Search arXiv⌕ Search

arXiv · 2306.17535

A multi-level analysis of data quality for formal software citation

Abstract

Software is a central part of modern science, and knowledge of its use is crucial for the scientific community with respect to reproducibility and attribution of its developers. Several studies have investigated in-text mentions of software and its quality, while the quality of formal software citations has only been analyzed superficially. This study performs an in-depth evaluation of formal software citation based on a set of manually annotated software references. It examines which resources are cited for software usage, to what extend they allow proper identification of software and its specific version, how this information is made available by scientific publishers, and how well it is represented in large-scale bibliographic databases. The results show that software articles are the most cited resource for software, while direct software citations are better suited for identification of software versions. Moreover, we found current practices by both, publishers and bibliographic databases, to be unsuited to represent these direct software citations, hindering large-scale analyses such as assessing software impact. We argue that current practices for representing software citations -- the recommended way to cite software by current citation standards -- stand in the way of their adaption by the scientific community, and urge providers of bibliographic data to explicitly model scientific software.

Explore related subjects

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

David Schindler, Tazin Hossain, Sascha Spors, Frank Krüger. 2024-04-17. A multi-level analysis of data quality for formal software citation. https://arxiv.org/abs/2306.17535

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

A framework for linking literature-based knowledge integration and infrastructure-supported knowledge integration: Opportunities and challenges from a case study

Integrating knowledge across disciplines is central to sustainability research, yet most evidence-synthesis methods rely on findings as reported in publications, limiting verification and reuse of underlying data and workflows. We develop a conceptual framework linking literature-based and infrastructure-supported knowledge integration, using a systematic review case study to examine when integration can extend beyond reported findings. We reviewed 37 studies on climate change, violent conflict, and household food security. Literature-based synthesis enabled integration across all included studies, whereas access to reusable outputs was limited: over half provided no data availability statement, 27% reported availability upon request, but reusable data and workflows were available for only 8%. To explore infrastructure-supported integration, we used the TIB Knowledge Loom to represent studies with accessible data and code as machine-readable outputs, and produced a knowledge gap map (KGM) from manually extracted and Loom-derived data, comparing manual and infrastructure-supported synthesis. Where outputs were reusable, synthesis could be produced directly from data and workflows rather than from publications. These findings show that literature-based synthesis can be complemented by infrastructure-supported integration where outputs are accessible and usable, and that advancing knowledge integration depends not only on infrastructures but on making data, code, and workflows accessible, executable, and reusable.

cs.DL↗

TiAb Review Plugin: A Browser-Based Tool for AI-Assisted Study Selection in Systematic Reviews

Server-based screening tools impose subscription costs, while open-source alternatives require coding skills, and full-text screening has remained outside the scope of no-code open-source tools. We developed TiAb Review Plugin, an open-source Chrome browser extension that provides no-code, serverless artificial intelligence (AI)-assisted study selection covering both title and abstract (T&A) screening and full-text screening. It uses Google Sheets as a shared database and Google Drive as a PDF store, and users supply their own large language model (LLM) API key. For T&A screening, it offers manual review, LLM batch screening, and machine learning (ML) active learning. For full-text screening, it retrieves open-access PDFs from PubMed Central, Europe PMC, Unpaywall, OpenAlex, and publisher pages, supports blinded dual review with structured exclusion reasons and adjudication, optionally obtains an LLM judgment with page-anchored evidence, and computes PRISMA 2020 flow counts. We re-implemented the default ASReview algorithm (TF-IDF with Naive Bayes) in TypeScript and compared it with the Python original using 10-fold cross-validation on six datasets. For LLM T&A screening, we compared 16 parameter configurations on a benchmark dataset, validated the best (Gemini 3.0 Flash, low thinking budget, TopP 0.95) on five public datasets (1,038 to 5,628 records; 0.5% to 2.0% prevalence), and benchmarked nine further models from four developers. The TypeScript classifier produced top-100 rankings identical to ASReview on all six datasets. LLM T&A screening achieved recall of 94% to 100% with precision of 2% to 15%, and work saved over sampling at 95% recall (WSS@95) of 46.3% to 89.3%. No additional model exceeded the 96.1% recall of the reference configuration; the most recent models traded recall for precision. The classification accuracy of the full-text stage has not yet been evaluated.

cs.DL↗

PaperAtlas: an automatically constructed atlas of computational methods and software from 6.4 million open-access articles

Computational methods and software are dispersed across a literature that is increasingly difficult to review manually, while curated registries capture only a subset of available resources. We present PaperAtlas, an automatically constructed atlas derived from the PubMed Central open-access corpus. Of 6,446,741 abstracts screened, 1,074,191 were classified as computational, with schema-valid records extracted for 1,074,140. Among these, 267,893 papers describing an algorithm, software package or web server formed 1,438 clusters, with 1,000 retained after restriction to parent-level biomedical categories. In 296 clusters linked to at least five bio.tools entries, the mean concentration of the most frequent EDAM topic was 61.7%, compared with 26.4% under permutation. Of 31,180 distinct software and web-server names, 61.0% lacked a strict match in bio.tools, PyPI, CRAN, Bioconductor or Bioconda. Among 12,207 bio.tools entries with defining papers in the corpus, 56.6% were recovered end to end, increasing to 83.6% among the 8,265 entries whose defining publication entered the atlas. PaperAtlas is fully open source and available as a web server at bhargavaresearch.org/paperatlas.

cs.DL↗