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

Mutations01:35

Mutations

31.2K
Mutations are changes in the sequence of DNA. These changes can occur spontaneously or they can be induced by exposure to environmental factors. Mutations can be characterized in a number of different ways: whether and how they alter the amino acid sequence of the protein, whether they occur over a small or large area of DNA, and whether they occur in somatic cells or germline cells.
Chromosomal Alterations Are Large-Scale Mutations
While point mutations are changes in a single nucleotide in...
31.2K
Mutations01:39

Mutations

66.8K
Overview
66.8K
Mutation, Gene Flow, and Genetic Drift01:09

Mutation, Gene Flow, and Genetic Drift

53.1K
In a population that is not at Hardy-Weinberg equilibrium, the frequency of alleles changes over time. Therefore, any deviations from the five conditions of Hardy-Weinberg equilibrium can alter the genetic variation of a given population. Conditions that change the genetic variability of a population include mutations, natural selection, non-random mating, gene flow, and genetic drift (small population size).
53.1K
Mismatch Repair01:20

Mismatch Repair

5.4K
Organisms are capable of detecting and fixing nucleotide mismatches that occur during DNA replication. This sophisticated process requires identifying the new strand and replacing the erroneous bases with correct nucleotides. Mismatch repair is coordinated by many proteins in both prokaryotes and eukaryotes.
The Mutator Protein Family Plays a Key Role in DNA Mismatch Repair
The human genome has more than 3 billion base pairs of DNA per cell. Prior to cell division, that vast amount of genetic...
5.4K
In-vitro Mutagenesis01:16

In-vitro Mutagenesis

14.8K
To learn more about the function of a gene, researchers can observe what happens when the gene is inactivated or “knocked out,” by creating genetically engineered knockout animals. Knockout mice have been particularly useful as models for human diseases such as cancer, Parkinson’s disease, and diabetes.
14.8K
Mutations in Microorganisms01:18

Mutations in Microorganisms

1.2K
Mutations are heritable changes in an organism’s genome involving alterations in the base sequence of DNA or RNA. These changes can influence cellular processes and phenotypic traits, potentially transforming the unaltered wild type into a mutant form. Such changes, termed forward mutations, are pivotal in shaping the genetic diversity of organisms.RNA viruses exhibit the highest mutation rates due to the absence of robust proofreading mechanisms during genome replication. In contrast,...
1.2K

You might also read

Related Articles

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

Sort by
Same author

Response strategies to acute and chronic environmental stress in the arctic breeding Lapland longspur (Calcarius lapponicus).

Communications biology·2024
Same author

A phospho-dawn of protein modification anticipates light onset in the picoeukaryote Ostreococcus tauri.

Journal of experimental botany·2023
Same author

HAIKU: A Semantic Framework for Surveillance of Healthcare-Associated Infections.

Procedia computer science·2020
Same author

The quail genome: insights into social behaviour, seasonal biology and infectious disease response.

BMC biology·2020
Same author

A Surveillance Infrastructure for Malaria Analytics: Provisioning Data Access and Preservation of Interoperability.

JMIR public health and surveillance·2018
Same author

From Cues to Nudge: A Knowledge-Based Framework for Surveillance of Healthcare-Associated Infections.

Journal of medical systems·2015
Same journal

Immune biomarkers, profiles, and responses: a vaccine ontology perspective.

Journal of biomedical semantics·2026
Same journal

A pragmatist approach to bridging tables and ontologies through LinkML and punning.

Journal of biomedical semantics·2026
Same journal

FAIR in practice: minimum metadata schema for bioinformatics analytics by machines.

Journal of biomedical semantics·2026
Same journal

Prenatal monitoring in primary health care: a design science research-based approach to FHIR interoperability.

Journal of biomedical semantics·2026
Same journal

From narrative evidence to computable knowledge: a decision-relevant corpus for medicinal herb-disease relationships.

Journal of biomedical semantics·2026
Same journal

BERTopic-driven term extraction from biomedical texts toward ontology population: evaluating vaccine ontology with Plotkin's vaccines corpus.

Journal of biomedical semantics·2026
See all related articles

Related Experiment Video

Updated: May 2, 2026

Studying Ribonucleotide Incorporation: Strand-specific Detection of Ribonucleotides in the Yeast Genome and Measuring Ribonucleotide-induced Mutagenesis
09:04

Studying Ribonucleotide Incorporation: Strand-specific Detection of Ribonucleotides in the Yeast Genome and Measuring Ribonucleotide-induced Mutagenesis

Published on: July 26, 2018

7.5K

Benchmarking infrastructure for mutation text mining.

Artjom Klein1, Alexandre Riazanov, Matthew M Hindle

  • 1Computer Science And Applied Statistics Department, University of New Brunswick, Saint John, Canada. artjom.unb@gmail.com.

Journal of Biomedical Semantics
|February 27, 2014
PubMed
Summary
This summary is machine-generated.

A new infrastructure for benchmarking mutation text mining systems has been developed. This system uses semantic standards and curated data to improve the evaluation of mutation information extraction.

More Related Videos

A Deep-sequencing-assisted, Spontaneous Suppressor Screen in the Fission Yeast Schizosaccharomyces pombe
07:55

A Deep-sequencing-assisted, Spontaneous Suppressor Screen in the Fission Yeast Schizosaccharomyces pombe

Published on: March 7, 2019

8.4K
An Array-based Comparative Genomic Hybridization Platform for Efficient Detection of Copy Number Variations in Fast Neutron-induced Medicago truncatula Mutants
09:32

An Array-based Comparative Genomic Hybridization Platform for Efficient Detection of Copy Number Variations in Fast Neutron-induced Medicago truncatula Mutants

Published on: November 8, 2017

7.3K

Related Experiment Videos

Last Updated: May 2, 2026

Studying Ribonucleotide Incorporation: Strand-specific Detection of Ribonucleotides in the Yeast Genome and Measuring Ribonucleotide-induced Mutagenesis
09:04

Studying Ribonucleotide Incorporation: Strand-specific Detection of Ribonucleotides in the Yeast Genome and Measuring Ribonucleotide-induced Mutagenesis

Published on: July 26, 2018

7.5K
A Deep-sequencing-assisted, Spontaneous Suppressor Screen in the Fission Yeast Schizosaccharomyces pombe
07:55

A Deep-sequencing-assisted, Spontaneous Suppressor Screen in the Fission Yeast Schizosaccharomyces pombe

Published on: March 7, 2019

8.4K
An Array-based Comparative Genomic Hybridization Platform for Efficient Detection of Copy Number Variations in Fast Neutron-induced Medicago truncatula Mutants
09:32

An Array-based Comparative Genomic Hybridization Platform for Efficient Detection of Copy Number Variations in Fast Neutron-induced Medicago truncatula Mutants

Published on: November 8, 2017

7.3K

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Natural Language Processing

Background:

  • Developing and evaluating mutation text mining systems is challenging due to the lack of standardized benchmarking infrastructure.
  • Existing evaluation frameworks primarily focus on other biological entities, leaving a gap for mutation-specific data.

Purpose of the Study:

  • To propose and develop a community-oriented infrastructure for the annotation and benchmarking of mutation text mining systems.
  • To facilitate the development, testing, benchmarking, and comparison of systems for extracting mutation information from text.

Main Methods:

  • Utilized semantic web standards, including RDF for annotations and an OWL ontology for data schema.
  • Employed SPARQL for computing performance metrics, minimizing the need for programming.
  • Created a substantial collection of manually curated documents for mutation grounding and impact extraction experiments.

Main Results:

  • Developed a core infrastructure comprising an ontology, SPARQL queries, and a curated document corpus.
  • The infrastructure supports the evaluation of mutation grounding and mutation impact extraction.
  • The system is designed for extensibility and out-of-the-box usability.

Conclusions:

  • The developed infrastructure provides a foundational tool for benchmarking mutation text mining tasks.
  • The use of RDF and OWL ensures the extensibility and semantic richness of the corpora.
  • The infrastructure is ready for community adoption and use in various applications.