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Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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NTR: dorsal interneuron caudal and rostral axon projection #8633

Closed gocentral closed 9 years ago

gocentral commented 13 years ago

Hi,

for annotation of Lhx1_chick (P53411) and Lhx9_chick (Q90881) in PMID:19545367 I will require the following new terms:

GO:0008045 motor axon guidance [defn:The process in which the migration of an axon growth cone of a motor neuron is directed to a specific target site in response to a combination of attractive and repulsive cues.] --< GO:NEW spinal sensory axon guidance [defn: The process in which the migration of an axon growth cone of a spinal sensory neuron is directed to a specific target site in response to a combination of attractive and repulsive cues. --< GO:NEW dorsal interneuron axon guidance [defn: The process in which the migration of an axon growth cone of a dorsal interneuron is directed to a specific target site in response to a combination of attractive and repulsive cues.] --< GO:NEW dorsal interneuron caudal axon projection [defn: The process in which the migration of an axon growth cone of a dorsal interneuron is directed caudially to a specific target site in response to a combination of attractive and repulsive cues.] (Lhx1/ IDA) --< GO:NEW dorsal interneuron rostral axon projection [defn: The process in which the migration of an axon growth cone of a dorsal interneuron is directed rostrally to a specific target site in response to a combination of attractive and repulsive cues.] (Lhx9/ IDA)

Thanks, Yasmin

Reported by: yafaruque

Original Ticket: geneontology/ontology-requests/8421

gocentral commented 13 years ago

Original comment by: paolaroncaglia

gocentral commented 13 years ago

Hi Yasmin,

I'm going to check with the Cell Type Ontology people about their general way of creating neuron type terms, to try and align GO to CL as much as possible. This said, here's what I'd do for the terms you need:

1) GO:0008045 motor axon guidance Rename to "motor neuron axon guidance" (consistently with CL:0000100 motor neuron). Add exact synonyms "motor axon guidance" and "motoneuron axon guidance".

2) GO:0007411 axon guidance

Sensory neurons are located in sensory organs, where they respond to stimuli and send their signals to the Central Nervous System (CNS, i.e. brain and spinal cord). Spinal sensory neurons are sensory neurons that project to the spinal cord. Motor neurons instead are located in the CNS and project their axons outside of it. Therefore, "spinal sensory neuron axon guidance" should be a child of the broader term GO:0007411 axon guidance, rather than of GO:0008045 motor (neuron) axon guidance as you seem to suggest, unless I got you wrong. I'll check with CL if they'd want to create a new term for spinal sensory neuron.

3) GO:0007411 axon guidance

Interneurons are different from motor neurons - they connect neurons within a same region of the CNS, same place where motor neurons are. Dorsal interneurons are interneurons located in the dorsal part of the spinal cord. I'll check with CL if they'd want to create a new term for dorsal spinal cord interneuron, or interneuron of the dorsal spinal cord (similarly to a term they have in the current pre-release version of CL, CL:0002611 neuron of the dorsal spinal cord)

4) GO:NEW6 dorsal spinal cord interneuron posterior axon guidance (broad or related synonym: dorsal interneuron caudal axon projection) is_a GO:NEW5 dorsal spinal cord interneuron axon guidance is_a GO:0033564 anterior/posterior axon guidance

5) GO:NEW7 dorsal spinal cord interneuron anterior axon guidance (broad or related synonym: dorsal interneuron rostral axon projection) is_a GO:NEW5 dorsal spinal cord interneuron axon guidance is_a GO:0033564 anterior/posterior axon guidance

Let me know if you disagree with any of this or if anything is not clear. Thanks for reading this far :-) Paola

Original comment by: paolaroncaglia

gocentral commented 13 years ago

Original comment by: paolaroncaglia

gocentral commented 13 years ago

Hi Yasmin,

Sorry this is taking so long. I'm still waiting for the new terms I requested from the Cell Ontology. I followed up with them yesterday, but they (he) might be on holiday. If so, this will have to wait until I come back from my trip. Should you need your terms sooner, please let me know. Thanks!

Paola

Original comment by: paolaroncaglia

gocentral commented 13 years ago

No worries Paola, I can wait Yasmin

Original comment by: yafaruque

gocentral commented 13 years ago

Hi Yasmin,

This request is still on hold, waiting for the Cell Ontology to create new terms for the neuron types below. We'll be talking to Chris about cell-type work in general, and neuro-cell work specifically, at the GOC meeting in London. Therefore, I'll have to keep this item open for a bit longer. Let me know if there's any problem with that.

Thanks, Paola

Original comment by: paolaroncaglia

gocentral commented 13 years ago

Setting this request to pending, while we wait for the Cell Type Ontology terms to be added. At the GOC-UCL meeting last week, Chris said these will be done, so don't despair.

Note for self: Cell Ontology request is at https://sourceforge.net/tracker/?func=detail&aid=3403196&group\_id=76834&atid=925065

Paola

Original comment by: paolaroncaglia

gocentral commented 13 years ago

Original comment by: paolaroncaglia

gocentral commented 12 years ago

Renamed GO:0008045 motor axon guidance to 'motor neuron axon guidance'. Added exact synonyms 'motor axon guidance and 'motoneuron axon guidance'. Added new terms: GO:0097374 sensory neuron axon guidance GO:0097375 spinal sensory neuron axon guidance GO:0097376 interneuron axon guidance GO:0097377 spinal cord interneuron axon guidance GO:0097378 dorsal spinal cord interneuron axon guidance GO:0097379 dorsal spinal cord interneuron posterior axon guidance GO:0097380 dorsal spinal cord interneuron anterior axon guidance

Leaving status as 'pending' only because the Cell Ontology terms haven't been created yet. Though, terms under 'axon guidance' don't actually have Dbxrefs to CL (yet?).

Original comment by: paolaroncaglia

gocentral commented 12 years ago

Original comment by: paolaroncaglia

gocentral commented 11 years ago

Added CL IDs as Dbxref to: GO:0008045 motor neuron axon guidance [CL:0000100] GO:0097374 sensory neuron axon guidance [CL:0000101] GO:0097375 spinal sensory neuron axon guidance [CL:0009000] GO:0097376 interneuron axon guidance [CL:0000099] GO:0097377 spinal cord interneuron axon guidance [CL:0005000]

Original comment by: paolaroncaglia

gocentral commented 11 years ago

Original comment by: paolaroncaglia