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obophenotype / upheno-dev

Framework for the automated construction of uPheno 2.0
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HP vs MP special cases #42

Open caufieldjh opened 1 year ago

caufieldjh commented 1 year ago

The following are all cases in which semantic similarity comparisons between HP and MP appear to be impacted by changes in Upheno (plots below):

  1. HP:0002607 vs MP:0003281
  2. HP:0002553 vs MP:0003761
  3. HP:0410188 vs MP:0005562
  4. HP:0002227 vs MP:0006242
  5. HP:0006611 vs MP:0010869
caufieldjh commented 1 year ago

Plot for 1: graph

Plot for 2: graph2

Plot for 3: graph3

Plot for 4: graph4

Plot for 5: graph5

caufieldjh commented 1 year ago

If we look at the 1000 HP vs MP pairs with the greatest negative semantic similarity difference between old and new scores (i.e., those which have increased the most) and find their common UPHENO ancestors, we find 85 nodes:

UPHENO:0001005 ! abnormal phenotype by ontology source
UPHENO:0002263 ! abnormality of immune system physiology
UPHENO:0002320 ! abnormality of muscle organ physiology
UPHENO:0002332 ! abnormality of anatomical entity physiology
UPHENO:0002343 ! abnormality of blood vessel physiology
UPHENO:0002405 ! abnormality of sweat gland physiology
UPHENO:0002433 ! abnormality of nervous system physiology
UPHENO:0002816 ! abnormal musculature
UPHENO:0002832 ! abnormal renal system
UPHENO:0003020 ! abnormal eyeball of camera-type eye
UPHENO:0003070 ! abnormal leg
UPHENO:0003964 ! abnormal pulmonary vein
UPHENO:0004536 ! abnormal respiratory system
UPHENO:0006276 ! increased width of metatarsal bone
UPHENO:0006432 ! increased width of metacarpal bone
UPHENO:0012541 ! decreased size of the anatomical entity in the independent continuant
UPHENO:0015324 ! abnormal anatomical entity morphology in the heart
UPHENO:0019224 ! abnormal cranial fossa morphology
UPHENO:0019487 ! abnormal kidney morphology
UPHENO:0019528 ! abnormal anus morphology
UPHENO:0019880 ! abnormal ureteropelvic junction morphology
UPHENO:0020158 ! abnormal cardiac muscle tissue morphology
UPHENO:0020178 ! abnormal olecranon morphology
UPHENO:0020351 ! abnormal blood vessel morphology
UPHENO:0020427 ! abnormal external female genitalia morphology
UPHENO:0020575 ! abnormal head of femur morphology
UPHENO:0020648 ! abnormal metacarpal bone morphology
UPHENO:0020651 ! abnormal phalanx morphology
UPHENO:0020706 ! abnormal atrioventricular node morphology
UPHENO:0020734 ! abnormal mouth morphology
UPHENO:0020736 ! abnormal head of radius morphology
UPHENO:0020738 ! abnormal renal system morphology
UPHENO:0020817 ! abnormal metatarsal bone morphology
UPHENO:0020868 ! abnormal ulna morphology
UPHENO:0020869 ! abnormal radius bone morphology
UPHENO:0020914 ! abnormal globus pallidus morphology
UPHENO:0020967 ! abnormal femur morphology
UPHENO:0020968 ! abnormal skeletal joint morphology
UPHENO:0020974 ! abnormal paranasal sinus morphology
UPHENO:0020980 ! abnormal humerus morphology
UPHENO:0020998 ! abnormal cornea morphology
UPHENO:0021062 ! abnormal heart morphology
UPHENO:0021276 ! abnormal alveolus of lung morphology
UPHENO:0021474 ! abnormal camera-type eye morphology
UPHENO:0021677 ! abnormal styloid process of ulna morphology
UPHENO:0021749 ! abnormal eyelid morphology
UPHENO:0026385 ! absent anatomical entity in the eyelid
UPHENO:0041360 ! shape epiphysis of radius
UPHENO:0048694 ! increased level of glutamine
UPHENO:0048696 ! increased level of glycine
UPHENO:0048702 ! increased level of ornithine
UPHENO:0048722 ! increased level of threonine
UPHENO:0048723 ! increased level of leucine
UPHENO:0048724 ! increased level of phenylalanine
UPHENO:0048726 ! increased level of arginine
UPHENO:0048727 ! increased level of lysine
UPHENO:0048728 ! increased level of methionine
UPHENO:0048729 ! increased level of serine
UPHENO:0048732 ! increased level of glutamic acid
UPHENO:0048735 ! increased level of isoleucine
UPHENO:0051804 ! abnormal blood chemical entity level
UPHENO:0069435 ! decreased size of the genital labium
UPHENO:0075679 ! abnormal vitreous body
UPHENO:0075997 ! abnormal orbital region
UPHENO:0076286 ! abnormal role blood level
UPHENO:0076718 ! abnormal bone of pectoral complex morphology
UPHENO:0076727 ! abnormal limb bone morphology
UPHENO:0076754 ! abnormal forelimb zeugopod bone morphology
UPHENO:0076767 ! abnormal skeletal joint morphology
UPHENO:0076779 ! abnormal kidney morphology
UPHENO:0076781 ! abnormal myocardium morphology
UPHENO:0076800 ! abnormal mouth morphology
UPHENO:0076806 ! abnormal bone of pelvic complex morphology
UPHENO:0077824 ! abnormal umbilical cord blood dioxygen level
UPHENO:0079822 ! decreased role blood level
UPHENO:0079872 ! abnormal anatomical entity morphology in the skeleton of pectoral complex
UPHENO:0080178 ! aplasia or hypoplasia of paranasal sinus
UPHENO:0081318 ! nail of pedal digit hypoplasia
UPHENO:0081435 ! abnormal anatomical entity morphology in the brain
UPHENO:0081558 ! abnormal head of femur morphology
UPHENO:0081566 ! abnormal skull morphology
UPHENO:0081790 ! anatomical entity hypoplasia in independent continuant
UPHENO:0081802 ! increased width of the anatomical entity in humerus
UPHENO:0083639 ! abnormal pedal digit 2 phalanx morphology
UPHENO:0084447 ! abnormal anatomical entity morphology in the skeleton of manus

Or by frequency:

    249 UPHENO:0076806
    110 UPHENO:0076754
     89 UPHENO:0076718
     84 UPHENO:0081558
     57 UPHENO:0020575
     47 UPHENO:0079872
     29 UPHENO:0004536
     27 UPHENO:0002433
     24 UPHENO:0020967
     23 UPHENO:0076727
     20 UPHENO:0012541
     19 UPHENO:0002332
     18 UPHENO:0003070
     13 UPHENO:0020998
     11 UPHENO:0021677
     11 UPHENO:0020178
     10 UPHENO:0021276
      9 UPHENO:0076767
      9 UPHENO:0002320
      8 UPHENO:0020351
      7 UPHENO:0081802
      7 UPHENO:0002405
      6 UPHENO:0083639
      6 UPHENO:0003020
      6 UPHENO:0001005
      5 UPHENO:0076286
      5 UPHENO:0020736
      4 UPHENO:0084447
      4 UPHENO:0020968
      3 UPHENO:0051804
      3 UPHENO:0020651
      3 UPHENO:0002832
      2 UPHENO:0080178
      2 UPHENO:0075997
      2 UPHENO:0048735
      2 UPHENO:0048732
      2 UPHENO:0048729
      2 UPHENO:0048728
      2 UPHENO:0048727
      2 UPHENO:0048726
      2 UPHENO:0048724
      2 UPHENO:0048723
      2 UPHENO:0048722
      2 UPHENO:0048702
      2 UPHENO:0048696
      2 UPHENO:0048694
      2 UPHENO:0041360
      2 UPHENO:0026385
      2 UPHENO:0021474
      2 UPHENO:0021062
      2 UPHENO:0020738
      2 UPHENO:0019528
      2 UPHENO:0002816
      1 UPHENO:0081790
      1 UPHENO:0081566
      1 UPHENO:0081435
      1 UPHENO:0081318
      1 UPHENO:0079822
      1 UPHENO:0077824
      1 UPHENO:0076800
      1 UPHENO:0076781
      1 UPHENO:0076779
      1 UPHENO:0075679
      1 UPHENO:0069435
      1 UPHENO:0021749
      1 UPHENO:0020980
      1 UPHENO:0020974
      1 UPHENO:0020914
      1 UPHENO:0020869
      1 UPHENO:0020868
      1 UPHENO:0020817
      1 UPHENO:0020734
      1 UPHENO:0020706
      1 UPHENO:0020648
      1 UPHENO:0020427
      1 UPHENO:0020158
      1 UPHENO:0019880
      1 UPHENO:0019487
      1 UPHENO:0019224
      1 UPHENO:0015324
      1 UPHENO:0006432
      1 UPHENO:0006276
      1 UPHENO:0003964
      1 UPHENO:0002343
      1 UPHENO:0002263

So why is UPHENO:0076806 (abnormal bone of pelvic complex morphology) the common ancestor in so many newly-high-scoring pairs? Only one HP term (HP:0040069 (Abnormal lower limb bone morphology) ) connects to it directly in PHENIO, but that term is in 31 other is_a relationships in HP, so there's potential for a local neighborhood of high similarity pairs.

caufieldjh commented 1 year ago

It's a bit of a mess, but this may illustrate the issue (click to zoom!). graph6

This is just is_a and part_of relationships so I'm puzzled as to why UPHENO terms like UPHENO:0012526 (decreased size of the anatomical entity in the phalanx of pes) are directly related to UPHENO:0076806 (abnormal bone of pelvic complex morphology), when the former bone is not part of the latter morphological region?

matentzn commented 1 year ago

This is all super useful, thank you.. Please keep more insights like this coming.

matentzn commented 1 year ago
sbello commented 1 year ago

Discussed 1 at the UPheno call on 11/17, requesting a new term from GO or as a back up NBO to use in a common pattern that should improve this.

matentzn commented 1 year ago

@sbello can you give more detail, I have difficulties relating your answer to this ticket here. Thank you!