owlcollab
Error in building of topology graph in solr loading
From [email protected] on November 03, 2014 16:36:15
Test case:
OWLTools-Solr/src/test/resources/topology-test.obo
See also:
http://jira.geneontology.org/browse/GO-626 The topology graph edge between GO:0030414 (peptidase inhibitor activity and GO:0008233 (peptidase activity) Should not be part_of. The paths are:
- P, NR
- I, R (which reduces to R) This is calculated directly by the OGW. For the topology graph, all that needs to be done is a straightforward translation of the list returned by OGW, with reduced paths of length>1 discarded. The problem here may reside in getEdgeLabel in OGWE, which makes a dangerous call to getSingleQuantifiedProperty.
Original issue: http://code.google.com/p/owltools/issues/detail?id=105
From [email protected] on November 04, 2014 15:05:58
There is now some better documentation for purpose and structure of the GOlr graphs (via BBOP JS): https://github.com/kltm/bbop-js/wiki/Graph https://github.com/kltm/bbop-js/wiki/TopologyGraph https://github.com/kltm/bbop-js/wiki/TransitivityGraph
From [email protected] on November 06, 2014 14:21:40
Pushed a fix for the issue in r2400 . The correct results are now calculated using the ExpressionMaterializingReasoner for Amigo/Solr. See also the test case OWLTools-Solr/src/test/java/owltools/solrj/TransitivityGraphTest.java
Status: Started
Labels: -Priority-Medium Priority-High
From [email protected] on November 21, 2014 11:07:03
A failing integration test related to GAF Solr loading revealed some issues on the memory requirements (and unnecessary computations) for the setup of the ExpressionMaterializingReasoner. The strategy is now to only create expressions for a requested subset of properties.