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

Fri Oct 10 00:33:43 PDT 2008

We're working with the Harvard Stem Cell Institute. Would it be worth
me trying to recruit someone from there to help?
-Alan

On Thu, Oct 9, 2008 at 8:53 PM, Chris Mungall <cjm at berkeleybop.org> wrote:
>
> 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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>>
>
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