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

Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...
Genomics02:02

Genomics

Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...

You might also read

Related Articles

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

Sort by
Same author

Knowledge Engineering for Open Science: Building and Deploying Knowledge Bases for Metadata Standards.

AI magazine·2026
Same author

The HuBMAP Framework for Advancing Data FAIRness.

bioRxiv : the preprint server for biology·2026
Same author

Longitudinal evaluation of serial ctDNA kinetics using joint modeling in patients with metastatic breast cancer.

NPJ precision oncology·2026
Same author

Towards responsible artificial intelligence in healthcare-getting real about real-world data and evidence.

Journal of the American Medical Informatics Association : JAMIA·2025
Same author

A Cloud-Based Platform for Harmonized COVID-19 Data: Design and Implementation of the Rapid Acceleration of Diagnostics (RADx) Data Hub.

JMIR public health and surveillance·2025
Same author

Ensuring Adherence to Standards in Experiment-Related Metadata Entered Via Spreadsheets.

Scientific data·2025
Same journal

The Essential Components and Critical Conditions for Success in a Learning Health System in Oncology.

Studies in health technology and informatics·2026
Same journal

Use of Artificial Intelligence in Screening for Adolescent Idiopathic Scoliosis: A Scoping Review.

Studies in health technology and informatics·2026
Same journal

Movement Related Biomechanics in Adolescent Idiopathic Scoliosis: A Review of Reviews.

Studies in health technology and informatics·2026
Same journal

The Impact of Surgical Correction of Adolescent Idiopathic Scoliosis Using Posterior Spinal Fusion on Selected Radiological Parameters and Respiratory Function.

Studies in health technology and informatics·2026
Same journal

Acute Effect of Physio-logic® Exercises on Muscle Tone and Stiffness in Adolescent Idiopathic Scoliosis Patients: A Preliminary Study.

Studies in health technology and informatics·2026
Same journal

Effects of Integrated Music and Occupational Therapy on Motor and Autonomic Function in Children with Neurogenic Scoliosis.

Studies in health technology and informatics·2026
See all related articles

Related Experiment Video

Updated: Jun 8, 2026

A Metadata Extraction Approach for Clinical Case Reports to Enable Advanced Understanding of Biomedical Concepts
07:50

A Metadata Extraction Approach for Clinical Case Reports to Enable Advanced Understanding of Biomedical Concepts

Published on: September 20, 2018

Semantic reasoning with XML-based biomedical information models.

Martin J O'Connor1, Amar Das

  • 1Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA, USA.

Studies in Health Technology and Informatics
|September 16, 2010
PubMed
Summary
This summary is machine-generated.

This study introduces a novel workflow for converting Extensible Markup Language (XML) biomedical data into ontologies. This enables semantic reasoning for enhanced data interpretation in fields like HIV and radiology.

More Related Videos

A Knowledge Graph Approach to Elucidate the Role of Organellar Pathways in Disease via Biomedical Reports
07:35

A Knowledge Graph Approach to Elucidate the Role of Organellar Pathways in Disease via Biomedical Reports

Published on: October 13, 2023

Evidence-based Knowledge Synthesis and Hypothesis Validation: Navigating Biomedical Knowledge Bases via Explainable AI and Agentic Systems
05:47

Evidence-based Knowledge Synthesis and Hypothesis Validation: Navigating Biomedical Knowledge Bases via Explainable AI and Agentic Systems

Published on: June 13, 2025

Related Experiment Videos

Last Updated: Jun 8, 2026

A Metadata Extraction Approach for Clinical Case Reports to Enable Advanced Understanding of Biomedical Concepts
07:50

A Metadata Extraction Approach for Clinical Case Reports to Enable Advanced Understanding of Biomedical Concepts

Published on: September 20, 2018

A Knowledge Graph Approach to Elucidate the Role of Organellar Pathways in Disease via Biomedical Reports
07:35

A Knowledge Graph Approach to Elucidate the Role of Organellar Pathways in Disease via Biomedical Reports

Published on: October 13, 2023

Evidence-based Knowledge Synthesis and Hypothesis Validation: Navigating Biomedical Knowledge Bases via Explainable AI and Agentic Systems
05:47

Evidence-based Knowledge Synthesis and Hypothesis Validation: Navigating Biomedical Knowledge Bases via Explainable AI and Agentic Systems

Published on: June 13, 2025

Area of Science:

  • Biomedical Informatics
  • Semantic Web Technologies
  • Ontology Engineering

Background:

  • Extensible Markup Language (XML) is widely adopted for biomedical data exchange.
  • Ontologies are increasingly used in biomedicine, offering semantic reasoning capabilities.
  • Standardized methods for integrating XML data with ontologies are lacking.

Purpose of the Study:

  • To develop a standardized workflow and tools for transforming XML-based biomedical information models into OWL ontologies.
  • To enable semantic reasoning over these ontologies for automated inference generation.
  • To demonstrate the application of these methods in specific biomedical domains.

Main Methods:

  • Developed a workflow and tools to convert XML information models into domain ontologies using Web Ontology Language (OWL).
  • Applied semantic reasoning techniques to the generated OWL ontologies.
  • Tested the methodology on information models from the HIV and radiological imaging domains.

Main Results:

  • Successfully transformed XML information models into OWL ontologies.
  • Automated the generation of domain-level inferences using semantic reasoning.
  • Validated the approach for HIV and radiological image data models.

Conclusions:

  • The developed workflow and tools provide a standardized approach for integrating XML data with ontologies.
  • Semantic reasoning can be effectively applied to ontology-encoded XML data for automated knowledge discovery.
  • This approach enhances the utility of biomedical data by enabling advanced semantic analysis.