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

Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

14.0K
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...
14.0K
Incomplete Dominance01:43

Incomplete Dominance

25.3K
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.
25.3K
Genomics02:02

Genomics

37.1K
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...
37.1K
Pleiotropy01:33

Pleiotropy

40.9K
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,...
40.9K
Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

15.7K
A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
15.7K
X-linked Traits01:19

X-linked Traits

55.2K
In most mammalian species, females have two X sex chromosomes and males have an X and Y. As a result, mutations on the X chromosome in females may be masked by the presence of a normal allele on the second X. In contrast, a mutation on the X chromosome in males more often causes observable biological defects, as there is no normal X to compensate. Trait variations arising from mutations on the X chromosome are called “X-linked”.
55.2K

You might also read

Related Articles

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

Sort by
Same author

RankVar: machine learning-based variant ranking and reinterpretation for rare genetic diseases.

Genome medicine·2026
Same author

Improving Retrieval-Augmented Generation without Taxonomy-based Error Categorization.

Proceedings of the conference. Association for Computational Linguistics. Meeting·2026
Same author

Evaluating unsupervised and rule-based phenotyping methods versus administrative code counts for systemic sclerosis identification.

Seminars in arthritis and rheumatism·2026
Same author

Hard to Halt: Automation Bias in Agent-Driven Sequencing Prior Authorization Workflows.

medRxiv : the preprint server for health sciences·2026
Same author

Unsupervised characterization of 100,272 EHR patients identifies high-risk groups and comorbidities linked to premature aging.

NPJ digital medicine·2026
Same author

TimeX: Phenotype Onset Extraction from Clinical Narratives.

npj health systems·2026

Related Experiment Video

Updated: Aug 31, 2025

In Vivo Functional Study of Disease-associated Rare Human Variants Using Drosophila
06:41

In Vivo Functional Study of Disease-associated Rare Human Variants Using Drosophila

Published on: August 20, 2019

13.8K

OARD: Open annotations for rare diseases and their phenotypes based on real-world data.

Cong Liu1, Casey N Ta1, Jim M Havrilla2

  • 1Department of Biomedical Informatics, Columbia University, New York, NY 10032, USA.

American Journal of Human Genetics
|August 23, 2022
PubMed
Summary

We introduce Open Annotation for Rare Diseases (OARD), a new resource using electronic health records to identify rare disease phenotypes. OARD significantly expands rare disease knowledge beyond manual curation, enabling data-driven research.

Keywords:
electronic health recordshuman phenotype ontologyknowledge graphnatural language processingopen data sharingphenotype associationrare disease

More Related Videos

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information
09:37

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information

Published on: August 15, 2019

9.9K
In Vivo Modeling of the Morbid Human Genome using Danio rerio
12:31

In Vivo Modeling of the Morbid Human Genome using Danio rerio

Published on: August 24, 2013

20.8K

Related Experiment Videos

Last Updated: Aug 31, 2025

In Vivo Functional Study of Disease-associated Rare Human Variants Using Drosophila
06:41

In Vivo Functional Study of Disease-associated Rare Human Variants Using Drosophila

Published on: August 20, 2019

13.8K
Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information
09:37

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information

Published on: August 15, 2019

9.9K
In Vivo Modeling of the Morbid Human Genome using Danio rerio
12:31

In Vivo Modeling of the Morbid Human Genome using Danio rerio

Published on: August 24, 2013

20.8K

Area of Science:

  • Genomics
  • Medical Informatics
  • Computational Biology

Background:

  • Rare genetic disease diagnosis relies on phenotype knowledgebases, often manually curated from case reports.
  • Electronic health records (EHRs) remain underutilized for deriving comprehensive rare disease annotations.

Purpose of the Study:

  • To present Open Annotation for Rare Diseases (OARD), a novel resource derived from real-world EHR data.
  • To enhance rare disease phenotyping by leveraging large-scale clinical data and advanced NLP.

Main Methods:

  • Developed OARD using EHR data from over 10 million individuals across two institutions.
  • Employed ontology mapping and natural-language-processing (NLP) to extract rare diseases and phenotypes from clinical narratives, billing codes, and lab tests.
  • Validated OARD's derived prevalence against existing knowledgebases.

Main Results:

  • OARD successfully extracted rare disease and phenotypic concepts from extensive EHR data.
  • Identified over 1 million novel disease-phenotype associations, with over 60% confirmed by manual review.
  • Demonstrated high correlation between OARD-derived and existing rare disease prevalence data.

Conclusions:

  • OARD offers a data-driven, scalable alternative to manual annotation for rare disease phenotypes.
  • This resource facilitates data-driven research by enabling privacy-preserving sharing of aggregated statistics.
  • OARD significantly expands the annotation of rare diseases and their associated phenotypes.