brat-peek 0.1.1

Simple utilities to read/write brat standoff files (peek module)

brat Peek 👀

Peek into corpora annotated using brat rapid annotation tool (brat).

brat Peek 👀 is a Python framework for working with annotations in brat's standoff format (.ann files).

Main features

• Load .ann files using an object-oriented framework that allows easy access and manipulation to complete corpora as well as to individual documents and annotations.
• Load .txt files to see annotations in context, check annotation spans and extract individual sentences.
• Print different annotation statistics and output corpus contents in multiple formats.
• Calculate evaluation metrics such as inter-annotator agreement and F-1 score between document collections.

How to use brat peek 👀

A full documentation and example notebooks are in the works. Meanwhile, take a look at some examples of how to use brat peek 👀:

• Framework for working with .ann files and collections.

    import peek
    corpus = peek.AnnCorpus('dummy_data/')
    # Access a random document...
    doc = corpus.get_random_doc()
    # ...or get one by its name
    doc = corpus.get_doc_by_name('PMID-1590827')
    # Or maybe just get those you're interested in
    docs = [doc for doc in corpus.docs if 'Organism' in doc.count['entities']]
    # Print document name and path
    print(doc.name, doc.path)
    # See the individual annotations in a document
    print(doc.anns.items())
  

• See the annotations in a corpus at a glance with stats and graphs.

    print('Corpus stats:', corpus.count)
    print('Entity labels found in corpus: ', corpus.text_labels)
    print('Document 42 annotations:', corpus.docs[41].anns)
    # Create a plot
    peek.stats.plot_tags(corpus)
    # Generate .tsv with statistics
    peek.stats.generate_corpus_stats_tsv(corpus, include_txt=True)
  

• Check out the most common annotated text spans.

    print(corpus.text_freq)
    print(corpus.text_freq['Organism'].most_common(5))
    print(corpus.text_freq_lower)
  

• Print a corpus's content to a .tsv file.

    # Create .tsv file from corpus (to_ignore is an optional argument)
    peek.rwsl.print_tsv_from_corpus(corpus, 'output_folder/', to_ignore=['Organism'])
    # Create .tsv with text frequencies
    peek.rwsl.print_tsv_from_text_freq(corpus, 'output_folder/', to_ignore=['Organism'], lower=False)
    # Create .tsv with codes column for normalization with a code reference file.
    peek.rwsl.print_tsv_for_norm(corpus, 'output_folder/', 'reference.tsv', to_ignore=['Organism'])
  

• Calculate metrics for different corpora.

    # Calculate IAA and print .tsv file with disagreements [code based on https://github.com/TeMU-BSC/iaa-computation]
    peek.metrics.show_iaa([corpus1, corpus2], ['filename', 'label', 'offset'], ['Organism'], tsv=True)
    # You can use specific labels, as shown above, or use the text_labels attribute to use all the labels in the corpus at once.
    peek.metrics.show_iaa([corpus1, corpus2], ['filename', 'label', 'offset'], corpus1.text_labels)
    # Calculate precision, recall and F-score between a Gold Standard and a set of predictions [code based on https://github.com/TeMU-BSC/meddoprof-evaluation-library/]
    peek.metrics.show_fscore(gs, pred, gs.text_labels)
  

• Extract sentences from documents to create customizable annotation files.

    # Set txt to True when creating an AnnCorpus object to also read .txt files
    corpus = peek.AnnCorpus('dummy_data/', txt=True)
    # Separate document into individual sentences, adjusting annotation spans in the way.
    sentences = [peek.txt.doc2sent(doc) for doc in corpus.docs]
    # Create a new document only with sentences that have organisms annotated.
    new_doc = peek.txt.sent2doc([sent for sent in sentences if any(ann.tag == 'Organism' for ann in frase_med.anns['entities'])])
  

• Save corpora as pickle objects to load them later (useful for big corpora).

    # Save
    peek.rwsl.save_corpus(corpus, 'temp/')
    # Load
    corpus = peek.rwsl.load_corpus('temp/dummy_data.pckl')
  

• Suggest annotations to speed up your annotation process (on the works - mostly untested)

    peek.txt.generate_suggestions_from_tsv(temp, tsv)
  

• Convert brat files into spaCy objects

    corpus = peek.AnnCorpus('dummy_data/', txt=True)
    nlp = spacy.load(...)
    spacy_docs = peek.rwsl.brat2spacy(corpus, nlp)
  

Contact

brat peek is a personal project, which means that currently new features are added as I personally need them. If you have any questions or suggestions, you can contact me at the following address:

• Salvador Lima: <salvador.limalopez gmail com>

For more information on brat, please visit its GitHub repository or homepage.