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

[Pankaj Jaiswal (OSU)]

Chris,

Go ahead and let Chih-Wei know what's the solution on (a)trichoblast 
cell types. She can work on it. Also if you can submit the SF-PO 
request, that would be great.

Pankaj

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):
> 
>     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 ***
> 
> 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 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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-- 
Pankaj Jaiswal
Assistant Professor
Dept. of Botany and Plant Pathology
3082 Cordley Hall
Oregon State University
Corvallis, OR, 97331-2902, USA

Ph.  +1-541-737-8471
Fax: +1-541-737-3573
Web: www.gramene.org
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