Database Commons

a catalog of worldwide biological databases

As the SARS-CoV-2 virus continues to remain a universal threat on a global scale, a large number of COVID-19 clinical trials and observational studies are being conducted and published. Currently, 9,202 COVID-19 clinical trials have been registered on ClinicalTrials.gov and 293,187 COVID-19 articles were indexed in PubMed. To fully capitalize on the voluminous number of publications reporting COVID-19 interventional and observational studies, their results should be freely accessible via an open-source harmonized shared resource. We introduced ReMeDy (https://remedy.mssm.edu/), an intelligent integrative informatics platform aimed to harmonize and cross-link diverse COVID-19 trial outcomes and observational data. We tested the potential of the platform by uploading 52 COVID-19 clinical trials and 48 COVID-19 observational retrospective studies. ReMeDy was validated based on its capability to store and organize diverse data. The next steps include developing a crowdsourcing functionality coupled with automated outcome extraction using natural language processing.

ABSTRACT: Recent regenerative medicine studies have emphasized the need for increased standardization, harmonization and sharing of information related to stem cell product characterization, to help drive these innovative interventions toward public availability and to increase collaboration in the scientific community. Although numerous attempts and numerous databases have been made to manage these data, a platform that incorporates all the heterogeneous data collected from stem cell projects into a harmonized project-based framework is still lacking. The aim of the database, which is described in this study, is to provide an intelligent informatics solution that integrates comprehensive characterization of diverse stem cell product characteristics with research subject and project outcome information. In the resulting platform, heterogeneous data are validated using predefined ontologies and stored in a relational database, to ensure data quality and ease of access. Testing was performed using 51 published, publically available induced pluripotent stem cell projects conducted in clinical, preclinical and in-vitro evaluations. Future aims of this project include further increasing the database size to include all published stem cell trials and develop additional data visualization tools to improve usability. Our testing demonstrated the robustness of the proposed platform, by seamlessly harmonizing diverse common data elements, and the potential of this platform for driving knowledge generation from the aggregation and harmonization of these diverse data.
DATABASE URL: https://remedy.mssm.edu/.

Advancements in regenerative medicine have highlighted the need for increased standardization and sharing of stem cell products to help drive these innovative interventions toward public availability and to increase collaboration in the scientific community. Although numerous attempts and numerous databases have been made to store this data, there is still a lack of a platform that incorporates heterogeneous stem cell information into a harmonized project-based framework. The aim of the platform described in this study, ReMeDy, is to provide an intelligent informatics solution which integrates diverse stem cell product characteristics with study subject and omics information. In the resulting platform, heterogeneous data is validated using predefined ontologies and stored in a relational database. In this initial feasibility study, testing of the ReMeDy functionality was performed using published, publically-available induced pluripotent stem cell projects conducted in in vitro, preclinical and intervention evaluations. It demonstrated the robustness of ReMeDy for storing diverse iPSC data, by seamlessly harmonizing diverse common data elements, and the potential utility of this platform for driving knowledge generation from the aggregation of this shared data. Next steps include increasing the number of curated projects by developing a crowdsourcing framework for data upload and an automated pipeline for metadata abstraction. The database is publically accessible at https://remedy.mssm.edu/.

Recent studies demonstrated that comparative analysis of stem cell research data sets originating from multiple studies can produce new information and help with hypotheses generation. Effective approaches for incorporating multiple diverse heterogeneous data sets collected from stem cell projects into a harmonized project-based framework have been lacking. Here, we provide an intelligent informatics solution for integrating comprehensive characterizations of stem cells with research subject and project outcome information. Our platform is the first to seamlessly integrate information from iPSCs and cancer stem cell research into a single platform, using a multi-modular common data element framework. Heterogeneous data is validated using predefined ontologies and stored in a relational database, to ensure data quality and ease of access. Testing was performed using 103 published, publicly-available iPSC and cancer stem cell projects conducted in clinical, preclinical and in vitro evaluations. We validated the robustness of the platform, by seamlessly harmonizing diverse data elements, and demonstrated its potential for knowledge generation through the aggregation and harmonization of data. Future aims of this project include increasing the database size using crowdsourcing and natural language processing functionalities. The platform is publicly available at https://remedy.mssm.edu/.