gnormplus.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 itertools
import os
import re
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{Wei2015,
author={Wei, Chih-Hsuan and Kao, Hung-Yu and Lu, Zhiyong},
title={GNormPlus: An Integrative Approach for Tagging Genes, Gene Families, and Protein Domains},
journal={BioMed Research International},
year={2015},
month={Aug},
day={25},
publisher={Hindawi Publishing Corporation},
volume={2015},
pages={918710},
issn={2314-6133},
doi={10.1155/2015/918710},
url={https://doi.org/10.1155/2015/918710}
}
"""

_DATASETNAME = "gnormplus"
_DISPLAYNAME = "GNormPlus"

_DESCRIPTION = """\
We re-annotated two existing gene corpora. The BioCreative II GN corpus is a widely used data set for benchmarking GN
tools and includes document-level annotations for a total of 543 articles (281 in its training set; and 262 in test).
The Citation GIA Test Collection was recently created for gene indexing at the NLM and includes 151 PubMed abstracts
with both mention-level and document-level annotations. They are selected because both have a focus on human genes.
For both corpora, we added annotations of gene families and protein domains. For the BioCreative GN corpus, we also
added mention-level gene annotations. As a result, in our new corpus, there are a total of 694 PubMed articles.
PubTator was used as our annotation tool along with BioC formats.
"""

_HOMEPAGE = "https://www.ncbi.nlm.nih.gov/research/bionlp/Tools/gnormplus/"

_LICENSE = "UNKNOWN"

_URLS = {
    _DATASETNAME: "https://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/tmTools/download/GNormPlus/GNormPlusCorpus.zip"
}

_SUPPORTED_TASKS = [Tasks.NAMED_ENTITY_RECOGNITION, Tasks.NAMED_ENTITY_DISAMBIGUATION]

_SOURCE_VERSION = "1.0.0"

_BIGBIO_VERSION = "1.0.0"


class GnormplusDataset(datasets.GeneratorBasedBuilder):
    """Dataset loader for GNormPlus corpus."""

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

    BUILDER_CONFIGS = [
        BigBioConfig(
            name="gnormplus_source",
            version=SOURCE_VERSION,
            description="gnormplus source schema",
            schema="source",
            subset_id="gnormplus",
        ),
        BigBioConfig(
            name="gnormplus_bigbio_kb",
            version=BIGBIO_VERSION,
            description="gnormplus BigBio schema",
            schema="bigbio_kb",
            subset_id="gnormplus",
        ),
    ]

    DEFAULT_CONFIG_NAME = "gnormplus_source"

    _re_tax_id = re.compile(r"(?P<db_id>\d+)\([tT]ax:(?P<tax_id>\d+)\)")

    def _info(self) -> datasets.DatasetInfo:
        if self.config.schema == "source":
            features = datasets.Features(
                {
                    "doc_id": datasets.Value("string"),
                    "passages": [
                        {
                            "text": datasets.Value("string"),
                            "type": datasets.Value("string"),
                            "location": {
                                "offset": datasets.Value("int64"),
                                "length": datasets.Value("int64"),
                            },
                        }
                    ],
                    "entities": [
                        {
                            "id": datasets.Value("string"),
                            "type": datasets.Value("string"),
                            "text": datasets.Sequence(datasets.Value("string")),
                            "offsets": datasets.Sequence([datasets.Value("int32")]),
                            "normalized": [
                                {
                                    "db_name": datasets.Value("string"),
                                    "db_id": datasets.Value("string"),
                                    "tax_id": datasets.Value("string"),
                                }
                            ],
                        }
                    ],
                }
            )
        elif self.config.schema == "bigbio_kb":
            features = kb_features
        else:
            raise NotImplementedError(self.config.schema)

        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[_DATASETNAME]
        data_dir = dl_manager.download_and_extract(urls)

        return [
            datasets.SplitGenerator(
                name=datasets.Split.TRAIN,
                # Whatever you put in gen_kwargs will be passed to _generate_examples
                gen_kwargs={
                    "filepaths": [
                        os.path.join(data_dir, "GNormPlusCorpus/BC2GNtrain.BioC.xml"),

                        # This sub-part of the corpus is part of the GIA Test Collection, however in
                        # the paper they used it only for training their models. So we also add it to the
                        # training split.
                        os.path.join(data_dir, "GNormPlusCorpus/NLMIAT.BioC.xml"),
                    ],
                },
            ),
            datasets.SplitGenerator(
                name=datasets.Split.TEST,
                gen_kwargs={
                    "filepaths": [
                        os.path.join(data_dir, "GNormPlusCorpus/BC2GNtest.BioC.xml"),
                    ]
                },
            ),
        ]

    def _parse_bioc_entity(self, uid, bioc_ann, db_id_key="NCBIGene", insert_tax_id=False):
        offsets, texts = get_texts_and_offsets_from_bioc_ann(bioc_ann)
        _type = bioc_ann.infons["type"]

        # parse db ids
        normalized = []
        if _type in bioc_ann.infons:
            for _id in bioc_ann.infons[_type].split(","):
                match = self._re_tax_id.match(_id)
                if match:
                    _id = match.group("db_id")

                n = {"db_name": db_id_key, "db_id": _id}
                if insert_tax_id:
                    n["tax_id"] = match.group("tax_id") if match else None

                normalized.append(n)
        return {
            "id": uid,
            "offsets": offsets,
            "text": texts,
            "type": _type,
            "normalized": normalized,
        }

    def _generate_examples(self, filepaths) -> Tuple[int, Dict]:
        uid = map(str, itertools.count(start=0, step=1))

        for filepath in filepaths:
            with open(filepath, "r") as fp:
                collection = biocxml.load(fp)

                for _, document in enumerate(collection.documents):
                    idx = next(uid)
                    text = " ".join([passage.text for passage in document.passages])

                    insert_tax = self.config.schema == "source"
                    entities = [
                        self._parse_bioc_entity(next(uid), entity, insert_tax_id=insert_tax)
                        for passage in document.passages
                        for entity in passage.annotations
                    ]

                    # Some of the entities have a off-by-one error. Correct these annotations!
                    self.adjust_entity_offsets(text, entities)

                    if self.config.schema == "source":
                        features = {
                            "doc_id": document.id,
                            "passages": [
                                {
                                    "text": passage.text,
                                    "type": passage.infons["type"],
                                    "location": {
                                        "offset": passage.offset,
                                        "length": passage.total_span.length,
                                    },
                                }
                                for passage in document.passages
                            ],
                            "entities": entities,
                        }

                        yield idx, features
                    elif self.config.schema == "bigbio_kb":
                        # passage offsets/lengths do not connect, recalculate them for this schema.
                        passage_spans = []
                        start = 0
                        for passage in document.passages:
                            end = start + len(passage.text)
                            passage_spans.append((start, end))
                            start = end + 1

                        features = {
                            "id": next(uid),
                            "document_id": document.id,
                            "passages": [
                                {
                                    "id": next(uid),
                                    "type": passage.infons["type"],
                                    "text": [passage.text],
                                    "offsets": [span],
                                }
                                for passage, span in zip(document.passages, passage_spans)
                            ],
                            "entities": entities,
                            "events": [],
                            "coreferences": [],
                            "relations": [],
                        }

                        yield idx, features
                    else:
                        raise NotImplementedError(self.config.schema)

    def adjust_entity_offsets(self, text: str, entities: List[Dict]):
        for entity in entities:
            start, end = entity["offsets"][0]
            entity_mention = entity["text"][0]
            if not text[start:end] == entity_mention:
                if text[start - 1 : end - 1] == entity_mention:
                    entity["offsets"] = [(start - 1, end - 1)]
                elif text[start : end - 1] == entity_mention:
                    entity["offsets"] = [(start, end - 1)]