Abstract
Increasing efforts are being dedicated towards improving cancer care via personalized medicine. These efforts depend to a large degree on the availability of a knowledge foundation. Unfortunately, existing knowledge linking cancer drugs and potential efficacy biomarkers is in its infancy; and where links are known, they are frequently unstructured and poorly documented. We have developed a new open-access knowledgebase for precision cancer medicine (the PCM Wiki and Knowledgebase). This knowledgebase was constructed using an innovative, two-pronged approach involving a structured knowledgebase at the back-end, and an intuitive knowledge-sharing interface and user-friendly query engine in front. The knowledgebase was seeded with several patient case reports and information was mined via text-mining and literature review by human curators. Using our novel Wiki-based platform to present and share knowledge stored in the PCM knowledgebase, users are able to suggest corrections, propose additions or point to errors in the knowledgebase. The result is a community-driven evolving knowledgebase holding integrated and consolidated knowledge of markers and indications for personalized cancer medicine. We suggest that the PCM Knowledgebase and Wiki could serve as an important tool for the advancement of clinical trials and care in the field of precision cancer medicine.
Highlights
Personalized, or precision medicine is the tailoring of specific therapeutics for a specific individual, utilizing pharmacogenetic and/or pharmacogenomic information [1,2]
We have developed a unique knowledgebase utilizing a novel approach for capturing, storing and sharing knowledge concerned with precision cancer medicine
The knowledgebase holds information mined from the literature regarding different types of cancers, drugs, genetic markers and their co-occurrences in publications, as well as case studies introduced through a specialized form
Summary
Personalized, or precision medicine is the tailoring of specific therapeutics for a specific individual, utilizing pharmacogenetic and/or pharmacogenomic information [1,2]. Increasing efforts are being dedicated towards improving cancer care via personalized medicine These endeavors are largely based on comparing the properties of a given tumor to prior knowledge about drug efficacy. WINTHER clinical trial [6], over- or under-expressed transcripts are considered for their value in predicting drug efficacy In this approach, tumor-specific gene expression patterns are compared to prior literature-based knowledge, using known or inferred links between drug efficacy and alterations in gene expression. The Integrity database [12], for example, contains a large amount of marker-related information, but was designed to support research rather than for clinical care Another related database, the My Cancer Genome database [13], provides users with information regarding cancer-associated genes, possible targeted therapies and related clinical trials. To demonstrate the usefulness of this approach, the knowledgebase was seeded with actual case reports and information mined from the relevant literature that can be edited by the community
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