Search

The way in which data are shared can affect their utility and reusability. Here, we demonstrate how data that we had previously shared in bulk can be mobilized further through a knowledge graph that allows for much more granular exploration and interrogation. The original dataset is about the computational reproducibility of GitHub-hosted Jupyter notebooks associated with biomedical publications. It contains rich metadata about the publications, associated GitHub repositories and Jupyter notebooks, and the notebooks' reproducibility. We took this dataset, converted it into semantic triples and loaded these into a triple store to create a knowledge graph, FAIR Jupyter, that we made accessible via a web service. This enables granular data exploration and analysis through queries that can be tailored to specific use cases. Such queries may provide details about any of the variables from the original dataset, highlight relationships between them or combine some of the graph's content with materials from corresponding external resources. We provide a collection of example queries addressing a range of use cases in research and education. We also outline how sets of such queries can be used to profile specific content types, either individually or by class. We conclude by discussing how such a semantically enhanced sharing of complex datasets can both enhance their FAIRness, i.e., their findability, accessibility, interoperability, and reusability, and help identify and communicate best practices, particularly with regards to data quality, standardization, automation and reproducibility.

Despite the importance of scientific software for research, it is often not formally recognized and rewarded. This is especially true for foundation libraries, which are used by the software packages visible to the users, being ``hidden'' themselves. The funders and other organizations need to understand the complex network of computer programs that the modern research relies upon. In this work we used CZ Software Mentions Dataset to map the dependencies of the software used in biomedical papers and find the packages critical to the software ecosystems. We propose the centrality metrics for the network of software dependencies, analyze three ecosystems (PyPi, CRAN, Bioconductor) and determine the packages with the highest centrality.

The sharing and citation of research data is becoming increasingly recognized as an essential building block in scientific research across various fields and disciplines. Sharing research data allows other researchers to reproduce results, replicate findings, and build on them. Ultimately, this will foster faster cycles in knowledge generation. Some disciplines, such as astronomy or bioinformatics, already have a long history of sharing data; many others do not. The current landscape of so-called research data repositories is diverse. This review aims to perform a technology review on existing data repositories/portals with a focus on mathematical research data.

Mathematical world knowledge is a fundamental component of Wikidata. However, to date, no expertly curated knowledge graph has focused specifically on contemporary mathematics. Addressing this gap, the Mathematical Research Data Initiative (MaRDI) has developed a comprehensive knowledge graph that links multimodal research data in mathematics. This encompasses traditional research data items like datasets, software, and publications and includes semantically advanced objects such as mathematical formulas and hypotheses. This paper details the abilities of the MaRDI knowledge graph, which is based on Wikibase, leading up to its inaugural public release, codenamed Bravo, available on https://portal.mardi4nfdi.de., Comment: Accepted at Wikidata'23: Wikidata workshop at ISWC 2023

Jupyter notebooks facilitate the bundling of executable code with its documentation and output in one interactive environment, and they represent a popular mechanism to document and share computational workflows. The reproducibility of computational aspects of research is a key component of scientific reproducibility but has not yet been assessed at scale for Jupyter notebooks associated with biomedical publications. We address computational reproducibility at two levels: First, using fully automated workflows, we analyzed the computational reproducibility of Jupyter notebooks related to publications indexed in PubMed Central. We identified such notebooks by mining the articles full text, locating them on GitHub and re-running them in an environment as close to the original as possible. We documented reproduction success and exceptions and explored relationships between notebook reproducibility and variables related to the notebooks or publications. Second, this study represents a reproducibility attempt in and of itself, using essentially the same methodology twice on PubMed Central over two years. Out of 27271 notebooks from 2660 GitHub repositories associated with 3467 articles, 22578 notebooks were written in Python, including 15817 that had their dependencies declared in standard requirement files and that we attempted to re-run automatically. For 10388 of these, all declared dependencies could be installed successfully, and we re-ran them to assess reproducibility. Of these, 1203 notebooks ran through without any errors, including 879 that produced results identical to those reported in the original notebook and 324 for which our results differed from the originally reported ones. Running the other notebooks resulted in exceptions. We zoom in on common problems, highlight trends and discuss potential improvements to Jupyter-related workflows associated with biomedical publications., Comment: arXiv admin note: substantial text overlap with arXiv:2209.04308

Jupyter notebooks allow to bundle executable code with its documentation and output in one interactive environment, and they represent a popular mechanism to document and share computational workflows, including for research publications. Here, we analyze the computational reproducibility of 9625 Jupyter notebooks from 1117 GitHub repositories associated with 1419 publications indexed in the biomedical literature repository PubMed Central. 8160 of these were written in Python, including 4169 that had their dependencies declared in standard requirement files and that we attempted to re-run automatically. For 2684 of these, all declared dependencies could be installed successfully, and we re-ran them to assess reproducibility. Of these, 396 notebooks ran through without any errors, including 245 that produced results identical to those reported in the original. Running the other notebooks resulted in exceptions. We zoom in on common problems and practices, highlight trends and discuss potential improvements to Jupyter-related workflows associated with biomedical publications.

To mitigate the spread of COVID-19 pandemic, decision-makers and public authorities have announced various non-pharmaceutical policies. Analyzing the causal impact of these policies in reducing the spread of COVID-19 is important for future policy-making. The main challenge here is the existence of unobserved confounders (e.g., vigilance of residents). Besides, as the confounders may be time-varying during COVID-19 (e.g., vigilance of residents changes in the course of the pandemic), it is even more difficult to capture them. In this paper, we study the problem of assessing the causal effects of different COVID-19 related policies on the outbreak dynamics in different counties at any given time period. To this end, we integrate data about different COVID-19 related policies (treatment) and outbreak dynamics (outcome) for different United States counties over time and analyze them with respect to variables that can infer the confounders, including the covariates of different counties, their relational information and historical information. Based on these data, we develop a neural network based causal effect estimation framework which leverages above information in observational data and learns the representations of time-varying (unobserved) confounders. In this way, it enables us to quantify the causal impact of policies at different granularities, ranging from a category of policies with a certain goal to a specific policy type in this category. Besides, experimental results also indicate the effectiveness of our proposed framework in capturing the confounders for quantifying the causal impact of different policies. More specifically, compared with several baseline methods, our framework captures the outbreak dynamics more accurately, and our assessment of policies is more consistent with existing epidemiological studies of COVID-19., Comment: 10 pages, 7 figures

Scholia is a tool to handle scientific bibliographic information in Wikidata. The Scholia Web service creates on-the-fly scholarly profiles for researchers, organizations, journals, publishers, individual scholarly works, and for research topics. To collect the data, it queries the SPARQL-based Wikidata Query Service. Among several display formats available in Scholia are lists of publications for individual researchers and organizations, publications per year, employment timelines, as well as co-author networks and citation graphs. The Python package implementing the Web service is also able to format Wikidata bibliographic entries for use in LaTeX/BIBTeX., Comment: 16 pages, 5 figures, Scientometrics 2017

There is much debate on how public participation and expertise can be brought together in collaborative knowledge environments. One of the experiments addressing the issue directly is Citizendium. In seeking to harvest the strengths (and avoiding the major pitfalls) of both user-generated wiki projects and traditional expert-approved reference works, it is a wiki to which anybody can contribute using their real names, while those with specific expertise are given a special role in assessing the quality of content. Upon fulfillment of a set of criteria like factual and linguistic accuracy, lack of bias, and readability by non-specialists, these entries are forked into two versions: a stable (and thus citable) approved "cluster" (an article with subpages providing supplementary information) and a draft version, the latter to allow for further development and updates. We provide an overview of how Citizendium is structured and what it offers to the open knowledge communities, particularly to those engaged in education and research. Special attention will be paid to the structures and processes put in place to provide for transparent governance, to encourage collaboration, to resolve disputes in a civil manner and by taking into account expert opinions, and to facilitate navigation of the site and contextualization of its contents., Comment: A contribution to OKCON 2010 (cf. http://okfn.org/okcon/). Contextualized on-wiki at http://en.citizendium.org/wiki/Open_Knowledge_Conference/Program/Collaborative_Structuring_of_Knowledge_by_Experts_and_the_Public. Available online at http://ceur-ws.org/Vol-575/paper5.pdf, Also at: http://sunsite.informatik.rwth-aachen.de/Publications/CEUR-WS/Vol-575/