dkNET Hypothesis Center: A Hub for FAIR Data, Online Resources and Hypothesis Generation
Authors: Lin Ko‐Wei , Guo Vicky , McIndoe Richard A. , Martone Maryann E. , McKenna Neil J. , Grethe Jeffrey S. 
Published: May 2022

Discovering and learning how to use fast‐growing publicly available online bioinformatics and data resources can be challenging for bench scientists. The NIDDK Information Network (dkNET; https://dknet.org) is an open community resource information portal for biomedical researchers supported by the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK). dkNET helps researchers find resources relevant to their research and provides up‐to‐date information on new tools, services, and mandates to support reproducible science. To help bench scientists utilize available online bioinformatics tools, dkNET has launched a “Hypothesis Center”(https://dknet.org/hypothesis‐center) that brings together tutorials for a collection of online tools to assist researchers in exploring datasets and utilize online analytics and visualization tools. Our goal is to help researchers not only follow the step‐by‐step tutorial but also gain more understanding about these online tools, how to interpret the results, and encourage researchers to combine and/or reuse more online resources. Based on the questions and examples that a researcher has selected, the system suggests tool(s) and detailed tutorials based on specific use cases. For example, the Hypothesis Center phenotype‐genotype analytics module utilizes tools from the Signaling Pathways Project (SPP), a FAIR knowledgebase that allows researchers to ask questions across thousands of annotated transcriptomic and ChIP‐Seq datasets, and the Mouse Metabolic Phenotyping Center (MMPC), that provides information on mammalian phenotypes associated with specific gene manipulations in mouse models. The Hypothesis Center also provides information on tools and tutorials from external resources, including resources such as the Human Islet Research Network (HIRN) and the Type 1 Diabetes Knowledge Portal, that enables browsing, searching, and analysis of human genetic information linked to type 1 diabetes and related traits. To evaluate whether the approach of the Hypothesis Center can help educate researchers on using online resources more efficiently, we conducted beta testing with 15 students ranging from undergraduate to graduate. Students were new to the specific online bioinformatics tools represented and were asked to use the Hypothesis Center to learn how to use these tools. Feedback about usability and learning experience was collected to help improve the Hypothesis Center. Students found that the Hypothesis Center was helpful in learning to use a new bioinformatics tool and suggested that integrating additional tools and modifying the tutorial selections based on the knowledge level of the users could benefit trainees. To increase awareness of publicly available resources, dkNET also hosts a webinar series introducing helpful resources and promotes these resources via social media channels and YouTube. Through detailed tutorials in the Hypothesis Center and associated webinars, dkNET has created a virtual training environment that can assist researchers in finding and learning how to use online resources to support their research, breaking down barriers to the utilization of bioinformatics tools by bench researchers, and improve the utility of publicly available bioinformatics resources.