Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Genomics

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...

Cancer Therapies

Cancer Therapies

Cancer therapies are various modes of treatment, such as surgery, radiation therapy, and chemotherapy that are administered to cancer patients.
However, cancer treatments can pose several challenges, as therapies used to kill cancer cells are generally also toxic to normal cells. Moreover, cancer cells mutate rapidly and can develop resistance to chemical agents or radiation therapy. Besides, all types of cancer cells may not respond to the same therapy. Some cancer cells respond to one...

Cancer-Critical Genes I: Proto-oncogenes

Cancer-Critical Genes I: Proto-oncogenes

Genes usually encode proteins necessary for the proper functioning of a healthy cell. Mutations can often cause changes to the gene expression pattern, thereby altering the phenotype.
When the function of certain critical genes, especially those involved in cell cycle regulation and cell growth signaling cascades, gets disrupted, it upsets the cell cycle progression. Such cells with unchecked cell cycles start proliferating uncontrollably and eventually develop into tumors.
Such genes that act...

Targeted Cancer Therapies

Targeted Cancer Therapies

The targeted cancer therapies, also known as “molecular targeted therapies,” take advantage of the molecular and genetic differences between the cancer cells and the normal cells. It needs a thorough understanding of the cancer cells to develop drugs that can target specific molecular aspects that drive the growth, progression, and spread of cancer cells without affecting the growth and survival of other normal cells in the body.
There are several types of targeted therapies against...

Cancer Survival Analysis

Cancer Survival Analysis

Cancer survival analysis focuses on quantifying and interpreting the time from a key starting point, such as diagnosis or the initiation of treatment, to a specific endpoint, such as remission or death. This analysis provides critical insights into treatment effectiveness and factors that influence patient outcomes, helping to shape clinical decisions and guide prognostic evaluations. A cornerstone of oncology research, survival analysis tackles the challenges of skewed, non-normally...

Cancer-Critical Genes II: Tumor Suppressor Genes

Cancer-Critical Genes II: Tumor Suppressor Genes

Genes usually encode proteins necessary for the proper functioning of a healthy cell. Mutations can often cause changes to the gene expression pattern, thereby altering the phenotype.
When the function of certain critical genes, especially those involved in cell cycle regulation and cell growth signaling cascades, gets disrupted, it upsets the cell cycle progression. Such cells with unchecked cell cycles start proliferating uncontrollably and eventually develop into tumors.
Such genes that act...

You might also read

Related Articles

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

Sort by

Same author

The role of protein embeddings for protein-protein interaction prediction with graph neural networks.

Briefings in bioinformatics·2026

Same author

Machine-guided design for bioengineering gene therapy vectors: Where are we and what lies ahead?

Biotechnology advances·2026

Same author

FAIR Omics Data Management: Overview, Challenges, and Best Practices.

Advances in experimental medicine and biology·2026

Same author

Exploring the limits of pre-trained embeddings in machine-guided protein design: a case study on predicting AAV vector viability.

Scientific reports·2026

Same author

The Portuguese Beacon: sharing genomic variant data safely.

Database : the journal of biological databases and curation·2026

Same author

Leveraging knowledge for explainable AI in personalized cancer treatment: challenges and future directions.

Frontiers in digital health·2025

Search research articles

Related Experiment Video

Updated: Sep 26, 2025

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

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

Published on: October 13, 2023

Ontologies and Knowledge Graphs in Oncology Research.

Marta Contreiras Silva¹, Patrícia Eugénio¹, Daniel Faria¹

¹LASIGE, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal.

|April 23, 2022

Summary

Biomedical ontologies and knowledge graphs are crucial for integrating complex cancer data. This review of 141 studies shows their growing use in cancer research for data accessibility and AI-driven insights.

Keywords:

cancer knowledge graph oncology ontologies review semantic technologies

More Related Videos

Author Spotlight: Advancing Personalized Medicine in Ovarian Cancer

Author Spotlight: Advancing Personalized Medicine in Ovarian Cancer

Published on: February 23, 2024

Development of Compendium for Esophageal Squamous Cell Carcinoma

Development of Compendium for Esophageal Squamous Cell Carcinoma

Published on: April 12, 2024

Related Experiment Videos

Last Updated: Sep 26, 2025

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

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

Published on: October 13, 2023

Author Spotlight: Advancing Personalized Medicine in Ovarian Cancer

Author Spotlight: Advancing Personalized Medicine in Ovarian Cancer

Published on: February 23, 2024

Development of Compendium for Esophageal Squamous Cell Carcinoma

Development of Compendium for Esophageal Squamous Cell Carcinoma

Published on: April 12, 2024

Area of Science:

Biomedical Informatics
Computational Biology
Cancer Research

Background:

Cancer research involves complex, heterogeneous data from multiple biomedical disciplines.
A holistic view of cancer is essential for precision medicine, requiring data integration.
Biomedical ontologies offer a solution for creating cohesive knowledge models.

Purpose of the Study:

To review the application of ontologies and knowledge graphs in cancer research.
To categorize the usage of these tools in published works.
To identify commonly used and emerging ontologies.

Main Methods:

Systematic literature review of 141 published works.
Categorization of studies based on ontology and knowledge graph application.
Analysis of ontology usage trends in cancer research.

Main Results:

Ontologies and knowledge graphs are increasingly adopted in biomedical and cancer research.
Studies were categorized under 14 hierarchical themes based on their application.
Identified trends in the use of established and novel ontologies.

Conclusions:

Ontologies enhance data accessibility, interoperability, and integration in cancer research.
Knowledge graphs facilitate AI applications for unlocking new insights from complex data.
The integration of ontologies and knowledge graphs supports a holistic approach to cancer research and precision medicine.