Related Experiment Video
Updated: May 5, 2026
07:35
A Knowledge Graph Approach to Elucidate the Role of Organellar Pathways in Disease via Biomedical Reports
Published on: October 13, 2023
2.6K
Mining Genotype-Phenotype Associations from Public Knowledge Sources via Semantic Web Querying.
Richard C Kiefer1, Robert R Freimuth, Christopher G Chute
1Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA.
Summary
This study uses Semantic Web technologies to improve disease-gene association data in GeneWiki+ and OMIM. SPARQL queries help validate existing and discover new genotype-phenotype links for chronic diseases.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- GeneWiki+ and OMIM are key resources for disease-gene and gene-SNP associations.
- Manual curation of these databases is time-consuming and prone to errors.
Purpose of the Study:
- To investigate Semantic Web technologies for validating and discovering genotype-phenotype associations.
- To assess the applicability of SPARQL queries for data in GeneWiki+ and OMIM.
Main Methods:
- Utilized Semantic Web technologies, specifically SPARQL queries.
- Applied queries to identify associations in GeneWiki+ and OMIM for chronic diseases.
Main Results:
- Demonstrated the effectiveness of SPARQL for identifying unstated associations.
- Reported preliminary findings on the coverage, completeness, and validity of identified associations.
Conclusions:
- Semantic Web querying offers benefits for validating existing disease-gene associations.
- Novel associations can be identified, but further evaluation is needed for practical application.
Related Concept Videos
01:11Genome-wide Association Studies-GWAS
12.6K
Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
GWAS does not require the identification of the target gene involved in...
12.6K
02:27Background and Environment Affect Phenotype
5.8K
Although the genetic makeup of an organism plays a major role in determining the phenotype, there are also several environmental factors, such as temperature, oxygen availability, presence of mutagens, that can alter an organism’s phenotype.
An example of how genetic background affects phenotype can be seen in horses. The Extension gene in horses is responsible for their coat color. A wild-type gene (EE) produces black pigment in the coat, while a mutant gene (ee) produces red pigment. A...
An example of how genetic background affects phenotype can be seen in horses. The Extension gene in horses is responsible for their coat color. A wild-type gene (EE) produces black pigment in the coat, while a mutant gene (ee) produces red pigment. A...
5.8K
02:46Genetic Screens
4.6K
Genetic screens are tools used to identify genes and mutations responsible for phenotypes of interest. Genetic screens help identify individuals or a group of people at risk of developing genetic diseases and help them with early intervention, targeted therapy, and reproductive options.
Forward genetic screens
Forward or “classical” genetic screens involve creating random mutations in an organism’s DNA using radiation, mutagens, or insertion of additional bases, which...
Forward genetic screens
Forward or “classical” genetic screens involve creating random mutations in an organism’s DNA using radiation, mutagens, or insertion of additional bases, which...
4.6K
01:33Pleiotropy
31.2K
Pleiotropy is the phenomenon in which a single gene impacts multiple, seemingly unrelated phenotypic traits. For example, defects in the SOX10 gene cause Waardenburg Syndrome Type 4, or WS4, which can cause defects in pigmentation, hearing impairments, and an absence of intestinal contractions necessary for elimination. This diversity of phenotypes results from the expression pattern of SOX10 in early embryonic and fetal development. SOX10 is found in neural crest cells that form melanocytes,...
31.2K
01:43Incomplete Dominance
19.0K
Gregor Mendel's work (1822 - 1884) was primarily focused on pea plants. Through his initial experiments, he determined that every gene in a diploid cell has two variants called alleles inherited from each parent. He suggested that amongst these two alleles, one allele is dominant in character and the other recessive. The combination of alleles determines the phenotype of a gene in an organism.
19.0K
01:29Pharmacogenetic Phenotypes: Alterations in Pharmacokinetics, Drug Targets and Biologic Milieu
159
Genetic variations significantly influence drug response through pharmacokinetics, receptor interactions, and biologic milieu modifications. Pharmacokinetic alterations impact drug metabolism and clearance, affecting efficacy and toxicity. Variants in drug-metabolizing enzymes, such as CYP2C9 and CYP2C19, alter drug activation and elimination. For example, CYP2C9 loss-of-function variants require lower warfarin doses to prevent excessive bleeding, while CYP2C19 variants reduce clopidogrel...
159