Improving Scientific Rigor and Reproducibility: Check Research Resources Information When Planning Experiments Using dkNET
Authors: Lin Ko-Wei , Bandrowski Anita E. , Guo Vicky , Hsu Chun-Nan , Ozyurt Ibrahim B. , Pascual Leo , Grethe Jeffrey S. , Martone Maryann E. 
Published: April 2020

Transparency of information on the effectiveness of research resources such as cell lines and antibodies is critical for enhancing scientific rigor and reproducibility. Horbach et al. showed that 32,755 published articles have used misidentified cell lines, and the problem keeps growing as more than half a million studies cite these papers
[1]. Tracking research resources has been a challenge because there was no standard way of citing resources and the information provided in methods sections was not always enough to unambiguously identify the resources. Research Resource Identifiers (RRIDs), unique identifiers for research resources, were introduced to help solve this issue. Using these RRIDs and text mining techniques, we developed dkNET (NIDDK Information Network,
https://dknet.org) Resource Reports to help researchers find key resource information, locate and track resources and compare their performance. These reports provide rating and validation information and issues that may be known about a particular resource. When searching for RRIDs or for resources, authors are provided this information. Babic et al. have shown that authors looking for and citing RRIDs in publications is associated with lower reported use of problematic cell lines
[2]. While the information from a Resource Report may be seen at the time of publication, it would be beneficial for researchers to get this information before they perform their experiments. To assist researchers in this task, dkNET also provides Authentication Reports (built on the foundation provided by Resource Reports) to assist researchers in getting information on their resources while also providing information to help in complying with NIH's mandates on Rigor and Reproducibility. Here we present a dkNET Resource Report use case to understand problematic cell lines used in biomedical research. We performed searches for "problematic" cell lines
[3] and refined the results by using Disease and Mentions facets. As of November 12, 2019, we found 1253 problematic cell lines. The top 3 disease models were Human papillomavirus‐related endocervical adenocarcinoma, bladder carcinoma, and colon adenocarcinoma. Out of the 203 problematic cell lines that were used in research and retrieved via our RRID mention pipeline, the top 3 are Hep‐G2 (Hepatoblastoma, RRID:CVCL_0027), SH‐SY5Y (Neuroblastoma, RRID:CVCL_0019), and U‐87MG ATCC (Glioblastoma, RRID:CVCL_0022). dkNET provides useful tools that can assist researchers in the early stages of research development in selecting the most appropriate resources. dkNET continuously updates this aggregated information, providing researchers up‐to‐date resource information. dkNET uses this information to help researchers identify key biological resources, track their usage, and find potential collaborators. Researchers should check their key resources via dkNET Resource Reports before planning experiments to enhance scientific rigor and reproducibility.

Support or Funding Information

NIH NIDDK U24DK097771

Resource Report for Hep‐G2 (RRID:CVCL_0027) Cell Line.

Figure 1

Resource Report usage information for Hep‐G2 (RRID:CVCL_0027) Cell Line.

Figure 2