Open pfey03 opened 4 years ago
We are trying to avoid "decreased and increased", in favour of:
decreased occurrence decreased rate
decreased all by itself means nothing logically - better to distinguish. Which one is it?
we have increased / decreased for pretty much every phenotype. And it's not always rate. Sure occurrence might be used but I won't change these phenotypes. @matentzn I have the phenotype 'increased actin wave formation' with synonym: 'increased actin wave development' to fit the pattern, but maybe that's wrong thinking? actin wave is a GO CC. What would it be? increased_occurrence_of_anatomical_entity ? That might fit my phenotype and I could add a synonym for increased occurrence
@pfey03 I think it would be increased occurrence of development in location (where location would be a cellular component in this case).
I think you could use this pattern: https://github.com/obophenotype/upheno/blob/master/src/patterns/dosdp-dev/abnormallyIncreasedOccurrenceOfBiologicalProcessInLocation.yaml
Is there a GO term that would work for you? Maybe GO:0032989 cellular component morphogenesis or GO:0032502 developmental process ?
@nicolevasilevsky I don't have a process as it's not in GO: 'actin wave formation' doesn't exist as a process. actin wave is a CC in GO. GO:0032989 cellular component morphogenesis is not a phenotype, not specific enough abnormally_increased_occurrence_of_anatomical_entity would help
also, a general question: is it ok to have the pattern fitting term as synonym and leave the commonly known in the Dicty field as primary term? e.g DDPHENO:0000026 | development arrests at mound stage pattern: abnormallyArrestedBiologicalProcess synonym: abnormally arrested aggregation involved in sorocarp development GO:0031152: aggregation involved in sorocarp development
I have not yet added the synonym, but in general, is this acceptable as it's in the ontology but not primary term?
Thanks @nicolevasilevsky, @matentzn
Thanks both; Just to be clear. We do not impose any restrictions on the terminological aspect of a term at all. You can name a phenotype "increased X" - this has no bearing on anything. But for the pattern (logical definition), we want to be able to distinguish things in a more semantically meaningful way - a process can either occur more often, or at a higher rate, or with a larger output - its usually one of these. Thats why for the EQ, we try to capture precisely the meaning of term!
So to your second question: Absolutely! The only thing you need to do to be uPheno conformant is to adhere to the logical definition - the rest is up to your personal gusto!
Hey @pfey03 can i close this issue? If not, what are the action item?
Hmm, so nothing being added right? It's a lot of different things and I will see if I can manage with abnormally_increased_occurrence_of_anatomical_entityInLocation if there is also decreased/absence of
InLocation I would have to use for both, anatomy term or GO CC
Ok check that out, and if sometning is missing, just say here: please add pattern x and y.
There is:
abnormalDevelopmentOfAnatomicalEntity
Please add the increased / decreased terms
Thanks!