicine

Genetic and epigenetic contribution to complex traits

Much of the recent advances in functional genomics owe to developments in next-generation sequencing technology, which has contributed to the exponential increase of genomic data available for different human disease and population samples. With functional sequencing assays available to query both the transcriptome and the epigenome, annotation of the non-coding, regulatory genome is steadily improving and providing means to interpret the functional consequences of genetic variants associated with human complex traits. This has highlighted the need to better understand the normal variation in various cellular phenotypes, such as epigenetic modifications, and their transgenerational inheritance. In this review, we discuss different aspects of epigenetic variation in the context of DNA sequence variation and its contribution to complex phenotype

Portuguese science needs a shakeup

info:eu-repo/semantics/publishedVersio