Tom Gillespie

``` mvn exec:java -Dexec.mainClass="io.scigraph.owlapi.loader.BatchOwlLoader" -Djdk.xml.entityExpansionLimit=99999999 -Dexec.args="-c ../devGraph.yaml" -X Apache Maven 3.2.5 (12a6b3acb947671f09b81f49094c53f426d8cea1; 2014-12-14T09:29:23-08:00) Maven home: /usr/share/maven-bin-3.2 Java version: 1.7.0_79, vendor: Oracle Corporation Java home: /opt/icedtea-bin-7.2.5.5/jre Default locale: en_US, platform encoding:...

Further investigation seems to suggest that this happens because of this line here: `at org.semanticweb.elk.owlapi.ElkReasoner.isConsistent(ElkReasoner.java:854)` fma is probably inconsistent and so it fails. This doesn't happen for nif.owl (for example)...

My concern was less with FMA (we don't need a reasoned version), so that is good. My main concern was the behavior wrt the reasonerConfiguration option which needs to be...

the entityExpansionLimit is unrelated. It is a issue with the java XML parser and occasionally shows up when loading other large ontologies. I included it in the bug report in...

See also https://github.com/SciCrunch/NIF-Ontology/commit/3f04cff65bfabe44239527c5336c71c850be76bd#diff-9b3526f6575cc729a142749e7ba60eff.

Have you defined SNOMED-CT as a curie in the scigraph graph load yaml file? I can produce this behavior by specifying an invalid curie in the prefix field. Try removing...

Hrm, another possibility: is the annotation property that SNOMED uses for synonyms mapped to synonym in the mappedProperties: section of the yaml file? e.g. ``` mappedProperties: - name: synonym properties:...

This would require the creation of a debug/development mode. Returning the trackback in production is a security risk.

Hrm. That might be useful. Not sure if 500 error is the right thing to return. Maybe a 400 error? Or is 400 reserved only for issues with the HTTP...

Currently curies are loaded by services and can be changed by restarting services. We have a number of use cases that make this behavior desirable. However, I have been writing...