Add 14 myenteric neuron terms for HubMap (issue #3471)#3585
Add 14 myenteric neuron terms for HubMap (issue #3471)#3585RiveraAndrea83 merged 12 commits intomasterfrom
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Added the following new CL terms with temporary IDs CL_9900001-CL_9900014: - CL_9900001: Dogiel type II neuron (prerequisite) - CL_9900002: intrinsic primary afferent neuron of myenteric plexus - CL_9900003: interneuron of myenteric plexus - CL_9900004: secretomotor/vasodilator neuron of myenteric plexus - CL_9900005: intestinofugal neuron - CL_9900006: ascending interneuron of myenteric plexus - CL_9900007: descending interneuron of myenteric plexus - CL_9900008: stubby Dogiel type I neuron of myenteric plexus - CL_9900009: spiny Dogiel type I neuron of myenteric plexus - CL_9900010: Dogiel type II neuron of myenteric plexus - CL_9900011: calretinin-positive IPAN of myenteric plexus - CL_9900012: calretinin-negative IPAN of myenteric plexus - CL_9900013: cholinergic neuron of myenteric plexus (defined class) - CL_9900014: nitrergic neuron of myenteric plexus (defined class) Signed-off-by: GitHub Copilot Co-authored-by: RiveraAndrea83 <205639972+RiveraAndrea83@users.noreply.github.com>
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#gogoeditdiff |
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@copilot please remove the axiom spiny Dogiel type I neuron of myenteric plexus SubClassOf inhibitory motor neuron |
Per @dosumis review: spiny Dogiel type I neuron of myenteric plexus should not have an is_a relationship to inhibitory motor neuron (CL_0008015). Signed-off-by: GitHub Copilot Co-authored-by: dosumis <112839+dosumis@users.noreply.github.com>
Done — removed |
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#gogoeditdiff |
Here's a diff of how these changes impact the classified ontology (on -base file):Ontology comparisonLeft
Right
Ontology importsOntology annotationsDogiel type II neuron
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Here's a diff of your edit file (unreasoned)Ontology comparisonLeft
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Ontology importsOntology annotationsDogiel type II neuron
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@copilot please make this term CL_9900001 subclass of enteric neuron |
…ea83 review CL_9900001 (Dogiel type II neuron) was only a subclass of CL_0000540 (neuron); adding CL_0007011 (enteric neuron) as an additional parent per reviewer request. Signed-off-by: GitHub Copilot Co-authored-by: RiveraAndrea83 <205639972+RiveraAndrea83@users.noreply.github.com>
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#gogoeditdiff |
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Good for now. Let's aim for a second round with more refs and slightly broadened terms.
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Adds 14 new CL terms covering the major neurochemical and morphological cell types of the myenteric plexus, as requested by HubMap. All terms use temporary IDs (
CL_99xxxxx) pending minting of permanent IDs.Hierarchy overview
Defined classes (EquivalentClasses)
enteric neuron ∧ has_soma_location(UBERON:0002439) ∧ capable_of(GO:0014055)— acetylcholine secretion; autoclassifies stubby Dogiel I, IPANs, ascending interneuronsenteric neuron ∧ has_soma_location(UBERON:0002439) ∧ capable_of(GO:0006809)— nitric oxide biosynthesis; autoclassifies spiny Dogiel I neuronsPost-review axiom changes
SubClassOf(CL_9900009, CL_0008015)— spiny Dogiel type I neuron of myenteric plexus is no longer asserted as a subclass of inhibitory motor neuron.SubClassOf(CL_9900001, CL_0007011)— Dogiel type II neuron is now also a subclass of enteric neuron (in addition to neuron).Per-term metadata
Each term includes: definition with inline PMID citations, exact/related synonyms (abbreviations flagged
OMO_0003000),SubClassOfparent axioms,RO_0002100soma location toUBERON_0002439,IAO_0000233tracker link,terms:creator, andterms:date.Original prompt
This section details on the original issue you should resolve
<issue_title>Links to #3471 Add myenteric neurons for hubmap</issue_title>
<issue_description>Links #3471
Copilot follow the information below and create new CL for the terms described below:
-## Term 1: Intrinsic primary afferent neuron of myenteric plexus
Preferred Label: intrinsic primary afferent neuron of myenteric plexus
Definition: A sensory neuron of the enteric nervous system whose soma resides in the myenteric plexus and which functions as the afferent limb of intrinsic reflex circuits controlling motility, secretion, and blood flow. This neuron is characterised by Dogiel type II morphology (large smooth soma with multiple long axon-like processes), AH-type electrophysiology (prolonged afterhyperpolarization following an action potential), and is immunopositive for choline acetyltransferase (ChAT) and immunonegative for neuronal nitric oxide synthase (NOS1).
References:
UBERON Terms:
Parent CL Terms:
Import Flags: None
Synonyms:
Term 2: Interneuron of myenteric plexus
Preferred Label: interneuron of myenteric plexus
Definition: An interneuron of the enteric nervous system whose soma resides in the myenteric plexus. Interneurons of the myenteric plexus integrate sensory input from intrinsic primary afferent neurons (IPANs) and modulate motor output to smooth muscle and secretory epithelia by synapsing onto motor neurons and other interneurons within the plexus.
References:
UBERON Terms:
Parent CL Terms:
Import Flags: None
Synonyms:
Term 3: Secretomotor/vasodilator neuron of myenteric plexus
Preferred Label: secretomotor/vasodilator neuron of myenteric plexus
Definition: An enteric neuron whose soma resides in the myenteric plexus and which controls mucosal secretion and blood flow by innervating secretory epithelia and submucosal blood vessels. This neuron is characterised by expression of vasoactive intestinal peptide (VIP). In mouse, two Glp2r+ subtypes have been identified: PSVN1 (VIP+, non-cholinergic) and PSVN2 (ChAT+, cholinergic). In human, only the VIP+ non-cholinergic subtype has been detected.
References:
UBERON Terms:
Parent CL Terms:
Import Flags: None
Synonyms:
Term 4: Intestinofugal neuron
Preferred Label: intestinofugal neuron
Definition: An enteric neuron whose soma resides in the myenteric plexus of the intestine and whose axon projects outside the gut wall to synapse on neurons in prevertebral sympathetic ganglia (celiac, superior mesenteric, or inferior mesenteric ganglia). This neuron provides a pathway for gut-to-brain communication via sympathetic prevertebral ganglia. In humans, 89% are immunopositive for choline acetyltransferase (ChAT); CART (cocaine- and amphetamine-regulated transcript) is NOT a human marker (0% CART+) but is present in rodent viscerofugal neurons.
References:
UBERON Terms:
Parent CL Terms:
Import Flags: None
Synonyms:
Term 5: Ascending interneuron of myenteric plexus
Preferred Label: ascending interneuron of myenteric plexus
Definition: An interneuron of the myenteric plexus whose axon projects orally (in the ascending direction) along the gut axis. This neuron is immunopositive for choline acetyltransferase (ChAT) and enkephalin (ENK), and forms the excitatory limb of ascending reflex pathways that coordinate peristalsis.
References:
UBERON Terms:
Parent CL Terms:
Import Flags: None
Synonyms:
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