Map APO modifiers to PATO
matentzn opened this issue · 10 comments
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 |
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. |
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
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
correction for haploproficient:
haploproficient != normal
therefore should be:
APO:0000330 | haploproficient | skos:broadMatch | PATO:0000069 | deviation (from_normal)
correction for premature:
should be:
APO:0000251 | premature | skos:exactMatch | PATO:0000694 | premature
last edit from me, protein/peptide accumulation should be:
APO:0000149 | protein/peptide accumulation | ? | PATO:0002269 | accumulation
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. |
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? 🚀
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!
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.