tutorial

The labeling tool can help us label protein and cell names, and also specify some properties of the labels(I also call them annotations). For example, your confidence for labeling this as a protein name (1.0 is the highest confidence and is set to default) and why you label it as a protein name (based on your knowledge or any resources you refer to) would be helpful annotations. Here I’ll show you how to use the labeling tool to: Add labels Add annotations Remove unwanted labels Label the identical names within one caption Save results Please remember to save before you close the main window View the original papers Use shortcut keys by going through some examples. Startup First download the minorthird.jar, your data directory and urlmap.txt from goblin, start the labeling tool by running java –cp PATH_to_minorthird.jar edu.cmu.minorthird.text.gui.TextBaseEditor DATA_DIRECTORY LabelsFlName urlmap.txt where PATH_to_minorthird.jar is the relative path to the minorthird.jar DATA_DIRECTORY is where your documents are stored, LabelsFlName is where you would like to save your labels (minorthird will create a LabelsFlName if it does not exist), and urlmap.txt is a file containing information about the original papers. For example, I’ll put minorthird.jar, my data directory ‘zhenzhen’ and urlmap.txt at /home/zkou/data_label/, ‘cd /home/zkou/data_label/’ and run java –cp minorthird.jar edu.cmu.minorthird.text.gui.TextBaseEditor ...