Creating an Ignorance-Base: Exploring Known Unknowns in the Scientific Literature

Background Research progresses through the process of making the unknown unknowns into known unknowns, then into knowns. Many knowledge-bases exist to capture the knowns and can be used by graduate students to explore a topic or help researchers contextualize experimental results using concept enrichment methods. The unknowns surrounding these applications are equally as important as the knowns to continue to find the most pertinent questions and their answers. Prior work on known unknowns has sought to understand the phenomenon, annotate it, and automate its identification. However, no knowledge-bases exist to capture them and facilitate the widespread search for questions in order to find new avenues for exploration from a given topic or experimental results. The prenatal nutrition field especially could benefit from this due to the ethical and legal considerations in studying this underserved population. Results We present the first ignorance-base, a knowledge-base created from combining ignorance and biomedical concept classifiers over the prenatal nutrition literature to annotate the known unknowns or ignorance statements. Motivated by a graduate student’s search for a thesis topic in vitamin D, we found three new interesting avenues for exploration (immune system, respiratory system, and brain development) that were buried among the many standard enriched concepts but were found by focusing on ignorance enriched concepts. We also used the ignorance-base to connect a vitamin D and spontaneous preterm birth gene list to ignorance statements and found an emerging topic of study (brain development) in relation to the gene list. This emerging topic also has an implied field (neuroscience) that could potentially help provide some answers to the ignorance statements. Conclusion Our goal is to help students, researchers, funders, and publishers better understand the state of our collective scientific ignorance (known unknowns) in order to help accelerate translational research through the continued illumination of and focus on the known unknowns and their respective goals for scientific knowledge. Graphical abstract