We present PubGraph, a new resource for studying scientific progress that takes the form of a large-scale knowledge graph (KG) with more than 385M entities, 13B main edges, and 1.5B qualifier edges. PubGraph is comprehensive and unifies data from various sources, including Wikidata, OpenAlex, and Semantic Scholar, using the Wikidata ontology. Beyond the metadata available from these sources, PubGraph includes outputs from auxiliary community detection algorithms and large language models. To further support studies on reasoning over scientific networks, we create several large-scale benchmarks extracted from PubGraph for the core task of knowledge graph completion (KGC). These benchmarks present many challenges for knowledge graph embedding models, including an adversarial community-based KGC evaluation setting, zero-shot inductive learning, and large-scale learning. All of the aforementioned resources are accessible at https://purl.archive.org/pubgraph and released under the CC-BY-SA license. We plan to update PubGraph quarterly to accommodate the release of new publications.

Given the sheer size of the dataset (> 2.2TB), this repository only holds the code for extracting the KG, the data itself can be accessed through the provided PURL.