Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Fates of Pyruvate01:20

Fates of Pyruvate

8.7K
Pyruvate is the end product of glycolysis, where glucose is oxidized to pyruvate, simultaneously reducing NAD+ to NADH. Two molecules of ATP are also produced by substrate-level phosphorylation.
In aerobic organisms, pyruvate is metabolized via the citric acid cycle to produce reduced coenzymes NADH and FADH2. These coenzymes are then oxidized in the electron transport chain to produce ATP and, in the process, regenerate the NAD+ and FAD. As seen in some cell types and organisms, fermentation...
8.7K
Hepatic Portal System01:21

Hepatic Portal System

1.5K
The hepatic portal system, a critical part of our circulatory framework, transports nutrient-laden, deoxygenated blood from the gastrointestinal tract and spleen to the liver. This ingenious system plays an indispensable role in maintaining our body's metabolic equilibrium.
At its core, the hepatic portal vein is the result of a confluence of the superior and inferior mesenteric veins along with the splenic vein. Each of these veins has a unique role. The superior mesenteric vein is...
1.5K
Purpose of Health Records II01:19

Purpose of Health Records II

995
Health records serve various essential purposes in the healthcare system. Here are some key purposes:
995
Integrated Healthcare System01:20

Integrated Healthcare System

1.7K
An integrated healthcare system (IHS) is a set of organizations that provides for or arranges to provide coordinated and continuous service to a defined population. The IHS takes responsibility for that particular population's health status and outcome, both clinically and fiscally. An integrated healthcare system is a well-organized, well-coordinated, and collaborative network. The integrated delivery system is a network that connects different healthcare providers to deliver organized,...
1.7K
Purpose of Health Records I01:11

Purpose of Health Records I

1.3K
The vital purpose of health records is to provide a complete and accurate account of a patient's medical history, including communication, diagnostic and therapeutic orders, care planning, research, and quality review.
Here's a breakdown of how health records serve these purposes:
1.3K
Health Information Technology and Healthcare Information System01:30

Health Information Technology and Healthcare Information System

875
Health Information Technology (HIT)
Health Information Technology, commonly called HIT, integrates advanced information systems and technology in healthcare settings. Its primary functions include:
875

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Extracting Medical Information From Unstructured Clinical Text Using Large Language Models to Enhance Health Care Interoperability: Proof-of-Concept Study.

Journal of medical Internet research·2026
Same author

Recent Advances in Automated Mitosis Detection in Digital Pathology: A PRISMA-Guided Systematic Review with Evaluation-Regime Stratification (2018-2025).

Biomedicines·2026
Same author

From Flow to Feature Using a Proof-of-Concept Spectral-Driven Machine Learning Approach Using Smart Urinary and Drainage Catheter Systems: Algorithm Development and Validation.

JMIR medical informatics·2026
Same author

Improving Retrieval Augmented Generation for Health Care by Fine-Tuning Clinical Embedding Models: Development and Evaluation Study.

Journal of medical Internet research·2026
Same author

The Effect of Contrast Media Formulations with Different Iodine Preparation Concentrations at a Constant Iodine Delivery Rate in Low-kV CT Angiography: An Experimental Animal Study.

RoFo : Fortschritte auf dem Gebiete der Rontgenstrahlen und der Nuklearmedizin·2026
Same author

International testing and refinement of AI algorithms predicting acute leukemia subtypes from routine laboratory data.

Nature communications·2026

Related Experiment Video

Updated: Jul 24, 2025

The Participant-Reported Implementation Update and Score PRIUS: A Novel Method for Capturing Implementation-Related Data Over Time
06:05

The Participant-Reported Implementation Update and Score PRIUS: A Novel Method for Capturing Implementation-Related Data Over Time

Published on: February 19, 2021

1.3K

FHIR-PYrate: a data science friendly Python package to query FHIR servers.

René Hosch1,2, Giulia Baldini3,4, Vicky Parmar1,2

  • 1Institute of Interventional and Diagnostic Radiology and Neuroradiology, University Hospital Essen, Hufelandstraße 55, Essen, 45147, Germany.

BMC Health Services Research
|July 6, 2023
PubMed
Summary

FHIR-PYrate simplifies clinical data extraction for research by automating cohort building and data retrieval from electronic health records. This Python package streamlines the process, saving researchers valuable time.

Keywords:
DataframeDicomElectronic patient recordFHIRInformation extractionPython

More Related Videos

Cloud-Based Phrase Mining and Analysis of User-Defined Phrase-Category Association in Biomedical Publications
09:20

Cloud-Based Phrase Mining and Analysis of User-Defined Phrase-Category Association in Biomedical Publications

Published on: February 23, 2019

8.8K
High Precision FRET at Single-molecule Level for Biomolecule Structure Determination
11:24

High Precision FRET at Single-molecule Level for Biomolecule Structure Determination

Published on: May 13, 2017

10.8K

Related Experiment Videos

Last Updated: Jul 24, 2025

The Participant-Reported Implementation Update and Score PRIUS: A Novel Method for Capturing Implementation-Related Data Over Time
06:05

The Participant-Reported Implementation Update and Score PRIUS: A Novel Method for Capturing Implementation-Related Data Over Time

Published on: February 19, 2021

1.3K
Cloud-Based Phrase Mining and Analysis of User-Defined Phrase-Category Association in Biomedical Publications
09:20

Cloud-Based Phrase Mining and Analysis of User-Defined Phrase-Category Association in Biomedical Publications

Published on: February 23, 2019

8.8K
High Precision FRET at Single-molecule Level for Biomolecule Structure Determination
11:24

High Precision FRET at Single-molecule Level for Biomolecule Structure Determination

Published on: May 13, 2017

10.8K

Area of Science:

  • Medical Informatics
  • Computational Biology
  • Health Data Science

Background:

  • Electronic patient records (EPRs) are central to modern healthcare, containing comprehensive patient histories.
  • Clinical research often involves repetitive, non-standardized processes for building study cohorts from EPRs.
  • Researchers currently spend significant time on boilerplate coding for data extraction, diverting focus from core research tasks.

Purpose of the Study:

  • To introduce FHIR-PYrate, a Python package designed to streamline clinical data collection and extraction for research.
  • To provide a unified interface for querying FHIR servers, downloading imaging studies, and filtering clinical documents.
  • To enhance the efficiency and performance of clinical research data handling processes.

Main Methods:

  • FHIR-PYrate offers a straightforward interface for interacting with FHIR servers and REST APIs.
  • It enables uniform querying across all FHIR resources, simplifying customization for various use cases.
  • Features such as parallelization and filtering are integrated to optimize data retrieval performance.

Main Results:

  • The package facilitates the analysis of prognostic significance using routine CT imaging and clinical data in breast cancer patients with lung metastases.
  • It automates the collection of patient cohorts using ICD-10 codes, survival information, and additional clinical data.
  • CT scans and clinical data are processed for survival analysis using deep learning models.

Conclusions:

  • FHIR-PYrate enables rapid and easy retrieval of FHIR data, image data, and keyword searching within medical documents.
  • The package automates the assembly of research cohorts, significantly accelerating the research process.
  • It provides a powerful tool for researchers working with complex clinical datasets.