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
Sekisui Diagnostics UK Ltd.

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


Print article

Channels

Clinical Chemistry

view channel
Image: The new ADLM guidance will help healthcare professionals navigate respiratory virus testing in a post-COVID world (Photo courtesy of 123RF)

New ADLM Guidance Provides Expert Recommendations on Clinical Testing For Respiratory Viral Infections

Respiratory tract infections, predominantly caused by viral pathogens, are a common reason for healthcare visits. Accurate and swift diagnosis of these infections is essential for optimal patient management.... Read more

Molecular Diagnostics

view channel
Image: The blood test uses AI to predict Parkinson’s seven years before onset of symptoms (Photo courtesy of Kateryna Kon/Shutterstock)

AI-Powered Blood Test Predicts Parkinson's Seven Years before Symptoms Appear

Parkinson’s disease is currently the fastest-growing neurodegenerative disorder worldwide, affecting nearly 10 million people globally. It is a progressive disease caused by the deterioration and death... Read more

Hematology

view channel
Image: The CAPILLARYS 3 DBS devices have received U.S. FDA 510(k) clearance (Photo courtesy of Sebia)

Next Generation Instrument Screens for Hemoglobin Disorders in Newborns

Hemoglobinopathies, the most widespread inherited conditions globally, affect about 7% of the population as carriers, with 2.7% of newborns being born with these conditions. The spectrum of clinical manifestations... Read more

Industry

view channel
Image: For 46 years, Roche and Hitachi have collaborated to deliver innovative diagnostic solutions (Photo courtesy of Roche)

Roche and Hitachi High-Tech Extend 46-Year Partnership for Breakthroughs in Diagnostic Testing

Roche (Basel, Switzerland) and Hitachi High-Tech (Tokyo, Japan) have renewed their collaboration agreement, committing to a further 10 years of partnership. This extension brings together their long-standing... Read more
Copyright © 2000-2024 Globetech Media. All rights reserved.