Petagraph: A large-scale unifying knowledge graph framework for integrating biomolecular and biomedical data.

Over the past decade, there has been substantial growth in both the quantity and complexity of available biomedical data. In order to more efficiently harness this extensive data and alleviate challenges associated with integration of multi-omics data, we developed Petagraph, a biomedical knowledge graph that encompasses over 32 million nodes and 118 million relationships. Petagraph leverages more than 180 ontologies and standards in the Unified Biomedical Knowledge Graph (UBKG) to embed millions of quantitative genomics data points.

Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas Construction and Usage.

The Human BioMolecular Atlas Program (HuBMAP) aims to construct a reference 3D structural, cellular, and molecular atlas of the healthy adult human body. The HuBMAP Data Portal (https://portal.hubmapconsortium.

Organizational Breast Cancer Data Mart: A Solution for Assessing Outcomes of Imaging and Treatment.

Purpose: In the United States, a comprehensive national breast cancer registry (CR) does not exist. Thus, care and coverage decisions are based on data from population subsets, other countries, or models. We report a prototype real-world research data mart to assess mortality, morbidity, and costs for breast cancer diagnosis and treatment.

Presentation Acuity and Surgical Outcomes for Patients With Health Insurance Living in Highly Deprived Neighborhoods.

Importance: Insurance coverage expansion has been proposed as a solution to improving health disparities, but insurance expansion alone may be insufficient to alleviate care access barriers.

Objective: To assess the association of Area Deprivation Index (ADI) with postsurgical textbook outcomes (TO) and presentation acuity for individuals with private insurance or Medicare.

Design, Setting, And Participants: This cohort study used data from the National Surgical Quality Improvement Program (2013-2019) merged with electronic health record data from 3 academic health care systems.

Limitations of Noninvasive Tests-Based Population-Level Risk Stratification Strategy for Nonalcoholic Fatty Liver Disease.

Background: Nonalcoholic fatty liver disease (NAFLD) and nonalcoholic steatohepatitis (NASH) are highly prevalent but underdiagnosed.

Aims: We used an electronic health record data network to test a population-level risk stratification strategy using noninvasive tests (NITs) of liver fibrosis.

Methods: Data were obtained from PCORnet sites in the East, Midwest, Southwest, and Southeast United States from patients aged [Formula: see text] 18 with or without ICD-10-CM diagnosis codes for NAFLD, NASH, and NASH-cirrhosis between 9/1/2017 and 8/31/2020.

Independent Associations of Neighborhood Deprivation and Patient-level Social Determinants of Health with Textbook Outcomes after Inpatient Surgery.

Objective: Assess associations of Social Determinants of Health (SDoH) using Area Deprivation Index (ADI), race/ethnicity and insurance type with Textbook Outcomes (TO).

Summary Background Data: Individual- and contextual-level SDoH affect health outcomes, but only one SDoH level is usually included.

Methods: Three healthcare system cohort study using National Surgical Quality Improvement Program (2013-2019) linked with ADI risk-adjusted for frailty, case status and operative stress examining TO/TO components (unplanned reoperations, complications, mortality, Emergency Department/Observation Stays and readmissions).

REDCap and the National Mesothelioma Virtual Bank-a scalable and sustainable model for rare disease biorepositories.

Objective: Rare disease research requires data sharing networks to power translational studies. We describe novel use of Research Electronic Data Capture (REDCap), a web application for managing clinical data, by the National Mesothelioma Virtual Bank, a federated biospecimen, and data sharing network.

Materials And Methods: National Mesothelioma Virtual Bank (NMVB) uses REDCap to integrate honest broker activities, enabling biospecimen and associated clinical data provisioning to investigators.

Organ Mapping Antibody Panels: a community resource for standardized multiplexed tissue imaging.

Multiplexed antibody-based imaging enables the detailed characterization of molecular and cellular organization in tissues. Advances in the field now allow high-parameter data collection (>60 targets); however, considerable expertise and capital are needed to construct the antibody panels employed by these methods. Organ mapping antibody panels are community-validated resources that save time and money, increase reproducibility, accelerate discovery and support the construction of a Human Reference Atlas.

ReDWINE: A clinical datamart with text analytical capabilities to facilitate rehabilitation research.

Rehabilitation research focuses on determining the components of a treatment intervention, the mechanism of how these components lead to recovery and rehabilitation, and ultimately the optimal intervention strategies to maximize patients' physical, psychologic, and social functioning. Traditional randomized clinical trials that study and establish new interventions face challenges, such as high cost and time commitment. Observational studies that use existing clinical data to observe the effect of an intervention have shown several advantages over RCTs.

A Surgical Desirability of Outcome Ranking (DOOR) Reveals Complex Relationships Between Race/Ethnicity, Insurance Type, and Neighborhood Deprivation.

Objective: Develop an ordinal Desirability of Outcome Ranking (DOOR) for surgical outcomes to examine complex associations of Social Determinants of Health.

Background: Studies focused on single or binary composite outcomes may not detect health disparities.

Methods: Three health care system cohort study using NSQIP (2013-2019) linked with EHR and risk-adjusted for frailty, preoperative acute serious conditions (PASC), case status and operative stress assessing associations of multilevel Social Determinants of Health of race/ethnicity, insurance type (Private 13,957; Medicare 15,198; Medicaid 2835; Uninsured 2963) and Area Deprivation Index (ADI) on DOOR and the binary Textbook Outcomes (TO).

Combination of antidepressants and antipsychotics as a novel treatment option for psychosis in Alzheimer's disease.

Psychotic symptoms are reported as one of the most common complications of Alzheimer's disease (AD), in whom they are associated with more rapid deterioration and increased mortality. Empiric treatments, namely first and second-generation antipsychotics, confer modest efficacy in patients with AD and with psychosis (AD+P) and themselves increase mortality. Recent studies suggested the use and beneficial effects of antidepressants among patients with AD+P.

Combination of Antidepressants and Antipsychotics as A Novel Treatment Option for Psychosis in Alzheimer's Disease.

Background: Psychotic symptoms are reported as one of the most common complications of Alzheimer's disease (AD), affecting approximately half of AD patients, in whom they are associated with more rapid deterioration and increased mortality. Empiric treatments, namely first and second-generation antipsychotics, confer modest efficacy in AD patients with psychosis (AD+P) and themselves increase mortality. A recent genome-wide meta-analysis and early clinical trials suggest the use and beneficial effects of antidepressants among AD+P patients.

Multiomics in primary and metastatic breast tumors from the AURORA US network finds microenvironment and epigenetic drivers of metastasis.

The AURORA US Metastasis Project was established with the goal to identify molecular features associated with metastasis. We assayed 55 females with metastatic breast cancer (51 primary cancers and 102 metastases) by RNA sequencing, tumor/germline DNA exome and low-pass whole-genome sequencing and global DNA methylation microarrays. Expression subtype changes were observed in ~30% of samples and were coincident with DNA clonality shifts, especially involving HER2.

Tissue registration and exploration user interfaces in support of a human reference atlas.

Seventeen international consortia are collaborating on a human reference atlas (HRA), a comprehensive, high-resolution, three-dimensional atlas of all the cells in the healthy human body. Laboratories around the world are collecting tissue specimens from donors varying in sex, age, ethnicity, and body mass index. However, harmonizing tissue data across 25 organs and more than 15 bulk and spatial single-cell assay types poses challenges.

Assessing the impact of privacy-preserving record linkage on record overlap and patient demographic and clinical characteristics in PCORnet®, the National Patient-Centered Clinical Research Network.

Objective: This article describes the implementation of a privacy-preserving record linkage (PPRL) solution across PCORnet®, the National Patient-Centered Clinical Research Network.

Material And Methods: Using a PPRL solution from Datavant, we quantified the degree of patient overlap across the network and report a de-duplicated analysis of the demographic and clinical characteristics of the PCORnet population.

Results: There were ∼170M patient records across the responding Network Partners, with ∼138M (81%) of those corresponding to a unique patient.

Establishing a framework for privacy-preserving record linkage among electronic health record and administrative claims databases within PCORnet, the National Patient-Centered Clinical Research Network.

Objective: The aim of this study was to determine whether a secure, privacy-preserving record linkage (PPRL) methodology can be implemented in a scalable manner for use in a large national clinical research network.

Results: We established the governance and technical capacity to support the use of PPRL across the National Patient-Centered Clinical Research Network (PCORnet). As a pilot, four sites used the Datavant software to transform patient personally identifiable information (PII) into de-identified tokens.

Open-source Software Sustainability Models: Initial White Paper From the Informatics Technology for Cancer Research Sustainability and Industry Partnership Working Group.

Background: The National Cancer Institute Informatics Technology for Cancer Research (ITCR) program provides a series of funding mechanisms to create an ecosystem of open-source software (OSS) that serves the needs of cancer research. As the ITCR ecosystem substantially grows, it faces the challenge of the long-term sustainability of the software being developed by ITCR grantees. To address this challenge, the ITCR sustainability and industry partnership working group (SIP-WG) was convened in 2019.

An atomic approach to the design and implementation of a research data warehouse.

Objective: As a long-standing Clinical and Translational Science Awards (CTSA) Program hub, the University of Pittsburgh and the University of Pittsburgh Medical Center (UPMC) developed and implemented a modern research data warehouse (RDW) to efficiently provision electronic patient data for clinical and translational research.

Materials And Methods: We designed and implemented an RDW named Neptune to serve the specific needs of our CTSA. Neptune uses an atomic design where data are stored at a high level of granularity as represented in source systems.

Using the Unified Medical Language System to Expand the Operative Stress Score - First Use Case.

Background: The Unified Medical Language System (UMLS) maps relationships between and within >100 biomedical vocabularies, including Current Procedural Terminology (CPT) codes, creating a powerful knowledge resource which can accelerate clinical research.

Methods: We used synonymy and concepts relating hierarchical structure of CPT codes within the UMLS, (1) guiding surgical experts in expanding the Operative Stress Score (OSS) from 565 originally rated CPT codes to additional, 1,853 related procedures; (2) establishing validity of the association between the added OSS ratings and 30-day outcomes in VASQIP (2015-2018).

Results: The UMLS Metathesaurus and Semantic Network was converted into an interactive graph database (https://github.

Association of Frailty and the Expanded Operative Stress Score with Preoperative Acute Serious Conditions, Complications, and Mortality in Males Compared to Females: A Retrospective Observational Study.

Objective: The aim of this study was to expand Operative Stress Score (OSS) increasing procedural coverage and assessing OSS and frailty association with Preoperative Acute Serious Conditions (PASC), complications and mortality in females versus males.

Summary Background Data: Veterans Affairs male-dominated study showed high mortality in frail veterans even after very low stress surgeries (OSS1).

Methods: Retrospective cohort using NSQIP data (2013-2019) merged with 180-day postoperative mortality from multiple hospitals to evaluate PASC, 30-day complications and 30-, 90-, and 180-day mortality.