Map APO modifiers to PATO

[matentzn]

The following characteristics from SGD need to be mapped to PATO.

pato_id	pato_id_name
APO:0000003	decreased
APO:0000004	increased
APO:0000112	inviable
APO:0000113	viable
APO:0000002	abnormal
APO:0000117	normal
APO:0000245	decreased rate
APO:0000152	haploinsufficient
APO:0000005	absent
APO:0000097	auxotrophy
APO:0000246	increased rate
APO:0000153	petite
APO:0000252	normal rate
APO:0000154	petite-negative
APO:0000250	arrested
APO:0000249	delayed
APO:0000330	haploproficient
APO:0000045	sterile
APO:0000248	increased duration
APO:0000251	premature
APO:0000247	decreased duration
APO:0000043	spore wall formation
APO:0000076	mitochondrial transport
APO:0000149	protein/peptide accumulation
APO:0000310	growth in exponential phase

[rays22]

My pairwise mappings:

APO id	APO label	predicate	PATO id	PATO label	REMARKS
APO:0000003	decreased	skos:exactMatch	PATO:0002301	decreased quality
APO:0000004	increased	skos:exactMatch	PATO:0002300	increased quality
APO:0000112	inviable	skos:exactMatch	PATO:0000718	lethal (sensu genetics)	Alternatively: PATO:0001422 dead
APO:0000113	viable	skos:exactMatch	PATO:0000719	viable
APO:0000002	abnormal	skos:exactMatch	PATO:0000069	deviation (from_normal)
APO:0000117	normal	skos:exactMatch	PATO:0000461	normal
APO:0000245	decreased rate	skos:exactMatch	PATO:0000911	decreased rate
APO:0000152	haploinsufficient	skos:broadMatch	PATO:0000069	deviation (from_normal)	This is a class which is an amalgam of phenotype and genotype.
APO:0000005	absent	skos:exactMatch	PATO:0000462	absent
APO:0000097	auxotrophy	skos:exactMatch	PATO:0000422	auxotrophic	I am assuming that this is a quality, not a process.
APO:0000246	increased rate	skos:exactMatch	PATO:0000912	increased rate
APO:0000153	petite	??	0	NONE	This is a complex phenotype. It can be modelled as 1: abnormal GO:0009060 aerobic respiration, or 2: decreased colony size.
APO:0000252	normal rate	skos:exactMatch	PATO:0045000	normal rate
APO:0000154	petite-negative	skos:broadMatch	APO:0000153	petite	This is a conditional phenotype, where the observable characteristics depend on a particular genotype. In other words, this class is an amalgam of phenotype and genotype.
APO:0000250	arrested	skos:exactMatch	PATO:0000297	arrested
APO:0000249	delayed	skos:exactMatch	PATO:0000502	delayed
APO:0000330	haploproficient	skos:broadMatch	PATO:0000461	normal	This is a class which is an amalgam of phenotype and genotype.
APO:0000045	sterile	skos:exactMatch	PATO:0000956	sterile
APO:0000248	increased duration	skos:exactMatch	PATO:0000498	increased duration
APO:0000251	premature	skos:exactMatch	PATO:0000498	increased duration
APO:0000247	decreased duration	skos:exactMatch	PATO:0000499	decreased duration
APO:0000043	spore wall formation	skos:exactMatch	GO:0030476	ascospore wall assembly	This does not look like a PATO quality.
APO:0000076	mitochondrial transport	skos:exactMatch	GO:0170036	import into the mitochondrion	This does not look like a PATO quality.
APO:0000149	protein/peptide accumulation	skos:broadMatch	PATO:0001470	proportionality to	Text definition appears to contradict label.
APO:0000310	growth in exponential phase	skos:broadMatch	GO:0016049	cell growth	This does not look like a PATO quality.

[ValWood]

hi @rays22 I think you have a typo on the

APO:0000251 | premature | skos:exactMatch | PATO:0000498 | increased duration
should be premature PATO:0000684
v

[srengel]

error on this line:

APO:0000154 | petite-negative | skos:broadMatch | APO:0000153 | petite

petite-negative != petite

but i don't have a better suggestion! :(

APO:0000154 | petite-negative | ?? | 0 | NONE

[srengel]

correction for haploproficient:

haploproficient != normal

therefore should be:
APO:0000330 | haploproficient | skos:broadMatch | PATO:0000069 | deviation (from_normal)

[srengel]

correction for premature:

should be:
APO:0000251 | premature | skos:exactMatch | PATO:0000694 | premature

[srengel]

last edit from me, protein/peptide accumulation should be:

APO:0000149 | protein/peptide accumulation | ? | PATO:0002269 | accumulation

[rays22]

Thank you @ValWood and @srengel for reviewing the table and the corrections.
Here is an updated table based on your feedback:

APO id	APO label	predicate	PATO id	PATO label	REMARKS
APO:0000003	decreased	skos:exactMatch	PATO:0002301	decreased quality
APO:0000004	increased	skos:exactMatch	PATO:0002300	increased quality
APO:0000112	inviable	skos:exactMatch	PATO:0000718	lethal (sensu genetics)	Alternatively: PATO:0001422 dead
APO:0000113	viable	skos:exactMatch	PATO:0000719	viable
APO:0000002	abnormal	skos:exactMatch	PATO:0000069	deviation (from_normal)
APO:0000117	normal	skos:exactMatch	PATO:0000461	normal
APO:0000245	decreased rate	skos:exactMatch	PATO:0000911	decreased rate
APO:0000152	haploinsufficient	skos:broadMatch	PATO:0000069	deviation (from_normal)	This is a class which is an amalgam of phenotype and genotype.
APO:0000005	absent	skos:exactMatch	PATO:0000462	absent
APO:0000097	auxotrophy	skos:exactMatch	PATO:0000422	auxotrophic	I am assuming that this is a quality, not a process.
APO:0000246	increased rate	skos:exactMatch	PATO:0000912	increased rate
APO:0000153	petite	??	0	NONE	This is a complex phenotype. It can be modelled as 1: abnormal GO:0009060 aerobic respiration, or 2: decreased colony size.
APO:0000252	normal rate	skos:exactMatch	PATO:0045000	normal rate
APO:0000154	petite-negative	??	0	NONE	This is a conditional phenotype, where the observable characteristics depend on a particular genotype. In other words, this class is an amalgam of phenotype and genotype.
APO:0000250	arrested	skos:exactMatch	PATO:0000297	arrested
APO:0000249	delayed	skos:exactMatch	PATO:0000502	delayed
APO:0000330	haploproficient	skos:broadMatch	PATO:0000069	deviation (from_normal)	This is a class which is an amalgam of phenotype and genotype.
APO:0000045	sterile	skos:exactMatch	PATO:0000956	sterile
APO:0000248	increased duration	skos:exactMatch	PATO:0000498	increased duration
APO:0000251	premature	skos:exactMatch	PATO:0000694	premature
APO:0000247	decreased duration	skos:exactMatch	PATO:0000499	decreased duration
APO:0000043	spore wall formation	skos:exactMatch	GO:0030476	ascospore wall assembly	This does not look like a PATO quality.
APO:0000076	mitochondrial transport	skos:exactMatch	GO:0170036	import into the mitochondrion	This does not look like a PATO quality.
APO:0000149	protein/peptide accumulation	skos:broadMatch	PATO:0002269	accumulation	Text definition shows a reciprocal relationship compared with what is implied by the label.
APO:0000310	growth in exponential phase	skos:broadMatch	GO:0016049	cell growth	This does not look like a PATO quality.

[matentzn]

Amazing @rays22 can you check this as a valid sssom file in https://github.com/monarch-initiative/monarch-mapping-commons (mappings dir) and make a PR? 🚀

[ValWood]

I have a (possibly minor) comment about viability (but it does affect many annotations)

In yeast biology "lethality" is used to refer to populations rather than cells

This means that here
PATO:0000718 | lethal (sensu genetics)
A viability quality inhering in a population by virtue of the bearer's long term survival inability.
is fine for
APO:0000112 | inviable | skos:exactMatch | PATO:0000718 | lethal (sensu genetics) | Alternatively: PATO:0001422 dead

because it refers to a population

but here
APO:0000113 | viable | skos:exactMatch | PATO:0000719 | viable
the viable term definition refers to a bearer or a population and so is not specific enough.

PomBase has many phenotypes for inviable cells at the single cell (organism) level, where population viability is decreased (because a high proportion cells are dead) but populations can be viable these need to be modelled as different phenotypes.

"Inviable cell (or organism)" vs "inviable population" is quite an important distinction for microbial communities. It might not affect your work here, if SGD do not annotate phenotypes related to dead individual cells but I wanted to mention it because it is currently a conflation in the PATO ontology.

Modelling death seems to be very tricky!

[srengel]

we have inviable for just 'nothing grows'. we also have 'viability', and then either increased or decreased. with these two ways of recording 'death', we address what Val has described above.