drseb/boqa

Bayesian ontology querying from Bauer et al.

BOQA

Simple usage by:

	// Test usage
	BoqaService service = new BoqaService(ontologyFile, annotationFile);
	service.scoreItemsForTestQuery();

	BOQACore.setAssociationFileType(Type.PAF);
	BOQACore boqaCore = new BOQACore(ontologyFile, annotationFile);

	List<Integer> queryAsBoqaIndices = new ArrayList<Integer>();
	queryAsBoqaIndices.add(1);
	queryAsBoqaIndices.add(2);
	queryAsBoqaIndices.add(3);

	List<ItemResultEntry> resultList = boqaCore.score(queryAsBoqaIndices);

	for (int i = 0; i < 10; i++) {

		int boqaId = resultList.get(i).getItemId();

		String itemName = boqaCore.getItemName(boqaId);

		double score = resultList.get(i).getScore();

		System.out.println("boqaId :" + boqaId);
		System.out.println("itemName :" + itemName);
		System.out.println("score :" + score);
		System.out.println();

	}
}

boqa's Issues

Ontologizer Dependencies

Hello, if you could assist me with getting your project to build it would be greatly appreciated. I'm having trouble locating the correct ontologizer dependencies. I see the ontologizerlib repo, but it does not contain many things that this project is looking for, for example ontologizer.association.AssociationParser, ontologizer.go.OBOParser, and I can't figure out where they are. Could you point me to them? Thanks

Handling of unknown TermIds

Currently an IllegalArgEx is thrown when unknown TermIds are given. Thus users have to filter before calling BOQA. I think it might be better to just run BOQA with the terms that can be found and print warnings for the ignored terms.

Javadoc errors using JDK8

Packaging this project using maven 3.5.1 and jdk8-openjdk 6.u144 will fail because of incomplete javadoc errors.
This is a broader issue as outlined here:
https://stackoverflow.com/questions/15886209/maven-is-not-working-in-java-8-when-javadoc-tags-are-incomplete

This issue can be fixed by disabling Xdoclint when compiling with jdk8. I have appended an edited pom.xml, which is usable for building against jdk8.

On a broader perspective it would be great if this issue could be fixed by completing documentation according to doclint requirements. Is there still ongoing work in this project?
pom.xml.txt

Help with Usage

@drseb Maybe this is the wrong repo, but I'm trying to basically run Phenomizer locally with a couple changes to the ontology and annotations, and I'm having a difficult time figuring out how to do that. The example gives back a list of phenotypes; how do I get the matching diseases? Thanks