We use cookies to understand how you use our site and to improve your experience. This includes personalizing content and advertising. To learn more, click here. By continuing to use our site, you accept our use of cookies. Cookie Policy.

Features Partner Sites Information LinkXpress
Sign In
Advertise with Us
LGC Clinical Diagnostics

Download Mobile App




Huge Modifiable Biomedical Database to Be Available on the Wikidata Site

By LabMedica International staff writers
Posted on 28 Apr 2016
Print article
Genome researchers are exploiting the power of the open Internet community Wikipedia database to create a comprehensive resource for geneticists, molecular biologists, and other interested life scientists.

While efficiency in generating scientific data improves almost daily, applying meaningful relationships between taxonomic and genetic entities requires a structured and integrative approach. Currently, knowledge is distributed across a multitude of sites from government-funded institutions to topic-focused databases to the supplemental tables of primary publications.

It is becoming increasingly difficult to organize this huge amount of information, since expert-curated databases are expensive to maintain and extend. To overcome these difficulties investigators at The Scripps Research Institute (La Jolla, CA, USA) have turned to the Wikimedia project Wikidata, an openly editable, semantic web compatible framework for knowledge representation. It is a project of the Wikimedia Foundation and offers knowledge integration capabilities ideally suited to the challenge of representing the exploding body of genomics information.

The investigators described initial priming of their Wikidata resource in a paper published in the March 17, 2016, online edition of the journal Database. They imported all human and mouse genes, and all human and mouse proteins into Wikidata. In total, 59,721 human genes and 73,355 mouse genes were imported from the [U.S.] National Center for Biotechnology Information (NCBI) and 27,306 human proteins and 16,728 mouse proteins were imported from the Swissprot subset of UniProt. As Wikidata is open and can be edited by anybody, this body of imported data is expected to serve as the starting point for integration of further data by scientists, the Wikidata community, and citizen scientists alike.

In a second paper, which was published in the March 28, 2016, online edition of the journal Database, the investigators focused on data of particular interest to molecular microbiologists and drug developers. This is an effort to develop a microbial specific data model, based on Wikidata’s semantic web compatibility, which represents bacterial species, strains, and the gene and gene products that define them. Currently, they have loaded 43,694 gene and 37,966 protein items for 21 species of bacteria, including the human pathogenic bacteria Chlamydia trachomatis. Using this pathogen as an example, they explored complex interactions between the pathogen, its host, associated genes, other microbes, disease, and drugs.

In the next phase of development, the investigators will add another 99 bacterial genomes and their gene and gene products, totaling about 900,000 additional entities.

“Open data is vital for progress and research,” said senior and contributing author Dr. Ben Good, assistant professor of molecular and experimental medicine at The Scripps Institute. “We need to break down those barriers.”

Related Links:
Scripps Research Institute

Platinum Member
COVID-19 Rapid Test
OSOM COVID-19 Antigen Rapid Test
HLX
Complement 3 (C3) Test
GPP-100 C3 Kit
New
Gold Member
Systemic Autoimmune Testing Assay
BioPlex 2200 ANA Screen with MDSS

Print article

Channels

Clinical Chemistry

view channel
Image: Reaching speeds up to 6,000 RPM, this centrifuge forms the basis for a new type of inexpensive, POC biomedical test (Photo courtesy of Duke University)

POC Biomedical Test Spins Water Droplet Using Sound Waves for Cancer Detection

Exosomes, tiny cellular bioparticles carrying a specific set of proteins, lipids, and genetic materials, play a crucial role in cell communication and hold promise for non-invasive diagnostics.... Read more

Molecular Diagnostics

view channel
Image: The study showed the blood-based cancer screening test detects 83% of people with colorectal cancer with specificity of 90% (Photo courtesy of Guardant Health)

Blood Test Shows 83% Accuracy for Detecting Colorectal Cancer

Colorectal cancer is the second biggest cause of cancer deaths among adults in the U.S., with forecasts suggesting 53,010 people might die from it in 2024. While fewer older adults are dying from this... Read more

Hematology

view channel
Image: The Gazelle Hb Variant Test (Photo courtesy of Hemex Health)

First Affordable and Rapid Test for Beta Thalassemia Demonstrates 99% Diagnostic Accuracy

Hemoglobin disorders rank as some of the most prevalent monogenic diseases globally. Among various hemoglobin disorders, beta thalassemia, a hereditary blood disorder, affects about 1.5% of the world's... Read more

Microbiology

view channel
Image: The new platform is designed to perform blood-based diagnoses of nontuberculosis mycobacteria (Photo courtesy of 123RF)

New Blood Test Cuts Diagnosis Time for Nontuberculous Mycobacteria Infections from Months to Hours

Breathing in nontuberculous mycobacteria (NTM) is a common experience for many people. These bacteria are present in water systems, soil, and dust all over the world and usually don't cause any problems.... Read more

Industry

view channel
Image: These new assays are being developed for use on the recently introduced DxI 9000 Immunoassay Analyzer (Photo courtesy of Beckman Coulter)

Beckman Coulter and Fujirebio Expand Partnership on Neurodegenerative Disease Diagnostics

Beckman Coulter Diagnostics (Brea, CA, USA) and Fujirebio Diagnostics (Tokyo, Japan) have expanded their partnership focused on the development, manufacturing and clinical adoption of neurodegenerative... Read more
Copyright © 2000-2024 Globetech Media. All rights reserved.