Background
Scientists have been searching for DNA methylation biomarkers to improve the diagnosis and management of cancer for over a decade, but for various reasons and despite all the resources that have been invested, translation of cancer biomarkers into routine clinical practice only rarely occurs.
In an attempt to address this so-called translational research valley of death, we are mobilizing an international team of scientists, scientific journals, academic institutions, funding agencies, private partners, biobanks and patient advocacy groups. Our goal is to improve the reliability, efficiency and translation of DNA methylation marker research.
To achieve our goal, we plan to build a FAIR database of all published cancer DNA methylation markers. Such a database would be a valuable resource for our field by itself, but we also aim to integrate it with existing biobanks and other infrastructure initiatives.
Development
My main responsibility in the atlas project is the construction of the marker database. This includes building an annotated corpus of relevant literature and the development of the online submission and search platforms. I am also implementing automated and NLP-based techniques to support the manual data extraction from scientific publications.