Related Experiment Video
Updated: Apr 12, 2026
09:37
Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information
Published on: August 15, 2019
10.6K
Identifying redundant and missing relations in the gene ontology
1ERIAS, INSERM U897, ISPED, University of Bordeaux, Bordeaux, France.
Studies in Health Technology and Informatics
|May 21, 2015
Summary
This study audited Gene Ontology (GO) relationships, finding over 1,000 redundant relations and 500 missing conditions. Automated reasoning successfully detected inconsistencies in GO
Area of Science:
- Bioinformatics
- Ontology Engineering
- Computational Biology
Background:
- The Gene Ontology (GO) is crucial for annotating gene and protein functions.
- Automated reasoning aids GO maintenance and coherence checks.
- Despite efforts, inconsistencies can persist within GO relationships.
Purpose of the Study:
- To audit Gene Ontology (GO) relationships for inconsistencies.
- To identify redundant relations and missing necessary and sufficient conditions within GO.
- To enhance the logical integrity of the GO database.
Main Methods:
- Applied automated reasoning to GO relationships.
- Detected redundant relations between GO concepts.
- Identified missing necessary and sufficient conditions using concept name structures.
Main Results:
- Discovered over 1,000 redundant relations in GO.
- Identified approximately 500 missing necessary and sufficient conditions.
- Demonstrated the effectiveness of the auditing approach.
Conclusions:
- The automated auditing approach successfully detected inconsistencies in GO relations.
- Further lexical analysis and use of synonyms/definitions could identify more conditions.
- Multiple necessary and sufficient conditions may signal potential GO inconsistencies.
Related Concept Videos
01:57Gene Families
10.3K
Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
10.3K
01:57Gene Families
4.0K
4.0K
02:37Gene Duplication and Divergence
8.3K
The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are...
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are...
8.3K
03:36Genome Annotation and Assembly
22.2K
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
22.2K
02:54Evolutionary Relationships through Genome Comparisons
7.3K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
7.3K
02:26Protein Networks
4.7K
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
4.7K