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

[Chris Mungall]

On Oct 8, 2008, at 4:15 AM, David Sutherland wrote:

> 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.]

I like this structure.

The problem is it would take a bit of effort to implement, as some of  
the existing types under 'stem cell' would have to be moved to be  
under progenitor cell.

Of course if someone else wants to take a crack at it...

Perhaps we can look again after the next release of FBbt

> 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.

I think it's important to make these distinctions in CL

>
>>     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'll pass this on to a vertebrate biologist..

>
>> 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.

OK, I'll try and come up with a proposed fix

>
>> 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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