Dataset Card for Flambe

FlaMBe is a dataset aimed at procedural knowledge extraction from biomedical texts, particularly focusing on single cell research methodologies described in academic papers. It includes annotations from 55 full-text articles and 1,195 abstracts, covering nearly 710,000 tokens, and is distinguished by its comprehensive named entity recognition (NER) and disambiguation (NED) for tissue/cell types, software tools, and computational methods. This dataset, to our knowledge, is the largest of its kind for tissue/cell types, links entities to identifiers in relevant knowledge bases and annotates nearly 400 workflow relations between tool-context pairs.

Citation Information

@inproceedings{,
  author    = {Dannenfelser, Ruth and Zhong, Jeffrey and Zhang, Ran and Yao, Vicky},
  title     = {Into the Single Cell Multiverse: an End-to-End Dataset for Procedural Knowledge Extraction in Biomedical Texts},
  publisher   = {Advances in Neural Information Processing Systems},
  volume    = {36},
  year      = {2024},
  url       = {https://proceedings.neurips.cc/paper_files/paper/2023/file/23e3d86c9a19d0caf2ec997e73dfcfbd-Paper-Datasets_and_Benchmarks.pdf},
}