List "allowable phenotypes" for genetic interaction types

[ValWood]

Most general phenotypes applicable to each genetic interaction type

GI	final phenotype terms term(s)	gene A phenotype terms
Dosage Growth Defect - Overexpression/increased dosage of one gene causes a growth defect in a strain that is mutated/deleted for another gene (e.g. PMID: 15166139).	FYPO:0000139 cell population growth phenotype	NORMAL POPULATION GROWTH
Dosage Lethality - Overexpression/increased dosage of one gene causes lethality in a strain that is mutated/deleted for another gene (e.g. PMID: 10805723, Fig. 3).	FYPO:0002059 inviable cell population	FYPO:0002058 viable cell population
Dosage Rescue - Overexpression/increased dosage of one gene rescues the lethality or growth defect of a strain mutated/deleted for another gene (e.g. PMID: 12207708, Fig. 3)	FYPO:0000139 cell population growth phenotype OR FYPO:0002059 inviable cell population	NORMAL POPULATION GROWTH OR FYPO:0002058 viable cell population
Negative Genetic - Mutations/deletions in separate genes, each of which alone causes a minimal phenotype, but when combined in the same cell results in a more severe fitness defect or lethality under a given condition (e.g. PMID: 20093466). This term is reserved for high or low throughput studies with scores.	N/A - excluded from Canto	-
Phenotypic Enhancement - Mutation/deletion/overexpression of one genes results in enhancement of any phenotype (other than lethality/growth defect) associated with mutation/deletion/overexpression of another gene, for example response to DNA damage or transcriptional output (e.g. PMID: 11890933, Fig. 2).	NOT (FYPO:0000139 cell population growth phenotype OR FYPO:0002059 inviable cell population)	SAME AS FINAL
Phenotypic Suppression - Mutation/deletion/overexpression of one gene results in suppression of any phenotype (other than lethality/growth defect) associated with mutation/deletion/overexpression of another gene (e.g. PMID: 10073572).	NOT (FYPO:0000139 cell population growth phenotype OR FYPO:0002059 inviable cell population)	SAME AS FINAL
Positive Genetic - Mutations/deletions in separate genes, each of which alone causes a minimal phenotype, but when combined in the same cell results in a less severe fitness defect than expected under a given condition.(e.g. PMID: 20093466). This term is reserved for high or low throughput studies with scores.	N/A - excluded from Canto	-
Synthetic Growth Defect - Mutations/deletions in separate genes, each of which alone causes a minimal phenotype, but when combined in the same cell results in a significant growth defect under a given condition (e.g. PMID: 12871902, Fig. 8).	FYPO:0000139 cell population growth phenotype (possibly can be more specific, reduced growth?)	-
Synthetic Haploinsufficiency - A genetic interaction is inferred when mutations or deletions in separate genes, at least one of which is hemizygous, cause a minimal phenotype alone but result in lethality when combined in the same cell under a given condition (e.g. PMID: 17167106).	FYPO:0002059 inviable cell population (MUST BE A HAPLOID/DIPLOID)	-
Synthetic Lethality - Mutations/deletions in separate genes, each of which alone causes a minimal phenotype, but when combined in the same cell results in lethality under a given condition (e.g. PMID: 14690608).	FYPO:0002059 inviable cell population	FYPO:0002058 viable cell population
Synthetic Rescue - Mutation/deletion of one gene rescues the lethality or growth defect of a strain mutated/deleted for another gene (e.g. PMID: 14734533, Fig. 1).	FYPO:0002058 viable cell population	FYPO:0002059 inviable cell population

[mah11]

Edited the table to reflect the fact that Negative Genetic and Positive Genetic aren't included in Canto, because they're used only for scored values that we collect in bulk-format files.

[ValWood]

I added gene "A" phenotype options (the ones we need) .

The other colum is the multi-allele phenotypes we want to capture if not already captured.

[mah11]

note: we've never used Synthetic Haploinsufficiency ...

[ValWood]

1. whether a phenotype is required will depend on interaction type. Therefore we need to add genotypes and interaction type before allowing phenotype selection
2. Relevant existing phenotypes (and their conditions) for the relevant single allele will be presented in the dropdown.
3. An option to add a phenotype and conditions if not already curated can be provided (this will also populate the single allele phenotype table
4. Later we can add prompts if there is no phenotype for the multi allele combination (and even capture it here)
5. Once the GI interface is in place, look into the possibility of having a "quick route" to create GI's for 2-gene interactions from the multi-gene phenotype route. We might be able to automatically create some of these. For example, if the user created 2 viable single gene genotypes and an enviable multi for the same allele combination we could automagically create the "synthetic lethal" GI.

Interaction type	Phenotype to report	FYPO branch restriction for phenotype acted on	Notes
Synthetic haploinsufficiency	omit, unused, keep it simple can add later if required
Dosage growth defect	enhanced growth phenotype (genotype1)	FYPO:0000046 decreased cell population growth
Dosage rescue	rescued phenotype (genotype1)	no term restriction
Phenotypic enhancement	enhanced phenotype (genotype1)	no term restriction
Phenotypic suppression	suppressed phenotype (genotype1)	no term restriction
Synthetic rescue	rescued phenotype (inviability or growth defect) (genotype1)	FYPO:0000046 decreased cell population growth OR FYPO:0002061 inviable vegetative cell population	prompt if no multi-allele annotation for allele combination in FYPO:0002060 viable vegetative cell population OR FYPO:0003937 increased cell population growth
Synthetic growth defect	outcome is compromised growth, do not need to record here?	n/a	prompt if no multi-allele annotation for allele combination in FYPO:0000046 decreased cell population growth branch
Synthetic lethality	outcome is inviability, do not need to record here	n/a	prompt if no multi-allele annotation for allele combination in FYPO:0002061 inviable vegetative cell population branch
Dosage lethality	outcome is inviability, do not need to record here	n/a	prompt if no multi-allele annotation for allele combination in FYPO:0002061 inviable vegetative cell population branch

[ValWood]

see https://github.com/pombase/canto/issues/2301#issuecomment-765535014