HP_0001842 Foot acroosteolysis and HP_0010177 Osteolytic defects of the phalanges of the toes are inferred to be equivalent

[nicolevasilevsky]

HP_0001842 Foot acroosteolysis and HP_0010177 Osteolytic defects of the phalanges of the toes are inferred to be equivalent

HP_0001842 Foot acroosteolysis 'has part' some (Osteolysis and ('inheres in part of' some 'phalanx of pes') and ('has modifier' some abnormal))

no text def

HP_0010177 Osteolytic defects of the phalanges of the toes 'has part' some (Osteolysis and ('inheres in' some 'phalanx of pes') and ('has modifier' some abnormal))

no text def

Osteolysis is an HP term (HP_0002797), I think we were trying to get away from using HP terms in the logical definitions?

Related to #149

@cmungall @pnrobinson

[nicolevasilevsky]

no explanation in protege:

[nicolevasilevsky]

If I try to revise the logical def for HP_0001842 Foot acroosteolysis to: 'has part' some (Osteolysis and ('inheres in part of' some pes) and ('has modifier' some abnormal))

it is still inferred to be equiv with HP_0010177 Osteolytic defects of the phalanges of the toes

I suggest we remove the logical def from HP_0001842 Foot acroosteolysis

@drseb @pnrobinson

[cmungall]

Osteolysis is an HP term (HP_0002797), I think we were trying to get away from using HP terms in the logical definitions?

There should be no design patterns of the form has-part some HP_nnnnn and ...

[cmungall]

Lots of terms without text defs here:

      is_a HP:0002797 ! Osteolysis ***  [DEF: "Osteolysis refers to the destruction of bone through bone resorption with removal or loss of calcium."]
       is_a HP:0000905 ! Progressive clavicular acroosteolysis [DEF: "Progressive bone resorption in the distal part of the clavicle."]
       is_a HP:0009139 ! Osteolysis involving bones of the lower limbs
        is_a HP:0006378 ! Osteolysis of patellae
        is_a HP:0009134 ! Osteolysis involving bones of the feet
         is_a HP:0001473 ! Metatarsal osteolysis [DEF: "Osteolysis involving metatarsal bones."]
         is_a HP:0006234 ! Osteolysis involving tarsal bones [DEF: "An increased resorption of bone matrix by osteoclasts leading to bony defects involving the tarsal bones."]
         is_a HP:0008095 ! Osteolysis of talus [DEF: "Osteolysis affecting the talus."]
         is_a HP:0010177 ! Osteolytic defects of the phalanges of the toes
       is_a HP:0010657 ! Patchy reduction of bone mineral density [DEF: "Patchy (irregular) reduction in bone density. This can take on many forms depending on severity and distribution as can be seen on x-rays."]
       is_a HP:0045039 ! Osteolysis involving bones of the upper limbs
        is_a HP:0001495 ! Carpal osteolysis [DEF: "Osteolysis affecting carpal bones."]
         is_a HP:0004238 ! Lytic defects of carpal bones
        is_a HP:0001504 ! Metacarpal osteolysis
         is_a HP:0010030 ! Osteolytic defects of the 1st metacarpal [DEF: "Dissolution or degeneration of bone tissue of the 1st metacarpal."]
        is_a HP:0004043 ! Lytic defects of ulnar metaphysis
        is_a HP:0009699 ! Osteolytic defects of the hand bones
         is_a HP:0006202 ! Osteolysis of scaphoids
         is_a HP:0009771 ! Osteolytic defects of the phalanges of the hand [DEF: "Dissolution or degeneration of bone tissue of the phalanges of the hand."]

All have owldefs.

OK, I suggest we split this into 2:

1. We need a pattern for osteolysis that avoids HP in genus. Ideally something like MPATH should work for this...
2. equivalence

[pnrobinson]

One issue is that it would be good to adopt more standardization for the term labels. In retrospect, I think that "Tarsal bone osteolysis" is better than "Osteolysis involving the tarsal bones", for instance. These terms were created ad hoc and any accrual, but now it is time to go back and review them. Also, I would like to add definitions manually and to provide the user a few hints as to what is meant. I do not think that computationally generated definitions are much use since there will not be much more meaning than in the term label.