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obophenotype / upheno

The Unified Phenotype Ontology (uPheno) integrates multiple phenotype ontologies into a unified cross-species phenotype ontology.
https://obophenotype.github.io/upheno/
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question about cell motility pattern #607

Open nicolevasilevsky opened 4 years ago

nicolevasilevsky commented 4 years ago

@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!

matentzn commented 4 years ago

@dosumis and @ybradford are better suited for that! Good question.

dosumis commented 4 years ago

Should check what's used in GO-plus and align with that.

dosumis commented 4 years ago

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

dosumis commented 4 years ago

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)

ybradford commented 4 years ago

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.

dosumis commented 4 years ago

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?

dosumis commented 4 years ago

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.

dosumis commented 4 years ago

At the risk of adding confusion - here's a potentially relevant old PATO ticket: https://github.com/pato-ontology/pato/issues/112

matentzn commented 4 years ago

see also https://github.com/obophenotype/upheno/issues/536

cmungall commented 2 years ago

in the interests of moving things forward, a proposal