FlyBase ROBOT Plugin

The FlyBase ROBOT plugin is a plugin for the ROBOT ontology manipulation tool. It provides additional commands that are used in FlyBase ontological pipelines.

Setup

Build with Maven by running:

mvn clean package

This will produce a flybase.jar file in the target directory. Place this file in your ROBOT plugins directory (by default ~/.robot/plugins).

Provided commands

flybase:rewrite-def

This command is intended to replace the EQWriter tool. It rewrites definitions that follow a given pattern.

Two types of rewriting are supported:

• rewriting of "DOT-definitions": definitions made of a single dot character (".") are replaced by an automatically generated definition that is a human-readable form of the logical definition of the class;
• rewriting of "SUB-definitions": definitions that are of the form "$sub_PFX:1234" are replaced by the definition of the PFX:1234 term.

To use, provide this command with an input ontology and specify which types of definitions should be replaced (-d for DOT definitions or -s for SUB definitions -- both options can be used simultaneously to replace both types of definition in a single operation).

You may use the -f option to restrict the command to work on terms that belong to a given namespace. For example, with -f FBbt, the command will only rewrite definitions for terms in the http://purl.obolibrary.org/FBbt_ namespace.

Definitions generated by this command may be annotated with extra annotations specified with the --add-annotation or --add-annotation-iri options. Both options expect a space-separated name value pair, where name is the annotation property IRI and value the value of the annotation. The difference between the two options is that with --add-annotation-iri, the value will be stored as an IRI instead of a string literal (which implies that the provided value must be a valid IRI or CURIE).

The output ontology is the input ontology with the rewritten definitions. In addition, you may also save the new definitions only in a separate file with the --write-to option.

Copying

The FlyBase ROBOT plugin is distributed under the terms of the MIT license.