Health informatics tools
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The Skyline ecosystem: Informatics for quantitative mass spectrometry proteomics Open
Skyline is a freely available, open‐source Windows client application for accelerating targeted proteomics experimentation, with an emphasis on the proteomics and mass spectrometry community as users and as contributors. This review covers…
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Clinical decision support systems for improving diagnostic accuracy and achieving precision medicine Open
As research laboratories and clinics collaborate to achieve precision medicine, both communities are required to understand mandated electronic health/medical record (EHR/EMR) initiatives that will be fully implemented in all clinics in th…
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Integrating pharmacogenomics into electronic health records with clinical decision support Open
The EHR with CDS is essential to curate pharmacogenomic data and disseminate patient-specific information at the point of care. As part of the successful implementation of pharmacogenomics into clinical settings, all relevant clinical reco…
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Integrated Informatics Analysis of Cancer-Related Variants Open
PURPOSE The modern researcher is confronted with hundreds of published methods to interpret genetic variants. There are databases of genes and variants, phenotype-genotype relationships, algorithms that score and rank genes, and in silico …
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Accrual to Clinical Trials (ACT): A Clinical and Translational Science Award Consortium Network Open
The Accrual to Clinical Trials (ACT) network is a federated network of sites from the National Clinical and Translational Science Award (CTSA) Consortium that has been created to significantly increase participant accrual to multi-site cli…
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The Observatory on LAkes (OLA) database: Sixty years of environmental data accessible to the public Open
Lakes are essential ecosystems that provide a large number of ecosystem services whose quality is strongly impacted by human pressures. Optimal uses of lakes require adapted management practices which in turn rely on physico-chemical and b…
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Pathway Tools version 28.0: Integrated Software for Pathway/Genome Informatics and Systems Biology Open
Pathway Tools is a bioinformatics software environment with a broad set of capabilities. The software provides genome-informatics tools such as a genome browser, sequence alignments, a genome-variant analyzer, and comparative-genomics oper…
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ftmsRanalysis: An R package for exploratory data analysis and interactive visualization of FT-MS data Open
The high-resolution and mass accuracy of Fourier transform mass spectrometry (FT-MS) has made it an increasingly popular technique for discerning the composition of soil, plant and aquatic samples containing complex mixtures of proteins, c…
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Information needs of physicians, care coordinators, and families to support care coordination of children and youth with special health care needs (CYSHCN) Open
Objectives: Identify and describe information needs and associated goals of physicians, care coordinators, and families related to coordinating care for medically complex children and youth with special health care needs (CYSHCN). Material…
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The Mass General Brigham Biobank Portal: an i2b2-based data repository linking disparate and high-dimensional patient data to support multimodal analytics Open
Objective Integrating and harmonizing disparate patient data sources into one consolidated data portal enables researchers to conduct analysis efficiently and effectively. Materials and Methods We describe an implementation of Informatics …
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Developing real‐world evidence from real‐world data: Transforming raw data into analytical datasets Open
Development of evidence‐based practice requires practice‐based evidence, which can be acquired through analysis of real‐world data from electronic health records (EHRs). The EHR contains volumes of information about patients—physical measu…
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Evaluating visual analytics for health informatics applications: a systematic review from the American Medical Informatics Association Visual Analytics Working Group Task Force on Evaluation Open
Objective This article reports results from a systematic literature review related to the evaluation of data visualizations and visual analytics technologies within the health informatics domain. The review aims to (1) characterize the var…
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Predicting the Functional Impact of KCNQ1 Variants of Unknown Significance Open
Background— An emerging standard-of-care for long-QT syndrome uses clinical genetic testing to identify genetic variants of the KCNQ1 potassium channel. However, interpreting results from genetic testing is confounded by the presence of va…
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Disseminating Metaproteomic Informatics Capabilities and Knowledge Using the Galaxy-P Framework Open
The impact of microbial communities, also known as the microbiome, on human health and the environment is receiving increased attention. Studying translated gene products (proteins) and comparing metaproteomic profiles may elucidate how mi…
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LipidFinder: A computational workflow for discovery of lipids identifies eicosanoid-phosphoinositides in platelets Open
Accurate and high-quality curation of lipidomic datasets generated from plasma, cells, or tissues is becoming essential for cell biology investigations and biomarker discovery for personalized medicine. However, a major challenge lies in r…
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Checklist for early recognition and treatment of acute illness: International collaboration to improve critical care practice Open
Processes to ensure world-wide best-practice for critical care delivery are likely to minimize preventable death, disability and costly complications for any healthcare system’s sickest patients, but no large-scale efforts have so far been…
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Antibodyomics: bioinformatics technologies for understanding B‐cell immunity to <span>HIV</span>‐1 Open
Summary Numerous antibodies have been identified from HIV ‐1‐infected donors that neutralize diverse strains of HIV ‐1. These antibodies may provide the basis for a B cell‐mediated HIV ‐1 vaccine. However, it has been unclear how to elicit…
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Collaborative, Multidisciplinary Evaluation of Cancer Variants Through Virtual Molecular Tumor Boards Informs Local Clinical Practices Open
PURPOSE The cancer research community is constantly evolving to better understand tumor biology, disease etiology, risk stratification, and pathways to novel treatments. Yet the clinical cancer genomics field has been hindered by redundant…
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Clinical informatics accelerates health system adaptation to the COVID-19 pandemic: examples from Colorado Open
Objective Large health systems responding to the coronavirus disease 2019 (COVID-19) pandemic face a broad range of challenges; we describe 14 examples of innovative and effective informatics interventions. Materials and Methods A team of …
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A mouse informatics platform for phenotypic and translational discovery Open
The International Mouse Phenotyping Consortium (IMPC) is providing the world's first functional catalogue of a mammalian genome by characterising a knockout mouse strain for every gene. A robust and highly structured informatics platform h…
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An Accessible Proteogenomics Informatics Resource for Cancer Researchers Open
Proteogenomics has emerged as a valuable approach in cancer research, which integrates genomic and transcriptomic data with mass spectrometry–based proteomics data to directly identify expressed, variant protein sequences that may have fun…
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Undergraduate Biocuration: Developing Tomorrow's Researchers While Mining Today's Data. Open
Biocuration is a time-intensive process that involves extraction, transcription, and organization of biological or clinical data from disjointed data sets into a user-friendly database. Curated data is subsequently used primarily for text …
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An Untargeted Metabolomics Workflow that Scales to Thousands of Samples for Population-Based Studies Open
The success of precision medicine relies upon collecting data from many individuals at the population level. Although advancing technologies have made such large-scale studies increasingly feasible in some disciplines such as genomics, the…
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Staring into the void: demystifying microbial metabolomics Open
Metabolites give us a window into the chemistry of microbes and are split into two subclasses: primary and secondary. Primary metabolites are required for life whereas secondary metabolites have historically been classified as those appear…
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LesionTracker: Extensible Open-Source Zero-Footprint Web Viewer for Cancer Imaging Research and Clinical Trials Open
Oncology clinical trials have become increasingly dependent upon image-based surrogate endpoints for determining patient eligibility and treatment efficacy. As therapeutics have evolved and multiplied in number, the tumor metrics criteria …
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Omics AnalySIs System for PRecision Oncology (OASISPRO): a web-based omics analysis tool for clinical phenotype prediction Open
Summary Precision oncology is an approach that accounts for individual differences to guide cancer management. Omics signatures have been shown to predict clinical traits for cancer patients. However, the vast amount of omics information p…
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Orders- Versus Encounters-Based Image Capture: Implications Pre- and Post-Procedure Workflow, Technical and Build Capabilities, Resulting, Analytics and Revenue Capture: HIMSS-SIIM Collaborative White Paper Open
The decision to implement an orders-based versus an encounters-based imaging workflow poses various implications to image capture and storage. The impacts include workflows before and after an imaging procedure, electronic health record bu…
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CGPE: an integrated online server for <i>C</i>ancer <i>G</i>ene and <i>P</i>athway <i>E</i>xploration Open
Summary Cancer Gene and Pathway Explorer (CGPE) is developed to guide biological and clinical researchers, especially those with limited informatics and programming skills, performing preliminary cancer-related biomedical research using tr…
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The Stanford Medicine data science ecosystem for clinical and translational research Open
Objective To describe the infrastructure, tools, and services developed at Stanford Medicine to maintain its data science ecosystem and research patient data repository for clinical and translational research. Materials and Methods The dat…
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Sleep and circadian informatics data harmonization: a workshop report from the Sleep Research Society and Sleep Research Network Open
The increasing availability and complexity of sleep and circadian data are equally exciting and challenging. The field is in constant technological development, generating better high-resolution physiological and molecular data than ever b…