Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases

Chen, Q.; Britto, R.; Erill, I.; Jeffery, C. J.; Liberzon, A.; Magrane, M.; Onami, J.-i.; Robinson-Rechavi, M.; Sponarova, J.; Zobel, J.; Verspoor, K.

doi:10.1101/788034

bioRxiv · 10.1101/788034

Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases

Chen, Q.·Britto, R.·Erill, I.·Jeffery, C. J.·Liberzon, A.·Magrane, M.·Onami, J.-i.·Robinson-Rechavi, M.·Sponarova, J.·Zobel, J.·Verspoor, K.

View original source ↗Export metadata ↓

Abstract

The volume of biological database records is growing rapidly, populated by complex records drawn from heterogeneous sources. A specific challenge is duplication, that is, the presence of redundancy (records with high similarity) or inconsistency (dissimilar records that correspond to the same entity). The characteristics (which records are duplicates), impact (why duplicates are significant), and solutions (how to address duplication), are not well understood. Studies on the topic are neither recent nor comprehensive. In addition, other data quality issues, such as inconsistencies and inaccuracies, are also of concern in the context of biological databases. A primary focus of this paper is to present and consolidate the opinions of over 20 experts and practitioners on the topic of duplication in biological sequence databases. The results reveal that survey participants believe that duplicate records are diverse; that the negative impacts of duplicates are severe, while positive impacts depend on correct identification of duplicates; and that duplicate detection methods need to be more precise, scalable, and robust. A secondary focus is to consider other quality issues. We observe that biocuration is the key mechanism used to ensure the quality of this data, and explore the issues through a case study of curation in UniProtKB/Swiss-Prot as well as an interview with an experienced biocurator. While biocuration is a vital solution for handling of data quality issues, a broader community effort is needed to provide adequate support for thorough biocuration in the face of widespread quality concerns.

Source connections

Published article ↗

Explore related subjects

scientific communication and education Preprint

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Chen, Q., Britto, R., Erill, I., Jeffery, C. J., Liberzon, A., Magrane, M., Onami, J.-i., Robinson-Rechavi, M., Sponarova, J., Zobel, J., Verspoor, K.. 2019-10-05. Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases. https://doi.org/10.1101/788034

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

KEEP EXPLORING

Related preprints

bioRxiv2026

Evaluating Large Language Models as Tools to Navigate Researchers in Rapidly Evolving Research Landscapes: A Case Study in Cancer Drug Response Prediction

Large Language Models (LLMs) have emerged as promising tools for assisting researchers in automating and accelerating the synthesis of literature reviews. However, their reliability is a significant concern due to issues like factual inaccuracies and hallucinations. The key question is whether LLMs can reliably provide comprehensive, up-to-date overviews and analyses. This study evaluates the performance of three leading LLMs (OpenAI's ChatGPT, Google's Gemini, and DeepSeek) on the complex task of generating a comprehensive survey paper on deep learning for cancer Drug Response Prediction (DRP). By testing both standard and Deep Research (DR) / Deep Think (DT) modes of LLMs with prompts of varying detail, this paper assesses key academic dimensions, including reference management, content quality, and analytical depth. Key findings reveal that while DR modes of LLMs significantly improve reliability by eliminating hallucinations, performance variations exist across models and prompts. A trade-off between reference quantity and integration quality was observed, and even the best-performing models lacked the analytical depth of human experts, often requiring extensive human supervision. The study concludes that LLMs currently serve as powerful assistive tools but still cannot replace the critical validation and synthesis provided by human researchers. Choosing the best LLM to use depends on the task in hand, while several strategies can be implemented to improve the produced output.

scientific communication and education↗

bioRxiv2019

Using a Systems Change Framework to Evaluate Academic Equity & Climate Efforts in a Graduate Program

While academia is moving forward in terms of diversifying recruitment of undergraduate and graduate students, diverse representation is still not found across the academic hierarchy. At the graduate level, new discussions are emerging around efforts to improve the experiences of women and underrepresented minorities through inclusive graduate programming. Inclusive graduate programs are that which actively center and prioritize support for diverse experiences, identities, career goals, and perspectives, from recruitment through graduation. Establishing regular and rigorous evaluation of equity and inclusion efforts and needs is a critical component of this work. This is recognized by funding agencies that increasingly require reporting on inclusion efforts; here we suggest use of a systems change framework for these evaluations. A systems change approach emphasizes three levels: explicit change (e.g. policies), semi-explicit change (e.g. power dynamics), and implicit change (e.g. biases). We use the Ecology, Evolution, and Behavior (EEB) PhD Program at the University of Texas at Austin in an exercise to (1) identify areas of concern regarding inclusive programming voiced by graduate students, (2) categorize efforts to address these concerns, and (3) integrating and evaluating which areas of the systems change framework show the greatest progress or potential for progress. We argue this framework is particularly useful for academic systems as they are complex, composed of variable individuals, and must address diverse stakeholder needs.

scientific communication and education↗

bioRxiv2019

Plagiarism in Brazil: A perspective of 25,000 PhD holders across the sciences

When it comes to ownership of ideas in science, Robert K. Merton (1957) observed in Priorities in Scientific Discovery: A Chapter in the Sociology of Science that "what is true of physics, chemistry, astronomy, medicine and mathematics is true also of all the other scientific disciplines, not excluding the social and psychological sciences". However, consensus over related issues, such as what constitutes plagiarism in these fields cannot be taken for granted. We conducted a comprehensive study on plagiarism views among PhD holders registered in the database of the Brazilian National Council for Scientific and Technological Development (CNPq). We collected 25,157 valid responses encompassing views and attitudes toward plagiarism from a probability sample of PhD holders across the fields, including biologists, physicists, mathematicians, and engineers as well as linguists, philosophers and anthropologists. The results suggest that core principles about plagiarism are shared among this multidisciplinary community and that they corroborate Mertons observations. Before this study, we could only speculate that this is the case. With these data from a probability sample of Brazilian academia (PhD holders), this study offers insight into the way plagiarism is perceived across the sciences, including the literature and arts, and sheds light on the problem in the context of international collaborative research networks. The data focus on a young research system in Latin America, but, given the cultural similarities that bind most Latin-American nations, these results may be relevant to other PhD populations in the region and should provide a comparison with studies from other emerging, non-Anglophone regions.

scientific communication and education↗