[Ontology-editors] [Obo-cell-type] stem cells [was Re: help wanted getting CL and GO consistent]

[David Sutherland]

Hi Chris,

Not alot of time to work on this right now as I'm in the thick of grant
writing.  One general comment though - given the current state of CL,
I'd be very careful about using it to infer links in GO.

On Tue, 2008-10-07 at 16:25 -0700, Chris Mungall wrote:
> What about these:
> 
> > ** GO:0048103 somatic stem cell division **
> > GO:0055057 neuroblast division
> 
> > ** GO:0048864 stem cell development **
> > GO:0014019 neuroblast development
> 
> > ** GO:0048863 stem cell differentiation **
> > GO:0010054 trichoblast differentiation
> > GO:0010055 atrichoblast differentiation
> > GO:0014016 neuroblast differentiation
> 
> I would have thought the neuroblast cases would be straightforward  
> examples of CL being right and GO needing to add the 3 links above.
> 
> However, fly_anatomy has neuroblast as a subtype of precursor cell and  
> sibling of stem cell (both undefined):
> 

Note - there was a whole thread on this about 18months back - I think on
the CL list.

The CL def of stem cell (from MESH) is not bad
def: "A relatively undifferentiated cell that retains the ability to
divide and proliferate throughout life to provide progenitor cells that
can differentiate into specialized cells." [MESH:A.11.872]

However - I'd dispute the 'throughout life' (plenty of evidence now for
stem cell replenishment by de-differentiation). I think that the
important point is that a stem cell retains its idenitity while budding
off cells which differentiate (or have progeny which do). Failure to
make that distinction (which I think is implicit in the MESH def) means
that any undifferentiated cell with progeny/descendants that
differentiate is a stem cell.

Here's my quick stab at a new heirarchy for CL:

precursor cell [Def: A relatively undifferentiated cell, some or all of
whose progeny form differentiated cells]
	is_a progenitor cell [Def: A relatively undifferentiated cell whose
identity is lost during division and whose descendants can differentiate
into specialised cells.]
	is_a stem cell  [Def: A relatively undifferentiated cell that retains
the ability to divide and proliferate. During division it retains its
identity while budding off provide progenitor cells that can
differentiate into specialized cells.]

Using this, the heirarchy arthropod neural precurors should be:

precursor cell
	is_a progenitor cell
		is_a ganglion mother cell
	is_a stem cell
		is_a neuroblast
(This is how it is in the development version of FBbt)

Note - ganglion mother cells are neuronal precursor cells, but they
don't retain their identity at division - all of their progeny
differentiate.


>      is_a FBbt:00007008 ! precursor cell
>        is_a FBbt:00001666 ! cardioblast
>        is_a FBbt:00004860 ! germ cell
>        is_a FBbt:00004874 ! oogonial cell
>        is_a FBbt:00004947 ! acroblast
>        is_a FBbt:00004994 ! epidermoblast
>        is_a FBbt:00005041 ! tracheal precursor cell
>        is_a FBbt:00005083 ! myoblast
>        is_a FBbt:00005145 ! glioblast
>        is_a FBbt:00005146 ! neuroblast ***  [DEF: "A neural stem cell  
> which delaminates from the ectoderm and which buds off new ganglion  
> mother cells during the course of development."]
>        is_a FBbt:00005149 ! ganglion mother cell
>        is_a FBbt:00005220 ! hemangioblast [DEF: "A cell type of the  
> cardiac mesoderm which gives rise to a subpopulation of the  
> cardioblasts and pericardial cells."]
>        is_a FBbt:00005605 ! imaginal tracheal precursor
>        is_a FBbt:00007014 ! stem cell
>        is_a FBbt:00007021 ! larval oenocyte precursor [DEF: "Larval  
> oenocyte precursors first become apparent during stage 11 when a small  
> group of cells encircling each chordotonal organ precursor cell C1  
> become sickle shaped, making a
> 


> ZFA is perfectly aligned with CL:
> 
>     is_a ZFA:0009000 ! cell
>      is_a ZFA:0009307 ! somatic stem cell
>       is_a ZFA:0009020 ! multi fate stem cell
>        is_a ZFA:0009019 ! neuronal stem cell
>         is_a ZFA:0009011 ! neuroblast ***
> 
Are you sure that vertebrate neuroblasts are stem cells by the above
definition?

> I'd like to get a plant person involved to make sure the  
> (a)trichoblast classification in CL is improved (currently these are  
> both animal and plant cells!)
> 
I also responded to this previously

I suspect the confusion comes from both plants and insects having
structures called trichomes.  Unlike a plant trichome, an insect
trichome is not a cell - it is a cell extension.

> I suggest the following:
> 
> - GO adds the 3 proposed neuroblast BP links
> - I will transfer the embedded GO definition of somatic stem cell to  
> CL (where it is currently undefined).
> 	"a stem cell that can give rise to cell types of the body other than  
> those of the germ-line" OR
> 	"undifferentiated cells in the embryo or adult which can undergo  
> unlimited division and give rise to cell types of the body other than  
> those of the germ-line"
> 
> 
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