Here, we present a protocol for retrieving, validating, and analyzing Web of Science Core Collection records on Caenorhabditis elegans and aging using CiteSpace, VOSviewer, Bibliometrix, and Scimago Graphica for reproducible bibliometric mapping.
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Method Article
* These authors contributed equally
Here, we present a protocol for retrieving, validating, and analyzing Web of Science Core Collection records on Caenorhabditis elegans and aging using CiteSpace, VOSviewer, Bibliometrix, and Scimago Graphica for reproducible bibliometric mapping.
Aging is a complex biological phenomenon characterized by the progressive deterioration of physiological functions and increased vulnerability to age-associated diseases. At the cellular level, this process is exemplified by senescence, in which cells experience an irreversible halt in division and enter a state of permanent growth arrest, without progressing to apoptosis. However, the underlying mechanisms remain incompletely understood. The nematode Caenorhabditis elegans (C. elegans), with a short lifespan and well-characterized genetics, is a powerful model for deciphering the molecular basis of aging. Nevertheless, a comprehensive bibliometric mapping of research at the intersection of C. elegans and aging is still lacking. Here, we present a protocol to retrieve records from the Web of Science Core Collection, perform data processing, and conduct reproducible bibliometric visualization using CiteSpace, Bibliometrix (R), VOSviewer, and Pajek, aiming to map the knowledge structure and identify emerging trends in C. elegans aging research. Using 6,117 articles published from 1970 through June 5, 2025, we analyzed country and institutional contributions, authorship, journal impact, citation patterns, and thematic evolution. The dataset comprised 6,117 records from 19,864 authors across 3,798 institutes in 91 countries. Annual publications increased from 312 in 2020 to 341 in 2021 and remained high thereafter. The United States led global output, followed by China, Germany, and the United Kingdom, with collaboration networks concentrated among these countries. The University of California system ranked first in productivity, while the Chinese Academy of Sciences ranked third. Topic evolution indicated a shift from foundational studies of insulin/insulin-like growth factor 1 signaling (IIS) pathways and stress responses toward emerging themes such as thermal control and mitophagy in C. elegans aging models. Overall, this protocol enables transparent, updatable bibliometric analyses and supports future studies of key directions, including caloric restriction and mitophagy.
Aging is a multifaceted biological process that refers to the loss of the proliferative capacity of normal somatic cells after a limited number of divisions. During the aging process, the physiological functions of the organism gradually decline, and susceptibility to age-related diseases increases1. At the cellular level, this process manifests as DNA damage, such as the accumulation of double-strand breaks and oxidative damage, and these damages exceed the handling capacity of the repair mechanisms. These cellular-level changes are reflected at the organismal level as the gradual deterioration of physiological functions. Furthermore, some studies have further demonstrated that aged cells drive age-related pathological processes by secreting senescence-associated secretory phenotype (SASP). These factors can disrupt the tissue microenvironment and promote fibrosis, leading to chronic inflammation and even cancer progression2. With the deepening of research on aging, it has been recognized that aging plays a significant role in the occurrence and development of various diseases, including cardiovascular diseases, type 2 diabetes, Alzheimer's disease, and cancer, among others3. With the acceleration of global aging, understanding the mechanisms of aging is crucial for extending healthy lifespan.
Over the past few decades, model organisms have played an indispensable role in revealing the genetic, molecular, and environmental determinants of aging. Model organisms exhibit distinct advantages, including short generation times, well-characterized genetic backgrounds, and high experimental tractability. Common model organisms include yeast, fruit flies, and mice4. In the 1960s, Caenorhabditis elegans (C. elegans) was first established as a novel model organism. Its core advantages for selection include a short life cycle and ease of cultivation, complemented by a suite of mature genetic tools. Moreover, due to its tiny size, it can be cultivated and manipulated on a large scale in a standardized manner, like microorganisms5. Most importantly, it effectively fills a significant gap in previous research, as single-celled organisms, despite being simple and easy to operate, are challenging to utilize for genetics research on complex life mechanisms. In addition, traditional model animals are limited in the efficiency of large-scale screening due to their complex operation. The application of C. elegans precisely solves the above problems6.
The use of C. elegans in aging research dates back to the 1980s7. It was not until 1993 that the field of C. elegans in aging research took a transformative leap. Mutagenesis screens led by Thomas Johnson and colleagues identified the first long-lived mutant, the age-1 gene8,9. This finding changed the prevailing view that aging was a stochastic, unregulated process, instead implicating specific genetic pathways in lifespan determination. Subsequent studies built on this foundation, revealing a conserved network of signaling pathways that coordinate aging. The IIS pathway has emerged as a central regulator. The mutation in daf-2, which encodes the C. elegans ortholog of the insulin/ insulin-like growth factor (IIGF-1) receptor, could reduce IIS activity, activating the FOXO transcription factor DAF-16, causing it to translocate from the cytoplasm to the nucleus, thereby promoting the expression of stress response genes, molecular chaperones, and detoxification enzymes, thus delaying the aging process and extending healthy lifespan10. DAF-16 translocates from the cytoplasm to the nucleus, promoting the expression of stress-resistance genes, molecular chaperones, and detoxification enzymes, thereby extending organismal health span and delaying the progression of aging and extending organismal healthspan11. Furthermore, C. elegans has illuminated other conserved mechanisms of aging. For example, the target of rapamycin (TOR) pathway, a key nutrient-sensing axis, was shown to modulate lifespan through interactions with IIS12.
In recent years, bibliometric methods have been widely applied to many fields. Bibliometric network analysis employs statistical methods to uncover development patterns, disciplinary structures, research hotspots, and trends in a field by examining the quantity, structure, distribution, and citation relationships of literature13. Despite extensive research on C. elegans in aging, no study has provided a comprehensive bibliometric analysis of this interdisciplinary field. In this study, we present a comprehensive, multi-method, and reproducible analysis that elucidates the collaborative framework, intellectual foundation, and dynamic thematic developments within the field, thereby identifying emerging trajectories for future research endeavors. This article reviews the landscape of recent aging research achievements in the C. elegans field. Furthermore, this study aims to: (1) analyze publication and citation trends in C. elegans aging research from 1970 to June 5, 2025; (2) assess contributions by countries and institutions and explore collaboration networks; (3) identify top authors and key journals by productivity and citation impact; (4) uncover the field's intellectual foundation through co-citation and citation-burst analysis; and (5) track major research themes and emerging trends using keyword co-occurrence and temporal analysis. Ultimately, these insights will facilitate a deeper comprehension of the field’s evolving trajectory.
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This study does not refer to ethical approval and consent to participate. The data used in this study were obtained from the Web of Science Core Collection (WoSCC).
1. Database selection
2. Search parameters
3. Data retrieval and format
4. Data preprocessing
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Overview of trends and evolution of C. elegans in the aging area
The bibliometric analysis included 6,117 publication records from 1,123 sources, selected from an initial 6,205 publications from WOSCC that met eligibility criteria. This included 45 early-access reviews and 145 proceedings papers. After excluding 87 irrelevant and one retracted publication, the data were analyzed for temporal distribution and document types. Over the past five decades, 4,949 articles (80.90%) and 1,168 review...
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To ensure reproducibility and interpretability, key steps in this workflow include: thoroughly reporting the retrieval strategy (database source, query, document types, language limits, retrieval date), conducting relevance screening and data validation to minimize off-topic records, consistently reporting tool parameters (time slicing, node types, pruning, thresholds, clustering), and exporting outputs in standard formats while documenting software versions for transparency and future updates. This protocol can be adjus...
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The authors have nothing to disclose.
The authors wish to express their appreciation to all the participants and researchers who contributed to this work. Furthermore, they are grateful for the analytical tools provided by CiteSpace, VOSviewer, Scimago Graphica, and R, which were instrumental in conducting this research.
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| Name | Company | Catalog Number | Comments |
|---|---|---|---|
| LEGION Savior Y7000 2019 laptop (SerialNumber PF1CGZJU) | Lenovo | https://pcsupport.lenovo.com/us/en/products/laptops-and-netbooks/legion-series/legion-y7000-2019 | Computer used for analyses |
| R (version 4.5.2) | R Foundation for Statistical Computing / R Core Team | https://www.r-project.org/ | Statistical computing environment |
| CiteSpace (version 6.3.R3) | CiteSpace / Chaomei Chen (Drexel University) | https://citespace.podia.com/ | Bibliometric visualization and analysis software |
| VOSviewer (version 1.6.20) | Leiden University CWTS (Nees Jan van Eck, Ludo Waltman) | https://www.vosviewer.com/ | Bibliometric mapping software |
| Pajek (version 64.6.01) | University of Ljubljana (Vladimir Batagelj, Andrej Mrvar) | http://mrvar.fdv.uni-lj.si/pajek/ | Network analysis and visualization software |
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