genia_relation_corpus.py

# coding=utf-8
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#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
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#     http://www.apache.org/licenses/LICENSE-2.0
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"""
The extraction of various relations stated to hold between biomolecular entities is one of the most frequently
addressed information extraction tasks in domain studies. Typical relation extraction targets involve protein-protein
interactions or gene regulatory relations. However, in the GENIA corpus, such associations involving change in the
state or properties of biomolecules are captured in the event annotation.

The GENIA corpus relation annotation aims to complement the event annotation of the corpus by capturing (primarily)
static relations, relations such as part-of that hold between entities without (necessarily) involving change.
"""

import os
from pathlib import Path
from typing import Dict, List, Tuple

import datasets

from .bigbiohub import kb_features
from .bigbiohub import BigBioConfig
from .bigbiohub import Tasks
from .bigbiohub import parse_brat_file
from .bigbiohub import brat_parse_to_bigbio_kb


_LANGUAGES = ['English']
_PUBMED = True
_LOCAL = False
_CITATION = """\
@inproceedings{pyysalo-etal-2009-static,
    title = "Static Relations: a Piece in the Biomedical Information Extraction Puzzle",
    author = "Pyysalo, Sampo  and
      Ohta, Tomoko  and
      Kim, Jin-Dong  and
      Tsujii, Jun{'}ichi",
    booktitle = "Proceedings of the {B}io{NLP} 2009 Workshop",
    month = jun,
    year = "2009",
    address = "Boulder, Colorado",
    publisher = "Association for Computational Linguistics",
    url = "https://aclanthology.org/W09-1301",
    pages = "1--9",
}

@article{article,
author = {Ohta, Tomoko and Pyysalo, Sampo and Kim, Jin-Dong and Tsujii, Jun'ichi},
year = {2010},
month = {10},
pages = {917-28},
title = {A reevaluation of biomedical named entity - term relations},
volume = {8},
journal = {Journal of bioinformatics and computational biology},
doi = {10.1142/S0219720010005014}
}

@MISC{Hoehndorf_applyingontology,
    author = {Robert Hoehndorf and Axel-cyrille Ngonga Ngomo and Sampo Pyysalo and Tomoko Ohta and Anika Oellrich and
    Dietrich Rebholz-schuhmann},
    title = {Applying ontology design patterns to the implementation of relations in GENIA},
    year = {}
}
"""

_DATASETNAME = "genia_relation_corpus"
_DISPLAYNAME = "GENIA Relation Corpus"

_DESCRIPTION = """\
The extraction of various relations stated to hold between biomolecular entities is one of the most frequently
addressed information extraction tasks in domain studies. Typical relation extraction targets involve protein-protein
interactions or gene regulatory relations. However, in the GENIA corpus, such associations involving change in the
state or properties of biomolecules are captured in the event annotation.

The GENIA corpus relation annotation aims to complement the event annotation of the corpus by capturing (primarily)
static relations, relations such as part-of that hold between entities without (necessarily) involving change.
"""

_HOMEPAGE = "http://www.geniaproject.org/genia-corpus/relation-corpus"

_LICENSE = 'GENIA Project License for Annotated Corpora'

_URLS = {
    _DATASETNAME: {
        "train": "http://www.nactem.ac.uk/GENIA/current/GENIA-corpus/Relation/GENIA_relation_annotation_training_data.tar.gz",
        "validation": "http://www.nactem.ac.uk/GENIA/current/GENIA-corpus/Relation/GENIA_relation_annotation_development_data.tar.gz",
        "test": "http://www.nactem.ac.uk/GENIA/current/GENIA-corpus/Relation/GENIA_relation_annotation_test_data.tar.gz",
    },
}

_SUPPORTED_TASKS = [Tasks.RELATION_EXTRACTION]

_SOURCE_VERSION = "1.0.0"

_BIGBIO_VERSION = "1.0.0"


class GeniaRelationCorpusDataset(datasets.GeneratorBasedBuilder):
    """GENIA Relation corpus."""

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

    BUILDER_CONFIGS = [
        BigBioConfig(
            name="genia_relation_corpus_source",
            version=SOURCE_VERSION,
            description="genia_relation_corpus source schema",
            schema="source",
            subset_id="genia_relation_corpus",
        ),
        BigBioConfig(
            name="genia_relation_corpus_bigbio_kb",
            version=BIGBIO_VERSION,
            description="genia_relation_corpus BigBio schema",
            schema="bigbio_kb",
            subset_id="genia_relation_corpus",
        ),
    ]

    DEFAULT_CONFIG_NAME = "genia_relation_corpus_source"

    def _info(self) -> datasets.DatasetInfo:
        if self.config.schema == "source":
            features = datasets.Features(
                {
                    "id": datasets.Value("string"),
                    "document_id": datasets.Value("string"),
                    "text": datasets.Value("string"),
                    "text_bound_annotations": [  # T line in brat, e.g. type or event trigger
                        {
                            "offsets": datasets.Sequence([datasets.Value("int32")]),
                            "text": datasets.Sequence(datasets.Value("string")),
                            "type": datasets.Value("string"),
                            "id": datasets.Value("string"),
                        }
                    ],
                    "relations": [  # R line in brat
                        {
                            "id": datasets.Value("string"),
                            "head": {
                                "ref_id": datasets.Value("string"),
                                "role": datasets.Value("string"),
                            },
                            "tail": {
                                "ref_id": datasets.Value("string"),
                                "role": datasets.Value("string"),
                            },
                            "type": datasets.Value("string"),
                        }
                    ],
                    "equivalences": [  # Equiv line in brat
                        {
                            "id": datasets.Value("string"),
                            "ref_ids": datasets.Sequence(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[_DATASETNAME]
        data_dir = dl_manager.download_and_extract(urls)
        return [
            datasets.SplitGenerator(
                name=split,
                gen_kwargs={
                    "data_dir": data_dir[split],
                },
            )
            for split in [
                datasets.Split.TRAIN,
                datasets.Split.VALIDATION,
                datasets.Split.TEST,
            ]
        ]

    def _generate_examples(self, data_dir) -> Tuple[int, Dict]:
        """Yields examples as (key, example) tuples."""
        for dirpath, _, filenames in os.walk(data_dir):
            for guid, filename in enumerate(filenames):
                if filename.endswith(".txt"):
                    txt_file_path = Path(dirpath, filename)
                    if self.config.schema == "source":
                        example = parse_brat_file(
                            txt_file_path, annotation_file_suffixes=[".a1", ".rel"]
                        )
                        example["id"] = str(guid)
                        for key in ["events", "attributes", "normalizations"]:
                            del example[key]
                        yield guid, example
                    elif self.config.schema == "bigbio_kb":
                        example = brat_parse_to_bigbio_kb(
                            parse_brat_file(txt_file_path)
                        )
                        example["id"] = str(guid)
                        yield guid, example