cmungall
commented
12 years ago Hi Chris,
My take on this is as follows:
- Cells that are capable of firing action potentials with a pacemaker (rhythmic) modality are present not only in the heart but also in the brain and intestine (and there are 'pacemakers' in some sperm flagella too, involved in motility).
- Therefore it might be useful to reflect this in the cells' names to avoid ambiguity. Though 'pacemaker' refers to heart pacemaker in most cases. The CL already has the intestinal pacemaker type (see my last point below). I wouldn't add other cell types for the time being; in neurobiology, afaik, 'pacemaker' refers to the type of firing pattern and resulting currents more than to a specific type of neuron.
- In heart, there are primary and secondary pacemakers (see e.g. http://en.wikipedia.org/wiki/Cardiac\_pacemaker). But for GO's uses, I think it's fine to have 'cardiac pacemaker cell' mean both; that's the way it's used in GO:0060926 pacemaker cell development GO:0060920 pacemaker cell differentiation GO:0060927 pacemaker cell fate commitment (see https://sourceforge.net/tracker/?func=detail&aid=3436150&group\_id=36855&atid=440764).
- Currently, the Cell Ontology has: (I'm looking at the prerelease version dated 9/6/12, cl-edit.obo)
1) id: CL:0002072 name: nodal myocyte def: "A specialized cardiac myocyte in the sinuatrial and atrioventricular nodes. The cell is slender and fusiform confined to the nodal center, circumferentially arranged around the nodal artery." [FMA:67101, GOC:tfm, http://63.198.234.228/OpenFMA/Nodal%20myocyte.html] synonym: "pacemaker cell" EXACT []
So this comprises both primary and secondary cardiac pacemaker cells. I'd make the existing synonym "pacemaker cell" broad rather than exact, and I'd add an exact synonym "cardiac pacemaker cell" similarly to what you suggest.
2) id: CL:0002088 name: interstitial cell of Cajal def: "This is a cell found in the gastrointestinal tract of mammals and serves as a pacemaker that triggers gut contraction. ICCs mediate inputs from the enteric nervous system to smooth muscle cells and are thought to be the cells from which gastrointestinal stromal tumors (GISTs) arise." [GOC:tfm, PMID:16460275, PMID:19520112]
I'd add an exact synonym "intestinal pacemaker cell"
3) id: CL:1000477 name: pacemaker cell of sinuatrial node def: "A nodal myocyte that is part of the sinuatrial node." [GOC:tfm] synonym: "pacemaker cell of sinoatrial node" EXACT []
(This is a descendant of CL:0002072 nodal myocyte) I'd change the name to "cardiac pacemaker cell of sinuatrial node", make "pacemaker cell of sinuatrial node" an exact synonym, and add an exact synonym "cardiac pacemaker cell of sinoatrial node".
As for the existing GO terms GO:0060926 pacemaker cell development GO:0060920 pacemaker cell differentiation GO:0060927 pacemaker cell fate commitment I'll change the name to "cardiac pacemaker etc.".
Does this make sense? Thanks, Paola
Original comment by: paolaroncaglia
See http://sourceforge.net/tracker/index.php?func=detail&aid=3436150&group\_id=36855&atid=440764
We have:
[Term] id: CL:0002072 name: nodal myocyte namespace: cell def: "A specialized cardiac myocyte in the sinuatrial and atrioventricular nodes. The cell is slender and fusiform confined to the nodal center, circumferentially arranged around the nodal artery." [FMA:67101, GOC:tfm, http://63.198.234.228/OpenFMA/Nodal%20myocyte.html] synonym: "Myocytus nodalis" EXACT [] synonym: "P cell" EXACT [] synonym: "Pacemaker cell" EXACT [] xref: BTO:0004190 xref: FMA:67101 is_a: CL:0002086 ! specialized cardiac myocyte
Should the exact syn not be "cardiac pacemaker cell"? Should we have the other kinds of pacemaker?
Original comment by: cmungall