biomedical

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Closes #501 : BEAR Dataset

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Closes #501 ### Checkbox - [x] 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...

karthikrangasai

Resolves #695 - Update DisTEMIST to final release used in shared task (5.1) - Included NED annotations from both entity linking training sets - Added configs for different subtracks (entities...

phlobo

## Describe the bug Some entity offsets for bc5cdr are off by a few characters ## Steps to reproduce the bug ```python from bigbio.dataloader import BigBioConfigHelpers data = conhelps.for_config_name("bc5cdr_bigbio_kb").load_dataset() for...

davidkartchner

Closes #637

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Add the plant-phenotype dataset. Closes #637 New location for dataset (that corrects errors of nested/missing entities): https://github.com/davidkartchner/PPRcorpus ### Checkbox - [x] Confirm that this PR is linked to the dataset...

davidkartchner

Multiple normalizations per entity

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Dear all, I am trying to add NED annotations for different datasets (e.g., [Quaero](https://github.com/bigscience-workshop/biomedical/issues/702) and [DisTEMIST](https://github.com/bigscience-workshop/biomedical/issues/695)), and I wonder how to use the `normalized` attribute when there are multiple concept...

phlobo

bc7_litcovid returns None instances

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## Describe the bug `bc7_litcovid` generates instances with out a `text` field, e.g., `{'id': '34', 'document_id': '34219343', 'text': None, 'labels': ['Prevention']}` ## Steps to reproduce the bug Iterate through the...

jason-fries

thomas2011 implementation issues -- missing passages / entity only implementation

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[thomas2011](https://github.com/bigscience-workshop/biomedical/blob/master/bigbio/biodatasets/thomas2011/thomas2011.py) does not implement passages, only entities, in the KB schema.

jason-fries

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...

holylovenia

_TAGS for fine-grained tasks

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### INTRO This introduces a metadata attribute `_TAGS`. The values in `_TAGS` are, well tags, to further classify the task. These tags are meant to be used together w/ `_SUPPORTED_TASKS`....

sg-wbi

Check for libraries like modin

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A number of these datasets (eg. `medal`) involves reading large CSV files. This can be considerably sped up if the dataset loader checks for the presence of a library like...

shamikbose