Closes #714 #721
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Closes #714 #721
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First pass at supporting bigbio_kb schema properly. WIP
Passes all tests
shamikbose
requested review from
hakunanatasha,
jason-fries,
sunnnymskang,
ruisi-su,
galtay,
leonweber,
sg-wbi and
debajyotidatta
as code owners
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@phlobo I transferred the bug fix to the hub implementation. Please have a look. Thanks! |
phlobo
requested changes
Dec 10, 2024
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@mariosaenger some minor issues, could you take a quick look, please?
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| _HOMEPAGE = "http://www.geniaproject.org/shared-tasks/bionlp-jnlpba-shared-task-2004" | ||
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| _LICENSE = 'Creative Commons Attribution 3.0 Unported' | ||
| _LICENSE = "CC_BY_3p0" |
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Not sure this is correct. The data archives contain a LICENSE file with "GENIA Project License for Annotated Corpora".
| The data came from the GENIA version 3.02 corpus (Kim et al., 2003). | ||
| This was formed from a controlled search on MEDLINE using the MeSH terms human, blood cells and transcription factors. | ||
| From this search 2,000 abstracts were selected and hand annotated according to a small taxonomy of 48 classes based on | ||
| a chemical classification. Among the classes, 36 terminal classes were used to annotate the GENIA corpus. | ||
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| _HOMEPAGE = "http://www.geniaproject.org/shared-tasks/bionlp-jnlpba-shared-task-2004" |
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The link does not work - If we can't find another one, maybe just a link to ACL Anthology?
| document["passages"] = [ | ||
| { | ||
| "id": next(uid), | ||
| "type": "", |
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Passage type should not be empty imho. I guess it is "sentence" in this dataset?
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biodatasets/my_dataset/my_dataset.py(please use only lowercase and underscore for dataset naming)._CITATION,_DATASETNAME,_DESCRIPTION,_HOMEPAGE,_LICENSE,_URLs,_SUPPORTED_TASKS,_SOURCE_VERSION, and_BIGBIO_VERSIONvariables._info(),_split_generators()and_generate_examples()in dataloader script.BUILDER_CONFIGSclass attribute is a list with at least oneBigBioConfigfor the source schema and one for a bigbio schema.datasets.load_datasetfunction.python -m tests.test_bigbio biodatasets/my_dataset/my_dataset.py.