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 Experiment Videos

GenXref. VI: Automatic generation of links between two heterogeneous databases

F Achard1, P Dessen

  • 1GIS Infobiogen, Villejuif, France.

Bioinformatics (Oxford, England)
|April 1, 1998
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

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

Sort by
Same author

Human degradation of tropical moist forests is greater than previously estimated.

Nature·2024
Same author

Long-term (1990-2019) monitoring of forest cover changes in the humid tropics.

Science advances·2021
Same author

The microRNA-205-5p is correlated to metastatic potential of 21T series: A breast cancer progression model.

PloS one·2017
Same author

DNMT3A(R882H) mutant and Tet2 inactivation cooperate in the deregulation of DNA methylation control to induce lymphoid malignancies in mice.

Leukemia·2016
Same author

A common variant in RAB27A gene is associated with fractional exhaled nitric oxide levels in adults.

Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology·2014
Same author

Thrombocytopenia induced by the histone deacetylase inhibitor abexinostat involves p53-dependent and -independent mechanisms.

Cell death & disease·2013

GenXref automatically links genome data across databases, overcoming manual cross-referencing limitations. This system successfully generated over 10,000 links between gene and sequence databases.

Area of Science:

  • Bioinformatics
  • Genomics
  • Information Retrieval

Background:

  • Public databases contain vast amounts of unlinked genomic information.
  • Manual cross-referencing of this data is resource-intensive and costly.
  • Automated solutions are needed to improve data integration and accessibility.

Purpose of the Study:

  • To develop an automated system, genXref, for inferring links between heterogeneous biological databases.
  • To address the challenge of insufficient cross-referencing in public genome data.
  • To reduce the reliance on expensive manual expertise for data integration.

Main Methods:

  • Utilized information retrieval technology for link inference.
  • Developed the genXref system for automated cross-referencing.

Related Experiment Videos

  • Applied the system to link gene data from GDB with human sequences from GenBank.

    • Main Results:

    • GenXref successfully generated over 10,000 links between GDB genes and GenBank human sequences.
    • Achieved a precision of 83% in the generated links.
    • Demonstrated a recall of approximately 32% for the inferred links.

    Conclusions:

    • Automated link inference systems like genXref can significantly enhance the cross-referencing of public genome data.
    • GenXref provides a scalable and efficient method for integrating information from heterogeneous biological databases.
    • The system demonstrates the potential of information retrieval techniques in bioinformatics for data linkage.