1. summary How inference of abnormality works

Introduction

The current design patterns are such that the abnormal qualifier is only added when the quality class in the definition is neutral.

However, we still need to be able to infer

* Hyoplasia of right ventricle SubClassOf Abnormality of right ventricle

Because the latter class definition includes qualifier some abnormal, the SubClassOf axiom will not be entailed unless the qualifier is explicitly stated or inferred

Details

We achieve this by including an axiom to PATO such that decreased sizes etc are inferred to be qualifier some abnormal.

We do this with an exiom in imports/extra.owl

* 'deviation(from normal)' SubClassOf qualifier some abnormal

Anything under 'increased', 'decreased' etc in PATO is pre-reasoned in PATO to be here.

See the following explanation:

http://phenotype-ontologies.googlecode.com/svn/trunk/doc/images/has-qualifier-inference.png

Limitations

For this strategy to work it requires the PATO classes themselves to be classified under deviation from normal. This may not always be the case

Notes

Do not be distracted by the fact the has-qualifier relation is named has-component at the moment

https://code.google.com/p/phenotype-ontologies/issues/detail?id=45

Notes