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

C4 Pathway and CAM01:27

C4 Pathway and CAM

48.9K
Most plants use the C3 pathway for carbon fixation. However, some plants, such as sugar cane, corn, and cacti that grow in hot conditions, use alternative pathways to fix carbon and conserve energy loss due to photorespiration. Photorespiration is the process that occurs when the oxygen concentration is high. Under such conditions, the rubisco enzyme in the Calvin cycle binds O2 instead of CO2, which halts photosynthesis and consumes energy.
C4 Pathway
The C4 pathway is used by plants such as...
48.9K
Mechanistic Models: Overview of Compartment Models01:21

Mechanistic Models: Overview of Compartment Models

371
Mechanistic models, a category encompassing both physiological and compartmental modeling, differ from empirical models' approaches to incorporating known factors about the systems being modeled. Empirical models describe data with minimal assumptions, while mechanistic models aim to provide a robust description of available data by specifying assumptions and integrating known factors about the system. Compartmental analysis is a key example of a mechanistic model in pharmacokinetics and...
371
Mechanistic Models: Compartment Models in Individual and Population Analysis01:23

Mechanistic Models: Compartment Models in Individual and Population Analysis

257
Mechanistic models are utilized in individual analysis using single-source data, but imperfections arise due to data collection errors, preventing perfect prediction of observed data. The mathematical equation involves known values (Xi), observed concentrations (Ci), measurement errors (εi), model parameters (ϕj), and the related function (ƒi) for i number of values. Different least-squares metrics quantify differences between predicted and observed values. The ordinary least...
257
Other Glycolytic Pathways01:24

Other Glycolytic Pathways

855
The pentose phosphate pathway (PPP) operates in parallel with glycolysis, facilitating the metabolism of both pentoses and glucose. This pathway consists of two distinct phases: the oxidative and non-oxidative phases. While it does not directly generate ATP, the intermediates formed during the process can integrate into glycolysis, contributing to cellular energy metabolism when required.Oxidative Phase: NADPH ProductionThe oxidative phase of the pentose phosphate pathway is primarily...
855
Respiration Pathways01:26

Respiration Pathways

723
Cellular respiration is a fundamental metabolic process that enables organisms to generate energy from organic molecules. One of its central pathways is the tricarboxylic acid (TCA) cycle, also known as the Krebs cycle, which plays a crucial role in energy production and biosynthetic processes.Conversion of Pyruvate to Acetyl-CoAThe pyruvate generated from glycolysis undergoes oxidative decarboxylation by the pyruvate dehydrogenase complex, producing acetyl-CoA, one molecule of NADH, and one...
723
Auditory Pathway01:15

Auditory Pathway

7.2K
Auditory pathways constitute the complex neural circuits responsible for transmitting and interpreting auditory information from the peripheral auditory system to the brain. Sound waves are initially captured by the outer ear, funneled through the ear canal, and reach the tympanic membrane (eardrum). These vibrations are transmitted via the middle ear's ossicles to the inner ear's cochlea.
When viewed cross-sectionally, the cochlea reveals the scala vestibuli and scala tympani flanking...
7.2K

You might also read

Related Articles

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

Sort by
Same author

Selecting medical research data platforms for translational biomedical research: a five-tier overview and requirement-weighted assessment framework.

Frontiers in digital health·2026
Same author

Trends in Computational Metabolomics: A Perspective on Five Years of Software Development, Challenges, and Opportunities (2021-2025).

Analytical chemistry·2026
Same author

VO: The Vaccine Ontology.

Scientific data·2026
Same author

The Cell Ontology in the age of single-cell omics.

Scientific data·2026
Same author

Correction to "Natural Products Have Increased Rates of Clinical Trial Success throughout the Drug Development Process".

Journal of natural products·2026
Same author

An Interactive Brain Atlas of Knowledge.

bioRxiv : the preprint server for biology·2025
Same journal

OpenIMC: an open-source platform for analyzing single-cell and spatial proteomics by imaging mass cytometry.

BMC bioinformatics·2026
Same journal

NAP: an open source pipeline for cross-domain microbiome profiling using Nanopore sequencing-derived amplicon data.

BMC bioinformatics·2026
Same journal

SurvGME: an R package for survival analysis with graphical and measurement error models.

BMC bioinformatics·2026
Same journal

SimMapNet: a Bayesian framework for gene regulatory network inference using gene ontology similarities as external hint.

BMC bioinformatics·2026
Same journal

Dual channel drug-drug interactions extraction based on cross attention.

BMC bioinformatics·2026
Same journal

FeSseqdb: a curated sequence-level database and interpretable machine learning framework for identifying iron-sulfur proteins.

BMC bioinformatics·2026
See all related articles

Related Experiment Video

Updated: Jan 24, 2026

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

2.1K

PathMe: merging and exploring mechanistic pathway knowledge.

Daniel Domingo-Fernández1,2, Sarah Mubeen3,4, Josep Marín-Llaó3

  • 1Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, 53754, Sankt Augustin, Germany. daniel.domingo.fernandez@scai.fraunhofer.de.

BMC Bioinformatics
|May 17, 2019
PubMed
Summary
This summary is machine-generated.

PathMe unifies pathway knowledge from multiple databases into a single schema, enabling better understanding of biological systems. This Python package and web tool facilitate pathway crosstalk analysis and consensus identification.

Keywords:
BioinformaticsBiological expression languageBiological networksDatabase integrationNetwork analysisPathways

More Related Videos

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

1.4K
Exploring the Role of Deontic Reasoning and World Knowledge in Wason´s Selection Task
06:08

Exploring the Role of Deontic Reasoning and World Knowledge in Wason´s Selection Task

Published on: July 22, 2025

929

Related Experiment Videos

Last Updated: Jan 24, 2026

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

2.1K
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

1.4K
Exploring the Role of Deontic Reasoning and World Knowledge in Wason´s Selection Task
06:08

Exploring the Role of Deontic Reasoning and World Knowledge in Wason´s Selection Task

Published on: July 22, 2025

929

Area of Science:

  • Systems Biology
  • Bioinformatics
  • Computational Biology

Background:

  • Biological systems complexity increases with multi-omics data.
  • Pathway databases aid molecular signature interpretation.
  • Lack of interoperability hinders pathway resource harmonization.

Purpose of the Study:

  • To unify pathway knowledge from disparate databases.
  • To develop a tool for harmonizing and exploring pathway data.
  • To enhance comprehension and modeling of biological systems.

Main Methods:

  • Developed PathMe, a Python package.
  • Utilized Biological Expression Language (BEL) as an integrative schema.
  • Created a complementary web application for user exploration.

Main Results:

  • Transformed pathway knowledge from three major databases into a unified abstraction.
  • Enabled comprehensive exploration of pathway crosstalk.
  • Facilitated comparison of consensus and discrepancies across databases.

Conclusions:

  • Harmonized major pathway databases into a unified schema for a holistic view.
  • Demonstrated PathMe's utility in integrating pathway landscapes.
  • Showcased PathMe's capability in comparing pathway consensus and exploring molecular-level crosstalk.