Precursor B cell and immature B cell: inverted hierarchy in CL vs. GO

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Hello,

Precursor B (pre-B) cell and immature B cell show an inverted hierarchy in CL 
vs. GO:

GO hierarchy:

          is_a GO:0002327 ! immature B cell differentiation
           is_a GO:0002329 ! pre-B cell differentiation ***

CL hierarchy - inverted!

          is_a CL:0000817 ! precursor B cell
            is_a CL:0000816 ! immature B cell ***

We need to solve this in order to put in logical definitions.
Could someone please look into this and let me know if we should change GO, or 
if the issue is rather in the naming and affecting both - is 'immature B cell' 
rather a synonym of 'precursor B cell'?

Thanks,
Paola

Original issue reported on code.google.com by pa...@ebi.ac.uk on 3 May 2013 at 10:33

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I am looking into the placement of 'immature B cell' in the CL.  I know Terry 
was trying to represent at least 2 different nomenclature systems for the 
developmental stages of B cells in the CL, so I am going back to the papers he 
looked at to see if I can resolve this.

-- Alex 

Original comment by addi...@buffalo.edu on 3 May 2013 at 3:44

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Hi Alex,

Hope all is well with you. Was there any update on this ticket please? In case 
I missed something. 

Thanks,
Paola.

Original comment by pa...@ebi.ac.uk on 1 May 2014 at 10:00

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Does this commit fix this?
https://code.google.com/p/cell-ontology/source/detail?r=412

Original comment by cmung...@gmail.com on 17 Sep 2014 at 4:23

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Very likely, yes. Is this one the correct file to look at, so I may visualize 
all details: cl-edit.owl in go-trunk/ontology/external/cell-ontology? Has a 
datestamp of Sept. 10th, day after commit. (BTW, Ontobee seems to be down today)

Thanks,
Paola

Original comment by pa...@ebi.ac.uk on 17 Sep 2014 at 7:43

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OK, looks like 'precursor B cell' and 'immature B cell' are now siblings under 
'B cell'.

 * GO folks: are we happy to follow CL and turn make the differentiation terms sibs? (assuming what GO calls a pre-B cell is what is properly called a precursor B cell - we should change label too)
 * MP folks: the same

If so, let's close this ticket and celebrate!!!

(The equiv axiom for precursor B cell is a bit dodgy I think, but that's 
another ticket...)

Original comment by cmung...@gmail.com on 17 Sep 2014 at 8:35

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Uhm, note that the def. comment of 'precursor B cell' says 'Representation 
needs to be aligned with GO' 
and 
the def. of 'immature B cell' says 'An immature B cell is a *precursor B cell* 
that has the phenotype surface IgM-positive and surface IgD-negative, and have 
not undergone class immunoglobulin class switching or peripheral encounter with 
antigen and activation.' 
so is this really resolved - should we really just change the GO terms? I'm 
happy to do that if so. Alex?

Thanks :-)
Paola

Original comment by pa...@ebi.ac.uk on 18 Sep 2014 at 10:08

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Original comment by vasil...@ohsu.edu on 2 Dec 2014 at 5:53

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Hi (Alex),

Just wondering if there's any follow-up to the discussion above please?

Many thanks,

Paola

Original comment by pa...@ebi.ac.uk on 27 Apr 2015 at 12:35

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Hi Paola,

The hierarchy is correct in CL.  I need to fix the definition of immature B 
cell to reference the proper genus.

-- Alex

Original comment by addi...@buffalo.edu on 27 Apr 2015 at 12:49

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Thanks Alex!

Note for self: when that's done, I can edit GO as above, and fix/close the 
relevant GO ticket
https://sourceforge.net/p/geneontology/ontology-requests/10166/

Original comment by pa...@ebi.ac.uk on 27 Apr 2015 at 1:05

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I fixed the definition for 'immature B Cell' to reference 'B cell' as the genus 
rather than 'precursor B cell'.  I also added the axiom 
lacks_plasma_membrane_part some 'IgM immunoglobulin complex' to 'precursor B 
cell' to distinguish the class better from 'immature B cell' and its children.  
Some precursor B cells bear the pre-BCR; the transition to immature B cell is 
when the pre-BCR is replaced by the surface IgM BCR upon successful completion 
of light chain somatic recombination.

Original comment by addi...@buffalo.edu on 5 May 2015 at 2:09