The future of publishing in preclinical TBI: PRECISE and ODC-TBI

It will come as no surprise to preclinical researchers or anyone who has been following the issues with reproducibility facing biomedical science that the current way of publishing our work is inadequate.  Our survey of 300 papers published in preclinical TBI to populate the Model Catalog highlighted current problems of which preclinical TBI researchers are well aware: little sharing of primary data, papers routinely omitting key data elements, e.g., weight of animals, or device used. When present, there is little standardization about how these key entities are reported. 

But that was then and this is now.  PRECISE seeks to transform the practice and reporting of pre-clinical TBI research to take advantage of advances in data science to achieve the full potential of pre-clinical research.  PRECISE is creating a data and knowledge community hub where researchers will be able to share FAIR data, access a comprehensive knowledge base of pre-clinical models and detailed experimental protocols, deploy powerful algorithms across  pools of AI-ready data aligned to Common Data Elements (CDEs) and understand best practices for working with harmonized data.  These goals are achieved through tight integration across the PRECISE Cores comprising the Model Catalog, Education, CDE and Informatics Cores. 

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Over the course of PRECISE, we hope to facilitate a dramatic shift in the rigor with which researchers conduct their research, routinely employing community-vetted best practices in choosing, executing and assessing TBI models. How do we do that?  We hope to introduce the pre-clinical TBI community to the “publication of the future”.  Instead of a static research article, each publication will actually comprise a linked set of research products:

• A data set shared through ODC-TBI complying with PRECISE recommendations for standards and best practices

• A detailed experimental protocol published in Protocols.io

• A collection of Common Data Elements (CDEs) that provides a common way to structure your data to help share and harmonize across datasets 

• A publication that provides the narrative description and links to these products

• Extraction of key findings into a large knowledge base of pre-clinical findings allowing powerful comparisons across studies

Thanks to PRECISE, all of this data and knowledge is being made freely available to the research community along with tools that will allow these resources to be used in planning, analyzing and publishing studies.  

Drs. Zezong Gu and Catherine Johnson of the PRECISE Education Core provide a first glimpse into the future imagined by PRECISE. They recently published a dataset from their Siedhoff et al. (2022) open field blast study in mice in the ODC-TBI. They used the ODC-TBI mapping tools to retrospectively map their data to the PRECISE recommended core CDE’s, thereby facilitating harmonization across future data within the ODC-TBI.  The data sets are accompanied by a detailed protocol published in protocols.io, providing critical details for reproducibility and interpretability.  Key parameters and outcomes from the paper were extracted and added to the PRECISE Model Catalog, so that these studies can be compared across key details with the over 300 additional entries.  The figure shows all of the different assessments that have been performed on the 24 instances of blast models we have in the PRECISE Model Catalog.

Why is publishing these linked products important?  Because each is published in a form that optimizes the potential for reuse.  The protocols in protocols.io are published and designed in a way that makes them easy to follow, discuss, compare and modify.  Compare that experience with the condensed methods section typically provided in papers that need to be transcribed and where key details are often scattered across multiple previous studies.  The data sets in ODC-TBI are published so that they are FAIR:  findable, accessible, interoperable and reusable, by both humans and computers: machine-friendly open format, ample metadata and documentation (e.g., a data dictionary) and adherence to community standards like CDE’s.  The PRECISE Model Catalog provides the necessary semantic framework for comparing key details across studies so that powerful analytics can be used to plan experiments, compare to clinical studies or visualize the pre-clinical TBI landscape.  

PRECISE is still in its early stages, but the work of Gu and Johnson show the power of the integrated tool suite it is developing.  We hope that the pre-clinical TBI embraces the publication of the future, propelling pre-clinical TBI towards a powerful data- and knowledge-driven future built on a foundation of rigorous and reproducible science.