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The TO hierarchy does not always follow PATO #302

Open cmungall opened 9 years ago

cmungall commented 9 years ago

Example:

/ TO:0000387 ! plant trait
  is_a TO:0000017 ! anatomy and morphology trait
   is_a TO:0000839 ! plant structure anatomy and morphology trait
    is_a TO:0000064 ! plant embryo anatomy and morphology trait
     is_a TO:0000193 ! embryo shape
      is_a TO:0000113 ! giant embryo ***

Originally we defined this as

embryo shape = shape and inheres_in some embryo
giant embryo = 'increased size' and inheres_in some embryo

however, if you try this in a reasoner, it then follows that 'increased size' SubClassOf 'shape', which is not what is in PATO (shape and size are different siblings under morphology). You then get a ton of weird inferences coming from that.

marieALaporte commented 9 years ago

For me, embryo shape is a trait whereas giant embryo is a phenotype (the value of the trait). So this last term should not be part of TO. Maybe that could explain the problem or at least part of it

Marie

Le 22 sept. 2015 à 19:05, Chris Mungall notifications@github.com a écrit :

Example:

/ TO:0000387 ! plant trait is_a TO:0000017 ! anatomy and morphology trait is_a TO:0000839 ! plant structure anatomy and morphology trait is_a TO:0000064 ! plant embryo anatomy and morphology trait is_a TO:0000193 ! embryo shape is_a TO:0000113 ! giant embryo *\ Originally we defined this as

embryo shape = shape and inheres_in some embryo giant embryo = 'increased size' and inheres_in some embryo however, if you try this in a reasoner, it then follows that 'increased size' SubClassOf 'shape', which is not what is in PATO (shape and size are different siblings under morphology). You then get a ton of weird inferences coming from that.

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cmungall commented 9 years ago

Some more

TO:0002617 ! fruit color        TO:0002629 ! fruit anatomy and morphology trait PATO:0000014 ! color    PATO:0000051 ! morphology

color is not a subclass of morphology

cmungall commented 9 years ago

This one is more subtle:

TO:0002694 ! fruit flavor trait TO:0000281 ! metabolite content related trait   PATO:0000043 ! flavor   PATO:0000070 ! amount

biologically it makes sense

but flavor is not a subclass of amount or any quality regarding composition:

 / PATO:0000001 ! quality
  is_a PATO:0001241 ! physical object quality
   is_a PATO:0001018 ! physical quality
    is_a PATO:0000043 ! flavor ***

If we want TO classes to be qualities, then the subclass hierarchy must be stricter. flavour would be in a different subclass hierarchy from content. However, there would be relationships such as influenced by between disjoint heirarchies

cmungall commented 9 years ago

Oh, you're quite right, it is unusual to see that in TO!

Maybe that was a bad example to choose, there are other examples of this kind of unhealthy mixing

On 22 Sep 2015, at 10:40, Marie-Angélique wrote:

For me, embryo shape is a trait whereas giant embryo is a phenotype (the value of the trait). So this last term should not be part of TO. Maybe that could explain the problem or at least part of it

Marie

cmungall commented 8 years ago

full list of problematic ones:

SubClass SubClassLabel SuperClass SuperClassLabel PATOSub PATOSubLabel PATOSuper PATOSuperLabel
TO:0000061 node shattering TO:0000051 stem strength PATO:0001662 fragility PATO:0001230 strength
TO:0000069 variegated leaf TO:0000326 leaf color PATO:0001533 multi-colored PATO:0000014 color
TO:0000097 amylopectin content TO:0000489 carbohydrate composition related trait PATO:0000070 amount PATO:0000025 composition
TO:0000113 giant embryo TO:0000193 embryo shape PATO:0000586 increased size PATO:0000052 shape
TO:0000196 amylose content TO:0000489 carbohydrate composition related trait PATO:0000070 amount PATO:0000025 composition
TO:0000200 brittle culm TO:0000051 stem strength PATO:0001362 fragile PATO:0001230 strength
TO:0000230 crown rootless TO:0002685 crown root number PATO:0001557 PATO:0000070 amount
TO:0000297 glucosamine content TO:0006008 carbohydrate derivative content PATO:0000070 amount PATO:0000025 composition
TO:0000298 chlorophyll ratio TO:0000495 chlorophyll content PATO:0001470 proportionality to PATO:0000070 amount
TO:0000339 stem thickness TO:0000051 stem strength PATO:0000915 thickness PATO:0001230 strength
TO:0000372 amylose to amylopectin ratio TO:0000291 carbohydrate content PATO:0001470 proportionality to PATO:0000070 amount
TO:0000411 seed length to width ratio TO:0000146 seed length PATO:0001470 proportionality to PATO:0000122 length
TO:0000452 leaf area to spikelet number ratio TO:0000540 leaf area PATO:0001470 proportionality to PATO:0001323 area
TO:0000478 abscisic acid concentration TO:0000476 growth hormone content PATO:0000033 concentration of PATO:0000070 amount
TO:0000494 pigment content TO:0000493 leaf composition trait PATO:0000070 amount PATO:0000025 composition
TO:0000538 large vascular bundle number to leaf area ratio TO:0000472 vascular bundle number PATO:0001470 proportionality to PATO:0001555 has number of
TO:0000542 leaf length to width ratio TO:0002637 leaf size PATO:0001470 proportionality to PATO:0000117 size
TO:0000543 leaf nitrogen content TO:0000493 leaf composition trait PATO:0000070 amount PATO:0000025 composition
TO:0000616 leaf perimeter TO:0000492 leaf shape PATO:0001711 perimeter PATO:0000052 shape
TO:0000639 seed fertility TO:0000420 fertility related trait PATO:0000274 fertility PATO:0000014 color
TO:0000639 seed fertility TO:0000420 fertility related trait PATO:0000274 fertility PATO:0000133 orientation
TO:0000702 starch concentration TO:0006007 polysaccharide content PATO:0000033 concentration of PATO:0000070 amount
TO:0001011 deep root weight ratio TO:0000279 root weight PATO:0001470 proportionality to PATO:0000128 weight
TO:0002617 fruit color TO:0002629 fruit anatomy and morphology trait PATO:0000014 color PATO:0000051 morphology
TO:0002694 fruit flavor trait TO:0000281 metabolite content related trait PATO:0000043 flavor PATO:0000070 amount
TO:0006001 salt tolerance TO:0000429 salt sensitivity PATO:0000515 tolerant to PATO:0000085 sensitivity toward
TO:0006008 carbohydrate derivative content TO:0000291 carbohydrate content PATO:0000025 composition PATO:0000070 amount
TO:0006045 phosphorus concentration TO:0001024 phosphorus content PATO:0000033 concentration of PATO:0000070 amount
TO:0020078 zeaxanthin content TO:0000301 xanthophyll content PATO:0000025 composition PATO:0000070 amount
TO:0020079 beta-cryptoxanthin content TO:0000301 xanthophyll content PATO:0000025 composition PATO:0000070 amount
TO:0020106 Indole-3-acetic acid content TO:0002672 auxin content PATO:0000025 composition PATO:0000070 amount
TO:0020118 neoxanthin content TO:0000301 xanthophyll content PATO:0000025 composition PATO:0000070 amount
TO:0020119 violaxanthin content TO:0000301 xanthophyll content PATO:0000025 composition PATO:0000070 amount