nlm_gene.py

# coding=utf-8
# Copyright 2022 The HuggingFace Datasets Authors and the current dataset script contributor.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
import collections
import itertools
from pathlib import Path
from typing import Dict, List, Tuple

import datasets
from bioc import biocxml

from .bigbiohub import kb_features
from .bigbiohub import BigBioConfig
from .bigbiohub import Tasks
from .bigbiohub import get_texts_and_offsets_from_bioc_ann


_LANGUAGES = ['English']
_PUBMED = True
_LOCAL = False
_CITATION = """\
@article{islamaj2021nlm,
  title        = {
    NLM-Gene, a richly annotated gold standard dataset for gene entities that
    addresses ambiguity and multi-species gene recognition
  },
  author       = {
    Islamaj, Rezarta and Wei, Chih-Hsuan and Cissel, David and Miliaras,
    Nicholas and Printseva, Olga and Rodionov, Oleg and Sekiya, Keiko and Ward,
    Janice and Lu, Zhiyong
  },
  year         = 2021,
  journal      = {Journal of Biomedical Informatics},
  publisher    = {Elsevier},
  volume       = 118,
  pages        = 103779
}
"""

_DATASETNAME = "nlm_gene"
_DISPLAYNAME = "NLM-Gene"

_DESCRIPTION = """\
NLM-Gene consists of 550 PubMed articles, from 156 journals, and contains more \
than 15 thousand unique gene names, corresponding to more than five thousand \
gene identifiers (NCBI Gene taxonomy). This corpus contains gene annotation data \
from 28 organisms. The annotated articles contain on average 29 gene names, and \
10 gene identifiers per article. These characteristics demonstrate that this \
article set is an important benchmark dataset to test the accuracy of gene \
recognition algorithms both on multi-species and ambiguous data. The NLM-Gene \
corpus will be invaluable for advancing text-mining techniques for gene \
identification tasks in biomedical text.
"""

_HOMEPAGE = "https://zenodo.org/record/5089049"

_LICENSE = 'Creative Commons Zero v1.0 Universal'

_URLS = {
    "source": "https://zenodo.org/record/5089049/files/NLM-Gene-Corpus.zip",
    "bigbio_kb": "https://zenodo.org/record/5089049/files/NLM-Gene-Corpus.zip",
}

_SUPPORTED_TASKS = [Tasks.NAMED_ENTITY_RECOGNITION, Tasks.NAMED_ENTITY_DISAMBIGUATION]

_SOURCE_VERSION = "1.0.0"
_BIGBIO_VERSION = "1.0.0"


class NLMGeneDataset(datasets.GeneratorBasedBuilder):
    """NLM-Gene Dataset for gene entities"""

    SOURCE_VERSION = datasets.Version(_SOURCE_VERSION)
    BIGBIO_VERSION = datasets.Version(_BIGBIO_VERSION)

    BUILDER_CONFIGS = [
        BigBioConfig(
            name="nlm_gene_source",
            version=SOURCE_VERSION,
            description="NlM Gene source schema",
            schema="source",
            subset_id="nlm_gene",
        ),
        BigBioConfig(
            name="nlm_gene_bigbio_kb",
            version=BIGBIO_VERSION,
            description="NlM Gene BigBio schema",
            schema="bigbio_kb",
            subset_id="nlm_gene",
        ),
    ]

    DEFAULT_CONFIG_NAME = "nlm_gene_source"

    def _info(self) -> datasets.DatasetInfo:

        if self.config.schema == "source":
            if self.config.schema == "source":
                # this is a variation on the BioC format
                features = datasets.Features(
                    {
                        "passages": [
                            {
                                "document_id": datasets.Value("string"),
                                "type": datasets.Value("string"),
                                "text": datasets.Value("string"),
                                "entities": [
                                    {
                                        "id": datasets.Value("string"),
                                        "offsets": [[datasets.Value("int32")]],
                                        "text": [datasets.Value("string")],
                                        "type": datasets.Value("string"),
                                        "normalized": [
                                            {
                                                "db_name": datasets.Value("string"),
                                                "db_id": datasets.Value("string"),
                                            }
                                        ],
                                    }
                                ],
                            }
                        ]
                    }
                )

        elif self.config.schema == "bigbio_kb":
            features = kb_features

        return datasets.DatasetInfo(
            description=_DESCRIPTION,
            features=features,
            homepage=_HOMEPAGE,
            license=str(_LICENSE),
            citation=_CITATION,
        )

    def _split_generators(self, dl_manager) -> List[datasets.SplitGenerator]:
        """Returns SplitGenerators."""
        urls = _URLS[self.config.schema]
        data_dir = Path(dl_manager.download_and_extract(urls))

        return [
            datasets.SplitGenerator(
                name=datasets.Split.TRAIN,
                gen_kwargs={
                    "filepath": data_dir / "Corpus",
                    "file_name": "Pmidlist.Train.txt",
                    "split": "train",
                },
            ),
            datasets.SplitGenerator(
                name=datasets.Split.TEST,
                gen_kwargs={
                    "filepath": data_dir / "Corpus",
                    "file_name": "Pmidlist.Test.txt",
                    "split": "test",
                },
            ),
        ]

    @staticmethod
    def _get_bioc_entity(
        span, db_id_key="NCBI Gene identifier", splitters=",;|-"
    ) -> dict:
        """Parse BioC entity annotation."""
        offsets, texts = get_texts_and_offsets_from_bioc_ann(span)
        db_ids = span.infons.get(db_id_key, "-1")

        # Correct an annotation error in PMID 24886643
        if db_ids.startswith('-222'):
            db_ids = db_ids.lstrip('-222,')

        # No listed entity for a mention
        if db_ids in ['-1','-000','-111','-']:
            normalized = []

        else:
            # Find connector between db_ids for the normalization, if not found, use default
            connector = "|"
            for splitter in list(splitters):
                if splitter in db_ids:
                    connector = splitter
            normalized = [
                {"db_name": "NCBIGene", "db_id": db_id} for db_id in db_ids.split(connector)
            ]

        return {
            "id": span.id,
            "offsets": offsets,
            "text": texts,
            "type": span.infons["type"],
            "normalized": normalized,
        }

    def _generate_examples(
        self, filepath: Path, file_name: str, split: str
    ) -> Tuple[int, Dict]:
        """Yields examples as (key, example) tuples."""

        if self.config.schema == "source":
            with open(filepath / file_name, encoding="utf-8") as f:
                contents = f.readlines()
            for uid, content in enumerate(contents):
                file_id = content.replace("\n", "")
                file_path = filepath / "FINAL" / f"{file_id}.BioC.XML"
                reader = biocxml.BioCXMLDocumentReader(file_path.as_posix())
                for xdoc in reader:
                    yield uid, {
                        "passages": [
                            {
                                "document_id": xdoc.id,
                                "type": passage.infons["type"],
                                "text": passage.text,
                                "entities": [
                                    self._get_bioc_entity(span)
                                    for span in passage.annotations
                                ],
                            }
                            for passage in xdoc.passages
                        ]
                    }
        elif self.config.schema == "bigbio_kb":
            with open(filepath / file_name, encoding="utf-8") as f:
                contents = f.readlines()
            uid = 0  # global unique id
            for i, content in enumerate(contents):
                file_id = content.replace("\n", "")
                file_path = filepath / "FINAL" / f"{file_id}.BioC.XML"
                reader = biocxml.BioCXMLDocumentReader(file_path.as_posix())
                for xdoc in reader:
                    data = {
                        "id": uid,
                        "document_id": xdoc.id,
                        "passages": [],
                        "entities": [],
                        "relations": [],
                        "events": [],
                        "coreferences": [],
                    }
                    uid += 1

                    char_start = 0
                    # passages must not overlap and spans must cover the entire document
                    for passage in xdoc.passages:
                        offsets = [[char_start, char_start + len(passage.text)]]
                        char_start = char_start + len(passage.text) + 1
                        data["passages"].append(
                            {
                                "id": uid,
                                "type": passage.infons["type"],
                                "text": [passage.text],
                                "offsets": offsets,
                            }
                        )
                        uid += 1
                    # entities
                    for passage in xdoc.passages:
                        for span in passage.annotations:
                            ent = self._get_bioc_entity(
                                span, db_id_key="NCBI Gene identifier"
                            )
                            ent["id"] = uid  # override BioC default id
                            data["entities"].append(ent)
                            uid += 1

                    yield i, data