Closes #873 and revises #874

[WangXII]

Closes #873 and revises #874 - Wrong entity offsets in the tmvar_v3 datasets

Wrong offsets in PMID 21904390 are already present in the source file https://ftp.ncbi.nlm.nih.gov/pub/lu/tmVar3/tmVar3Corpus.txt

Solution: Manually corrected the wrong offsets in PMID 21904390 as the wrong offsets do not seem to follow any pattern.

Compared to #874, this pull request reverts the offsets in the standard 'source' dataset back to original (but wrong) offsets provided by the original dataset and adds a new 'source_fixed' dataset with corrected offsets

Checkbox

• Confirm that this PR is linked to the dataset issue.
• 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.

[leonweber]

Imho this can be merged after the two comments have been resolved. Please also update to the lastest version of main. At the moment there is a conflict that prevents merging.

[WangXII]

Thanks for the review @leonweber. Looking into the merge conflict, the branch is already up-to-date with main. It seems more like a simple change that the automatic merging strategies fails to recognize. The branch version adds an if-clause to just show the fixed annotations in the source version if the user explicitly requests it ("_source_fixed" vs "_source")

<<<<<<< tmvar_v3_fix
                if "_fixed" in self.config.name:
                    document["entities"] = self._correct_wrong_offsets(
                        document["entities"], doc.pmid
                    )
=======
                document["entities"] = self._correct_wrong_offsets(
                    document["entities"], doc.pmid
                )
>>>>>>> main