Genetic interactions interface: refining the pull-down options for genetic interaction annotations.

[ValWood]

Improving the available options for genetic interaction annotations.

• [x] If one of the alleles is "overexpression" only display: Dosage Growth Defect Dosage Lethality Dosage Rescue Phenotypic Enhancement Phenotypic Suppression

[ValWood]

• [ ] If both alleles are deletion, only display:

Phenotypic Suppression Synthetic Growth Defect Synthetic Lethality Synthetic Rescue

(corrected)

[ValWood]

• [ ] if double mutant phenotype is a population phenotype, only show Dosage Growth Defect Dosage Lethality Dosage Rescue Synthetic Growth Defect Synthetic Lethality Synthetic Rescue

[ValWood]

Note, these are 'additive' So, if If one of the alleles is "overexpression" AND if double mutant phenotype is a population phenotype, only show

only display Dosage Growth Defect Dosage Lethality Dosage Rescue

[ValWood]

if double mutant phenotype NOT is a population phenotype, only show Phenotypic Enhancement Phenotypic Suppression

[ValWood]

I just saw this ticket, I think there is partial overlap here https://github.com/pombase/canto/issues/1988

[kimrutherford]

It would be helpful to come up with grouping names for these sets of evidence codes so that the configuration is understandable. For example is there an ECO parent term that contains each set?

[kimrutherford]

Val to add labels for each group.

[ValWood]

These are the restrictions:

Some combinations of allele types/ phenoticpic class and evidence code are disallowed and so we will not display them in he avaiable evidence codes. (I.e ) you cant have evidence which require an overexpression if both alleles are deleted.

DGD = Dosage growth defect DL = Dosage lethal DR = Dosage rescue SGD = Synthetic growth defect SL = Synthetic lethal SR = Synthetic rescue PE = Phenotypic enhancement PS = Phenotypic supression

The 'types' are Only Pop (DGD, DL, DR, SGD, SL,SR) Not Pop (PE,PS) both delta (SGD,SL,SR) only O-EX (DGD, DL, DR, PE,PS) And the intersect combinations Only POP + only O-EX (DG, DL, DR)

We don’t need these Not POP + only O-EX (PE,PS) is the same set as “Not POP’ and Only POP + both delta is the same as “Both delta’

For any other combination that is none of the above display all codes

Doe that help?

[kimrutherford]

est. 2 days

[kimrutherford]

I've made a first attempt at implementing this but I haven't done a lot of testing. I'm heading to bed and I'll do more tomorrow.

The test Canto will have the change in 30 minutes or so. It's currently updating its ontology database which was necessary to implement the code that makes use of the population phenotype term. The new code won't work properly until the update finishes.

[kimrutherford]

I've done a bit more testing and it seems OK. Could you have a try and let me know?

[kimrutherford]

I've done a bit more testing and it seems OK.

I obviously didn't test very well because while implementing #2533 I noticed that the evidence codes for when one allele is overexpressed were mis-configured. Fixed now.

[ValWood]

I tested and this is looking pretty good. I only found the relevant combinations of evidence codes.

a useful test would be to see if any of our existing GIs violate these combinations! (for later)

I think we will notice pretty quickly if we have blocked something that should be allewed.

[ValWood]

I just tried to add an interaction to:

I was going to complain that only one evidence code was available (PS), but I followed the logic and this is correct. I think I got the logic a bit wrong 9subtly) although you encoded correctly.

Only O-E means if one allele is over expression it MUST be one of these types, NOT the inverse only allow these types for O-E alleles

This would mean that for the allele and phenotype combination above I would also see PE and PS

[ValWood]

I will just re-cast the restrictions more explicitly for you to check

if one allele is overexpression, only display Dosage Growth Defect Dosage Lethality Dosage Rescue Phenotypic Enhancement Phenotypic Suppression

SGD,SL,SR and should only be displayed if both alleles are delta (BUT other types COULD be relevant to both alleles being delta, it is just that these particular evidence would not be relevant to any other allele combinations)

[ValWood]

SO, if both allels are delta, AND the phenotype is nOT a population phenotype PE and PS should. be displayed

[kimrutherford]

if one allele is overexpression, only display

That list is what is currently configured.

SO, if both allels are delta, AND the phenotype is nOT a population phenotype PE and PS should. be displayed

OK, I've added Phenotypic Enhancement to the configuration for double deletion. You'll probably need to shift-reload.

[ValWood]

OK that worked. I am not sure if some of these combinations ever occur in reality. That is something many could perhaps look at, as we might be able to block other combinations. I think we are good here though.

[kimrutherford]

Should we close this issue?

[ValWood]

yep