Add increased/decreased DevelopmentOfAnatomicalEntity

[pfey03]

There is:

abnormalDevelopmentOfAnatomicalEntity

Please add the increased / decreased terms

Thanks!

[matentzn]

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?

[pfey03]

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

[nicolevasilevsky]

@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
?

[pfey03]

@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

[pfey03]

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

[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!

[matentzn]

Hey @pfey03 can i close this issue? If not, what are the action item?

[pfey03]

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

[matentzn]

Ok check that out, and if sometning is missing, just say here: please add pattern x and y.