Causal relation extraction (CRE) is central to biomedical text mining, but current resources often conflate causal relations with broader associations, restrict annotation to sentence-level examples, or focus mainly on explicit causal cues. This limits their usefulness for evaluating whether models can recover causal claims as they are actually expressed in biomedical text. We introduce PubMedCausal, a span-level annotated corpus for biomedical CRE built from PubMed abstracts. The corpus contains 30,000 paragraph-level rows, including 3,945 causal rows and 6,491 adjudicated cause–effect pairs. Each causal relation is annotated with full-text cause and effect spans, causality type, and sententiality, enabling evaluation of both causal detection and full-span causal extraction. We benchmark discriminative encoders and open-source generative models across detection and extraction settings. For causal detection, biomedical encoders are strongest, with PubMedBERT reaching an F₁ score of 0.7391. For span-level extraction, the best generative baseline is DeepSeek-R1-32B with few-shot prompting, reaching a Cosine Pair F₁ of 0.6765. We further test transfer learning by evaluating PubMedCausal-trained encoders on external causal relation datasets, showing that the resource supports cross-dataset evaluation beyond its original biomedical setting. Our results show that biomedical CRE remains difficult under class imbalance, long causal spans, implicit causality, inter-sentential relations, and prompt sensitivity. PubMedCausal provides a high-quality benchmark for studying causal detection, full-span extraction, and the limits of current language models in biomedical causal reasoning.

We introduce CoDe-KG, an open-source, end-to-end pipeline for extracting sentence-level knowledge graphs by combining robust coreference resolution with syntactic sentence decomposition. Using our model, we contribute a dataset of over 150 000 knowledge triples, which is open source. We also contribute a training corpus of 7248 rows for sentence complexity, 200 rows of gold human annotations for coreference resolution using lung-cancer abstracts from PubMed, 900 rows of gold human annotations for sentence conversion policies from sentences in the abstract, and 398 triples of gold human annotations. We systematically select optimal prompt-model pairs across five complexity categories, showing that hybrid chain-of-thought and few-shot prompting yields up to 99.8% exact-match accuracy on sentence simplification. On relation extraction (RE), our pipeline achieves 65.8% macro-F1 on REBEL, an 8-point gain over the prior state of the art, and 75.7% micro-F1 on WebNLG2, while matching or exceeding performance on Wiki-NRE and CaRB. Ablation studies demonstrate that integrating coreference and decomposition increases recall on rare relations by over 20%