Building Weighted PubMed Citation Graphs at Scale: A Pipeline and an Audit of Edge-Similarity Features

Abstract

Studies of scientific literature often combine citation links with article metadata, but the data preparation needed to do so at the scale of millions of papers is laborious and error-prone. This paper describes a pipeline that turns PubMed metadata and a citation network into a graph whose edges carry seven similarity features: bibliographic coupling and co-citation (each as a count and as a Jaccard coefficient), publication-year proximity, MeSH-term similarity, and similarity of MedCPT title-abstract embeddings. Applied to a citation network derived from the cell biology research literature, the pipeline yields 7,445,898 nodes and 57,512,086 edges with complete year, MeSH, title, and abstract metadata. The paper reports how nodes are matched across sources, how duplicate identifiers are resolved, and which intermediate tables grew to hundreds of gigabytes. An audit of the full feature table shows that 47.2% of the edges share neither references nor citing documents, so their topological features are zero, and that the MeSH feature is nonzero on only 0.28% of edges. Where both kinds of signal exist, they agree: edges with higher coupling also have more similar abstracts and closer publication years. In a pilot, replacing the median by a mean or best-match aggregation makes the MeSH feature nonzero on nearly all article pairs, and near-identical texts point to possible duplicate records that identifier checks miss. The parsing, graph-construction, and feature code are public; the paper states which data are released and which are not. A companion paper uses the resulting weighted graph for clustering.