AnnotationFrequency

[pnrobinson]

We probably want to keep this because we want to have the actual numerator and denominator (the frequency is not enough!)

@ielis @iimpulse

[ielis]

I am not sure I understand the big picture of the issue. NB, the latest phenol parses the HPOA data in 2 steps:

• HpoaDiseaseDataLoader just reads whatever is in the HPOA file, resulting in collections of objects with no preprocessing (HpoaDiseaseDataContainer). This is useful if one is interested in doing custom preprocessing or just presenting the HPOA data.
• HpoDiseaseLoader uses HpoaDiseaseDataLoader in the first step and then transforms the data into HpoDiseases (a container with disease objects)

So, if you want to access the primary data, use the HpoaDiseaseDataLoader. If you are OK with the transformation, use HpoDiseases etc.

[ielis]

@pnrobinson can you pls be more specific regarding what is the issue here?

I want to replace the org.monarchinitiative.phenol.annotations.formats.hpo.AnnotationFrequency interface by Ratio which is a like AnnotationFrequency but also provides the counts.

So, I'm closing the issue because I think the issue should be resolved, but pls comment if you think it should be re-opened.