Related Experiment Video
Updated: May 24, 2026
08:03
Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
Published on: December 7, 2021
BioQ: tracing experimental origins in public genomic databases using a novel data provenance model
Scott F Saccone1, Jiaxi Quan, Peter L Jones
1Department of Psychiatry, Washington University, Saint Louis, MO 63110, USA. ssaccone@wustl.edu
Bioinformatics (Oxford, England)
|March 20, 2012
Summary
BioQ is a new web application that traces the experimental origins of genomic data, enhancing reliability in genetic studies. It helps researchers assess data integrity by linking it to original subjects and biologics.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- Public genomic databases are crucial for human disease genetic studies and genomic medicine.
- Current databases often lack systematic tools to determine the experimental origins of data.
- Assessing data reliability is essential for accurate genomic research.
Purpose of the Study:
- To introduce a novel data provenance model for assessing the reliability of genomic data.
- To implement this model in a public web application, BioQ.
- To enable systematic tracing of experimental origins for genomic data.
Main Methods:
- Developed a data provenance model.
- Implemented the model in a public web application called BioQ.
- BioQ visualizes data provenance and allows exploration of experimental process flow.
- Integrated human genetic variation databases like HapMap and 1000 Genomes.
Main Results:
- BioQ enables systematic tracing of genomic data back to original subjects and biologics.
- The application provides tools for detailed data exploration and documentation.
- Investigators can visualize and explore data provenance effectively.
- Enhanced reliability assessment for data in public genomic databases.
Conclusions:
- BioQ provides a robust solution for data provenance in genomic medicine.
- The tool improves the systematic assessment of genomic data reliability.
- Facilitates more trustworthy in silico integrative genomics research.
Related Concept Videos
02:02Genomics
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...
02:54Evolutionary Relationships through Genome Comparisons
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...
03:00Next-generation Sequencing
The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
01:29Modern Molecular Taxonomy
Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
02:32Exon Recombination
The evolution of new genes is critical for speciation. Exon recombination, also known as exon shuffling or domain shuffling, is an important means of new gene formation. It is observed across vertebrates, invertebrates, and in some plants such as potatoes and sunflowers. During exon recombination, exons from the same or different genes recombine and produce new exon-intron combinations, which might evolve into new genes.
Exon shuffling follows “splice frame rules.” Each exon has three reading...
Exon shuffling follows “splice frame rules.” Each exon has three reading...
01:57Sanger Sequencing
DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...