Profiling risk factors for chronic uveitis in juvenile idiopathic arthritis: a new model for EHR-based research.

BackgroundJuvenile idiopathic arthritis is the most common rheumatic disease in children. Chronic uveitis is a common and serious comorbid condition of juvenile idiopathic arthritis, with insidious presentation and potential to cause blindness. Knowledge of clinical associations will improve risk stratification. Based on clinical observation, we hypothesized that allergic conditions are associated with chronic uveitis in juvenile idiopathic arthritis patients.MethodsThis study is a retrospective cohort study using Stanford's clinical data warehouse containing data from Lucile Packard Children's Hospital from 2000-2011 to analyze patient characteristics associated with chronic uveitis in a large juvenile idiopathic arthritis cohort. Clinical notes in patients under 16 years of age were processed via a validated text analytics pipeline. Bivariate-associated variables were used in a multivariate logistic regression adjusted for age, gender, and race. Previously reported associations were evaluated to validate our methods. The main outcome measure was presence of terms indicating allergy or allergy medications use overrepresented in juvenile idiopathic arthritis patients with chronic uveitis. Residual text features were then used in unsupervised hierarchical clustering to compare clinical text similarity between patients with and without uveitis.ResultsPreviously reported associations with uveitis in juvenile idiopathic arthritis patients (earlier age at arthritis diagnosis, oligoarticular-onset disease, antinuclear antibody status, history of psoriasis) were reproduced in our study. Use of allergy medications and terms describing allergic conditions were independently associated with chronic uveitis. The association with allergy drugs when adjusted for known associations remained significant (OR 2.54, 95% CI 1.22-5.4).ConclusionsThis study shows the potential of using a validated text analytics pipeline on clinical data warehouses to examine practice-based evidence for evaluating hypotheses formed during patient care. Our study reproduces four known associations with uveitis development in juvenile idiopathic arthritis patients, and reports a new association between allergic conditions and chronic uveitis in juvenile idiopathic arthritis patients

Addendum to Informatics for Health 2017: Advancing both science and practice

This article presents presentation and poster abstracts that were mistakenly omitted from the original publication

TLAD 2010 Proceedings:8th international workshop on teaching, learning and assesment of databases (TLAD)

This is the eighth in the series of highly successful international workshops on the Teaching, Learning and Assessment of Databases (TLAD 2010), which once again is held as a workshop of BNCOD 2010 - the 27th International Information Systems Conference. TLAD 2010 is held on the 28th June at the beautiful Dudhope Castle at the Abertay University, just before BNCOD, and hopes to be just as successful as its predecessors.The teaching of databases is central to all Computing Science, Software Engineering, Information Systems and Information Technology courses, and this year, the workshop aims to continue the tradition of bringing together both database teachers and researchers, in order to share good learning, teaching and assessment practice and experience, and further the growing community amongst database academics. As well as attracting academics from the UK community, the workshop has also been successful in attracting academics from the wider international community, through serving on the programme committee, and attending and presenting papers.This year, the workshop includes an invited talk given by Richard Cooper (of the University of Glasgow) who will present a discussion and some results from the Database Disciplinary Commons which was held in the UK over the academic year. Due to the healthy number of high quality submissions this year, the workshop will also present seven peer reviewed papers, and six refereed poster papers. Of the seven presented papers, three will be presented as full papers and four as short papers. These papers and posters cover a number of themes, including: approaches to teaching databases, e.g. group centered and problem based learning; use of novel case studies, e.g. forensics and XML data; techniques and approaches for improving teaching and student learning processes; assessment techniques, e.g. peer review; methods for improving students abilities to develop database queries and develop E-R diagrams; and e-learning platforms for supporting teaching and learning

TLAD 2010 Proceedings:8th international workshop on teaching, learning and assesment of databases (TLAD)

This is the eighth in the series of highly successful international workshops on the Teaching, Learning and Assessment of Databases (TLAD 2010), which once again is held as a workshop of BNCOD 2010 - the 27th International Information Systems Conference. TLAD 2010 is held on the 28th June at the beautiful Dudhope Castle at the Abertay University, just before BNCOD, and hopes to be just as successful as its predecessors.The teaching of databases is central to all Computing Science, Software Engineering, Information Systems and Information Technology courses, and this year, the workshop aims to continue the tradition of bringing together both database teachers and researchers, in order to share good learning, teaching and assessment practice and experience, and further the growing community amongst database academics. As well as attracting academics from the UK community, the workshop has also been successful in attracting academics from the wider international community, through serving on the programme committee, and attending and presenting papers.This year, the workshop includes an invited talk given by Richard Cooper (of the University of Glasgow) who will present a discussion and some results from the Database Disciplinary Commons which was held in the UK over the academic year. Due to the healthy number of high quality submissions this year, the workshop will also present seven peer reviewed papers, and six refereed poster papers. Of the seven presented papers, three will be presented as full papers and four as short papers. These papers and posters cover a number of themes, including: approaches to teaching databases, e.g. group centered and problem based learning; use of novel case studies, e.g. forensics and XML data; techniques and approaches for improving teaching and student learning processes; assessment techniques, e.g. peer review; methods for improving students abilities to develop database queries and develop E-R diagrams; and e-learning platforms for supporting teaching and learning

An ontology to standardize research output of nutritional epidemiology : from paper-based standards to linked content

Background: The use of linked data in the Semantic Web is a promising approach to add value to nutrition research. An ontology, which defines the logical relationships between well-defined taxonomic terms, enables linking and harmonizing research output. To enable the description of domain-specific output in nutritional epidemiology, we propose the Ontology for Nutritional Epidemiology (ONE) according to authoritative guidance for nutritional epidemiology. Methods: Firstly, a scoping review was conducted to identify existing ontology terms for reuse in ONE. Secondly, existing data standards and reporting guidelines for nutritional epidemiology were converted into an ontology. The terms used in the standards were summarized and listed separately in a taxonomic hierarchy. Thirdly, the ontologies of the nutritional epidemiologic standards, reporting guidelines, and the core concepts were gathered in ONE. Three case studies were included to illustrate potential applications: (i) annotation of existing manuscripts and data, (ii) ontology-based inference, and (iii) estimation of reporting completeness in a sample of nine manuscripts. Results: Ontologies for food and nutrition (n = 37), disease and specific population (n = 100), data description (n = 21), research description (n = 35), and supplementary (meta) data description (n = 44) were reviewed and listed. ONE consists of 339 classes: 79 new classes to describe data and 24 new classes to describe the content of manuscripts. Conclusion: ONE is a resource to automate data integration, searching, and browsing, and can be used to assess reporting completeness in nutritional epidemiology

A visual and curatorial approach to clinical variant prioritization and disease gene discovery in genome-wide diagnostics

Background: Genome-wide data are increasingly important in the clinical evaluation of human disease. However, the large number of variants observed in individual patients challenges the efficiency and accuracy of diagnostic review. Recent work has shown that systematic integration of clinical phenotype data with genotype information can improve diagnostic workflows and prioritization of filtered rare variants. We have developed visually interactive, analytically transparent analysis software that leverages existing disease catalogs, such as the Online Mendelian Inheritance in Man database (OMIM) and the Human Phenotype Ontology (HPO), to integrate patient phenotype and variant data into ranked diagnostic alternatives. Methods: Our tool, “OMIM Explorer” (http://www.omimexplorer.com), extends the biomedical application of semantic similarity methods beyond those reported in previous studies. The tool also provides a simple interface for translating free-text clinical notes into HPO terms, enabling clinical providers and geneticists to contribute phenotypes to the diagnostic process. The visual approach uses semantic similarity with multidimensional scaling to collapse high-dimensional phenotype and genotype data from an individual into a graphical format that contextualizes the patient within a low-dimensional disease map. The map proposes a differential diagnosis and algorithmically suggests potential alternatives for phenotype queries—in essence, generating a computationally assisted differential diagnosis informed by the individual’s personal genome. Visual interactivity allows the user to filter and update variant rankings by interacting with intermediate results. The tool also implements an adaptive approach for disease gene discovery based on patient phenotypes. Results: We retrospectively analyzed pilot cohort data from the Baylor Miraca Genetics Laboratory, demonstrating performance of the tool and workflow in the re-analysis of clinical exomes. Our tool assigned to clinically reported variants a median rank of 2, placing causal variants in the top 1 % of filtered candidates across the 47 cohort cases with reported molecular diagnoses of exome variants in OMIM Morbidmap genes. Our tool outperformed Phen-Gen, eXtasy, PhenIX, PHIVE, and hiPHIVE in the prioritization of these clinically reported variants. Conclusions: Our integrative paradigm can improve efficiency and, potentially, the quality of genomic medicine by more effectively utilizing available phenotype information, catalog data, and genomic knowledge

BlogForever D2.6: Data Extraction Methodology

This report outlines an inquiry into the area of web data extraction, conducted within the context of blog preservation. The report reviews theoretical advances and practical developments for implementing data extraction. The inquiry is extended through an experiment that demonstrates the effectiveness and feasibility of implementing some of the suggested approaches. More specifically, the report discusses an approach based on unsupervised machine learning that employs the RSS feeds and HTML representations of blogs. It outlines the possibilities of extracting semantics available in blogs and demonstrates the benefits of exploiting available standards such as microformats and microdata. The report proceeds to propose a methodology for extracting and processing blog data to further inform the design and development of the BlogForever platform