Establishment of a integrative multi-omics expression database CKDdb in the context of chronic kidney disease (CKD)

Complex human traits such as chronic kidney disease (CKD) are a major health and financial burden in modern societies. Currently, the description of the CKD onset and progression at the molecular level is still not fully understood. Meanwhile, the prolific use of high-throughput omic technologies in disease biomarker discovery studies yielded a vast amount of disjointed data that cannot be easily collated. Therefore, we aimed to develop a molecule-centric database featuring CKD-related experiments from available literature publications. We established the Chronic Kidney Disease database CKDdb, an integrated and clustered information resource that covers multi-omic studies (microRNAs, genomics, peptidomics, proteomics and metabolomics) of CKD and related disorders by performing literature data mining and manual curation. The CKDdb database contains differential expression data from 49395 molecule entries (redundant), of which 16885 are unique molecules (non-redundant) from 377 manually curated studies of 230 publications. This database was intentionally built to allow disease pathway analysis through a systems approach in order to yield biological meaning by integrating all existing information and therefore has the potential to unravel and gain an in-depth understanding of the key molecular events that modulate CKD pathogenesis

Identifying Gene-Gene Interactions that are Highly Associated with Body Mass Index Using Quantitative Multifactor Dimensionality Reduction (QMDR)

Despite heritability estimates of 40–70% for obesity, less than 2% of its variation is explained by Body Mass Index (BMI) associated loci that have been identified so far. Epistasis, or gene-gene interactions are a plausible source to explain portions of the missing heritability of BMI. Using genotypic data from 18,686 individuals across five study cohorts – ARIC, CARDIA, FHS, CHS, MESA – we filtered SNPs (Single Nucleotide Polymorphisms) using two parallel approaches. SNPs were filtered either on the strength of their main effects of association with BMI, or on the number of knowledge sources supporting a specific SNP-SNP interaction in the context of BMI. Filtered SNPs were specifically analyzed for interactions that are highly associated with BMI using QMDR (Quantitative Multifactor Dimensionality Reduction). QMDR is a nonparametric, genetic model-free method that detects non-linear interactions associated with a quantitative trait

Knowledge-based Biomedical Data Science 2019

Knowledge-based biomedical data science (KBDS) involves the design and implementation of computer systems that act as if they knew about biomedicine. Such systems depend on formally represented knowledge in computer systems, often in the form of knowledge graphs. Here we survey the progress in the last year in systems that use formally represented knowledge to address data science problems in both clinical and biological domains, as well as on approaches for creating knowledge graphs. Major themes include the relationships between knowledge graphs and machine learning, the use of natural language processing, and the expansion of knowledge-based approaches to novel domains, such as Chinese Traditional Medicine and biodiversity.Comment: Manuscript 43 pages with 3 tables; Supplemental material 43 pages with 3 table

Structuring research methods and data with the research object model:genomics workflows as a case study

Background: One of the main challenges for biomedical research lies in the computer-assisted integrative study of large and increasingly complex combinations of data in order to understand molecular mechanisms. The preservation of the materials and methods of such computational experiments with clear annotations is essential for understanding an experiment, and this is increasingly recognized in the bioinformatics community. Our assumption is that offering means of digital, structured aggregation and annotation of the objects of an experiment will provide necessary meta-data for a scientist to understand and recreate the results of an experiment. To support this we explored a model for the semantic description of a workflow-centric Research Object (RO), where an RO is defined as a resource that aggregates other resources, e. g., datasets, software, spreadsheets, text, etc. We applied this model to a case study where we analysed human metabolite variation by workflows. Results: We present the application of the workflow-centric RO model for our bioinformatics case study. Three workflows were produced following recently defined Best Practices for workflow design. By modelling the experiment as an RO, we were able to automatically query the experiment and answer questions such as "which particular data was input to a particular workflow to test a particular hypothesis?", and "which particular conclusions were drawn from a particular workflow?". Conclusions: Applying a workflow-centric RO model to aggregate and annotate the resources used in a bioinformatics experiment, allowed us to retrieve the conclusions of the experiment in the context of the driving hypothesis, the executed workflows and their input data. The RO model is an extendable reference model that can be used by other systems as well. Availability: The Research Object is available at http://www.myexperiment.org/packs/428 The Wf4Ever Research Object Model is available at http://wf4ever.github.io/r

Mining User-generated Content of Mobile Patient Portal: Dimensions of User Experience

Patient portals are positioned as a central component of patient engagement through the potential to change the physician-patient relationship and enable chronic disease self-management. The incorporation of patient portals provides the promise to deliver excellent quality, at optimized costs, while improving the health of the population. This study extends the existing literature by extracting dimensions related to the Mobile Patient Portal Use. We use a topic modeling approach to systematically analyze users’ feedback from the actual use of a common mobile patient portal, Epic\u27s MyChart. Comparing results of Latent Dirichlet Allocation analysis with those of human analysis validated the extracted topics. Practically, the results provide insights into adopting mobile patient portals, revealing opportunities for improvement and to enhance the design of current basic portals. Theoretically, the findings inform the social-technical systems and Task-Technology Fit theories in the healthcare field and emphasize important healthcare structural and social aspects. Further, findings inform the humanization of healthcare framework, support the results of existing studies, and introduce new important design dimensions (i.e., aspects) that influence patient satisfaction and adherence to patient portal

Mining User-generated Content of Mobile Patient Portal: Dimensions of User Experience

Patient portals are positioned as a central component of patient engagement through the potential to change the physician-patient relationship and enable chronic disease self-management. The incorporation of patient portals provides the promise to deliver excellent quality, at optimized costs, while improving the health of the population. This study extends the existing literature by extracting dimensions related to the Mobile Patient Portal Use. We use a topic modeling approach to systematically analyze users’ feedback from the actual use of a common mobile patient portal, Epic’s MyChart. Comparing results of Latent Dirichlet Allocation analysis with those of human analysis validated the extracted topics. Practically, the results provide insights into adopting mobile patient portals, revealing opportunities for improvement and to enhance the design of current basic portals. Theoretically, the findings inform the social-technical systems and Task-Technology Fit theories in the healthcare field and emphasize important healthcare structural and social aspects. Further, findings inform the humanization of healthcare framework, support the results of existing studies, and introduce new important design dimensions (i.e., aspects) that influence patient satisfaction and adherence to patient portal