Review request: basic muscle cell hierarchy

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I would like to request a review of the basic muscle cell hierarchy. By basic I 
mean the core types of: cardiac, skeletal, smooth, striated.

specifically

 * definitions signed off
 * consistency of synonyms (e.g. use of "fiber" as synonym)
 * if possible, logical defs in terms of GO CCs (e.g. myofibrils)
 * generalization across taxa to appropriate level
 * checks against external sources
 * develops_from
 * part_of
 * DisjointUnion axioms (or at least Disjoint)

currently we have:

------is_a CL:0002371 ! somatic cell
--------is_a CL:0000187 ! muscle cell
----------is_a CL:0000188 ! skeletal muscle cell *** 
----------is_a CL:0000192 ! smooth muscle cell *** 
----------is_a CL:0000737 ! striated muscle cell *** 
------------is_a CL:0000746 ! cardiac muscle cell *** 

(this is just a subset of the DAG - e.g. cardiac isa cardiocyte not shown)

Do we agree with this? Many sources group skeletal and cardiac together under 
striated. i.e. in OWL terms

  'muscle cell' DisjointUnionOf 'smooth muscle cell', 'striated muscle cell'

This is somewhat supported by the not-very-good-yet wikipedia article
https://en.wikipedia.org/wiki/Striated_muscle

This is also supported, at least in humans, by the FMA:

----is_a FMA:72300 ! Somatic cell
------is_a FMA:67328 ! Muscle cell
--------is_a FMA:14072 ! Smooth muscle cell *** 
--------is_a FMA:86936 ! Striated muscle cell
----------is_a FMA:14067 ! Cardiac myocyte *** (aka Cardiac muscle cell)
----------is_a FMA:9727 ! Skeletal muscle cell *** 

Just for comparison, BTO has:

--/ BTO:0000000 ! tissues, cell types and enzyme sources
----is_a BTO:0000042 ! animal
------is_a BTO:0001489 ! whole body
--------po BTO:0001485 ! muscular system
----------is_a BTO:0001369 ! vertebrate muscular system
------------po BTO:0001103 ! skeletal muscle *** 
--------------is_a BTO:0002916 ! striated muscle cell *** 

But aside from mixing cells and tissues in the isa hierarchy I think this is a 
mistake?

For definitions we have:

 *  CL:0000188 ! skeletal muscle cell [DEF: "A somatic cell located in skeletal muscle."]
 *  CL:0000192 ! smooth muscle cell [DEF: "A non-striated, elongated, spindle-shaped cell found lining the digestive tract, uterus, and blood vessels. They develop from specialized myoblasts (smooth muscle myoblast)."]
 *  CL:0000737 ! striated muscle cell [DEF: "Muscle cell which has as its direct parts myofilaments organized into sarcomeres."]
 *  CL:0000746 ! cardiac muscle cell [DEF: "Cardiac muscle cells are striated muscle cells that are responsible for heart contraction. In mammals, the contractile fiber resembles those of skeletal muscle but are only one third as large in diameter, are richer in sarcoplasm, and contain centrally located instead of peripheral nuclei."]

I'm not so keen on the first two. In contrast:

----is_a FMA:72300 ! Somatic cell [DEF: "Nucleated cell which has one of more 
diploid sets (46 pairs) of chromosomes."]
------is_a FMA:67328 ! Muscle cell [DEF: "Somatic cell which has as direct 
parts of its cytoplasm myofibrils organized in various patterns."]
--------is_a FMA:14072 ! Smooth muscle cell ***  [DEF: "Muscle cell which has 
as its direct parts myofilaments attached to cytoplasmic dense bodies."]
--------is_a FMA:86936 ! Striated muscle cell [DEF: "Muscle cell which has as 
its direct parts myofilaments organized into sarcomeres."]
----------is_a FMA:14067 ! Cardiac myocyte ***  [DEF: "Striated muscle cell 
which has as its direct parts one or two centrally placed nuclei."]
----------is_a FMA:9727 ! Skeletal muscle cell ***  [DEF: "Striated muscle cell 
which has as its direct parts two or more peripherally located nuclei."]

Note that here the definitions are intrinsic - no reference to the tissues in 
which they are found.

Some of the relevant CC terms from GO that may be useful here:

----------is_a GO:0043232 ! intracellular non-membrane-bounded organelle
------------is_a GO:0043292 ! contractile fiber *** 
--------------po GO:0005859 ! muscle myosin complex
----------------is_a GO:0005863 ! striated muscle myosin thick filament
--------------is_a GO:0030016 ! myofibril
----------------po GO:0030017 ! sarcomere
----------------po GO:0036379 ! myofilament
----------------po GO:0043034 ! costamere
--------------is_a GO:0030485 ! smooth muscle contractile fiber
----------------po GO:0030486 ! smooth muscle dense body
--------------po GO:0044449 ! contractile fiber part
----------------is_a GO:0005859 ! muscle myosin complex
------------------is_a GO:0005863 ! striated muscle myosin thick filament
----------------is_a GO:0005861 ! troponin complex
----------------is_a GO:0005862 ! muscle thin filament tropomyosin
----------------is_a GO:0014705 ! C zone
----------------is_a GO:0030017 ! sarcomere
----------------is_a GO:0030018 ! Z disc
----------------is_a GO:0030485 ! smooth muscle contractile fiber
------------------po GO:0030486 ! smooth muscle dense body
----------------is_a GO:0030486 ! smooth muscle dense body
----------------is_a GO:0031430 ! M band
----------------is_a GO:0031672 ! A band
----------------is_a GO:0031673 ! H zone
----------------is_a GO:0031674 ! I band
----------------is_a GO:0036379 ! myofilament
----------------is_a GO:0043034 ! costamere
----------------is_a GO:0055120 ! striated muscle dense body

Original issue reported on code.google.com by cmung...@gmail.com on 30 May 2013 at 10:39

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There is some discussion of muscle cells in the old CL tracker.

http://sourceforge.net/tracker/index.php?func=detail&aid=3436074&group_id=76834&
atid=925065
http://sourceforge.net/tracker/index.php?func=detail&aid=3555196&group_id=76834&
atid=925065
http://sourceforge.net/tracker/index.php?func=detail&aid=3426095&group_id=76834&
atid=925065

I know there was a discussion on the CL developmental hierarchy for muscle 
cells in 2006 on the obo-cell-type-request list.

Original comment by cer...@gmail.com on 30 May 2013 at 11:05

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See also: 
http://sourceforge.net/p/geneontology/ontology-requests/10199/

(scroll to page 2)

Original comment by cmung...@gmail.com on 30 Jul 2013 at 8:39

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Made slow muscle fiber a related synonym of slow muscle cell.  

Original comment by zfinf...@gmail.com on 30 Jul 2013 at 8:51

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Check position in hierarchy of the 'myocyte of atrioventricular node' and 
'myocyte of sinoatrial node'.  Probably cardiac muscle cells.

Original comment by zfinf...@gmail.com on 30 Jul 2013 at 8:55