Error code: ConfigNamesError Exception: ImportError Message: To be able to use bigbio/nlm_gene, you need to install the following dependency: bioc. Please install it using 'pip install bioc' for instance. Traceback: Traceback (most recent call last): File "/src/services/worker/src/worker/job_runners/dataset/config_names.py", line 66, in compute_config_names_response config_names = get_dataset_config_names( File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/inspect.py", line 347, in get_dataset_config_names dataset_module = dataset_module_factory( File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/load.py", line 1914, in dataset_module_factory raise e1 from None File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/load.py", line 1880, in dataset_module_factory return HubDatasetModuleFactoryWithScript( File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/load.py", line 1504, in get_module local_imports = _download_additional_modules( File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/load.py", line 354, in _download_additional_modules raise ImportError( ImportError: To be able to use bigbio/nlm_gene, you need to install the following dependency: bioc. Please install it using 'pip install bioc' for instance.

Dataset Card for NLM-Gene

NLM-Gene consists of 550 PubMed articles, from 156 journals, and contains more than 15 thousand unique gene names, corresponding to more than five thousand gene identifiers (NCBI Gene taxonomy). This corpus contains gene annotation data from 28 organisms. The annotated articles contain on average 29 gene names, and 10 gene identifiers per article. These characteristics demonstrate that this article set is an important benchmark dataset to test the accuracy of gene recognition algorithms both on multi-species and ambiguous data. The NLM-Gene corpus will be invaluable for advancing text-mining techniques for gene identification tasks in biomedical text.

Citation Information

@article{islamaj2021nlm,
  title        = {
    NLM-Gene, a richly annotated gold standard dataset for gene entities that
    addresses ambiguity and multi-species gene recognition
  },
  author       = {
    Islamaj, Rezarta and Wei, Chih-Hsuan and Cissel, David and Miliaras,
    Nicholas and Printseva, Olga and Rodionov, Oleg and Sekiya, Keiko and Ward,
    Janice and Lu, Zhiyong
  },
  year         = 2021,
  journal      = {Journal of Biomedical Informatics},
  publisher    = {Elsevier},
  volume       = 118,
  pages        = 103779
}