Java Event Based Parser for OBO

Getting Started

The Java event-based parser is part of the OBO-Edit source code, in the org.geneontology.oboedit.dataadapter package.

OBO-Edit can load files in both OBO 1.0 and OBO 1.2 syntax.

We apologize in advance for the very sparse documentation in these source files.

The classes of interest are:

• GOBOParser
• DefaultGOBOParser
• GOBOParseEngine

The basic idea is that GOBOParseEngine reads and parses a collection of OBO files to generate events (like readID and readDefinition). Each GOBOParseEngine is associated with an implementation of GOBOParser. Each time GOBOParseEngine generates an event, the corresponding GOBOParser method is called. Thus, if GOBOParseEngine sees the line "name: kinase" in an OBO file, it will call GOBOParseEngine.readName("kinase", null).

DefaultGOBOParser is an implementation of GOBOParser that populates the OBO-Edit data models from an OBO file. If you want to use OBO-Edit's data models, you can use DefaultGOBOParser like so:

public static OBOSession getSession(String path) {
	DefaultGOBOParser parser = new DefaultGOBOParser();
	GOBOParseEngine engine = new GOBOParseEngine(parser);
	// GOBOParseEngine can parse several files at once
	// and create one munged-together ontology,
	// so we need to provide a Collection to the setPaths() method
	Collection paths = new LinkedList();
	paths.add(path);
	engine.setPaths(paths);
	engine.parse();
	OBOSession session = parser.getSession();
	return session;
}

If you're populating a database, or doing something else where it would just be a waste of memory to use the OBO-Edit data models, you can create your own implementation of GOBOParser, and skip the data model generation step altogether.

If you feel inspired to add some developer documentation to the OBO-Edit code (particularly the data model and data adapter interfaces), please do! We're always happy to integrate code contributions!

If you have any additional questions, please contact gohelp@geneontology.org (the GO helpdesk).

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