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1. Get Annotator URI with single Dictionary.

You can easily annotate text by uploading text to the PubAnnotation web service. For annotation, you need to provide the PubDictionary's annotatori URI to the PubAnnotation as described in this manual.

Follow the instructions to get an Annotator URI for a single dictionary. If you want to use multiple dictionaries to annotate text, look at the bottom of this page.


  • 01 - Select a dictionary.
  • 02 - Cilck the Get Annotator URI button.
  • 03 - Input annotation option values.
  • 04 - Click the Generate URI button and use the URI for annotation.


2. Get Annotator URI with multiple Dictionary.

Obtain the annotator URI for multiple dictionaries.

  • 01 - Cilck the Get Annotator URI button.
  • 02 - Click the Select button to select dictionaries.
  • 03 - Choose dictionaries and add them to annotator dictionary list.
  • 04 - Input option values and click the Generate URI button.
  • 05 - Use the URI for annotation.


3. Annotate text using PubAnnotation

Annotate text (e.g., PubMed abstracts) by using the PubAnnotation and PubDictionaries services.
  1. Go to the PubDictionaries site and obtain the annotator URI as explained above.
  2. Use the PubAnnotation service to create a project.
  3. Add text into the project. PubMed abstracts can be easily added by using PubMed ID.
  4. Annotate the text by using the annotator URI.

  • 01 - Sign in to the PubAnnotation.
  • 02 - Create a new project.
  • 03 - Input information and click the Create Project button.
  • 04 - Click the second tab to add PubMed abstract.
  • 05 - Input PubMed ID.
  • 06 - Click the Show button to see the added abstract.
  • 07 - Paste the annotator URI of the PubDictionaries and click the Get button.
  • 08 - 33 mentions are automatically annotated.
  • 09 - Table format view of the annotated entity mentions.