keyword
https://read.qxmd.com/read/37900350/an-approach-for-collaborative-development-of-a-federated-biomedical-knowledge-graph-based-question-answering-system-question-of-the-month-challenges
#1
JOURNAL ARTICLE
Karamarie Fecho, Chris Bizon, Tursynay Issabekova, Sierra Moxon, Anne E Thessen, Shervin Abdollahi, Sergio E Baranzini, Basazin Belhu, William E Byrd, Lawrence Chung, Andrew Crouse, Marc P Duby, Stephen Ferguson, Aleksandra Foksinska, Laura Forero, Jennifer Friedman, Vicki Gardner, Gwênlyn Glusman, Jennifer Hadlock, Kristina Hanspers, Eugene Hinderer, Charlotte Hobbs, Gregory Hyde, Sui Huang, David Koslicki, Philip Mease, Sandrine Muller, Christopher J Mungall, Stephen A Ramsey, Jared Roach, Irit Rubin, Shepherd H Schurman, Anath Shalev, Brett Smith, Karthik Soman, Sarah Stemann, Andrew I Su, Casey Ta, Paul B Watkins, Mark D Williams, Chunlei Wu, Colleen H Xu
Knowledge graphs have become a common approach for knowledge representation. Yet, the application of graph methodology is elusive due to the sheer number and complexity of knowledge sources. In addition, semantic incompatibilities hinder efforts to harmonize and integrate across these diverse sources. As part of The Biomedical Translator Consortium, we have developed a knowledge graph-based question-answering system designed to augment human reasoning and accelerate translational scientific discovery: the Translator system...
2023: Journal of Clinical and Translational Science
https://read.qxmd.com/read/37066514/evaluating-robustness-of-a-generalized-linear-model-when-applied-to-electronic-health-record-data-accessed-using-an-open-api
#2
JOURNAL ARTICLE
Priya Sharma, Perry Haaland, Ashok Krishnamurthy, Bo Lan, Patrick L Schmitt, Meghamala Sinha, Hao Xu, Karamarie Fecho
The Integrated Clinical and Environmental Exposures Service (ICEES) provides open regulatory-compliant access to clinical data, including electronic health record data, that have been integrated with environmental exposures data. While ICEES has been validated in the context of an asthma use case and several other use cases, the regulatory constraints on the ICEES open application programming interface (OpenAPI) result in data loss when using the service for multivariate analysis. In this study, we investigated the robustness of the ICEES OpenAPI through a comparative analysis, in which we applied a generalized linear model (GLM) to the OpenAPI data and the constraint-free source data to examine factors predictive of asthma exacerbations...
2023: Health Informatics Journal
https://read.qxmd.com/read/36271753/vergence-accommodative-therapy-for-symptomatic-convergence-insufficiency-in-children-time-course-of-improvements-in-convergence-function
#3
JOURNAL ARTICLE
Erin C Jenewein, Susan Cotter, Tawna Roberts, Marjean Kulp, G Lynn Mitchell, Lisa A Jones-Jordan, Angela M Chen, Kristine Hopkins, Kristine Huang, Deborah Amster, Gregory Fecho, Julie Tyler, Shivakhaami Meiyeppen, Mitchell Scheiman
PURPOSE: To evaluate the time course of improvements in clinical convergence measures for children with symptomatic convergence insufficiency treated with office-based vergence/accommodative therapy. METHODS: We evaluated convergence measures from 205, 9- to 14-year-old children with symptomatic convergence insufficiency randomised to office-based vergence/accommodative therapy in the Convergence Insufficiency Treatment Trial - Attention and Reading Trial (CITT-ART)...
October 22, 2022: Ophthalmic & Physiological Optics: the Journal of the British College of Ophthalmic Opticians (Optometrists)
https://read.qxmd.com/read/36125173/biolink-model-a-universal-schema-for-knowledge-graphs-in-clinical-biomedical-and-translational-science
#4
REVIEW
Deepak R Unni, Sierra A T Moxon, Michael Bada, Matthew Brush, Richard Bruskiewich, J Harry Caufield, Paul A Clemons, Vlado Dancik, Michel Dumontier, Karamarie Fecho, Gustavo Glusman, Jennifer J Hadlock, Nomi L Harris, Arpita Joshi, Tim Putman, Guangrong Qin, Stephen A Ramsey, Kent A Shefchek, Harold Solbrig, Karthik Soman, Anne E Thessen, Melissa A Haendel, Chris Bizon, Christopher J Mungall
Within clinical, biomedical, and translational science, an increasing number of projects are adopting graphs for knowledge representation. Graph-based data models elucidate the interconnectedness among core biomedical concepts, enable data structures to be easily updated, and support intuitive queries, visualizations, and inference algorithms. However, knowledge discovery across these "knowledge graphs" (KGs) has remained difficult. Data set heterogeneity and complexity; the proliferation of ad hoc data formats; poor compliance with guidelines on findability, accessibility, interoperability, and reusability; and, in particular, the lack of a universally accepted, open-access model for standardization across biomedical KGs has left the task of reconciling data sources to downstream consumers...
August 2022: Clinical and Translational Science
https://read.qxmd.com/read/35837616/leveraging-open-electronic-health-record-data-and-environmental-exposures-data-to-derive-insights-into-rare-pulmonary-disease
#5
JOURNAL ARTICLE
Karamarie Fecho, Stanley C Ahalt, Michael Knowles, Ashok Krishnamurthy, Margaret Leigh, Kenneth Morton, Emily Pfaff, Max Wang, Hong Yi
Research on rare diseases has received increasing attention, in part due to the realized profitability of orphan drugs. Biomedical informatics holds promise in accelerating translational research on rare disease, yet challenges remain, including the lack of diagnostic codes for rare diseases and privacy concerns that prevent research access to electronic health records when few patients exist. The Integrated Clinical and Environmental Exposures Service (ICEES) provides regulatory-compliant open access to electronic health record data that have been integrated with environmental exposures data, as well as analytic tools to explore the integrated data...
2022: Frontiers in artificial intelligence
https://read.qxmd.com/read/35611543/progress-toward-a-universal-biomedical-data-translator
#6
REVIEW
Karamarie Fecho, Anne E Thessen, Sergio E Baranzini, Chris Bizon, Jennifer J Hadlock, Sui Huang, Ryan T Roper, Noel Southall, Casey Ta, Paul B Watkins, Mark D Williams, Hao Xu, William Byrd, Vlado Dančík, Marc P Duby, Michel Dumontier, Gustavo Glusman, Nomi L Harris, Eugene W Hinderer, Greg Hyde, Adam Johs, Andrew I Su, Guangrong Qin, Qian Zhu
Clinical, biomedical, and translational science has reached an inflection point in the breadth and diversity of available data and the potential impact of such data to improve human health and well-being. However, the data are often siloed, disorganized, and not broadly accessible due to discipline-specific differences in terminology and representation. To address these challenges, the Biomedical Data Translator Consortium has developed and tested a pilot knowledge graph-based "Translator" system capable of integrating existing biomedical data sets and "translating" those data into insights intended to augment human reasoning and accelerate translational science...
May 25, 2022: Clinical and Translational Science
https://read.qxmd.com/read/35605411/nicotine-vaping-for-relaxation-and-coping-race-ethnicity-differences-and-social-connectedness-mechanisms
#7
JOURNAL ARTICLE
Candice D Donaldson, David A Stupplebeen, Cassandra L Fecho, Tiffany Ta, Xueying Zhang, Rebecca J Williams
The current study examined race- and ethnicity-based differences in the reasons that youth report for vaping, with an emphasis on understanding the relationship between race/ethnicity and vaping for relaxation and stress/anxiety coping. This work also sought to go beyond examining race-based differences as a cause of tobacco-use disparities by assessing social connectedness factors that mediate relationships between race/ethnicity and vaping for relaxation and coping. Research questions were tested using data from the 2019-2020 California Student Tobacco Survey, a representative school-based survey of 10th and 12th grade public school students throughout schools in California...
May 13, 2022: Addictive Behaviors
https://read.qxmd.com/read/35363149/development-and-application-of-an-open-tool-for-sharing-and-analyzing-integrated-clinical-and-environmental-exposures-data-asthma-use-case
#8
JOURNAL ARTICLE
Karamarie Fecho, Stanley C Ahalt, Stephen Appold, Saravanan Arunachalam, Emily Pfaff, Lisa Stillwell, Alejandro Valencia, Hao Xu, David B Peden
BACKGROUND: The Integrated Clinical and Environmental Exposures Service (ICEES) serves as an open-source, disease-agnostic, regulatory-compliant framework and approach for openly exposing and exploring clinical data that have been integrated at the patient level with a variety of environmental exposures data. ICEES is equipped with tools to support basic statistical exploration of the integrated data in a completely open manner. OBJECTIVE: This study aims to further develop and apply ICEES as a novel tool for openly exposing and exploring integrated clinical and environmental data...
April 1, 2022: JMIR Formative Research
https://read.qxmd.com/read/34769911/open-application-of-statistical-and-machine-learning-models-to-explore-the-impact-of-environmental-exposures-on-health-and-disease-an-asthma-use-case
#9
JOURNAL ARTICLE
Bo Lan, Perry Haaland, Ashok Krishnamurthy, David B Peden, Patrick L Schmitt, Priya Sharma, Meghamala Sinha, Hao Xu, Karamarie Fecho
ICEES (Integrated Clinical and Environmental Exposures Service) provides a disease-agnostic, regulatory-compliant approach for openly exposing and analyzing clinical data that have been integrated at the patient level with environmental exposures data. ICEES is equipped with basic features to support exploratory analysis using statistical approaches, such as bivariate chi-square tests. We recently developed a method for using ICEES to generate multivariate tables for subsequent application of machine learning and statistical models...
October 29, 2021: International Journal of Environmental Research and Public Health
https://read.qxmd.com/read/34652275/adoption-of-machine-learning-systems-for-medical-diagnostics-in-clinics-qualitative-interview-study
#10
JOURNAL ARTICLE
Luisa Pumplun, Mariska Fecho, Nihal Wahl, Felix Peters, Peter Buxmann
BACKGROUND: Recently, machine learning (ML) has been transforming our daily lives by enabling intelligent voice assistants, personalized support for purchase decisions, and efficient credit card fraud detection. In addition to its everyday applications, ML holds the potential to improve medicine as well, especially with regard to diagnostics in clinics. In a world characterized by population growth, demographic change, and the global COVID-19 pandemic, ML systems offer the opportunity to make diagnostics more effective and efficient, leading to a high interest of clinics in such systems...
October 15, 2021: Journal of Medical Internet Research
https://read.qxmd.com/read/34462722/enabling-longitudinal-exploratory-analysis-of-clinical-covid-data
#11
David Borland, Irena Brain, Karamarie Fecho, Emily Pfaff, Hao Xu, James Champion, Chris Bizon, David Gotz
As the COVID-19 pandemic continues to impact the world, data is being gathered and analyzed to better understand the disease. Recognizing the potential for visual analytics technologies to support exploratory analysis and hypothesis generation from longitudinal clinical data, a team of collaborators worked to apply existing event sequence visual analytics technologies to a longitudinal clinical data from a cohort of 998 patients with high rates of COVID-19 infection. This paper describes the initial steps toward this goal, including: (1) the data transformation and processing work required to prepare the data for visual analysis, (2) initial findings and observations, and (3) qualitative feedback and lessons learned which highlight key features as well as limitations to address in future work...
August 25, 2021: ArXiv
https://read.qxmd.com/read/34283031/a-biomedical-knowledge-graph-system-to-propose-mechanistic-hypotheses-for-real-world-environmental-health-observations-cohort-study-and-informatics-application
#12
JOURNAL ARTICLE
Karamarie Fecho, Chris Bizon, Frederick Miller, Shepherd Schurman, Charles Schmitt, William Xue, Kenneth Morton, Patrick Wang, Alexander Tropsha
BACKGROUND: Knowledge graphs are a common form of knowledge representation in biomedicine and many other fields. We developed an open biomedical knowledge graph-based system termed Reasoning Over Biomedical Objects linked in Knowledge Oriented Pathways (ROBOKOP). ROBOKOP consists of both a front-end user interface and a back-end knowledge graph. The ROBOKOP user interface allows users to posit questions and explore answer subgraphs. Users can also posit questions through direct Cypher query of the underlying knowledge graph, which currently contains roughly 6 million nodes or biomedical entities and 140 million edges or predicates describing the relationship between nodes, drawn from over 30 curated data sources...
July 20, 2021: JMIR Medical Informatics
https://read.qxmd.com/read/34084496/modified-blue-protocol-ultrasonography-can-diagnose-thrombotic-complications-of-covid-19-with-normal-lung-ultrasound
#13
Tamer Mohamed Zaalouk, Zouheir Ibrahim Bitar, Ossama Sajeh Maadarani, Ragab Desouky Ragab Elshabasy
The BLUE protocol provides an excellent step-by-step approach for diagnosis of acute dyspnea. Adding FECHO (Focused Echocardiography) to the BLUE protocol completes the picture and helps make solid diagnoses, especially in submassive and massive PE (Pulmonary embolism). COVID-19 infection can present with thrombotic manifestations like DVT (Deep vein thrombosis) and PE with no ultrasonographic evidence of lung parenchymal affection.
May 2021: Clinical Case Reports
https://read.qxmd.com/read/33882430/vaping-identity-in-adolescent-e-cigarette-users-a-comparison-of-norms-attitudes-and-behaviors
#14
JOURNAL ARTICLE
Candice D Donaldson, Cassandra L Fecho, Tiffany Ta, Tam D Vuong, Xueying Zhang, Rebecca J Williams, April G Roeseler, Shu-Hong Zhu
INTRODUCTION: Using the tenets underlying social identity theory and the theory of planned behavior, the current study compared the perceptions, attitudes, and behaviors of e-cigarette users that reported vaping as self-defining ("vapers") compared to users that denied vaping was central to their identity ("non-vapers"). METHOD: Secondary analyses of data from the 2017-2018 California Student Tobacco Survey were utilized. A weighted, multivariable regression model (N = 82,217) compared the demographic characteristics, beliefs, and behaviors of vapers and non-vapers...
April 18, 2021: Drug and Alcohol Dependence
https://read.qxmd.com/read/33742785/application-of-mcat-questions-as-a-testing-tool-and-evaluation-metric-for-knowledge-graph-based-reasoning-systems
#15
JOURNAL ARTICLE
Karamarie Fecho, James Balhoff, Chris Bizon, William E Byrd, Sui Hang, David Koslicki, Stefano E Rensi, Patrick L Schmitt, Mathias J Wawer, Mark Williams, Stanley C Ahalt
'Knowledge graphs' (KGs) have become a common approach for representing biomedical knowledge. In a KG, multiple biomedical datasets can be linked together as a graph representation, with nodes representing entities such as 'chemical substance' or 'genes' and edges representing predicates such as 'causes' or 'treats'. Reasoning and inference algorithms can then be applied to the KG and used to generate new knowledge. We developed three KG-based question-answering systems as part of the Biomedical Data Translator program...
March 20, 2021: Clinical and Translational Science
https://read.qxmd.com/read/33226347/visualization-environment-for-federated-knowledge-graphs-development-of-an-interactive-biomedical-query-language-and-web-application-interface
#16
JOURNAL ARTICLE
Steven Cox, Stanley C Ahalt, James Balhoff, Chris Bizon, Karamarie Fecho, Yaphet Kebede, Kenneth Morton, Alexander Tropsha, Patrick Wang, Hao Xu
BACKGROUND: Efforts are underway to semantically integrate large biomedical knowledge graphs using common upper-level ontologies to federate graph-oriented application programming interfaces (APIs) to the data. However, federation poses several challenges, including query routing to appropriate knowledge sources, generation and evaluation of answer subsets, semantic merger of those answer subsets, and visualization and exploration of results. OBJECTIVE: We aimed to develop an interactive environment for query, visualization, and deep exploration of federated knowledge graphs...
November 23, 2020: JMIR Medical Informatics
https://read.qxmd.com/read/32908843/point-of-care-ultrasound-can-suggest-covid-19
#17
JOURNAL ARTICLE
Ossama Maadarani, Zouheir Bitar, Tamer Zaalouk, Mohammad Mohsen, Ragab Elshabasy
Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the World Health Organization (WHO) declared it a pandemic on 11 March 2020. Point-of-care ultrasound (POCUS) is a real-time bedside tool used by physicians to guide rapid, focused and accurate evaluation in order to identify or rule out various pathologies. We describe the case of an elderly man who had fallen at home 3 days previously and was hypoxic at presentation to the emergency department (ED)...
2020: European Journal of Case Reports in Internal Medicine
https://read.qxmd.com/read/32708093/translator-exposure-apis-open-access-to-data-on-airborne-pollutant-exposures-roadway-exposures-and-socio-environmental-exposures-and-use-case-application
#18
JOURNAL ARTICLE
Alejandro Valencia, Lisa Stillwell, Stephen Appold, Saravanan Arunachalam, Steven Cox, Hao Xu, Charles P Schmitt, Shepherd H Schurman, Stavros Garantziotis, William Xue, Stanley C Ahalt, Karamarie Fecho
Environmental exposures have profound effects on health and disease. While public repositories exist for a variety of exposures data, these are generally difficult to access, navigate, and interpret. We describe the research, development, and application of three open application programming interfaces (APIs) that support access to usable, nationwide, exposures data from three public repositories: airborne pollutant estimates from the US Environmental Protection Agency; roadway data from the US Department of Transportation; and socio-environmental exposures from the US Census Bureau's American Community Survey...
July 21, 2020: International Journal of Environmental Research and Public Health
https://read.qxmd.com/read/32160884/fhir-pit-an-open-software-application-for-spatiotemporal-integration-of-clinical-data-and-environmental-exposures-data
#19
JOURNAL ARTICLE
Hao Xu, Steven Cox, Lisa Stillwell, Emily Pfaff, James Champion, Stanley C Ahalt, Karamarie Fecho
BACKGROUND: Informatics tools to support the integration and subsequent interrogation of spatiotemporal data such as clinical data and environmental exposures data are lacking. Such tools are needed to support research in environmental health and any biomedical field that is challenged by the need for integrated spatiotemporal data to examine individual-level determinants of health and disease. RESULTS: We have developed an open-source software application-FHIR PIT (Health Level 7 Fast Healthcare Interoperability Resources Patient data Integration Tool)-to enable studies on the impact of individual-level environmental exposures on health and disease...
March 11, 2020: BMC Medical Informatics and Decision Making
https://read.qxmd.com/read/31769676/robokop-kg-and-kgb-integrated-knowledge-graphs-from-federated-sources
#20
JOURNAL ARTICLE
Chris Bizon, Steven Cox, Jim Balhoff, Yaphet Kebede, Patrick Wang, Kenneth Morton, Karamarie Fecho, Alexander Tropsha
A proliferation of data sources has led to the notional existence of an implicit Knowledge Graph (KG) that contains vast amounts of biological knowledge contributed by distributed Application Programming Interfaces (APIs). However, challenges arise when integrating data across multiple APIs due to incompatible semantic types, identifier schemes, and data formats. We present ROBOKOP KG (https://robokopkg.renci.org), which is a KG that was initially built to support the open biomedical question-answering application, ROBOKOP (Reasoning Over Biomedical Objects linked in Knowledge-Oriented Pathways) (https://robokop...
November 26, 2019: Journal of Chemical Information and Modeling
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