Datasets:

ncbi
/

ncbi_disease

- {"ncbi_disease": {"description": "This paper presents the disease name and concept annotations of the NCBI disease corpus, a collection of 793 PubMed\nabstracts fully annotated at the mention and concept level to serve as a research resource for the biomedical natural\nlanguage processing community. Each PubMed abstract was manually annotated by two annotators with disease mentions\nand their corresponding concepts in Medical Subject Headings (MeSH\u00ae) or Online Mendelian Inheritance in Man (OMIM\u00ae).\nManual curation was performed using PubTator, which allowed the use of pre-annotations as a pre-step to manual annotations.\nFourteen annotators were randomly paired and differing annotations were discussed for reaching a consensus in two\nannotation phases. In this setting, a high inter-annotator agreement was observed. Finally, all results were checked\nagainst annotations of the rest of the corpus to assure corpus-wide consistency.\n\nFor more details, see: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3951655/\n\nThe original dataset can be downloaded from: https://www.ncbi.nlm.nih.gov/CBBresearch/Dogan/DISEASE/NCBI_corpus.zip\nThis dataset has been converted to CoNLL format for NER using the following tool: https://github.com/spyysalo/standoff2conll\nNote: there is a duplicate document (PMID 8528200) in the original data, and the duplicate is recreated in the converted data.\n", "citation": "@article{dougan2014ncbi,\n title={NCBI disease corpus: a resource for disease name recognition and concept normalization},\n author={Dogan, Rezarta Islamaj and Leaman, Robert and Lu, Zhiyong},\n journal={Journal of biomedical informatics},\n volume={47},\n pages={1--10},\n year={2014},\n publisher={Elsevier}\n}\n", "homepage": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3951655/", "license": "", "features": {"id": {"dtype": "string", "id": null, "_type": "Value"}, "tokens": {"feature": {"dtype": "string", "id": null, "_type": "Value"}, "length": -1, "id": null, "_type": "Sequence"}, "ner_tags": {"feature": {"num_classes": 3, "names": ["O", "B-Disease", "I-Disease"], "names_file": null, "id": null, "_type": "ClassLabel"}, "length": -1, "id": null, "_type": "Sequence"}}, "post_processed": null, "supervised_keys": null, "builder_name": "ncbi_disease", "config_name": "ncbi_disease", "version": {"version_str": "1.0.0", "description": null, "major": 1, "minor": 0, "patch": 0}, "splits": {"train": {"name": "train", "num_bytes": 2355516, "num_examples": 5433, "dataset_name": "ncbi_disease"}, "validation": {"name": "validation", "num_bytes": 413900, "num_examples": 924, "dataset_name": "ncbi_disease"}, "test": {"name": "test", "num_bytes": 422842, "num_examples": 941, "dataset_name": "ncbi_disease"}}, "download_checksums": {"https://github.com/spyysalo/ncbi-disease/raw/master/conll/train.tsv": {"num_bytes": 1140476, "checksum": "5f87b0de649eccff21e6d6e49e304aace808056ecae55225ea31602192517be9"}, "https://github.com/spyysalo/ncbi-disease/raw/master/conll/devel.tsv": {"num_bytes": 200352, "checksum": "b4e1e7efcc2a35047bf2f3d281648357470e674f555d4a26a0049ac37d59cc61"}, "https://github.com/spyysalo/ncbi-disease/raw/master/conll/test.tsv": {"num_bytes": 205664, "checksum": "8f088ce45dc4746592188f9e69de3d89d87f3bb8f0ed8c4a287d018123fa148d"}}, "download_size": 1546492, "post_processing_size": null, "dataset_size": 3192258, "size_in_bytes": 4738750}}