Open nicolevasilevsky opened 4 years ago
@dosumis and @ybradford are better suited for that! Good question.
Should check what's used in GO-plus and align with that.
IN this case - GO already has the term - https://www.ebi.ac.uk/ols/ontologies/go/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FGO_0097722
So it should be used directly
If you click on the neighbourhood tab here http://amigo.geneontology.org/amigo/term/GO:0097722
You can see the relation used to link to CL. Unfortunately there's a rendering issue, but looking up in OLS => https://www.ebi.ac.uk/ols/ontologies/ro/properties?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FRO_0002565
So - 'abnormal sperm motility' should be just abnormal BP pattern, but we should also have an abnormal cell motility pattern that allows a cell type to be slotted in:
suggest:
has_part some 'process quality' and inhere_in some ('cell motility' and results_in_movement_of some X)
Where X is a pattern slot for cell type. (should, of course, align with generic abnormal BP)
ZFIN uses the PATO term 'cellular motility' ( http://purl.obolibrary.org/obo/PATO_0001488 ) to say that the motility of a cell is abnormal - used most frequently for cells that are moving from one place to another.
PATO term 'cellular motility' ( http://purl.obolibrary.org/obo/PATO_0001488 )
Ughhhh - I don't see any justification for this being a quality - esp when we have a perfectly good GO term: cell motility http://purl.obolibrary.org/obo/GO_004887. I suggest obsoleting in PATO and switching to an 'abnormal cell motility' pattern referencing the GO term.
Or am I missing something?
Looking at the definition of the PATO term:
"A cellular quality inhering in a cell by virtue of whether the bearer exhibits the ability to move spontaneously."
From this it sounds like 'bearer_of' some cellular motility is equivalent to asserting 'capable of' some GO:cell motility. So - any use to define cells could be switched to use GO.
At the risk of adding confusion - here's a potentially relevant old PATO ticket: https://github.com/pato-ontology/pato/issues/112
in the interests of moving things forward, a proposal
characteristic-of some capable-of some P
allowing us to shadow e.g. GO BP
@matentzn we have this pattern for cell motility that is for cellular components: https://github.com/obophenotype/upheno/blob/master/src/patterns/dosdp-dev/abnormalMotilityOfCellularComponent.yaml
HPO has a cell motility term using sperm: http://purl.obolibrary.org/obo/HP_0012206 Abnormal sperm motility
The logical def is: 'has part' some ('cellular motility' and ('inheres in' some sperm) and ('has modifier' some abnormal))
Should we create a new pattern that fits the logical def above, or create a new pattern that is similar to the abnormalMotilityOfCellularComponent.yaml pattern (but uses anatomical entity (including cells)?
Thanks!