NTR: GO term request with composed uberon terms

[cerivs]

I need to add new terms that compose 2 uberon terms in a single term name in the development tree of GO.
I need to add midbrain neuron development and hindbrain neuron development.

The template needs to have term 1 part_of term 2 and development part of could be replaced by better relation if desired.

To follow the pattern for forebrain development I came up with the following hierarchy:

[NEW] hindbrain generation of neurons
The process in which nerve cells are generated in the hindbrain. This includes the production of neuroblasts from and their differentiation into neurons.
is_a: GO:0048699 generation of neurons
part_of GO:0030902 hindbrain development

[NEW] hindbrain neuron differentiation
The process in which a relatively unspecialized cell acquires specialized features of a neuron that will reside in the hindbrain.
is_a: GO:0021953 central nervous system neuron differentiation
part_of:[NEW] hindbrain generation of neurons

[NEW]hindbrain neuron development
The process whose specific outcome is the progression of a neuron that resides in the hindbrain, from its initial commitment to its fate, to the fully functional differentiated cell.
is_a: GO:0021954 central nervous system neuron development
part_of: [NEW] hindbrain neuron differentiation

[cerivs]

@cmungall Haven't figured out how to assign this to you.

[cmungall]

cc @dosumis

I think generation of neurons should be the occurs in template (@cerivs - sorry, should have noticed this one, you can go ahead and add this now). E.g. 'generation of neurons' and occurs_in some hindbrain

Are all your terms for cell types like 'hindbrain neuron', ie. cell types that have extrinsic differentia rather than intrinsic?

You actually have two options with the existing templates for e.g. hindbrain neuron differentiation:

1. cell differentiation template (but note you will need to go to cl.termgenie.org and request hindbrain neuron)
2. occurs in template ('neuron differenaton' and occurs_in some hindbrain)

We don't really have any docs saying when to use which, we need this.

My criteria would be:

• use (1) if the neuron is defined intrinsically (e.g. interneuron, GABAergic, ...)
• use (2) if the neuron is discriminated purely from location (e.g. hindbrain neuron)

If so, @cerivs is good to go?

[cerivs]

This is use 2, gota love researchers. There are many instances of zebrafish researchers saying a gene affects development of a cell type in a structure in a mutant.

[cmungall]

OK, I'm confident in saying you should go ahead and use the existing occurs_in template, I think you have permission. I'll leave this open til we discuss how best to document the choices here.

Just curious, what does a line of your pheno.txt file look like for this? Maybe the GO annotation can be automated?

[cmungall]

We need to do a bit of work on the GO side: https://sourceforge.net/p/geneontology/ontology-requests/11756/

[cerivs]

hindbrain interneuron - increased amount
Mauthner neuron - increased amount
hindbrain:dorsal region - has fewer parts of type - neuron

I could request subtypes for the hindbrain neuron development but these will get researchers to the right part of the brain.

[cerivs]

Need to request midbrain neuron development tree for completeness since it doesn't make sense to have forebrain neuron development in the GO but not midbrain or hindbrain.

[dosumis]

Hi @cerivs, do you have any references you could share for these?

I think that generally the pattern should be:

• In CL, define neuron class, including its location (via some link to Uberon) if this can be specified.
  • 'hindbrain neuron' could simply be "neuron that part_of some hindbrain". But some hindbrain neurons may extend to other regions. So, it might be better to use "neuron that has_soma_location* some hindbrain" (* this is a type of overlap)
• Define GO differentiation term for cell type.

GO then needs to leverage CL part/overlaps relationships to Uberon structure to make part relationships in GO. (This step is a general problem for GO).

For the "hindbrain generation of neurons", we need to be careful:

• Does the development occur in the hindbrain or in some precursor structure?
• Do any neurons developing in the hindbrain (or its precursor) migrate? If so:
  • not all of the resulting neurons will be hindbrain neurons (as defined above)
  • 'part of' some 'hindbrain development' seems slightly dodgy. (perhaps ambitious, but we may be able to automate much of this partonomy too. The GCIs at least are straightforward: "results_in_differentiation of some (part_of some hindbrain) SubClassOf part_of some hindbrain development.")

[cerivs]

I followed the pattern for forebrain neurons from GO. The paper I am curating GO for is PMID:9007241. We annotate phenotype and GO based on the author's statements in the pub so if they say hindbrain neurons are affected I am not going to say they aren't in the hindbrain. For what it is worth hindbrain starts at 10 somites in the ZFA and the fate mapping is widely accpeted.

[dosumis]

I followed the pattern for forebrain neurons from GO.

This is defined with reference to a CL term, as I suggested:

forebrain neuron differentiation
EquivalentTo: 'cell differentiation'
and ('results in acquisition of features of' some 'neuron of the forebrain')

But it does also have the potentially dubious axiom:
SubClassOf: part_of some 'forebrain generation of neuron'

'forebrain generation of neurons' does not have the axiom 'occurs in' some forebrain, but the definition suggests this. The ontology therefore has the implicit assumption that all neurons that develop in the forebrain contribute to it. This may be true, but I wouldn't want to assume it. The term has no reference attached and is the only instance of this pattern in the ontology, so I'm not happy with using this as a general pattern.

The paper I am curating GO for is PMID:9007241. We annotate phenotype and GO based on the author's statements in the pub so if they say hindbrain neurons are affected I am not going to say they aren't in the hindbrain. For what it is worth hindbrain starts at 10 somites in the ZFA and the fate mapping is widely accepted.

We define CL & GO terms based on what we know generally from the literature and we may need to make finer distinctions than this particular paper does e.g. do we define hindbrain neuron as 'neuron that has_soma_location some hindbrain', rather than 'neuron that part_of some hindbrain'.

[dosumis]

Discussion from Editor's meeting:

Agreement:

1. Use CL TG to make cell X part term
   It better to use has_soma_location, but we should punt this for now. Comment & add examples on ticket Should cells defined by location use part_of or has_soma_part obophenotype/cell-ontology#182
2. Follow standard GO pattern for cell differentiation - can use TG.
3. Should fill in missing axiomatistaion in GO following this pattern.

[cmungall]

For 3, we need:

[Term]
id: GO:0002329 ! pre-B cell differentiation
name: pre-B cell differentiation

[Term]
id: GO:0002333 ! transitional one stage B cell differentiation
name: transitional one stage B cell differentiation

[Term]
id: GO:0002334 ! transitional two stage B cell differentiation
name: transitional two stage B cell differentiation

[Term]
id: GO:0003255 ! endocardial precursor cell differentiation
name: endocardial precursor cell differentiation

[Term]
id: GO:0003292 ! cardiac septum cell differentiation
name: cardiac septum cell differentiation

[Term]
id: GO:0003349 ! epicardium-derived cardiac endothelial cell differentiation
name: epicardium-derived cardiac endothelial cell differentiation

[Term]
id: GO:0007289 ! spermatid nucleus differentiation
name: spermatid nucleus differentiation

[Term]
id: GO:0007548 ! sex differentiation
name: sex differentiation

[Term]
id: GO:0008583 ! mystery cell differentiation
name: mystery cell differentiation

[Term]
id: GO:0021524 ! visceral motor neuron differentiation
name: visceral motor neuron differentiation

[Term]
id: GO:0021526 ! medial motor column neuron differentiation
name: medial motor column neuron differentiation

[Term]
id: GO:0021527 ! spinal cord association neuron differentiation
name: spinal cord association neuron differentiation

[Term]
id: GO:0021529 ! spinal cord oligodendrocyte cell differentiation
name: spinal cord oligodendrocyte cell differentiation

[Term]
id: GO:0021709 ! cerebellar basket cell differentiation
name: cerebellar basket cell differentiation

[Term]
id: GO:0021711 ! cerebellar unipolar brush cell differentiation
name: cerebellar unipolar brush cell differentiation

[Term]
id: GO:0021712 ! candelabrum cell differentiation
name: candelabrum cell differentiation

[Term]
id: GO:0021886 ! hypothalamus gonadotrophin-releasing hormone neuron differentiation
name: hypothalamus gonadotrophin-releasing hormone neuron differentiation

[Term]
id: GO:0021979 ! hypothalamus cell differentiation
name: hypothalamus cell differentiation

[Term]
id: GO:0022036 ! rhombomere cell differentiation
name: rhombomere cell differentiation

[Term]
id: GO:0030706 ! germarium-derived oocyte differentiation
name: germarium-derived oocyte differentiation

[Term]
id: GO:0030859 ! polarized epithelial cell differentiation
name: polarized epithelial cell differentiation

[Term]
id: GO:0033078 ! extrathymic T cell differentiation
name: extrathymic T cell differentiation

[Term]
id: GO:0035163 ! embryonic hemocyte differentiation
name: embryonic hemocyte differentiation

[Term]
id: GO:0035164 ! embryonic plasmatocyte differentiation
name: embryonic plasmatocyte differentiation

[Term]
id: GO:0042490 ! mechanoreceptor differentiation
name: mechanoreceptor differentiation

[Term]
id: GO:0042705 ! ocellus photoreceptor cell differentiation
name: ocellus photoreceptor cell differentiation

[Term]
id: GO:0043696 ! dedifferentiation
name: dedifferentiation

[Term]
id: GO:0043697 ! cell dedifferentiation
name: cell dedifferentiation

[Term]
id: GO:0044671 ! sorocarp spore cell differentiation
name: sorocarp spore cell differentiation

[Term]
id: GO:0046660 ! female sex differentiation
name: female sex differentiation

[Term]
id: GO:0046661 ! male sex differentiation
name: male sex differentiation

[Term]
id: GO:0048052 ! R1/R6 cell differentiation
name: R1/R6 cell differentiation

[Term]
id: GO:0048054 ! R2/R5 cell differentiation
name: R2/R5 cell differentiation

[Term]
id: GO:0048056 ! R3/R4 cell differentiation
name: R3/R4 cell differentiation

[Term]
id: GO:0048321 ! axial mesodermal cell differentiation
name: axial mesodermal cell differentiation

[Term]
id: GO:0048342 ! paraxial mesodermal cell differentiation
name: paraxial mesodermal cell differentiation

[Term]
id: GO:0048371 ! lateral mesodermal cell differentiation
name: lateral mesodermal cell differentiation

[Term]
id: GO:0048392 ! intermediate mesodermal cell differentiation
name: intermediate mesodermal cell differentiation

[Term]
id: GO:0048505 ! regulation of timing of cell differentiation
name: regulation of timing of cell differentiation

[Term]
id: GO:0048824 ! pigment cell precursor differentiation
name: pigment cell precursor differentiation

[Term]
id: GO:0048908 ! anterior lateral line ganglion neuron differentiation
name: anterior lateral line ganglion neuron differentiation

[Term]
id: GO:0050933 ! early stripe melanocyte differentiation
name: early stripe melanocyte differentiation

[Term]
id: GO:0050934 ! late stripe melanocyte differentiation
name: late stripe melanocyte differentiation

[Term]
id: GO:0055012 ! ventricular cardiac muscle cell differentiation
name: ventricular cardiac muscle cell differentiation

[Term]
id: GO:0060113 ! inner ear receptor cell differentiation
name: inner ear receptor cell differentiation

[Term]
id: GO:0060164 ! regulation of timing of neuron differentiation
name: regulation of timing of neuron differentiation

[Term]
id: GO:0060165 ! regulation of timing of subpallium neuron differentiation
name: regulation of timing of subpallium neuron differentiation

[Term]
id: GO:0060290 ! transdifferentiation
name: transdifferentiation

[Term]
id: GO:0060318 ! definitive erythrocyte differentiation
name: definitive erythrocyte differentiation

[Term]
id: GO:0060479 ! lung cell differentiation
name: lung cell differentiation

[Term]
id: GO:0060508 ! lung basal cell differentiation
name: lung basal cell differentiation

[Term]
id: GO:0060645 ! peripheral mammary gland bud epithelial cell differentiation
name: peripheral mammary gland bud epithelial cell differentiation

[Term]
id: GO:0060646 ! internal mammary gland bud epithelial cell differentiation
name: internal mammary gland bud epithelial cell differentiation

[Term]
id: GO:0060889 ! limb basal epidermal cell differentiation
name: limb basal epidermal cell differentiation

[Term]
id: GO:0060890 ! limb spinous cell differentiation
name: limb spinous cell differentiation

[Term]
id: GO:0060891 ! limb granular cell differentiation
name: limb granular cell differentiation

[Term]
id: GO:0060938 ! epicardium-derived cardiac fibroblast cell differentiation
name: epicardium-derived cardiac fibroblast cell differentiation

[Term]
id: GO:0060942 ! neural crest-derived cardiac fibroblast cell differentiation
name: neural crest-derived cardiac fibroblast cell differentiation

[Term]
id: GO:0060947 ! cardiac vascular smooth muscle cell differentiation
name: cardiac vascular smooth muscle cell differentiation

[Term]
id: GO:0060951 ! neural crest-derived cardiac glial cell differentiation
name: neural crest-derived cardiac glial cell differentiation

[Term]
id: GO:0060983 ! epicardium-derived cardiac vascular smooth muscle cell differentiation
name: epicardium-derived cardiac vascular smooth muscle cell differentiation

[Term]
id: GO:0061103 ! carotid body glomus cell differentiation
name: carotid body glomus cell differentiation

[Term]
id: GO:0061207 ! mesonephric juxtaglomerulus cell differentiation
name: mesonephric juxtaglomerulus cell differentiation

[Term]
id: GO:0061223 ! mesonephric mesenchymal cell differentiation
name: mesonephric mesenchymal cell differentiation

[Term]
id: GO:0061250 ! mesonephric glomerular epithelial cell differentiation
name: mesonephric glomerular epithelial cell differentiation

[Term]
id: GO:0061253 ! mesonephric glomerular parietal epithelial cell differentiation
name: mesonephric glomerular parietal epithelial cell differentiation

[Term]
id: GO:0061259 ! mesonephric glomerular mesangial cell differentiation
name: mesonephric glomerular mesangial cell differentiation

[Term]
id: GO:0061260 ! mesonephric mesangial cell differentiation
name: mesonephric mesangial cell differentiation

[Term]
id: GO:0061266 ! mesonephric interstitial fibroblast differentiation
name: mesonephric interstitial fibroblast differentiation

[Term]
id: GO:0061329 ! Malpighian tubule principal cell differentiation
name: Malpighian tubule principal cell differentiation

[Term]
id: GO:0061443 ! endocardial cushion cell differentiation
name: endocardial cushion cell differentiation

[Term]
id: GO:0072062 ! proximal convoluted tubule segment 1 cell differentiation
name: proximal convoluted tubule segment 1 cell differentiation

[Term]
id: GO:0072069 ! DCT cell differentiation
name: DCT cell differentiation

[Term]
id: GO:0072139 ! glomerular parietal epithelial cell differentiation
name: glomerular parietal epithelial cell differentiation

[Term]
id: GO:0072162 ! metanephric mesenchymal cell differentiation
name: metanephric mesenchymal cell differentiation

[Term]
id: GO:0072184 ! renal vesicle progenitor cell differentiation
name: renal vesicle progenitor cell differentiation

[Term]
id: GO:0072192 ! ureter epithelial cell differentiation
name: ureter epithelial cell differentiation

[Term]
id: GO:0072195 ! kidney smooth muscle cell differentiation
name: kidney smooth muscle cell differentiation

[Term]
id: GO:0072209 ! metanephric mesangial cell differentiation
name: metanephric mesangial cell differentiation

[Term]
id: GO:0072240 ! metanephric DCT cell differentiation
name: metanephric DCT cell differentiation

[Term]
id: GO:0072245 ! metanephric glomerular parietal epithelial cell differentiation
name: metanephric glomerular parietal epithelial cell differentiation

[Term]
id: GO:0072251 ! metanephric juxtaglomerulus cell differentiation
name: metanephric juxtaglomerulus cell differentiation

[Term]
id: GO:0072254 ! metanephric glomerular mesangial cell differentiation
name: metanephric glomerular mesangial cell differentiation

[Term]
id: GO:0072258 ! metanephric interstitial fibroblast differentiation
name: metanephric interstitial fibroblast differentiation

[Term]
id: GO:0072311 ! glomerular epithelial cell differentiation
name: glomerular epithelial cell differentiation

[Term]
id: GO:0072312 ! metanephric glomerular epithelial cell differentiation
name: metanephric glomerular epithelial cell differentiation

[Term]
id: GO:0072497 ! mesenchymal stem cell differentiation
name: mesenchymal stem cell differentiation

[rebeccafoulger]

What's the next step on this issue, so I can go ahead and add in the 'midbrain dopaminergic neuron differentiation' terms in geneontology/go-ontology#12039?

Thank you.