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Over the past decade there has been a significant growth in bioinformatics databases, tools and resources. Although, bioinformatics is becoming more specific, increasing the number of bioinformatics-wares has made it difficult for…
Despite the success of PubMed and other search engines in managing the massive volume of biomedical literature and the retrieval of individual publications, grant-related data remains scattered and relatively inaccessible. This is…
Papers, patents, and clinical trials are essential scientific resources in biomedicine, crucial for knowledge sharing and dissemination. However, these documents are often stored in disparate databases with varying management standards and…
In this article, we describe the Registry of Scientometric Data Sources (RSDS) and several scientometric data sources recorded in this open registry that could be of interest for scientometricians, institutional researchers, librarians,…
Automated relation extraction (RE) from biomedical literature is critical for many downstream text mining applications in both research and real-world settings. However, most existing benchmarking datasets for bio-medical RE only focus on…
The aim of this article is to introduce a reporting framework for reproducible, interactive research applied to Big Clinical Data, based on open source technologies. The framework is constituted by the following three axes: (i) data, (ii)…
Machine Learning (ML) has garnered considerable attention from researchers and practitioners as a new and adaptable tool for disease diagnosis. With the advancement of ML and the proliferation of papers and research in this field, a…
Open and reproducible research in materials science relies on the availability of data, code, and common metadata standards. Journal research data policies (RDPs) remain a primary mechanism by which publication norms are defined and…
Researchers in biomedical research, public health, and the life sciences often spend weeks or months discovering, accessing, curating, and integrating data from disparate sources, significantly delaying the onset of actual analysis and…
In many academic disciplines, software is created during the research process or for a research purpose. The crucial role of software for research is increasingly acknowledged. The application of software engineering to research software…
The number of biomedical research articles published has doubled in the past 20 years. Search engine based systems naturally center around searching, but researchers may not have a clear goal in mind, or the goal may be expressed in a query…
Computational methods have reshaped the landscape of modern biology. While the biomedical community is increasingly dependent on computational tools, the mechanisms ensuring open data, open software, and reproducibility are variably…
Biomedical research yields a wealth of information, much of which is only accessible through the literature. Consequently, literature search is an essential tool for building on prior knowledge in clinical and biomedical research. Although…
Despite the excitement behind biomedical artificial intelligence (AI), access to high-quality, diverse, and large-scale data - the foundation for modern AI systems - is still a bottleneck to unlocking its full potential. To address this…
Many research groups aspire to make data and code FAIR and reproducible, yet struggle because the data and code life cycles are disconnected, executable environments are often missing from published work, and technical skill requirements…
Curation of biomedical knowledge bases (KBs) relies on extracting accurate multi-entity relational facts from the literature - a process that remains largely manual and expert-driven. An essential step in this workflow is retrieving…
Public data archives are the backbone of modern biological and biomedical research. While archives for biological molecules and structures are well-established, resources for imaging data do not yet cover the full range of spatial and…
Biomedical research centers can empower basic discovery and novel therapeutic strategies by leveraging their large-scale datasets from experiments and patients. This data, together with new technologies to create and analyze it, has ushered…
Reproducibility should be a cornerstone of science as it enables validation and reuse. In recent years, the scientific community and the general public became increasingly aware of the reproducibility crisis, i.e. the wide-spread inability…
We have established an RNA Mapping Database (RMDB) to enable a new generation of structural, thermodynamic, and kinetic studies from quantitative single-nucleotide-resolution RNA structure mapping (freely available at…