Knowtator2 annotation project creation - UCDenver-ccp/CRAFT GitHub Wiki

Much of the annotation work in CRAFT was done using the original Knowtator plugin for Protégé. This plugin has been deprecated as it only works on a very old version of Protégé. A new Protégé plugin, Knowatator2, is now available for use. The Clojure Boot script that can generate alternative annotation file formats (see Creating annotation files in alternative formats) is also capable of creating the directory structure required for Knowtator2 annotation projects.

For instructions on how to install/use Knowtator2, please visit the Knowtator2 home page.

System requirements (please install before proceeding)

  • Java 8 (or better)
  • Clojure Boot (see installation instructions here)

Important: run boot from the base directory of the distribution

Clojure Boot is a command line utility. It makes use of the build.boot file that is in the base directory of the CRAFT distribution. Make sure you are in the base directory of the distribution (where the build.boot file is located) when trying to run a boot command. If you see an error message containing java.lang.IllegalArgumentException: No such task ([TASK_NAME]) then you may not be in the correct directory, or you may have a typo in [TASK_NAME].

Example: Create a Knowtator2 project using all concept annotations

boot all-concepts knowtator-project -o /tmp/all-concepts-knowtator-project

converting (:UBERON :SO :PR :NCBITaxon :MOP :GO_MF :GO_CC :GO_BP :CL :CHEBI) annotations to :knowtator2 ...
output directory: /tmp/all-concepts-knowtator-project/Annotations

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