Annotate Biomedical Documents

Review publications, index your documents, or create text corpora

Help us understand your needs with this survey


That easy:

  1. Import Documents

    Submit PubMed PMIDs or PMCIDs, or upload any text, pdf, or xml.

  2. Annotate, Manually and Automatically

    Use the web editor to manually annotate entities, relations, or classify documents. Or use our machines to annotate it for you automatically. If you spot any error in our predictions, we will learn from your feedback to get it right next time.

  3. Get the Results

    Download the annotation results in your favorite format: json, xml, or tsv. That's it!


  • On the Web

    Nothing to install. Just use your favorite browser.

  • Annotation Editor

    Use our web editor to annotate entities (e.g. proteins or subcellular locations), relations (e.g. diseases caused by mutations), and to classify documents.

  • Full-Text Articles (Tons of them)

    Import abstracts or full texts. Decide to focus on specific sections (e.g. Results), leave out others (e.g. Introduction), and annotate the captions of figures and tables.

    Work with millions of documents with ease as everything is handled on the cloud. Ready for Big Data.

  • Machine Learning & Interactive Interface

    You can opt for automatic annotations and accept or reject them on an individual basis. Your feedback is used to re-train our machines thus obtaining better results.

  • Team Collaboration

    Invite other users to help you. You will all work with the same information for seamless integration.

  • Entity Normalization

    Link the annotated entities to unique ids from standard databases such as UniProt or ChEBI.

    You can also upload your own dictionaries to map the annotations to the ids of your internal database.


FlyBase is an online bioinformatics database and the most recognized repository of genetic and molecular data for the insect family Drosophilidae. Read the published paper of our collaboration.
Interested? Start now!