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

Fri Oct 10 01:19:36 PDT 2008

On Fri, 10 Oct 2008, Alan Ruttenberg wrote:

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

Makes sense to me.
David

> -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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