I use co-citation netwroks to identfy knowledge base in medical article collections. Bibliometric coupling for scientific frontiers.
In Web of Scince and Scopus you can directly perform these analysis with bibliometrix package of R. But bibliometrix do not support PubMed.
Also citation reports are not directly avaliabli in PubMED as Web of Science and Scopus.
You have to write your own script. My early scripts were in VBA and I had performed co-citation and bibliometric analysis in Sci2. PubMed updated its API interface and VBA scirpt do not work properly after that update.
I have migrated my scripts in R. I found igraph very usefull in co-citation analysis. All software have limitation in bibliomet coupling analysis. Historical or significant articles have very dense citation relation. A hundred of important article in orthopedic literature published in 1980s retrived hundred millions of edges in bibliometric coupling. Simplification of this netwrok is not easy. However cocitation analysis on this article set can be performed after some optimization.
PubMed is important because it is a non commerical foundation. However Web of Science and Scopus are commercial. If you dont work in a univesity hospital or if you work in private practive PubMed become unique information portal.
PMC subset of PubMED consist of %100 free full full text articles.
I especialy prefere to study on PubMed to indetify information flow between scientist and medical workers in private practice and developing countires.
In medical literature these kinds of studies on PUBMED is very rare. The studies on Web of Science and Scopus are not rare.
By this reason igraph may play an important role in PubMed Studies.
I am not sure what can be a practical solution. Big data packages ? a new additional small package with parse matrix for Pubmed ? a function which suports work on cluster ?
You can find early findings of one of my cocitation study on COVID19 (will published in Journal of WORK in June ) https://www.linkedin.com/in/rafet-irmak-4211bb70/detail/recent-activity/posts/
I can sent full study with raw data. More details on cocitation studies on Pubmed