obophenotype
names that are too broad for their definitions (ciliary epithelial cells)
TICKET: These terms have names that are too broad for their definitions, or
definitions that are two narrow for their names:
id: CL:0002304
name: non-pigmented ciliary epithelial cell
def: "A multi-ciliated cell of the retina that lacks visual pigment and
contributes to aqueous humor by secreting chloride ions. This cell type
maintains gap junctions with pigmented epithelial cells." [GOC:tfm,
PMID:15106942]
[Term]
id: CL:0002303
name: pigmented ciliary epithelial cell
def: "A ciliated epithelial cell of the retina, this cell type uptakes sodium
chloride and passes it to non-pigmented ciliary epithelial cells."
[PMID:15106942]
Original issue reported on code.google.com by [email protected] on 27 Feb 2012 at 5:41
@dosumis
TICKET: These terms have names that are too broad for their definitions, or definitions that are two narrow for their names: id: CL:0002304 name: non-pigmented ciliary epithelial cell def: "A multi-ciliated cell of the retina that lacks visual pigment and contributes to aqueous humor by secreting chloride ions. This cell type maintains gap junctions with pigmented epithelial cells." [GOC:tfm, PMID:15106942] [Term] id: CL:0002303 name: pigmented ciliary epithelial cell def: "A ciliated epithelial cell of the retina, this cell type uptakes sodium chloride and passes it to non-pigmented ciliary epithelial cells." [PMID:15106942]Original issue reported on code.google.com by
[email protected]on 27 Feb 2012 at 5:41
Would you be ok with
- [ ] renaming CL:0002304 'non-pigmented ciliary epithelial cell' as 'retinal multi-ciliated non-pigmented epithelial cell'
- [ ] adding part_of 'retina'
- [ ] editing CL:0002303 'pigmented ciliary epithelial cell' so it's a subclass of 'ciliated epithelial cell' (rather than 'multi-ciliated epithelial cell'; rename it as 'retinal pigmented ciliary epithelial cell'; make it part_of retina ? Also,
- [ ] fix typo in def of CL:0005012 'multi-ciliated epithelial cell' "A ciliated epithelial cell with many cilium." (cilium => cilia)
@dosumis, unless you have other feedback, I will proceed with Paola's suggestions above.
After taking a closer look at this, it appears the inconsistency in the original definitions is causing confusion rather than this being a narrow vs broad issue.
A 'non-pigmented ciliary epithelial cell', as it is referenced in the dbxref annotation, is not a retinal cell. It is part of the ciliary body, which is part of the uvea. These cells do contribute to production of the aqueous humour, but I have not found a reference that describes them as having cilia or being "multi-ciliated".
Similarly, a 'pigmented ciliary epithelial cell' is part of the ciliary body, not part of the retina. They do participate in the production of aqueous humour with the non-pigmented ciliary epithelial cells, but I have not found any reference that describes them as having cilia.
Proposed solution to come....
As noted above, there is currently misalignment between:
- the text definitions and some of the assertions of these classes and
- the labels and references of these classes
This misalignment may have stemmed from a misreading of "ciliary" as "ciliated" and misattributing the ciliary epithelium as being part of the retina (it is part of the ciliary body, not the retina).
It is prudent to use the current references and labels as the intended meaning of the concept and make the following revisions:
CL:0002303 ‘pigmented ciliary epithelial cell’
[x] Revise text definition
CURRENT: A ciliated epithelial cell of the retina, this cell type uptakes sodium chloride and passes it to non-pigmented ciliary epithelial cells.
REVISED: A cell that is part of pigmented ciliary epithelium. This cell type uptakes sodium and chloride ions from stromal interstitium and passes the ions to non-pigmented ciliary epithelial cells via gap junctions.
[x] Remove parent class ‘multi-ciliated epithelial cell’
[x] Add subclass 'part of' some ‘ciliary epithelium’
Of note, ‘pigmented ciliary epithelium’ is not found in Uberon, but BTO term ‘pigmented ciliary epithelium’ does exist.
[x] Revise exact synonym
CURRENT: PE
REVISED: PE cell (dbxref: https://doi.org/10.1016/j.exer.2003.09.021)
[x] Add comment: In a consensus model of unidirectional secretion, aqueous humour is formed by transferring solute, principally NaCl, from stroma to posterior chamber, with water passively following the osmotic gradient. Unidirectional secretion comprises three sequential steps. First, NaCl is transferred from the stromal interstitium into the pigmented ciliary epithelial (PE) cells… Second, solute passes from the PE into the non-pigmented ciliary epithelial (NPE) cells through gap junctions. Finally, NPE cells release Na+ and Cl− into the aqueous humour… (dbxref: https://doi.org/10.1016/j.exer.2003.09.021)
CL:0002304 ‘non-pigmented ciliary epithelial cell’
[x] Revise text definition
CURRENT: A multi-ciliated cell of the retina that lacks visual pigment and contributes to aqueous humor by secreting chloride ions. This cell type maintains gap junctions with pigmented epithelial cells.
REVISED: A cell that is part of non-pigmented ciliary epithelium. This cell type participates in aqueous humor formation by releasing solute, principally sodium and chloride ions received from pigmented epithelial cells via gap junctions, into the aqueous humor of the eye.
[x] Remove parent class ‘multi-ciliated epithelial cell’
[x] Add subclass 'part of' some ‘ciliary epithelium’
Of note, ‘nonpigmented ciliary epithelium’ is not found in Uberon, but BTO term ‘nonpigmented ciliary epithelium’ does exist.
[x] Revise exact synonym
CURRENT: NPE
REVISED: NPE cell (dbxref: https://doi.org/10.1016/j.exer.2003.09.021)
[x] Add exact synonym: nonpigmented ciliary epithelial cell dbxref: PMID:10913011
[x] Add comment: In a consensus model of unidirectional secretion, aqueous humor is formed by transferring solute, principally NaCl, from stroma to posterior chamber, with water passively following the osmotic gradient. Unidirectional secretion comprises three sequential steps. First, NaCl is transferred from the stromal interstitium into the pigmented ciliary epithelial (PE) cells… Second, solute passes from the PE into the non-pigmented ciliary epithelial (NPE) cells through gap junctions. Finally, NPE cells release Na+ and Cl− into the aqueous humour… (dbxref: https://doi.org/10.1016/j.exer.2003.09.021)
Additionally: [x] fix typo in def of CL:0005012 'multi-ciliated epithelial cell' "A ciliated epithelial cell with many cilium." (cilium => cilia)