Ontology Enrichment from Texts (OET): A Biomedical Dataset for Concept Discovery and Placement

A biomedical dataset supporting ontology enrichment from texts, by concept discovery and placement, adapting the MedMentions dataset (PubMed abstracts) with SNOMED CT of versions in 2014 and 2017 under the Diseases (disorder) sub-category and the broader categories of Clinical finding, Procedure, and Pharmaceutical / biologic (CPP) product.

The dataset is documented in the work, Ontology Enrichment from Texts: A Biomedical Dataset for Concept Discovery and Placement, on arXiv: https://arxiv.org/abs/2306.14704

ver2: we revised the mention-level data by only keeping out-of-KB mentions (or "NIL" mentions) associated with one-hop edges (including leaf nodes, as <leaf node, NULL>) and two-hop edges in the ontology (SNOMED CT 20140901).