RRD-Bio: Building An Integrated Research Resource Database for Biomedicine

TL;DR

RRD-Bio is a comprehensive, publicly accessible database that consolidates over 2.5 million biomedical research resources from 40 million papers, enhancing resource discoverability and research reproducibility.

Contribution

This work introduces a large, integrated database of biomedical research resources extracted from extensive literature, addressing resource dispersion and accessibility issues.

Findings

Contains 2,555,116 research resources with URLs and descriptions

Built from 40 million biomedical papers from PubMed and PMC

Publicly available to improve resource visibility and reproducibility

Abstract

Research resources (RRs) such as data, software, and tools are essential pillars of scientific research. The field of biomedicine, a critical scientific discipline, is witnessing a surge in research publications resulting in the accumulation of a substantial number of RRs. However, these resources are dispersed among various biomedical articles and can be challenging to locate and reuse due to their transient nature. In this paper, we report our recent progress in biomedical data curation - building a large research resource database for biomedicine (RRD-Bio), based on a collection of 40 million papers from two large biomedical literature databases, PubMed and PubMed Central. The database contains 2,555,116 RRs, each identified by a location on the Internet (URL) and descriptive information (Context). We made the RRD-Bio database publicly available (\url{https://zenodo.org/records/10526493}) to enhance the visibility of biomedical research resources, the ability to preserve important resources and the reproducibility of biomedical research.