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Fixed link to BC5CDR dataset (Closes #909) #910

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merged 1 commit into from
Jan 17, 2024

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drAbreu
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@drAbreu drAbreu commented Dec 4, 2023

  • Dataset: BC5CDR
  • Description of the problem: The links to the bc5cdr dataset are no longer valid.
  • Data: official, mirror

Solution
I change the links of the data to this mirrored repository since the new domain of BioCreative seems to still have problems.

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  • Confirm that this PR is linked to the dataset issue.
  • Create the dataloader script hub/hub_repos/my_dataset/my_dataset.py (please use only lowercase and underscore for dataset naming).
  • Provide values for the _CITATION, _DATASETNAME, _DESCRIPTION, _HOMEPAGE, _LICENSE, _URLs, _SUPPORTED_TASKS, _SOURCE_VERSION, and _BIGBIO_VERSION variables.
  • Implement _info(), _split_generators() and _generate_examples() in dataloader script.
  • Make sure that the BUILDER_CONFIGS class attribute is a list with at least one BigBioConfig for the source schema and one for a bigbio schema.
  • Confirm dataloader script works with datasets.load_dataset function.
  • Confirm that your dataloader script passes the test suite run with python -m tests.test_bigbio_hub <dataset_name> [--data_dir /path/to/local/data] --test_local.

@drAbreu drAbreu changed the title Fixed link to BC5CDR dataset Fixed link to BC5CDR dataset (Closes #909) Dec 4, 2023
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@WojciechKusa WojciechKusa left a comment

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thanks, looks good to me! 🎉

@WojciechKusa WojciechKusa merged commit c6c0cda into bigscience-workshop:main Jan 17, 2024
@dinhngoc267
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Hi, @drAbreu Do you have link to the MeSH dictionary which use for this dataset? I have found in another repo but the bc5cdr has some mention ids which don't exist in the MeSH dictionary, I need to find the right version.

phlobo pushed a commit to davidkartchner/biomedical that referenced this pull request Oct 21, 2024
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3 participants