A cloud-based pipeline for analysis of FHIR and long-read data
FHIR RESOURCES
All of the major cloud providers have their own implementation of an FHIR server that can readily be used with other cloud services. Amazon supports ‘FHIR Works’ on Amazon Web Services (AWS), Microsoft supports an ‘Azure API for FHIR’ on Azure, Google supports a ‘Cloud Healthcare API’ on Google Cloud and IBM supports an ‘IBM FHIR Server’ on the IBM Cloud.
academic.oup.com/bioinformat…
BioData Catalyst Consortium
NHLBI BioData Catalyst® (BDC) is a cloud-based ecosystem offering researchers analytical tools, applications, and workflows in secure workspaces where researchers can find, access, share, store, and compute on hosted data or data they bring to it. BDC is also an NHLBI data repository where researchers share scientific data so they and others can reproduce findings and reuse data to advance science. The TOPMed Imputation Server, where researchers can upload their own phased or unphased GWAS genotypes and receive phased and imputed genomes in return, is also part of the BDC ecosystem
biodatacatalyst.nhlbi.nih.go…
Portable Format for Bioinformatics_FHIR (pfb_fhir): A utility to extract clinical data systems into a portable format
“A carrier format for describing raw data and the data model in which it is structured, based on an efficient binary format (AVRO). PFB allows an entire cohort of metadata to be loaded into a research data system. Here, we describe an open source utility that will scan FHIR based systems and create PFB based archives.”
medrxiv.org/content/10.1101/…
1 day before the plandemic this drops coincidence? I think not.
Flat FHIR files created (Synthetic data can be embedded)
March 4, 2020
High Performance Computing on Flat FHIR Files Created with the New SMART/HL7 Bulk Data Access Standard
pmc.ncbi.nlm.nih.gov/article…
Journal of Biomedical Semantics
Pathling: analytics on FHIR
jbiomedsem.biomedcentral.com…
Upper level FHIR concepts
The purpose of this vignette is to explore relationships between concepts underlying FHIR foundational concepts and aspects of implementation in BiocFHIR.
bioconductor.org/packages/de…
Stakeholder capitalism in healthcare
The CARIN (Creating Access to Real-time Information Now through Consumer-Directed Exchange) Alliance is an HL7 FHIR Accelerator program which brings implementers together to advance the use of HL7 FHIR standards in health care.
build.fhir.org/ig/HL7/carin-…
The CARIN Code of Conduct
onyxhealth.io/carin-code-of-…
Data Science for Merged FHIR and PacBio VCF Data on Azure Machine Learning Notebooks
techcommunity.microsoft.com/…
SYNTHEA
Synthea™ Novel coronavirus (COVID-19) model and synthetic data set
sciencedirect.com/science/ar…
A builder for converting the Synthea fake data to the OPOM CDM
ohdsi.github.io/ETL-Synthea/
The Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) is an open-source data standard that organizes observational healthcare data into a common format.
ohdsi.org/data-standardizati…
Synthea synthetic patient generator data in OMOP Common Data Model
The Synthea generated data is provided here as a 1,000 person (1k), 100,000 person (100k), and 2,800,000 persom (2.8m) data sets in the OMOP Common Data Model format.
registry.opendata.aws/synthe…
Transforming Healthcare Analytics with FHIR: A Framework for Standardizing and Analyzing Clinical Data
researchgate.net/publication…
Real‐world evidence in the cloud: Tutorial on developing an end‐to‐end data and analytics pipeline using Amazon Web Services resources
researchgate.net/publication…
Generating Synthetic CDISC Clinical Trial Data
PDF DOWNLOAD
lexjansen.com/pharmasug/2021…
◽Clinical Data Interchange Standards Consortium
Electronic Source Data Interchange (eSDI) Group
Leveraging the CDISC Standards to
Facilitate the use of Electronic Source
Data within Clinical Trials
PDF DOWNLOAD
acrpnet.org/wp-content/uploa…
Use of HL7 FHIR as eSource to Pre-populate CDASH Case Report Forms using a CDISC ODM API
cdisc.org/kb/articles/use-hl…