OncoMX: A Knowledgebase for Exploring Cancer Biomarkers in the Context of Related Cancer and Healthy Data.

Details

Serval ID
serval:BIB_BC34650B96ED
Type
Article: article from journal or magazin.
Collection
Publications
Title
OncoMX: A Knowledgebase for Exploring Cancer Biomarkers in the Context of Related Cancer and Healthy Data.
Journal
JCO clinical cancer informatics
Author(s)
Dingerdissen H.M., Bastian F., Vijay-Shanker K., Robinson-Rechavi M., Bell A., Gogate N., Gupta S., Holmes E., Kahsay R., Keeney J., Kincaid H., King C.H., Liu D., Crichton D.J., Mazumder R.
ISSN
2473-4276 (Electronic)
ISSN-L
2473-4276
Publication state
Published
Issued date
03/2020
Peer-reviewed
Oui
Volume
4
Pages
210-220
Language
english
Notes
Publication types: Journal Article
Publication Status: ppublish
Abstract
The purpose of OncoMX <sup>1</sup> knowledgebase development was 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.
Cancer mutation, cancer differential expression, cancer expression specificity, healthy gene expression from human and mouse, literature mining for cancer mutation and cancer expression, and biomarker data were integrated, unified by relevant biomedical ontologies, and subjected to rule-based automated quality control before ingestion into the database.
OncoMX provides integrated data encompassing more than 1,000 unique biomarker entries (939 from the Early Detection Research Network [EDRN] and 96 from the US Food and Drug Administration) mapped to 20,576 genes that have either mutation or differential expression in cancer. Sentences reporting mutation or differential expression in cancer were extracted from more than 40,000 publications, and healthy gene expression data with samples mapped to organs are available for both human genes and their mouse orthologs.
OncoMX has prioritized user feedback as a means of guiding development priorities. By mapping to and integrating data from several cancer genomics resources, it is hoped that OncoMX will foster a dynamic engagement between bioinformaticians and cancer biomarker researchers. This engagement should culminate in a community resource that substantially improves the ability and efficiency of exploring cancer biomarker data and related multidimensional data.
Pubmed
Open Access
Yes
Create date
10/03/2020 16:53
Last modification date
13/03/2020 7:26
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