Europe PMC Full Text Corpus

This repository contains the Europe PMC full text corpus, a collection of 300 articles from the Europe PMC Open Access subset. Each article contains 3 core entity types, manually annotated by curators: Gene/Protein, Disease and Organism.

Corpus Directory Structure

annotations/: contains annotations of the 300 full-text articles in the Europe PMC corpus. Annotations are provided in 3 different formats.
 

• hypothesis/csv/: contains raw annotations fetched from the annotation platform Hypothes.is in comma-separated values (CSV) format.  
• GROUP0/: contains raw manual annotations made by curator GROUP0.
• GROUP1/: contains raw manual annotations made by curator GROUP1.
• GROUP2/: contains raw manual annotations made by curator GROUP2.

• IOB/: contains automatically extracted annotations using raw manual annotations in hypothesis/csv/, which is in Inside–Outside–Beginning tagging format.  
• dev/: contains IOB format annotations of 45 articles, suppose to be used a dev set in machine learning task.
• test/: contains IOB format annotations of 45 articles, suppose to be used a test set in machine learning task.
• train/: contains IOB format annotations of 210 articles, suppose to be used a training set in machine learning task.

• JSON/: contains automatically extracted annotations using raw manual annotations in hypothesis/csv/, which is in JSON format.
• README.md: a detailed description of all the annotation formats.

articles/: contains the full-text articles annotated in Europe PMC corpus.
 

• Sentencised/: contains XML articles whose text has been split into sentences using the Europe PMC sentenciser.
• XML/: contains XML articles directly fetched using Europe PMC Article Restful API.
• README.md: a detailed description of the sentencising and fetching of XML articles.

docs/: contains related documents that were used for generating the corpus.
 

• Annotation guideline.pdf: annotation guideline that is provided to curators to assist the manual annotation.
• demo to molecular conenctions.pdf: annotation platform guideline that is provided to curator to help them get familiar with the Hypothes.is platform.
• Training set development.pdf: initial document that details the paper selection procedures.

pilot/: contains annotations and articles that were used in a pilot study.
 

• annotations/csv/: contains raw annotations fetched from the annotation platform Hypothes.is in comma-separated values (CSV) format.
• articles/: contains the full-text articles annotated in the pilot study.  
  • Sentencised/: contains XML articles whose text has been split into sentences using the Europe PMC sentenciser.
  • XML/: contains XML articles directly fetched using Europe PMC Article Restful API.
• README.md: a detailed description of the sentencising and fetching of XML articles.

src/: source codes for cleaning annotations and generating IOB files
 

• metrics/ner_metrics.py: Python script contains SemEval evaluation metrics.
• annotations.py: Python script used to extract annotations from raw Hypothes.is annotations.
• generate_IOB_dataset.py: Python script used to convert JSON format annotations to IOB tagging format.
• generate_json_dataset.py: Python script used to extract annotations to JSON format.
• hypothesis.py: Python script used to fetch raw Hypothes.is annotations.

License

CCBY

Feedback

For any comment, question, and suggestion, please contact us through helpdesk@europepmc.org or Europe PMC contact page.