Bratify

Bratify is a program that produces Brat-formatted class hierarchy and labels from an OWL file.

Running the program

Edit the following information in the run_bratify.py file (see example below).

Specify the paths to:

• the input OWL file
• the output file formatted for brat visual.conf
• the output file formatted for brat annotation.conf

Specify the output format (1 or 2) of the labels for Brat's system and for visualization.conf.

1 = brat_syst_format | normal term format | ID

For example:

Matthew-Wood_syndrome | Matthew-Wood syndrome | DOID_0050819

2 = ID | normal term format

For example:

DOID_0050819 | Matthew-Wood syndrome

Specify the SPARQL query to get the labels and the PURLs for each class in the OWL file.

Run bratify.py for the specified ontology by adding a call to the function.

Example

def name_of_ontology():

    # Specify the paths to:
    # - the input OWL file
    # - the output file formatted for brat visual.conf
    # - the output file formatted for brat annotation.conf
    owl = "./path_to/owl_file.owl"
    visualization_path = "./for_configuration_files/labels_for_visualization.txt"
    annotation_path = "./for_configuration_files/hierarchy_for_annotation.txt"
        
    # Specify the output format of the labels for Brat's system and for visualization.conf
    # 1 = brat_syst_format | normal term format | ID 
    # 2 = ID | normal term format 
    output_style = "1"

    # Specify the SPARQL query to get the labels and the PURLs for each class in the OWL file
    query = """ SELECT DISTINCT ?child_label ?child_id ?parent_label ?parent_id
                WHERE {
                    ?child rdfs:subClassOf ?parent .
                    ?child a owl:Class .
                    ?parent a owl:Class .
                    ?child rdfs:label ?child_label .
                    ?parent rdfs:label ?parent_label .
                    ?child oboInOwl:id ?child_id .
                    ?parent oboInOwl:id ?parent_id .

                    FILTER ( ?parent != ?child )
                }
                #LIMIT 10
            """

    # Run bratify.py for the specified ontology
    run_bratify(owl, query, visualization_path, annotation_path, output_style)

if __name__ == '__main__':
    name_of_ontology()

Output examples

Hierarchy

DOID_4
    DOID_630
        DOID_0050177
            DOID_14793
            DOID_0050738
            DOID_0050739
                DOID_0050736
                    DOID_14213
                    DOID_9467
                    DOID_14702

Labels

DOID_0001816 | angiosarcoma
DOID_0002116 | pterygium
DOID_0014667 | disease of metabolism
DOID_0050004 | seminal vesicle acute gonorrhea
DOID_0050012 | chikungunya
DOID_0050013 | carbohydrate metabolism disease
DOID_0050025 | human granulocytic anaplasmosis
DOID_0050026 | human monocytic ehrlichiosis
DOID_0050032 | mineral metabolism disease
DOID_0050035 | African tick-bite fever