Nav: Home

OncoMX knowledgebase enables research of cancer biomarkers and related evidence

March 23, 2020

WASHINGTON (March 23, 2020) -- The OncoMX knowledgebase will improve the exploration and research of cancer biomarkers in the context of related evidence, according to a recent article from the George Washington University (GW). The article is published in the Journal of Clinical Oncology Clinical Cancer Informatics and is part of a special series called "Informatics Tools for Cancer Research and Care."

Cancer biomarkers, a sort of biological fingerprint, are molecules in bodily fluids or tissues that can indicate processes associated with various cancers. With increased research and funding, more potentially novel cancer biomarkers are being reported. However, challenges remain when it comes to reproducibility of initial findings, clinical validation, and access to harmonized biomarker data.

OncoMX, a knowledgebase and web portal for exploring cancer biomarker data and related evidence, was developed to integrate cancer biomarker and relevant data types into a meta-portal, enabling the research of cancer biomarkers side by side with other pertinent multidimensional data types.

"Many research groups and consortia have conducted studies reporting potentially actionable and available cancer biomarker data," said Hayley Dingerdissen, a PhD student at the GW Institute for Biomedical Sciences and first author of the paper. "It seems reasonable that these data could be combined into a single meta-resource to facilitate more efficient cancer biomarker research and exploration, but the reality is there are numerous challenges to combining heterogeneously structured data in a unified way."

To address the challenges associated with data collection and access, the OncoMX team worked to integrate public cancer biomarker data from the Early Detection Research Network (EDRN) and the FDA, as well as additional related data around persistent identifiers, which are long-lasting references to a document, file, webpage, or other object. The team integrated information such as cancer mutation, cancer differential expression, cancer expression specificity, healthy gene expression from human and mouse, and biomarker data.

The resulting data provides the foundation for integration of heterogeneous biomarker evidence, using the BioCompute Object framework, into OncoMX for improved cancer biomarker exploration.

"OncoMX is designed to combine existing biomarker-relevant data with newly generated data as it becomes available, establishing a resource customized for cancer biomarker research," said Raja Mazumder, PhD, professor of biochemistry and molecular medicine at the GW School of Medicine and Health Sciences, a member of the GW Cancer Center, and senior author on the study. "The focus on ontology-driven unification of biomarker data and cross comparison of various related experimental data, particularly inclusion of large-scale literature mining findings, NCI's EDRN and FDA biomarkers, and healthy gene expression data from Bgee are unique to OncoMX compared to other integrated cancer resources."

Moving forward, the OncoMX team is actively seeking new data types, such as imaging, glycan biomarkers, drug targets, alternative splicing, and more. They also continue to work on extending the data model to new types, integrating FDA data sets for additional cancers upon user request, and expanding cross references to key cancer resources.
-end-
The team at GW collaborated with researchers at NASA Jet Propulsion Laboratory, the SIB Swiss Institute of Bioinformatics, and the University of Delaware.

The article, titled "OncoMX: A Knowledgebase for Exploring Cancer Biomarkers in the Context of Related Cancer and Healthy Data," is published in the Journal of Clinical Oncology Clinical Cancer Informatics and is available at ascopubs.org/doi/full/10.1200/CCI.19.00117.

George Washington University

Related Cancer Articles:

Cancer mortality continues steady decline, driven by progress against lung cancer
The cancer death rate declined by 29% from 1991 to 2017, including a 2.2% drop from 2016 to 2017, the largest single-year drop in cancer mortality ever reported.
Stress in cervical cancer patients associated with higher risk of cancer-specific mortality
Psychological stress was associated with a higher risk of cancer-specific mortality in women diagnosed with cervical cancer.
Cancer-sniffing dogs 97% accurate in identifying lung cancer, according to study in JAOA
The next step will be to further fractionate the samples based on chemical and physical properties, presenting them back to the dogs until the specific biomarkers for each cancer are identified.
Moffitt Cancer Center researchers identify one way T cell function may fail in cancer
Moffitt Cancer Center researchers have discovered a mechanism by which one type of immune cell, CD8+ T cells, can become dysfunctional, impeding its ability to seek and kill cancer cells.
More cancer survivors, fewer cancer specialists point to challenge in meeting care needs
An aging population, a growing number of cancer survivors, and a projected shortage of cancer care providers will result in a challenge in delivering the care for cancer survivors in the United States if systemic changes are not made.
New cancer vaccine platform a potential tool for efficacious targeted cancer therapy
Researchers at the University of Helsinki have discovered a solution in the form of a cancer vaccine platform for improving the efficacy of oncolytic viruses used in cancer treatment.
American Cancer Society outlines blueprint for cancer control in the 21st century
The American Cancer Society is outlining its vision for cancer control in the decades ahead in a series of articles that forms the basis of a national cancer control plan.
Oncotarget: Cancer pioneer employs physics to approach cancer in last research article
In the cover article of Tuesday's issue of Oncotarget, James Frost, MD, PhD, Kenneth Pienta, MD, and the late Donald Coffey, Ph.D., use a theory of physical and biophysical symmetry to derive a new conceptualization of cancer.
Health indicators for newborns of breast cancer survivors may vary by cancer type
In a study published in the International Journal of Cancer, researchers from the UNC Lineberger Comprehensive Cancer Center analyzed health indicators for children born to young breast cancer survivors in North Carolina.
Few women with history of breast cancer and ovarian cancer take a recommended genetic test
More than 80 percent of women living with a history of breast or ovarian cancer at high-risk of having a gene mutation have never taken the test that can detect it.
More Cancer News and Cancer Current Events

Trending Science News

Current Coronavirus (COVID-19) News

Top Science Podcasts

We have hand picked the top science podcasts of 2020.
Now Playing: TED Radio Hour

Listen Again: Reinvention
Change is hard, but it's also an opportunity to discover and reimagine what you thought you knew. From our economy, to music, to even ourselves–this hour TED speakers explore the power of reinvention. Guests include OK Go lead singer Damian Kulash Jr., former college gymnastics coach Valorie Kondos Field, Stockton Mayor Michael Tubbs, and entrepreneur Nick Hanauer.
Now Playing: Science for the People

#562 Superbug to Bedside
By now we're all good and scared about antibiotic resistance, one of the many things coming to get us all. But there's good news, sort of. News antibiotics are coming out! How do they get tested? What does that kind of a trial look like and how does it happen? Host Bethany Brookeshire talks with Matt McCarthy, author of "Superbugs: The Race to Stop an Epidemic", about the ins and outs of testing a new antibiotic in the hospital.
Now Playing: Radiolab

Dispatch 6: Strange Times
Covid has disrupted the most basic routines of our days and nights. But in the middle of a conversation about how to fight the virus, we find a place impervious to the stalled plans and frenetic demands of the outside world. It's a very different kind of front line, where urgent work means moving slow, and time is marked out in tiny pre-planned steps. Then, on a walk through the woods, we consider how the tempo of our lives affects our minds and discover how the beats of biology shape our bodies. This episode was produced with help from Molly Webster and Tracie Hunte. Support Radiolab today at Radiolab.org/donate.