Causal relationships between phenotypes

[dosumis]

We have multiple potential use cases for recording causal relationships between phenotypes:

• Defining phenotypes that specify aetiology - e.g. hemolytic anemia MP:0001585 DEF: deficiency of red cells resulting from an increased rate of erythrocyte destruction (more examples here: Representing complex phenotypes #590
• Causal link between enzyme levels and activity: question re: logical def for children of HP_0012379 'Abnormal enzyme/coenzyme activity'. human-phenotype-ontology#4924
• Causal links between developmental process and morphological phenotypes (These are often recorded using is_a at present) e.g.
  
• Causal links between two existing phenotype terms e.g. link hydrocephaly to enlarged brain ventricles?

But first we need to define some relations.

Draft definitions:

phenotype results from: "A relationship between two phenotypes where one phenotype results from another. This relation can be used within phenotype definitions when we wish to restrict to a particular cause. Examples: part of the definition of 'hemolytic anemia' is that it results from hemolysis; part of the definition of cyanosis is that it results from decreased oxygenation of the blood. It can also be used between phenotypes. e.g. we might record that developmental phenotype results from a morphological phenotype in a precursor structure.

phenotype results in: "A relationship between two phenotypes where one phenotype results in another. This may be used between phenotypes (e.g. hydrocephalus results in enlarged brain ventricles) or in the internal definition of phenotypes e.g. abnormal sporulation resulting in formation of ascus containing non-uniform spores (FYPO) could be decomposed into two causally linked phenotypes."

Pull request here: oborel/obo-relations#351
RO ticket here: oborel/obo-relations#350

Please review and comment (& also link any other relevant tickets).

In all except cases where the phenotype definition specifies aetiology, the relationship is unlikely to strictly apply in every case. Do we recommend that the relations only be used where the relationship applies in the vase majority of cases? Do we provide some guidance or leave to the judgment of users. Should we have more relations to use when the relationship only sometimes applies? (my instinct is not).

[pnrobinson]

This looks good. One small thing to consider is that we might want to use the phrase 'phenotypic feature' because many people use phenotype to mean a disease (with multiple phenotypic features). HPO probably should have been called HPFO, but it is too late now.

[mah11]

FYPO really, really needs these. Great to see some progress!

[sbello]

Another example alopecia (http://purl.obolibrary.org/obo/MP_0000414) and Hypotrichosis (HPO) (http://purl.obolibrary.org/obo/HP_0001006) both use the same eq
has part some (
decreased amount and
inheres in some strand of hair and
has modifier some abnormal)
But differ in the cause, alopecia is from hair LOSS, hypotrichosis is failure of hair to ever grow. Both terms are missing an important part of the defnition in the current eq.