Loading YAGO Ontology with OWL API

Question

I’m using the OWL API (3.4.8 for compatibility reasons) for the first time, and I’m trying to load an ontology that is provided as part of the YAGO knowledge base (http://resources.mpi-inf.mpg.de/yago-naga/yago3.1/yagoSimpleTaxonomy.ttl.7z). However I keep getting the following warning:

[main] WARN org.obolibrary.oboformat.parser.OBOFormatParser - LINE: 629693 Expected white space at pos: 44  LINE:
<wikicat_Gardens_in_Aomori_Prefecture>  rdfs:subClassOf <yagoGeoEntity> .

(I just copied one example, but I get this warning for every line in the turtle file, and the printed position is always the colon.)

Here’s the code that produces those warnings:

OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
OWLOntology ontology = manager.loadOntologyFromOntologyDocument(new File("../data/yago/yagoSimpleTaxonomy.ttl"));

Even though they are just logged as warnings and there is no exception thrown, the program gets stuck at this point. So, it seems like there is some kind of issue that I need to sort out. Could anyone tell me what’s going on here?

I tried it with Protege 5.2.0 (OWL API 4.x based) and there are a lot of warnings due to white space misusage. How much memory did you allocate? A 52MB Turtle file needs definitely more than 500MB for the -Xmx setting — UninformedUser
I was able to figure it out (see my answer), but thanks for your help anyway! Appreciate it! — pho7

pho7 pho7 · Accepted Answer · 2017-08-29T07:56:18

As it turned out, some of the URIs in the YAGO ontology contain \n. Removing those \ns from the URIs that were concerned fixed the problem.

Loading YAGO Ontology with OWL API

1 Answers