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ÇOKLU-OMİK VERİLER İÇİN BİRLEŞTİRME YÖNTEMLERİ: BİBLİYOMETRİK BİR ANALİZ

Year 2025, Volume: 34 Issue: 2, 274 - 284, 15.08.2025
https://doi.org/10.34108/eujhs.1585598

Abstract

Bu çalışmanın temel amacı, görsel haritalama tekniklerini kullanarak Web of Science veritabanında 2013-2023 yılları arasında çoklu-omik yayınların bibliyometrik analizini yapmaktır. İncelenen dönemdeki yayınların eğilimleri göstermek için Biblioshiny ve VOSviewer yazılımları kullanılarak ağ haritaları oluşturuldu. 298 dergiden 714 makalenin kapsamlı bir incelemesi, çoklu-omik alanındaki entelektüel yapıyı ve oluşan eğilimleri ortaya çıkarmayı amaçladı. Bu amaçla, ülke, kurum, kaynak, yazar ve anahtar kelime üretkenliği için ortak-yazarlık, bibliyografik bağlantı ve eş-dizimlilik analizleri yapıldı. Çalışma süresince, Çin çoklu-omik yayınlara önde gelen katkıda bulunan ülke olarak ortaya çıkarken, ABD en fazla çoklu-omik yayını atıf sayısına ulaştı. Yazarın anahtar kelimelerinde en sık görülen terimler "çoklu-omik", "veri entegrasyonu" ve "metabolomik" olarak belirlendi. Çalışma ayrıca "Biyoinformatik Brifingleri" dergisini hem en ilgili kaynak hem de en çok atıf yapılan kaynak olarak belirledi. Zamansal analiz, 2013'dan 2022' ye kadar yayınlarda kayda değer bir artış olduğunu gösterdi. Bu gözlem, belirtilen dönemde çoklu-omik alanında ilgi ve araştırma faaliyetlerinde önemli bir artış olduğunu gösteriyor.

References

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  • Gallo Cantafio ME, Grillone K, Caracciolo D, et al. From Single Level Analysis to Multi-Omics Integrative Approaches: A Powerful Strategy towards the Precision Oncology. High-throughput. 2018;7(4):33. doi:10.3390/ht7040033.
  • Ritchie MD, Holzinger ER, Li R, Pendergrass SA, Kim D. Methods of integrating data to uncover genotype-phenotype interactions. Nat Rev Genet. 2015;16(2):85-97. doi:10.1038/nrg3868.
  • Subramanian I, Verma S, Kumar S, Jere A, Anamika K. Multi-omics Data Integration, Interpretation, and Its Application. Bioinform Biol Insights. 2020;14:1177932219899051. doi:10.1177/1177932219899051.
  • Cavill R, Jennen D, Kleinjans J, Briedé JJ. Transcriptomic and metabolomic data integration. Brief Bioinform. 2016;17(5):891-901. doi:10.1093/bib/bbv090.
  • Lin E, Lane HY. Machine learning and systems genomics approaches for multi-omics data. Biomark Res. 2017;5:2. doi:10.1186/s40364-017-0082-y.
  • Ivanisevic T, Sewduth RN. Multi-Omics Integration for the Design of Novel Therapies and the Identification of Novel Biomarkers. Proteomes. 2023:11(4):34. doi:10.3390/proteomes11040034.
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  • Chen C. CiteSpace II: Detecting and visualizing emerging trends and transient patterns in scientific literature. J Am Soc Inf Sci Technol. 2006;57(3):359-377. doi:10.1002/asi.20317.
  • Donthu N, Kumar S, Mukherjee D, Pandey N, Lim WM. How to conduct a bibliometric analysis: An overview and guidelines. J Bus Res. 2021;133:285-296.
  • Hashem E AR, Md Salleh NZ, Abdullah M, et al. Research trends, developments, and future perspectives in brand attitude: A bibliometric analysis utilizing the Scopus database (1944-2021). Heliyon. 2022;9(1):e12765. doi:10.1016/j.heliyon.2022.e12765.
  • Aria M, Cuccurullo C. Bibliometrix: An R-tool for Comprehensive Science Mapping Analysis. J Informetr. 2017;11:959-975. doi:10.1016/j.joi.2017.08.007.
  • Argelaguet R, Velten B, Arnol D, et al. Multi-Omics Factor Analysis-a framework for unsupervised integration of multi-omics data sets. Mol Syst Biol. 2018;14(6):e8124. doi:10.15252/msb.20178124.
  • Chaudhary K, Poirion OB, Lu L, Garmire LX. Deep Learning-Based Multi-Omics Integration Robustly Predicts Survival in Liver Cancer. Clin cancer res. 2018;24(6):1248-1259. doi:10.1158/1078-0432.CCR-17-0853.
  • Pang Z, Zhou G, Ewald J, et al. Using MetaboAnalyst 5.0 for LC-HRMS spectra processing, multi-omics integration and covariate adjustment of global metabolomics data. Nat Protoc. 2022;17(8):1735-1761. doi:10.1038/s41596-022-00710-w.
  • Pinu FR, Beale DJ, Paten AM, et al. Systems Biology and Multi-Omics Integration: Viewpoints from the Metabolomics Research Community. Metabolites. 2019;9(4):76. doi:10.3390/metabo9040076.
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  • Wang TJ, Larson MG, Vasan RS. Metabolite profiles and the risk of developing diabetes. Nature Medicine. 2011;17(4):448-453. doi:10.1038/nm.2307

INTEGRATION METHODS FOR MULTI-OMICS DATA: A BIBLIOMETRIC ANALYSIS

Year 2025, Volume: 34 Issue: 2, 274 - 284, 15.08.2025
https://doi.org/10.34108/eujhs.1585598

Abstract

The primary objective of this study is to conduct a bibliometric analysis of multi-omics publications from 2013 to 2023 in the Web of Science database, utilizing visual mapping techniques. Network maps were generated using Biblioshiny and VOS viewer software to illustrate the published trends over the investigated period. A comprehensive examination of 714 articles from 298 journals aimed to unveil the intellectual structure and emerging trends in the multi-omics field. For this purpose, co-authorship, bibliographic coupling, and co-occurrence analyses were conducted for country, institution, source, author, and keyword productivity. During the study period, China emerged as the leading contributor to multi-omics publications, while the USA secured the highest number of multi-omics citations. The most frequently occurring terms in the author's keywords were identified as "multi-omics," "data-integration," and "metabolomics." The study also determined "Bioinformatics Briefings" as both the most relevant source and the most cited. Temporal analysis indicated a noteworthy increase in publications from 2013 to 2022. This observation suggests a significant rise in interest and research activity in the multi-omics field during the specified period.

References

  • Zhong Y, Peng Y, Lin Y, et al. MODILM: towards better complex diseases classification using a novel multi-omics data integration learning model. BMC Med Inform Decis Mak. 2023;23 (82). doi:10.1186/s12911-023-02173-9.
  • Gallo Cantafio ME, Grillone K, Caracciolo D, et al. From Single Level Analysis to Multi-Omics Integrative Approaches: A Powerful Strategy towards the Precision Oncology. High-throughput. 2018;7(4):33. doi:10.3390/ht7040033.
  • Ritchie MD, Holzinger ER, Li R, Pendergrass SA, Kim D. Methods of integrating data to uncover genotype-phenotype interactions. Nat Rev Genet. 2015;16(2):85-97. doi:10.1038/nrg3868.
  • Subramanian I, Verma S, Kumar S, Jere A, Anamika K. Multi-omics Data Integration, Interpretation, and Its Application. Bioinform Biol Insights. 2020;14:1177932219899051. doi:10.1177/1177932219899051.
  • Cavill R, Jennen D, Kleinjans J, Briedé JJ. Transcriptomic and metabolomic data integration. Brief Bioinform. 2016;17(5):891-901. doi:10.1093/bib/bbv090.
  • Lin E, Lane HY. Machine learning and systems genomics approaches for multi-omics data. Biomark Res. 2017;5:2. doi:10.1186/s40364-017-0082-y.
  • Ivanisevic T, Sewduth RN. Multi-Omics Integration for the Design of Novel Therapies and the Identification of Novel Biomarkers. Proteomes. 2023:11(4):34. doi:10.3390/proteomes11040034.
  • van Eck NJ, Waltman L. Software survey: VOSviewer, a computer program for bibliometric mapping. Scientometrics. 2010;84(2):523-538. doi:10.1007/s11192-009-0146-3.
  • Chen C. CiteSpace II: Detecting and visualizing emerging trends and transient patterns in scientific literature. J Am Soc Inf Sci Technol. 2006;57(3):359-377. doi:10.1002/asi.20317.
  • Donthu N, Kumar S, Mukherjee D, Pandey N, Lim WM. How to conduct a bibliometric analysis: An overview and guidelines. J Bus Res. 2021;133:285-296.
  • Hashem E AR, Md Salleh NZ, Abdullah M, et al. Research trends, developments, and future perspectives in brand attitude: A bibliometric analysis utilizing the Scopus database (1944-2021). Heliyon. 2022;9(1):e12765. doi:10.1016/j.heliyon.2022.e12765.
  • Aria M, Cuccurullo C. Bibliometrix: An R-tool for Comprehensive Science Mapping Analysis. J Informetr. 2017;11:959-975. doi:10.1016/j.joi.2017.08.007.
  • Argelaguet R, Velten B, Arnol D, et al. Multi-Omics Factor Analysis-a framework for unsupervised integration of multi-omics data sets. Mol Syst Biol. 2018;14(6):e8124. doi:10.15252/msb.20178124.
  • Chaudhary K, Poirion OB, Lu L, Garmire LX. Deep Learning-Based Multi-Omics Integration Robustly Predicts Survival in Liver Cancer. Clin cancer res. 2018;24(6):1248-1259. doi:10.1158/1078-0432.CCR-17-0853.
  • Pang Z, Zhou G, Ewald J, et al. Using MetaboAnalyst 5.0 for LC-HRMS spectra processing, multi-omics integration and covariate adjustment of global metabolomics data. Nat Protoc. 2022;17(8):1735-1761. doi:10.1038/s41596-022-00710-w.
  • Pinu FR, Beale DJ, Paten AM, et al. Systems Biology and Multi-Omics Integration: Viewpoints from the Metabolomics Research Community. Metabolites. 2019;9(4):76. doi:10.3390/metabo9040076.
  • Mertins P, Mani DR, Ruggles KV, et al. Proteogenomics connects somatic mutations to signalling in breast cancer. Nature. 2016;534(7605):55-62. doi:10.1038/nature18003.
  • Wang TJ, Larson MG, Vasan RS. Metabolite profiles and the risk of developing diabetes. Nature Medicine. 2011;17(4):448-453. doi:10.1038/nm.2307
There are 18 citations in total.

Details

Primary Language English
Subjects Medical Genetics (Excl. Cancer Genetics)
Journal Section Research Article
Authors

Ahu Cephe 0000-0001-9374-4495

Early Pub Date July 28, 2025
Publication Date August 15, 2025
Submission Date November 14, 2024
Acceptance Date July 13, 2025
Published in Issue Year 2025 Volume: 34 Issue: 2

Cite

APA Cephe, A. (2025). INTEGRATION METHODS FOR MULTI-OMICS DATA: A BIBLIOMETRIC ANALYSIS. Sağlık Bilimleri Dergisi, 34(2), 274-284. https://doi.org/10.34108/eujhs.1585598
AMA Cephe A. INTEGRATION METHODS FOR MULTI-OMICS DATA: A BIBLIOMETRIC ANALYSIS. JHS. August 2025;34(2):274-284. doi:10.34108/eujhs.1585598
Chicago Cephe, Ahu. “INTEGRATION METHODS FOR MULTI-OMICS DATA: A BIBLIOMETRIC ANALYSIS”. Sağlık Bilimleri Dergisi 34, no. 2 (August 2025): 274-84. https://doi.org/10.34108/eujhs.1585598.
EndNote Cephe A (August 1, 2025) INTEGRATION METHODS FOR MULTI-OMICS DATA: A BIBLIOMETRIC ANALYSIS. Sağlık Bilimleri Dergisi 34 2 274–284.
IEEE A. Cephe, “INTEGRATION METHODS FOR MULTI-OMICS DATA: A BIBLIOMETRIC ANALYSIS”, JHS, vol. 34, no. 2, pp. 274–284, 2025, doi: 10.34108/eujhs.1585598.
ISNAD Cephe, Ahu. “INTEGRATION METHODS FOR MULTI-OMICS DATA: A BIBLIOMETRIC ANALYSIS”. Sağlık Bilimleri Dergisi 34/2 (August2025), 274-284. https://doi.org/10.34108/eujhs.1585598.
JAMA Cephe A. INTEGRATION METHODS FOR MULTI-OMICS DATA: A BIBLIOMETRIC ANALYSIS. JHS. 2025;34:274–284.
MLA Cephe, Ahu. “INTEGRATION METHODS FOR MULTI-OMICS DATA: A BIBLIOMETRIC ANALYSIS”. Sağlık Bilimleri Dergisi, vol. 34, no. 2, 2025, pp. 274-8, doi:10.34108/eujhs.1585598.
Vancouver Cephe A. INTEGRATION METHODS FOR MULTI-OMICS DATA: A BIBLIOMETRIC ANALYSIS. JHS. 2025;34(2):274-8.