[DEPRECATED] Gene Ontology / Ontology requests / #11013 NTR: somatodendritic compartment

#11013 NTR: somatodendritic compartment

Milestone: PARL-UCL

Status: closed-accepted

Owner: RFoulger

Labels: cellular component (34) New Term Request (38)

Priority: 5

Updated: 2014-07-29

Created: 2014-07-22

Creator: RFoulger

Private: No

A new term suggestion from Paul Denny:

somatodendritic compartment ; GO:NEW
The region of a neuron that includes the cell body (cell soma) and the dendrite, but excludes the axon.
is_a: cell part ; GO:0044464
has_part: neuronal cell body ; GO:0043025
has_part: dendrite ; GO:0030425
PMID:15009133
GOC:pad, GOC:PARL

Adding here for comments, thanks.

Discussion

David Hill - 2014-07-23

An interesting union term. Seems to work, but wouldn't it be somatodendritic?
According to the cell ontology 'Each neuron consists of a body, an axon, and dendrites'. So an alternative arrangement could be to have neuronal cell body part_of somatodendritic compartment and dendrite part_of somatodendritic compartment.

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David Hill - 2014-07-23

assigned_to: David Hill
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RFoulger - 2014-07-23

summary: NTR: sematodendritic compartment --> NTR: somatodendritic compartment

Description has changed:

Diff:

--- old +++ new @@ -1,6 +1,6 @@ A new term suggestion from Paul Denny: -sematodendritic compartment ; GO:NEW +somatodendritic compartment ; GO:NEW The region of a neuron that includes the cell body (cell soma) and the dendrite, but excludes the axon. is_a: cell part ; GO:0044464 has_part: neuronal cell body ; GO:0043025
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RFoulger - 2014-07-23

doh-not sure if thats an auto-correct error, or too much sema-signaling on the brain: I've updated the ticket.

The part_ofs look like they'd work. Should be is_a: neuron_part (GO:0097458) too, for a more specific is_a parent.

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David Hill - 2014-07-23

Yup, neuron part is better. Shall I add or do you still add terms?

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RFoulger - 2014-07-23

assigned_to: David Hill --> RFoulger
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RFoulger - 2014-07-23

I still edit so I'll add this in tomorrow when I'm back at my desk.... (i just make SF tickets for the ones that might not be straightforward or as reminders to me).

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RFoulger - 2014-07-24

status: open --> closed-accepted
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RFoulger - 2014-07-24

Added: somatodendritic compartment ; GO:0036477

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Paul Denny - 2014-07-29

Thx for adding this - Protein2GO doesn't recognise somatodendritic compartment ; GO:0036477 - should I ask Tony Sawford about this?

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