The dataset viewer is not available for this dataset.
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.Need help to make the dataset viewer work? Make sure to review how to configure the dataset viewer, and open a discussion for direct support.
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
}
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