owlcollab / owlcollab/owltools
Error in building of topology graph in solr loading
Nobody has claimed this yet.
- Dominant language
- Java
- Stars
- 115
- Forks
- 34
- PR merge metrics
- No merged PRs in 30d
Description
From cmung...@gmail.com 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
Contributor guide
No contributing guide indexed for this repository
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with OWLTools-Solr/src/test/resources/topology-test.obo and trace the topology graph handling described in the issue. Inspect getEdgeLabel and its call to getSingleQuantifiedProperty, then compare the OGW path list with the topology translation. Done means the edge between GO:0030414 and GO:0008233 is not labeled part_of.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- java
- Domain
- search
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100