Changes required to align (SubClassOf vs part_of) go with uberon

cmungall commented 10 years ago

We introduced uberon axioms to GO, this lead to some inferences A SubClasOf B where GO already asserts A SubClassOf part_of some B

heart

POTENTIAL REDUNDANT AXIOMS GO:0003164 'His-Purkinje system development' part_of 'part_of' GO:0003161 'cardiac conduction system development' is also a simple SubClassOf.

Classification in GO reflects ZFA, FMA and others but this could be changed
nervous system

POTENTIAL REDUNDANT AXIOMS GO:0021729 'superior reticular formation development' part_of 'part_of' GO:0021723 'medullary reticular formation development' is also a simple SubClassOf.

Uberon will change

POTENTIAL REDUNDANT AXIOMS GO:0021739 'mesencephalic trigeminal nucleus development' part_of 'part_of' GO:0021730 'trigeminal sensory nucleus development' is also a simple SubClassOf.

GO should change to is_a

POTENTIAL REDUNDANT AXIOMS GO:0021740 'principal sensory nucleus of trigeminal nerve development' part_of 'part_of' GO:0021730 'trigeminal sensory nucleus development' is also a simple SubClassOf

GO should change to is_a.

POTENTIAL REDUNDANT AXIOMS GO:0021741 'spinal trigeminal nucleus development' part_of 'part_of' GO:0021730 'trigeminal sensory nucleus development' is also a simple SubClassOf.

GO should change to is_a

POTENTIAL REDUNDANT AXIOMS GO:0021783 'preganglionic parasympathetic nervous system development' part_of 'part_of' GO:0048486 'parasympathetic nervous system development' is also a simple SubClassOf.

Uberon will change

POTENTIAL REDUNDANT AXIOMS GO:0021784 'postganglionic parasympathetic nervous system development' part_of 'part_of' GO:0048486 'parasympathetic nervous system development' is also a simple SubClassOf.

Uberon will change

POTENTIAL REDUNDANT AXIOMS GO:0048484 'enteric nervous system development' part_of 'part_of' GO:0048483 'autonomic nervous system development' is also a simple SubClassOf.

Uberon will change

POTENTIAL REDUNDANT AXIOMS GO:0048485 'sympathetic nervous system development' part_of 'part_of' GO:0048483 'autonomic nervous system development' is also a simple SubClassOf.

Uberon will change

POTENTIAL REDUNDANT AXIOMS GO:0048486 'parasympathetic nervous system development' part_of 'part_of' GO:0048483 'autonomic nervous system development' is also a simple SubClassOf.

skeletal

POTENTIAL REDUNDANT AXIOMS GO:0051216 'cartilage development' part_of 'part_of' GO:0048513 'organ development' is also a simple SubClassOf.

Change go to is_a
(Uberon has both cart. organ and cart. tissue, looking at the GO hierarchy organ is more appropriate)
renal

POTENTIAL REDUNDANT AXIOMS GO:0072025 'distal convoluted tubule development' part_of 'part_of' GO:0072017 'distal tubule development' is also a simple SubClassOf.

Change is_a in uberon to part_of

cmungall commented 10 years ago

Updated:

heart

POTENTIAL REDUNDANT AXIOMS GO:0003164 'His-Purkinje system development' part_of 'part_of' GO:0003161 'cardiac conduction system development' is also a simple SubClassOf.

TBD

nervous system

POTENTIAL REDUNDANT AXIOMS GO:0021729 'superior reticular formation development' part_of 'part_of' GO:0021723 'medullary reticular formation development' is also a simple SubClassOf.

DONE

POTENTIAL REDUNDANT AXIOMS GO:0021739 'mesencephalic trigeminal nucleus development' part_of 'part_of' GO:0021730 'trigeminal sensory nucleus development' is also a simple SubClassOf.

GO should change to is_a

POTENTIAL REDUNDANT AXIOMS GO:0021740 'principal sensory nucleus of trigeminal nerve development' part_of 'part_of' GO:0021730 'trigeminal sensory nucleus development' is also a simple SubClassOf

GO should change to is_a.

POTENTIAL REDUNDANT AXIOMS GO:0021741 'spinal trigeminal nucleus development' part_of 'part_of' GO:0021730 'trigeminal sensory nucleus development' is also a simple SubClassOf.

GO should change to is_a

POTENTIAL REDUNDANT AXIOMS GO:0021783 'preganglionic parasympathetic nervous system development' part_of 'part_of' GO:0048486 'parasympathetic nervous system development' is also a simple SubClassOf.

DONE

POTENTIAL REDUNDANT AXIOMS GO:0021784 'postganglionic parasympathetic nervous system development' part_of 'part_of' GO:0048486 'parasympathetic nervous system development' is also a simple SubClassOf.

DONE

POTENTIAL REDUNDANT AXIOMS GO:0048484 'enteric nervous system development' part_of 'part_of' GO:0048483 'autonomic nervous system development' is also a simple SubClassOf.

DONE

POTENTIAL REDUNDANT AXIOMS GO:0048485 'sympathetic nervous system development' part_of 'part_of' GO:0048483 'autonomic nervous system development' is also a simple SubClassOf.

DONE

POTENTIAL REDUNDANT AXIOMS GO:0048486 'parasympathetic nervous system development' part_of 'part_of' GO:0048483 'autonomic nervous system development' is also a simple SubClassOf.

DONE

skeletal

POTENTIAL REDUNDANT AXIOMS GO:0051216 'cartilage development' part_of 'part_of' GO:0048513 'organ development' is also a simple SubClassOf.

Change go to is_a
(Uberon has both cart. organ and cart. tissue, looking at the GO hierarchy organ is more appropriate)

renal

POTENTIAL REDUNDANT AXIOMS GO:0072025 'distal convoluted tubule development' part_of 'part_of' GO:0072017 'distal tubule development' is also a simple SubClassOf.

DONE

cmungall commented 10 years ago

Notes from http://wiki.geneontology.org/index.php/Ontology_meeting_2014-07-17

David H was less keen on cartilage as organ but we're going with that for now
Uberon will modify its representation of cardiac conduction system components and use part_of.

cmungall commented 10 years ago

Recommend also that ZFA uses part_of rather than is_a for nervous and cardiac conducton system parts. thoughts @cerivs?

cerivs commented 10 years ago

Need more context. Cardiac conduction system is part_of heart and is_a anatomical system. What is a better is_a parent, mouse apparently doesn't have an is_a parent, nor does human.

Nervous system is_a anatomical system. What would you propose as the is_a parent for nervous system? Didn't make a part of parent since is part_of whole organism.

cmungall commented 10 years ago

Sorry, my tickets can be kind of cryptic

It's the stuff below NS that's the issue:

  is_a ZFA:0000037 ! anatomical structure
   is_a ZFA:0001512 ! anatomical group
    is_a ZFA:0001439 ! anatomical system
     is_a ZFA:0000396 ! nervous system 
      is_a ZFA:0000012 ! central nervous system
      is_a ZFA:0000142 ! peripheral nervous system
      is_a ZFA:0001574 ! autonomic nervous system
       is_a ZFA:0001155 ! enteric nervous system
       is_a ZFA:0001575 ! parasympathetic nervous system
       is_a ZFA:0001576 ! sympathetic nervous system

we agree NS SubClassOf AS

and the stuff below CCS

  is_a ZFA:0000037 ! anatomical structure
   is_a ZFA:0001512 ! anatomical group
    is_a ZFA:0001439 ! anatomical system
     is_a ZFA:0005063 ! cardiac conduction system *** 
      is_a ZFA:0005071 ! distal conduction system
      is_a ZFA:0005074 ! central cardiac conduction system
      is_a ZFA:0005075 ! peripheral cardiac conduction system

we think these should be part_of

the relationship between CCS and AS is more problematic. FMA has CCS (what it calls conducting system of heart) as a type of tissue

cerivs commented 10 years ago

Part of the problem with the conduction system is that in zebrafish the anatomy hasn't been looked at in adult fish to any degree of detail. So the people have measured and disrupted the conduction in these systems so we know they exist but they but haven't described the structures. If they are part of the ccs then what should the is_a parent be?

For the NS would PNS be is_a anatomical system, part_of nervous system and CNS is_a anatomical system, part_of nervous system etc? This seems somewhat circular.

uberon commented 10 years ago

This is mostly a question of modeling rather than something that can be determined by an experiment. At the end of the day, for any class that has more than one instance in any given organism there is a partially arbitrary decision as to whether this is modeled as a mereological sum or a superclass.

See the latest Uberon for modeling of the NS. For the superclass of PNS etc we lifted 'organ system subdivision' from FMA (not in CARO). This is tagged with upper_level so that Bgee and others can present a biologist-friendly view.

On 17 Jul 2014, at 16:46, cerivs wrote:

Part of the problem with the conduction system is that in zebrafish the anatomy hasn't been looked at in adult fish to any degree of detail. So the people have measured and disrupted the conduction in these systems so we know they exist but they but haven't described the structures. If they are part of the ccs then what should the is_a parent be?

For the NS would PNS be is_a anatomical system, part_of nervous system and CNS is_a anatomical system, part_of nervous system etc? This seems somewhat circular.

Reply to this email directly or view it on GitHub: https://github.com/obophenotype/uberon/issues/527#issuecomment-49380747

cmungall commented 10 years ago

Closing this ticket as GO and Uberon are now aligned w.r.t isa vs partof

More works needs to be done on unifying this across AOs. I opted not to file a ZFA ticket for the NS terms for now, we can look at this en masse later

gouttegd commented 3 years ago

WARNING: This issue has been automatically closed because it has not been updated in more than 3 years. Please re-open it if you still need this to be addressed addressed addressed – we are now getting some resources to deal with such issues.

obophenotype / uberon