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Uncovered cardio terms below top-level term UPHENO:0004507: cardiovascular system phenotype #966

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hansenp opened this issue Dec 18, 2024 · 4 comments
Open
1 of 58 tasks

Uncovered cardio terms below top-level term UPHENO:0004507: cardiovascular system phenotype #966

hansenp opened this issue Dec 18, 2024 · 4 comments
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@matentzn

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hansenp commented Dec 18, 2024 •
edited by matentzn
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Top-level term UPHENO:0004507 does not include all terms that have something to do with the cardiovascular system.

Here is a list of uncovered terms whose label contains the word "cardiac":

  • UPHENO:0050573: cardiac muscle progenitor cell migration to the midline involved in heart field formation phenotype
  • UPHENO:0077441: decreased occurrence of cardiac muscle progenitor cell migration to the midline involved in heart field formation
  • UPHENO:0018886: arrested cardiac muscle contraction
  • UPHENO:0051310: cardiac muscle contraction phenotype
  • UPHENO:0083070: membrane repolarization during ventricular cardiac muscle cell action potential phenotype
  • UPHENO:0086084: decreased size of the cardiac muscle cell
  • UPHENO:0018914: arrested cardiac muscle cell proliferation
  • UPHENO:0053434: decreased qualitatively regulation of cardiac muscle contraction by calcium ion signaling
  • UPHENO:0050292: regulation of ventricular cardiac muscle cell membrane repolarization phenotype
  • UPHENO:0050633: cardiac atrium development phenotype
  • UPHENO:0083089: membrane repolarization during cardiac muscle cell action potential phenotype
  • UPHENO:0053898: localised cardiac neural crest
  • UPHENO:0050542: cardiac muscle tissue morphogenesis phenotype
  • UPHENO:0079481: increased occurrence of cardiac muscle cell proliferation
  • UPHENO:0050768: atrial cardiac muscle cell action potential phenotype
  • UPHENO:0086345: cardiac muscle cell degeneration
  • UPHENO:0085535: increased number of cardiac muscle cell
  • UPHENO:0053342: decreased qualitatively membrane repolarization during cardiac muscle cell action potential
  • UPHENO:0077742: decreased occurrence of atrial cardiac muscle cell differentiation
  • UPHENO:0085372: decreased number of cardiac muscle cell
  • UPHENO:0085218: increased size of the cardiac muscle cell
  • UPHENO:0018811: arrested cardiac conduction
  • UPHENO:0088203: disorganized cardiac muscle cell
  • UPHENO:0077749: decreased occurrence of cardiac muscle cell differentiation
  • UPHENO:0005948: decreased cardiac muscle cell membrane repolarization
  • UPHENO:0053161: decreased qualitatively cardiac muscle cell proliferation
  • UPHENO:0064521: decreased number of future cardiac ventricle
  • UPHENO:0050657: cardiac ventricle morphogenesis phenotype
  • UPHENO:0006779: increased width of future cardiac atrium
  • UPHENO:0050654: cardiac chamber formation phenotype
  • UPHENO:0077723: decreased occurrence of cardiac jelly development
  • UPHENO:0085667: decreased qualitatively atrial cardiac muscle cell differentiation
  • UPHENO:0051270: cardiac conduction phenotype
  • UPHENO:0000574: delayed cardiac muscle progenitor cell migration to the midline involved in heart field formation
  • UPHENO:0088448: delayed ventricular cardiac muscle cell membrane repolarization
  • UPHENO:0047215: decreased length of future cardiac ventricle
  • UPHENO:0006840: increased width of future cardiac ventricle
  • UPHENO:0015188: increased number of future cardiac atrium
  • UPHENO:0077745: decreased occurrence of ventricular cardiac muscle cell differentiation
  • UPHENO:0050199: cardiac ventricle development phenotype
  • UPHENO:0088611: absent desmosome in the cardiac muscle cell
  • UPHENO:0051514: cardiac cell fate specification phenotype
  • UPHENO:0077739: decreased occurrence of cardiac muscle tissue regeneration
  • UPHENO:0053310: decreased qualitatively ventricular cardiac muscle cell action potential
  • UPHENO:0002060: increased size of the future cardiac atrium
  • UPHENO:0085639: cardiac muscle cell physiology phenotype (
  • UPHENO:0053045: decreased qualitatively cardiac chamber morphogenesis
  • UPHENO:0053065: decreased qualitatively cardiac ventricle morphogenesis
  • UPHENO:0053012: decreased qualitatively cardiac conduction
  • UPHENO:0083988: decreased qualitatively cardiac muscle cell contraction
  • UPHENO:0078507: absent ventricular cardiac muscle cell action potential
  • UPHENO:0085668: decreased qualitatively ventricular cardiac muscle cell differentiation
  • UPHENO:0005858: decreased cardiac conduction
  • UPHENO:0050918: cardiac conduction system development phenotype
  • UPHENO:0052827: decreased qualitatively cardiac muscle progenitor cell migration to the midline involved in heart field formation
  • UPHENO:0070090: decreased size of the future cardiac ventricle
  • UPHENO:0054163: localised future cardiac ventricle
  • UPHENO:0052776: decreased qualitatively cardiac muscle tissue morphogenesis

For example, term UPHENO:0086084: decreased size of the cardiac muscle cell from the list is not below the top-level term UPHENO:0004507: cardiovascular system phenotype.

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@hansenp hansenp mentioned this issue Dec 18, 2024
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circulatory system phenotype because uses "primary circulatory organ" instead of "heart"

cardiac muscle cell physiology phenotype

Many of these have severely complicated reasons for not being included under "cardiovascular phenptyep"

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@hansenp I have published a new upheno release; how hard / easy would it be for you to check it again?

Note one major issue: cardiovascular system is not a good grouping, you should use circulatory system instead. The reason for this is that only some species actually have something like a heart in the strict sense, and what they have is instead called a "primary circulatory organ". Please let me know if this makes sense.

There will be still some ungrouped terms, but just eyeballing I can see some being correctly grouped now!

@matentzn matentzn self-assigned this Jan 12, 2025
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hansenp commented Jan 13, 2025

@matentzn This should be pretty easy, but I'm working on other things at the moment. Do you need quick feedback? I assume you're referring to this release: https://github.com/obophenotype/upheno-dev/releases/tag/2025-01-11

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I dont need quick feedback :P Thanks for checking in! Later in January is fine.

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