practicality of 'warning' messages for annotation checks

[ANiknejad]

WARN org.bgee.pipeline.annotations.SimilarityAnnotation

• 'warning' messages report Uberon ID and Taxon ID: could you please add the ID name for both?
  @fbastian
  @vrechdelaval

• 'warning' messages, 4 different types of message, each needing different checks, and each being differently time-consuming for annotation check:

1.-
There exist negative annotation(s)...There are also positive annotations in parent taxa for same HOM ID - Uberon ID, but some miss a corresponding negative annotation. Negative annotations potentially missing in taxa:

-> should generate an error, no? If parent taxa has positive annotations, none negative annotation should be accepted for sub-taxa...
-> please explain 'some' @fbastian

2.-
There exist negative annotation(s) with no associated positive annotations in same taxon or in sub-taxa....There is no corresponding positive annotation for the same taxon, or for any sub-taxon.

-> this warning is the more easy to understand for me

3.-
There exist negative annotation(s) with corresponding positive annotations in only ONE sub-taxon (most likely, there should be several).

-> this warning is the more easy to skip, depending on the number of sub-taxon

4.-
An annotation uses multiple entity IDs, but there is no annotation for the individual entity:

-> this warning is the more time-consuming, needs some literature check

[fbastian]

• It is an warning and not an error, because maybe a structure could have disapeared and later reapeared in a taxon. I agree that this is very unlikely.
• The method checkNegativeAnnotsParentTaxa identifies the annotations for generating this warning message. Notably, it generates the warning only if there is also no NOT annotation in the parent taxon having the positive annotation (conflicting evidence in a taxon, so that having a NOT annotation in the sub-taxon is plausible).
• Another good check would be to see if there is a positive annotation in the sub-taxon with the NOT annotation: this would be here again the capture of conflicting evidence.

=> If this latter point is implemented. then this warning could likely become an error.