Project description:The PDBe aggregated API is an open-access and open-source RESTful API that provides programmatic access to a wealth of macromolecular structural data and their functional and biophysical annotations through 80+ API endpoints. The API is powered by the PDBe graph database (https://pdbe.org/graph-schema), an open-access integrative knowledge graph that can be used as a discovery tool to answer complex biological questions. The PDBe aggregated API provides up-to-date access to the PDBe graph database, which has weekly releases with the latest data from the Protein Data Bank, integrated with updated annotations from UniProt, Pfam, CATH, SCOP and the PDBe-KB partner resources. The complete list of all the available API endpoints and their descriptions are available at https://pdbe.org/graph-api. The source code of the Python 3.6+ API application is publicly available at https://gitlab.ebi.ac.uk/pdbe-kb/services/pdbe-graph-api. Supplementary data are available at Bioinformatics online.
Project description:The Office of National Coordinator for Health Information Technology final rule implementing the interoperability and information blocking provisions of the 21st Century Cures Act requires support for two SMART (Substitutable Medical Applications, Reusable Technologies) application programming interfaces (APIs) and instantiates Health Level Seven International (HL7) Fast Healthcare Interoperability Resources (FHIR) as a lingua franca for health data. We sought to assess the current state and near-term plans for the SMART/HL7 Bulk FHIR Access API implementation across organizations including electronic health record vendors, cloud vendors, public health contractors, research institutions, payors, FHIR tooling developers, and other purveyors of health information technology platforms. We learned that many organizations not required through regulation to use standardized bulk data are rapidly implementing the API for a wide array of use cases. This may portend an unprecedented level of standardized population-level health data exchange that will support an apps and analytics ecosystem. Feedback from early adopters on the API's limitations and unsolved problems in the space of population health are highlighted.
Project description:The inconsistency of polymer indexing caused by the lack of uniformity in expression of polymer names is a major challenge for widespread use of polymer related data resources and limits broad application of materials informatics for innovation in broad classes of polymer science and polymeric based materials. The current solution of using a variety of different chemical identifiers has proven insufficient to address the challenge and is not intuitive for researchers. This work proposes a multi-algorithm-based mapping methodology entitled ChemProps that is optimized to solve the polymer indexing issue with easy-to-update design both in depth and in width. RESTful API is enabled for lightweight data exchange and easy integration across data systems. A weight factor is assigned to each algorithm to generate scores for candidate chemical names and optimized to maximize the minimum value of the score difference between the ground truth chemical name and the other candidate chemical names. Ten-fold validation is utilized on the 160 training data points to prevent overfitting issues. The obtained set of weight factors achieves a 100% test accuracy on the 54 test data points. The weight factors will evolve as ChemProps grows. With ChemProps, other polymer databases can remove duplicate entries and enable a more accurate "search by SMILES" function by using ChemProps as a common name-to-SMILES translator through API calls. ChemProps is also an excellent tool for auto-populating polymer properties thanks to its easy-to-update design.
Project description:BackgroundThe Medicare Rural Hospital Flexibility Program of the 1997 Balanced Budget Act allowed hospitals meeting certain criteria to convert to critical access hospitals (CAH) and changed their Medicare reimbursement mechanism from prospective payment system (PPS) to cost-based.ObjectiveTo examine the impact of CAH conversion on hospital patient safety.Data sourceSecondary data on hospital patient safety indicators (PSIs), hospital CAH status, patient case-mix, and market variables, for 89 Iowa rural hospitals during 1997-2004.Study designWe employed quasi-experimental designs that use both control groups and pretests. The hospital-year was the unit of analysis. We used generalized estimating equations logit and random-effects Tobit models to assess the effects of CAH conversion on hospital patient safety. The models were adjusted for patient case-mix and market variables. Sensitivity analyses, which varied by sample and statistical model, were used to examine the robustness of our findings.Data extraction methodsPSIs were computed from Iowa State Inpatient Databases (SIDs) using Agency for Healthcare Research and Quality indicators software. Hospital CAH status was extracted from Iowa Hospital Association. Patient case-mix variables were extracted from Iowa SIDs. Market variables came from Area Resource File (ARF).Principal findingsCAH conversion in Iowa rural hospitals was associated with better performance of risk-adjusted rates of iatrogenic pneumothorax, selected infections due to medical care, accidental puncture or laceration, and composite score of four PSIs, but had no significant impact on the observed rates of death in low-mortality diagnosis-related groups (DRGs), foreign body left during procedure, risk-adjusted rate of decubitus ulcer, or composite score of six PSIs. Conclusion. CAH conversion is associated with enhanced performance of certain PSIs.
Project description:VIPERdb (http://viperdb.scripps.edu) is a relational database and a web portal for icosahedral virus capsid structures. Our aim is to provide a comprehensive resource specific to the needs of the virology community, with an emphasis on the description and comparison of derived data from structural and computational analyses of the virus capsids. In the current release, VIPERdb(2), we implemented a useful and novel method to represent capsid protein residues in the icosahedral asymmetric unit (IAU) using azimuthal polar orthographic projections, otherwise known as Phi-Psi (Phi-Psi) diagrams. In conjunction with a new Application Programming Interface (API), these diagrams can be used as a dynamic interface to the database to map residues (categorized as surface, interface and core residues) and identify family wide conserved residues including hotspots at the interfaces. Additionally, we enhanced the interactivity with the database by interfacing with web-based tools. In particular, the applications Jmol and STRAP were implemented to visualize and interact with the virus molecular structures and provide sequence-structure alignment capabilities. Together with extended curation practices that maintain data uniformity, a relational database implementation based on a schema for macromolecular structures and the APIs provided will greatly enhance the ability to do structural bioinformatics analysis of virus capsids.
Project description:BackgroundPatient access to electronic health records (EHRs) is associated with increased patient engagement and health care quality outcomes. However, the adoption of patient portals and personal health records (PHRs) that facilitate this access is impeded by barriers. The Clinical Adoption Framework (CAF) has been developed to analyze EHR adoption, but this framework does not consider the patient as an end-user.ObjectiveWe aim to extend the scope of the CAF to patient access to EHRs, develop guidance documentation for the application of the CAF, and assess the interrater reliability.MethodsWe systematically reviewed existing systematic reviews on patients' access to EHRs and PHRs. Results of each review were mapped to one of the 43 CAF categories. Categories were iteratively adapted when needed. We measured the interrater reliability with Cohen's unweighted kappa and statistics regarding the agreement among reviewers on mapping quotes of the reviews to different CAF categories.ResultsWe further defined the framework's inclusion and exclusion criteria for 33 of the 43 CAF categories and achieved a moderate agreement among the raters, which varied between categories.ConclusionsIn the reviews, categories about people, organization, system quality, system use, and the net benefits of system use were addressed more often than those about international and regional information and communication technology infrastructures, standards, politics, incentive programs, and social trends. Categories that were addressed less might have been underdefined in this study. The guidance documentation we developed can be applied to systematic literature reviews and implementation studies, patient and informal caregiver access to EHRs, and the adoption of PHRs.
Project description:Recent advancements in technology and methodology have led to growing amounts of increasingly complex neuroscience data recorded from various species, modalities, and levels of study. The rapid data growth has made efficient data access and flexible, machine-readable data annotation a crucial requisite for neuroscientists. Clear and consistent annotation and organization of data is not only an important ingredient for reproducibility of results and re-use of data, but also essential for collaborative research and data sharing. In particular, efficient data management and interoperability requires a unified approach that integrates data and metadata and provides a common way of accessing this information. In this paper we describe GNData, a data management platform for neurophysiological data. GNData provides a storage system based on a data representation that is suitable to organize data and metadata from any electrophysiological experiment, with a functionality exposed via a common application programming interface (API). Data representation and API structure are compatible with existing approaches for data and metadata representation in neurophysiology. The API implementation is based on the Representational State Transfer (REST) pattern, which enables data access integration in software applications and facilitates the development of tools that communicate with the service. Client libraries that interact with the API provide direct data access from computing environments like Matlab or Python, enabling integration of data management into the scientist's experimental or analysis routines.
Project description:The Open Databases Integration for Materials Design (OPTIMADE) consortium has designed a universal application programming interface (API) to make materials databases accessible and interoperable. We outline the first stable release of the specification, v1.0, which is already supported by many leading databases and several software packages. We illustrate the advantages of the OPTIMADE API through worked examples on each of the public materials databases that support the full API specification.
Project description:BackgroundDigital medicine and smartphone-enabled health technologies provide a novel source of human health and human biology data. However, in part due to its intricacies, few methods have been established to analyze and interpret data in this domain. We previously conducted a six-month interventional trial examining the efficacy of a comprehensive smartphone-based health monitoring program for individuals with chronic disease. This included 38 individuals with hypertension who recorded 6,290 blood pressure readings over the trial.MethodsIn the present study, we provide a hypothesis testing framework for unstructured time series data, typical of patient-generated mobile device data. We used a mixed model approach for unequally spaced repeated measures using autoregressive and generalized autoregressive models, and applied this to the blood pressure data generated in this trial.ResultsWe were able to detect, roughly, a 2 mmHg decrease in both systolic and diastolic blood pressure over the course of the trial despite considerable intra- and inter-individual variation. Furthermore, by supplementing this finding by using a sequential analysis approach, we observed this result over three months prior to the official study end-highlighting the effectiveness of leveraging the digital nature of this data source to form timely conclusions.ConclusionsHealth data generated through the use of smartphones and other mobile devices allow individuals the opportunity to make informed health decisions, and provide researchers the opportunity to address innovative health and biology questions. The hypothesis testing framework we present can be applied in future studies utilizing digital medicine technology or implemented in the technology itself to support the quantified self.