On adopting Ontology Alignment techniques within the Phenotype Acquisition Process

The work presented in this paper is framed within the context of the BigMed project, aproject funded by the Norwegian Research Council. One of the objectives of BigMed isto enhance the phenotype acquisition process in newborns with a monogenetic disorder,one of the four patient groups studied in the project. The use of the Human PhenotypeOntology (HPO) [1] to tag phenotypes and systems like PhenoTips have substantiallycontributed to the overall phenotype acquisition workflow. PhenoTips [2] is a systemfor the acquisition of phenotypic information in patients with a genetic disease. Phe-noTips also suggests, given a selected set of HPO terms, candidate diagnoses usingOMIM (Online Mendelian Inheritance in Man) codes, and related genes for a subse-quent genetic test. Although PhenoTips represents a fantastic effort, we believe it couldbe extended with suitable Semantic Web solutions. In this paper, we present the firststeps to adopt ontology alignment techniques to contribute to the diagnostic process

Finding Data Should be Easier than Finding Oil

The competitiveness of modern enterprises heavily depends on their ability to make the right business decisions by relying on efficient and timely analysis of the right business critical data. In large and data intensive companies such as Equinor, a Norwegian multinational oil and gas company with more than 20,000 employees, gathering such data is not a trivial task due to the growing size and complexity of corporate information sources. As a result, the data gathering task is often the most time-consuming part of the decision making process, in particular when it comes to the work processes of Equinor's exploration geologists that should find in a timely manner new exploitable accumulations of oil or gas in given areas by analysing data about these areas. In this work we present our experience in addressing this data challenge tast at Equinor. We have developed and deployed at Equinor a semantic data access system that relies on the Ontology Based Data Access (OBDA) approach. Our system is based on our solid theoretical contributions and has been extensively evaluated at Equinor

Matching disease and phenotype ontologies in the ontology alignment evaluation initiative

Background: The disease and phenotype track was designed to evaluate the relative performance of ontology matching systems that generate mappings between source ontologies. Disease and phenotype ontologies are important for applications such as data mining, data integration and knowledge management to support translational science in drug discovery and understanding the genetics of disease. Results: Eleven systems (out of 21 OAEI participating systems) were able to cope with at least one of the tasks in the Disease and Phenotype track. AML, FCA-Map, LogMap(Bio) and PhenoMF systems produced the top results for ontology matching in comparison to consensus alignments. The results against manually curated mappings proved to be more difficult most likely because these mapping sets comprised mostly subsumption relationships rather than equivalence. Manual assessment of unique equivalence mappings showed that AML, LogMap(Bio) and PhenoMF systems have the highest precision results. Conclusions: Four systems gave the highest performance for matching disease and phenotype ontologies. These systems coped well with the detection of equivalence matches, but struggled to detect semantic similarity. This deserves more attention in the future development of ontology matching systems. The findings of this evaluation show that such systems could help to automate equivalence matching in the workflow of curators, who maintain ontology mapping services in numerous domains such as disease and phenotype

Optique: Zooming in on Big Data

Despite the dramatic growth of data accumulated by enterprises, obtaining value out of it is extremely challenging. In particular, the data access bottleneck prevents domain experts from getting the right piece of data within a constrained time frame. The Optique Platform unlocks the access to Big Data by providing end users support for directly formulating their information needs through an intuitive visual query interface. The submitted query is then transformed into highly optimized queries over the data sources, which may include streaming data, and exploiting massive parallelism in the backend whenever possible. The Optique Platform thus responds to one major challenge posed by Big Data in data-intensive industrial settings

Ontology Based Data Access in Statoil

Ontology Based Data Access (OBDA) is a prominent approach to query databases which uses an ontology to expose data in a conceptually clear manner by abstracting away from the technical schema-level details of the underlying data. The ontology is ‘connected’ to the data via mappings that allow to automatically translate queries posed over the ontology into data-level queries that can be executed by the underlying database management system. Despite a lot of attention from the research community, there are still few instances of real world industrial use of OBDA systems. In this work we present data access challenges in the data-intensive petroleum company Statoil and our experience in addressing these challenges with OBDA technology. In particular, we have developed a deployment module to create ontologies and mappings from relational databases in a semi-automatic fashion; a query processing module to perform and optimise the process of translating ontological queries into data queries and their execution over either a single DB of federated DBs; and a query formulation module to support query construction for engineers with a limited IT background. Our modules have been integrated in one OBDA system, deployed at Statoil, integrated with Statoil’s infrastructure, and evaluated with Statoil’s engineers and data

Body size and thyroid cancer in two million Norwegian men and women

We investigated relations between measured body mass index (BMI) and stature and thyroid cancer (3046 cases) in a large Norwegian cohort of more than two million individuals. The risk of thyroid cancer, especially of the papillary and follicular types, increased moderately with increasing BMI and height in both sexes

International variation in prescribing antihypertensive drugs: Its extent and possible explanations

BACKGROUND: Inexpensive antihypertensive drugs are at least as effective and safe as more expensive drugs. Overuse of newer, more expensive antihypertensive drugs is a poor use of resources. The potential savings are substantial, but vary across countries, in large part due to differences in prescribing patterns. We wanted to describe prescribing patterns of antihypertensive drugs in ten countries and explore possible reasons for inter-country variation. METHODS: National prescribing profiles were determined based on information on sales and indications for prescribing. We sent a questionnaire to academics and drug regulatory agencies in Canada, France, Germany, UK, US and the Nordic countries, asking about explanations for differences in prescribing patterns in their country compared with the other countries. We also conducted telephone interviews with medical directors of drug companies in the UK and Norway, the countries with the largest differences in prescribing patterns. RESULTS: There is considerable variation in prescribing patterns. In the UK thiazides account for 25% of consumption, while the corresponding figure for Norway is 6%. In Norway alpha-blocking agents account for 8% of consumption, which is more than twice the percentage found in any of the other countries. Suggested factors to explain inter-country variation included reimbursement policies, traditions, opinion leaders with conflicts of interests, domestic pharmaceutical production, and clinical practice guidelines. The medical directors also suggested hypotheses that: Norwegian physicians are early adopters of new interventions while the British are more conservative; there are many clinical trials conducted in Norway involving many general practitioners; there is higher cost-awareness among physicians in the UK, in part due to fund holding; and there are publicly funded pharmaceutical advisors in the UK. CONCLUSION: Two compelling explanations the variation in prescribing that warrant further investigation are the promotion of less-expensive drugs by pharmaceutical advisors in UK and the promotion of more expensive drugs through "seeding trials" in Norway

Periprandial changes of the sympathetic–parasympathetic balance related to perceived satiety in humans

Food intake regulation involves various central and peripheral mechanisms. In this study the relevance of physiological responses reflecting the autonomic nervous system were evaluated in relation to perceived satiety. Subjects were exposed to a lunch-induced hunger-satiety shift, while profiling diverse sensory, physiological, and biochemical characteristics at 15 min intervals. Sensory ratings comprised questionnaires with visual analogues scales about their feeling of satiety, desire to eat, fullness, and hunger. Physiological characteristics included heart rate, heart rate variability, and blood pressure, while biochemical markers such as cortisol levels and α-amylase activity were monitored in saliva. The four sensory ratings correlated with heart rate and salivary α-amylase suggesting a higher sympathetic tone during satiety. Furthermore, heart rate variability was associated with age and waist-to-hip ratio and cortisol levels negatively correlated with body mass index. Finally, neither chewing nor swallowing contributed to a heart rate increase at food consumption, but orosensory stimulation, as tested with modified sham feeding, caused a partial increase of heart rate. In conclusion, after meal ingestion critical physiological alterations reveal a elevated sympathetic tone, which is a potential measure of satiety

Morbidity, Including Fatal Morbidity, throughout Life in Men Entering Adult Life as Obese

Background: The association between obesity in adults and excess morbidity and mortality is well established, but the health impact throughout adult life of being obese in early adulthood needs elucidation. We investigated somatic morbidity, including fatal morbidity, throughout adulthood in men starting adult life as obese. Methods: Among 362,200 Danish young men, examined for military service between 1943 and 1977, all obese (defined as BMI$31.0 kg/m 2), and, as controls, a random 1 % sample of the others was identified. In the age range of 18–25 years, there were 1,862 obese, which encompass the men above the 99.5 percentile, and 3,476 controls. Information on morbidity was obtained via national registers. Cox regression models were used to estimate the relative morbidity assessed as first incidence of disease, occurrence of disease in the year preceding death and prevalent disease at time of death. Results: From age 18 through 80 years the obese had an increased risk of becoming diseased by or die from a broad range of diseases. Generally, the incidence of first event, occurrence in the year prior to death, and prevalence at time of death showed the same pattern. As an example, the relative hazard of type 2 diabetes was constant throughout life at 4.9 (95% confidence intervals [CI]: 4.1–5.9), 5.2 (95 % CI: 3.6–7.5), and 6.8 (95 % CI: 4.6–10.1), respectively. Conclusions: Our findings strongly support the continued need to avoid beginning adult life as obese, as obese young me