Issues loading Individuals OWL

[Robbie1977]

Continuing for #18

full size was loaded as VFB
and a smaller version loaded as VFB_test

neither seem to ever load?

How are we supposed to diagnose OWL loading errors?

[leechuck]

@reality @MiguelAngelRG How hard would it be to provide the exception message when loading of ontology fails in an infobox in AberOWL? I think it could be kept in Redis.

VFB fails to load because the URL is not valid (http://purl.obolibrary.org.obo/fbbt/vfb/fbbt_vfb_ind_prc_nr.owl). I changed the URL to point to the right file, reloading now, let's see if this works. For VFB_test, I get an InputFormatException, which is likely due to it's not being valid XML or RDF/XML.

[leechuck]

The VFB ontology is now available at http://aber-owl.net/ontology/VFB/, fully classified.

@reality I still have to manually reload the ontology after changing the URL (using the reload API command) before it actually loads the ontology; I guess the update script would pick it up once a day, but somewhere it should be documented that ontologies are only loaded from URLs once a day.

[dosumis]

Thanks Robert. Now trying to run queries for individuals using 'realize'

http://aber-owl.net/service/api/runQuery.groovy?type=realize&query=%3Chttp://purl.obolibrary.org/obo/FBbt_00007683%3E&ontology=VFB

=> {"result":[],"time":169}

Should find 276 individuals

Is the realize method not yet implemented on the site? I can see it here:

https://github.com/bio-ontology-research-group/AberOWL/blob/master/src/QueryEngine.groovy#L74

Cheers,
David

[leechuck]

Problem seems to be that we don't index instances in Lucene, and the classes2info function only returns OWLEntities for which we can find a label in our Lucene index. I might have temporarily fixed it by making the URI remainder a label should everything else fail, but we should properly index annotation properties of instances in Lucene.

Needs restart of AberOWL.

[leechuck]

It now returns some information for the instance query, but not 276 individuals. I will debug tomorrow, maybe @reality can have a look, too.

[leechuck]

Can this issue be closed? It may be covered by #13

[leechuck]

@dosumis Does this work for you with the recent updates to AberOWL? VFB does load again and will update frequently, and the results from the query above seem ok.