Annotating input data using graphs via a user interface is disclosed, including: receiving a selection of an imported ontological subgraph to import into an annotation of input data presenting at least a portion of the imported ontological subgraph in a user interface associated with editing the annotation of the input data; receiving, via the user interface, a user input to associate a selected portion associated with the input data with a previously defined node associated with the presented at least portion of the imported ontological subgraph; and updating the annotation of the input data based at least in part on the user input and the imported ontological subgraph.