Create an extendable set of lint-like checks

[GoogleCodeExporter]

Create code for the verification of ontologies.

In addition to being part of the release process, they can be called by GOLD to 
avoid opaque database errors

TODO
1. Decide on how 'extendable' is implemented.
2. What and when should be verified?
3. How should be verified (on syntax level and/or with a reasoner)

Initial problem: Incomplete/self-references in definitions

> [Term]
> id: GO:0090388  ! phagosome-lysosome docking involved in apoptotic cell 
clearance
> intersection_of: GO:0090384  ! phagosome-lysosome docking
> intersection_of: part_of GO:0043277  ! apoptotic cell clearance

Original issue reported on code.google.com by HDie...@lbl.gov on 19 Sep 2011 at 11:45

[GoogleCodeExporter]

added framework to oort to run checks on an ontology during release. Use class 
references, annotations and reflections to identify checks.

Checks are run at three stages in the release process (after loading, after 
mireot, and after reasoning).

TODO: add checks, currently there are only empty checks for demonstration 
purposes.

Original comment by HDie...@lbl.gov on 22 Sep 2011 at 8:16

• Changed state: Started
• Added labels: ****
• Removed labels: ****

[GoogleCodeExporter]

checks are now in use, e.g. cycle checks over is_a

Original comment by HDie...@lbl.gov on 18 Sep 2012 at 10:29

• Changed state: Fixed
• Added labels: ****
• Removed labels: ****