Closes #27 - Add S800

biodatasets/s800/s800.py

@@ -0,0 +1,254 @@
+# 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.
+
+"""
+S800 Corpus: a novel abstract-based manually annotated corpus for Named Entity Recognition.
+S800 comprises 800 PubMed abstracts in which organism mentions were identified and mapped to the corresponding NCBI Taxonomy identifiers.
+
+To increase the corpus taxonomic mention diversity the S800 abstracts were collected by selecting 100 abstracts from the following 8 categories: bacteriology, botany, entomology, medicine, mycology, protistology, virology and zoology.
+S800 has been annotated with a focus at the species level; however, higher taxa mentions (such as genera, families and orders) have also been considered.
+"""
+
+import os
+from pathlib import Path
+from typing import Any, List, Tuple, Dict
+
+import datasets
+import pandas as pd
+from bigbio.utils import schemas
+from bigbio.utils.configs import BigBioConfig
+from bigbio.utils.constants import Tasks
+
+_CITATION = """\
+@article{,
+    title = {The SPECIES and ORGANISMS Resources for Fast and Accurate Identification of Taxonomic Names in Text},
+    author = {Pafilis, Evangelos AND Frankild, Sune P. AND Fanini, Lucia AND Faulwetter, Sarah AND Pavloudi, Christina AND Vasileiadou, Aikaterini AND Arvanitidis, Christos AND Jensen, Lars Juhl},
+    journal = {PLOS ONE},
+    publisher = {Public Library of Science},
+    year = {2013},
+    month = {06},
+    volume = {8},
+    pages = {1-6},
+    number = {6},
+    url = {https://doi.org/10.1371/journal.pone.0065390},
+    doi = {10.1371/journal.pone.0065390},
+    biburl    = {https://journals.plos.org/plosone/article/citation/bibtex?id=10.1371/journal.pone.0065390},
+    bibsource = {https://journals.plos.org/plosone/article/citation?id=10.1371/journal.pone.0065390}
+}
+"""
+
+_DATASETNAME = "s800"
+
+_DESCRIPTION = """\
+S800 Corpus: a novel abstract-based manually annotated corpus.
+S800 comprises 800 PubMed abstracts in which organism mentions were identified and mapped to the corresponding NCBI Taxonomy identifiers.
+
+To increase the corpus taxonomic mention diversity the S800 abstracts were collected by selecting 100 abstracts from the following 8 categories: bacteriology, botany, entomology, medicine, mycology, protistology, virology and zoology.
+S800 has been annotated with a focus at the species level; however, higher taxa mentions (such as genera, families and orders) have also been considered.
+"""
+
+_HOMEPAGE = "https://species.jensenlab.org/"
+
+_LICENSE = "Creative Commons License Attribution-ShareAlike 4.0 International"
+
+_URLS = {
+    _DATASETNAME: "https://species.jensenlab.org/files/S800-1.0.tar.gz",
+}
+
+_SUPPORTED_TASKS = [Tasks.NAMED_ENTITY_RECOGNITION]
+
+_SOURCE_VERSION = "1.0.0"
+
+_BIGBIO_VERSION = "1.0.0"
+
+
+class S800Dataset(datasets.GeneratorBasedBuilder):
+    """S800 comprises 800 PubMed abstracts in which organism mentions were identified and mapped to the corresponding NCBI Taxonomy identifiers."""
+
+    SOURCE_VERSION = datasets.Version(_SOURCE_VERSION)
+    BIGBIO_VERSION = datasets.Version(_BIGBIO_VERSION)
+
+    BUILDER_CONFIGS = [
+        BigBioConfig(
+            name=f"{_DATASETNAME}_source",
+            version=SOURCE_VERSION,
+            description=f"{_DATASETNAME} source schema",
+            schema="source",
+            subset_id=f"{_DATASETNAME}",
+        ),
+        BigBioConfig(
+            name=f"{_DATASETNAME}_bigbio_kb",
+            version=BIGBIO_VERSION,
+            description=f"{_DATASETNAME} BigBio schema",
+            schema="bigbio_kb",
+            subset_id=f"{_DATASETNAME}",
+        ),
+    ]
+
+    DEFAULT_CONFIG_NAME = f"{_DATASETNAME}_source"
+
+    def _info(self) -> datasets.DatasetInfo:
+        if self.config.schema == "source":
+            features = datasets.Features(
+                {
+                    "doc_id": datasets.Value("string"),
+                    "s800_doc_id": datasets.Value("string"),
+                    "pmid": datasets.Value("string"),
+                    "entities": {
+                        "offsets": [datasets.Value("int64")],
+                        "text": datasets.Value("string"),
+                        "ncbi_txid": datasets.Value("string"),
+                    },
+                    "category": datasets.Value("string"),
+                    "category_id": datasets.Value("int64"),
+                    "journal": datasets.Value("string"),
+                    "text": datasets.Value("string"),
+                }
+            )
+
+        elif self.config.schema == "bigbio_kb":
+            features = schemas.kb_features
+
+        return datasets.DatasetInfo(
+            description=_DESCRIPTION,
+            features=features,
+            homepage=_HOMEPAGE,
+            license=_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={
+                    "data_dir": Path(data_dir),
+                    "split": "train",
+                },
+            ),
+        ]
+
+    def _generate_examples(self, data_dir: Path, split: str) -> Tuple[int, Dict]:
+        """Yields examples as (key, example) tuples."""
+        if self.config.schema == "source":
+            for key, example in self._read_example_from_file(data_dir):
+                yield key, example
+
+        elif self.config.schema == "bigbio_kb":
+            for key, example in self._read_example_from_file_in_kb_schema(data_dir):
+                yield key, example
+
+    def _read_example_from_file(self, data_dir: Path) -> Tuple[str, Dict]:
+        abstract_dir = data_dir / "abstracts"
+        df_s800 = pd.read_csv(
+            data_dir / "S800.tsv",
+            sep="\t",
+            header=None,
+            names=["nbci_taxonomy_id", "doc_id", "start", "end", "phrase"],
+        ).assign(
+            ncbi_txid=lambda dft: dft["nbci_taxonomy_id"].apply(
+                lambda x: f"NCBI:txid{x}"
+            )
+        )
+
+        df_pubmed = pd.read_csv(
+            data_dir / "pubmedid.tsv",
+            sep="\t",
+            header=None,
+            names=["s800_doc_id", "pmid", "category", "category_id", "journal"],
+        )
+
+        df = (
+            df_s800.groupby("doc_id")
+            .agg(list)
+            .reset_index()
+            .merge(
+                df_pubmed.assign(
+                    doc_id=lambda dft: (
+                        dft["s800_doc_id"] + ":" + dft["pmid"]
+                    ).str.replace("PMID:", "")
+                ),
+                on="doc_id",
+                how="left",
+            )
+        )
+        for _, row in df.iterrows():
+            key = row.doc_id
+            entities = [
+                dict(offsets=[s, e], text=p, ncbi_txid=ncbi_txid)
+                for s, e, p, ncbi_txid in zip(
+                    row.start, row.end, row.phrase, row.ncbi_txid
+                )
+            ]
+            doc_abstract_path = abstract_dir / f"{row.s800_doc_id}.txt"
+            with open(doc_abstract_path, encoding="utf-8") as fp:
+                text = fp.read()
+            example = {
+                "doc_id": key,
+                "s800_doc_id": row.s800_doc_id,
+                "pmid": row.pmid,
+                "entities": entities,
+                "category": row.category,
+                "category_id": row.category_id,
+                "journal": row.journal,
+                "text": text,
+            }
+            yield key, example
+
+    def _parse_example_to_kb_schema(self, example) -> Dict[str, Any]:
+        text = example["text"]
+        doc_id = example["doc_id"]
+        passages = [
+            {
+                "id": f"{doc_id}-P0",
+                "type": "abstract",
+                "text": [text],
+                "offsets": [[0, len(text)]],
+            }
+        ]
+        entities = []
+        for i, entity in enumerate(example["entities"]):
+            cs, ce = entity["offsets"]
+            ce = ce + 1  # Add 1 to make the offset exclusive
+            entity = {
+                "id": f"{doc_id}-E{i}",
+                "text": [entity["text"]],
+                "offsets": [[cs, ce]],
+                "type": "species",
+                "normalized": [
+                    {"db_id": entity["ncbi_txid"], "db_name": "NBCI Taxonomy"}
+                ],
+            }
+            entities.append(entity)
+        data = {
+            "id": doc_id,
+            "document_id": doc_id,
+            "passages": passages,
+            "entities": entities,
+            "relations": [],
+            "events": [],
+            "coreferences": [],
+        }
+        return data
+
+    def _read_example_from_file_in_kb_schema(self, data_dir: Path) -> Tuple[str, Dict]:
+        for key, example in self._read_example_from_file(data_dir):
+            example = self._parse_example_to_kb_schema(example)
+            yield key, example