Create dataloader for PMC-Patients Task 1: Patient Note Recognition (PNR)

[holylovenia]

Hello, I noticed that this repo has pmc_patients for PMC-Patients Task 2: Patient-Patient Similarity (PPS), but there was no dataloader for PMC-Patients Task 1: Patient Note Recognition (PNR), so I created this pull request for this addition. I also don't know if it's best to merge this addition to the previous dataloader (pmc_patients) or not, so for now I make this as a separate dataloader.

Regarding the dataloader schema, since the PMC-Patients PNR is not suitable for all the schemas that have been provided here, I followed @galtay's recommendation (via @SamuelCahyawijaya; thanks for relaying the info to me) to implement the source schema only and leave the _SUPPORTED_TASKS empty.

Please let me know if there's anything I can help.

• Name: PMC-Patients PNR
• Description: PMC-Patients dataset consists of 4 tasks. One of the task is Patient Note Recognition (PNR). PMC-Patients PNR dataset is modeled as a paragraph-level sequential labeling task, similar to the named entity recognition (NER) task. For each article, given input as a sequence of texts p1, p2, ..., pn, where n is the number of paragraphs, the output is a sequence of BIO tags t1, t2, ..., tn.
• Paper: PMC-Patients: A Large-scale Dataset of Patient Notes and Relations Extracted from Case Reports in PubMed Central
• Data: Google Drive

Checkbox

• [ ] Confirm that this PR is linked to the dataset issue.
• [x] Create the dataloader script biodatasets/my_dataset/my_dataset.py (please use only lowercase and underscore for dataset naming).
• [x] Provide values for the _CITATION, _DATASETNAME, _DESCRIPTION, _HOMEPAGE, _LICENSE, _URLs, _SUPPORTED_TASKS, _SOURCE_VERSION, and _BIGBIO_VERSION variables.
• [x] 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.
• [x] Confirm dataloader script works with datasets.load_dataset function.
• [x] Confirm that your dataloader script passes the test suite run with python -m tests.test_bigbio biodatasets/my_dataset/my_dataset.py.
• [ ] If my dataset is local, I have provided an output of the unit-tests in the PR (please copy paste). This is OPTIONAL for public datasets, as we can test these without access to the data files.