neuroNER

named entity recognizer for neuronal cells, based on UIMA Ruta rules

Use

TODO how to apply NER to simple text

Developer Install

NeuroNER uses Ruta (site, documentation), a workbench to develop and test NLP rules.

• Download Eclipse

• Install RUTA plugin

  • Help > Install New Software...
    • Work with: http://www.apache.org/dist/uima/eclipse-update-site/
    • Add...
      • Name: RUTA, OK
    • Select Apache UIMA Eclipse tooling and runtime support and Apache UIMA Ruta
      • Next, Next, Finish

• Open Ruta

  • Window > Open Perspective > Other...
    • Select: Uima Ruta

• Install neuroNER

  • File > Import
    • General > Existing Project into Workspace, Next
    • Select archive file
    • Browse... to your neuroNER folder
      • Finish
  • The project should appear in your Script Browser on the left

• Now let's apply the rules on some text.

  • Open script script/neuroNER/NeuroNER.ruta. This is where rules are defined. Check Ruta documentation to understand the syntax.
  • Right click, Debug As, UIMA Ruta
  • Open Console view to see progress, wait until it's <terminated>

• View results

  • Open files in output/
    • Select Type System NeuroNERTypeSystem.xml
  • Click on Eclipse View Annotation Browser View (tabed window on the right)
    • Select checkboxes, to reveal the annotations we added.

• Inspect results

  • This allows to see which rules have been applied to which sentence.
  • Window > Open Perspective > Ruta Explain
  • See what rules have been applied
    • Click on Eclipse View Applied Rules