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Stomatogastric ganglion crab lobster #3445

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merged 11 commits into from
Dec 19, 2024
Merged

Stomatogastric ganglion crab lobster #3445

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6ba77a5
new_changes
stevevanhooser Nov 27, 2024
3d796fd
added nerves to new_changes
andreagaede Dec 9, 2024
ba77a5d
Update new_changes.txt
stevewds Dec 11, 2024
45eea71
integrated new changes
stevevanhooser Dec 12, 2024
083d922
moving edits to uberon-edit.obo, making 6005096 is_a 8910000
stevevanhooser Dec 16, 2024
34b032e
Merge branch 'master' into stomatogastric_ganglion_crab_lobster
stevevanhooser Dec 16, 2024
a365958
removed special characters
stevevanhooser Dec 17, 2024
80c52e9
Merge branch 'stomatogastric_ganglion_crab_lobster' of https://github…
stevevanhooser Dec 17, 2024
2eaf985
fixed ID used twice, incomplete synonym statements, typo
stevevanhooser Dec 17, 2024
e97f859
fixed error in is_a command
stevevanhooser Dec 18, 2024
82772a4
changed double part_of statements to overlaps
stevevanhooser Dec 18, 2024
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168 changes: 168 additions & 0 deletions src/ontology/uberon-edit.obo
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Expand Up @@ -219794,6 +219794,7 @@ synonym: "stomodeal nervous system" RELATED [FlyBase:FBrf0111704]
is_a: UBERON:0011216 ! organ system subdivision
relationship: in_taxon NCBITaxon:6656 ! Arthropoda
relationship: part_of UBERON:0001017 ! central nervous system
relationship: is_a UBERON:8910000 ! stomatogastic nervous system
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[Term]
id: UBERON:6005168
Expand Down Expand Up @@ -224750,6 +224751,173 @@ is_a: UBERON:0012449 ! mechanoreceptor
relationship: dc-contributor https://orcid.org/0000-0003-2473-2313
property_value: dcterms-date "2024-06-12T13:51:05Z" xsd:string

[Term]
id: UBERON:8910000
name: stomatogastric nervous system
def: "The part of the nervous system that controls the stomach, such as in crabs, lobsters, and flies" [FlyBase:FBrf0089570, PMID:12966498, PMID:27450880, DOI:10.1016/B0-12-370878-8/00177-4]
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is_a: UBERON:0011216 ! organ system subdivision
relationship: in_taxon NCBITaxon:6656 ! Arthropoda
relationship: dc-contributor https://orcid.org/0000-0002-1909-7004

[Term]
id: UBERON:8910001
name: stomatogastric ganglion
def: "The stomatogastric ganglion (STG) consists of about 30 neurons that form two central pattern generator circuits in crustaceans. STG neurons have large soma (~50-100 um) and have complex branches. The crustacean stomach is a complex mechanical structure that grinds and filters foods. The STG contains the motor neurons that innervate the striated muscles that move the gastric mill and pyloric regions of the stomach." [PMID: 17009928]
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synonym: "STG"
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is_a: UBERON:0011216 ! organ system subdivision
relationship: part_of UBERON:8910000 ! stomatogastric nervous system
relationship: dc-contributor https://orcid.org/0000-0002-1909-7004
relationship: in_taxon NCBITaxon:6712 ! Astacidea
relationship: in_taxon NCBITaxon:6752 ! Brachyura

[Term]
id: UBERON:8910010
name: stomatogastric nerve (sensu Cancer borealis)
def: "The stomatogastric nerve (SGN) is made up of four separate nerves that emerge from the paired commissural ganglia, the superior and inferior esophageal nerves (SONs and IONs)." [DOI:10.1016/B0-12-370878-8/00177-4]
synonym: "SGN (sensu Cancer borealis)" EXACT [DOI:10.1016/B0-12-370878-8/00177-4]
is_a: UBERON:0035014 ! functional part of brain
relationship: dc-contributor https://orcid.org/0000-0002-1909-7004
relationship: in_taxon NCBITaxon:6712 ! Astacidea
relationship: in_taxon NCBITaxon:6752 ! Brachyura
relationship: part_of UBERON:8910000 ! stomatogastric nervous system

[Term]
id: UBERON:8910011
name: dorsal gastric nerve (sensu Cancer borealis)
def: "Nerve carrying dorsal gastric (DG) neurons which control the medial tooth movements in crustaceans." [PMID: 17009928]
is_a: UBERON:0035014 ! functional part of brain
relationship: dc-contributor https://orcid.org/0000-0002-1909-7004
relationship: in_taxon NCBITaxon:6712 ! Astacidea
relationship: in_taxon NCBITaxon:6752 ! Brachyura
relationship: part_of UBERON:8910000 ! stomatogastric nervous system
relationship: part_of UBERON:8910001 ! stomatogastric ganglion
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Suggested change
relationship: part_of UBERON:8910000 ! stomatogastric nervous system
relationship: part_of UBERON:8910001 ! stomatogastric ganglion
relationship: part_of UBERON:8910001 ! stomatogastric ganglion

Keep only one of the two axioms.

  • Explanation:
    If the stomatogastric ganglion is part of the stomatogastric nervous system, and another anatomical entity is part of the stomatogastric ganglion, then it is redundant to assert that the anatomical entity is also part of the stomatogastric nervous system. (The part of relationship is transitive.) Multiple classifications chains resulting from redundant assertions make the ontology difficult to edit and maintain in the long run.

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This is an interesting question we should unpack further. Many of these nerves are partially comprised of processes that originate from the stomatogastric ganglion, but then they extend far outside the ganglion around other parts of the stomatogastric nervous system. If you cut out the stomatogastric ganglion, many of these processes would still be there and would still be part of the stomatogastric nervous system.

Is there a different way we should capture the relationship?

This comment is similar for the other cases...

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This is an interesting question we should unpack further. Many of these nerves are partially comprised of processes that originate from the stomatogastric ganglion, but then they extend far outside the ganglion around other parts of the stomatogastric nervous system. If you cut out the stomatogastric ganglion, many of these processes would still be there and would still be part of the stomatogastric nervous system.

Is there a different way we should capture the relationship?

This comment is similar for the other cases...

I see. There is the RO:0002131 overlaps relationship that might capture this.


[Term]
id: UBERON:8910012
name: gastropyloric nerve (sensu Cancer borealis)
def: "Consists of gastropyloric receptor (GPR) neurons, which are stretch receptors that innervate stomach muscles in crustaceans." [PMID: 17009928, PMID: 26888106]
is_a: UBERON:0035014 ! functional part of brain
relationship: dc-contributor https://orcid.org/0000-0002-1909-7004
relationship: in_taxon NCBITaxon:6712 ! Astacidea
relationship: in_taxon NCBITaxon:6752 ! Brachyura
relationship: part_of UBERON:8910000 ! stomatogastric nervous system
relationship: part_of UBERON:8910001 ! stomatogastric ganglion
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Suggested change
relationship: part_of UBERON:8910000 ! stomatogastric nervous system
relationship: part_of UBERON:8910001 ! stomatogastric ganglion
relationship: part_of UBERON:8910001 ! stomatogastric ganglion


[Term]
id: UBERON:8910013
name: lateral gastric nerve (sensu Cancer borealis)
def: "Consists of lateral gastric (LG) neurons. The alternation between the lateral gastric neurons/medial gastric neurons and the lateral posterior gastric neurons control the movements of the lateral teeth in crustaceans." [PMID: 17009928]
is_a: UBERON:0035014 ! functional part of brain
relationship: dc-contributor https://orcid.org/0000-0002-1909-7004
relationship: in_taxon NCBITaxon:6712 ! Astacidea
relationship: in_taxon NCBITaxon:6752 ! Brachyura
relationship: part_of UBERON:8910000 ! stomatogastric nervous system
relationship: part_of UBERON:8910001 ! stomatogastric ganglion
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Suggested change
relationship: part_of UBERON:8910000 ! stomatogastric nervous system
relationship: part_of UBERON:8910001 ! stomatogastric ganglion
relationship: part_of UBERON:8910001 ! stomatogastric ganglion


[Term]
id: UBERON:8910013
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name: lateral ventricular nerve (sensu Cancer borealis)
def: "The motor axons that project into the dorsal ventricular nerve bifurcate and then project into both lateral ventricular nerves." [PMID: 10561445]
is_a: UBERON:0035014 ! functional part of brain
relationship: dc-contributor https://orcid.org/0000-0002-1909-7004
relationship: in_taxon NCBITaxon:6712 ! Astacidea
relationship: in_taxon NCBITaxon:6752 ! Brachyura
relationship: part_of UBERON:8910000 ! stomatogastric nervous system

[Term]
id: UBERON:8910014
name: pyloric nerve (sensu Cancer borealis)
def: "Innervates pyloric region of the stomach." [PMID: 2876096]
is_a: UBERON:0035014 ! functional part of brain
relationship: dc-contributor https://orcid.org/0000-0002-1909-7004
relationship: in_taxon NCBITaxon:6712 ! Astacidea
relationship: in_taxon NCBITaxon:6752 ! Brachyura
relationship: part_of UBERON:8910000 ! stomatogastric nervous system

[Term]
id: UBERON:8910015
name: pyloric dilator nerve (sensu Cancer borealis)
def: "Innervates muscles that dilate valves of the pylorus motor neurons involved in filtering in crustaceans. Anterior burster neurons are intrinsic oscillators that are electrically coupled with pyloric dilator neurons, causing them to fire bursts of action potentials. Together these neurons inhibit lateral pyloric and pyloric neurons, forcing them to fire in alternation with the pyloric dilator neurons." [PMID: 2876096, PMID: 17009928]
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is_a: UBERON:0035014 ! functional part of brain
relationship: dc-contributor https://orcid.org/0000-0002-1909-7004
relationship: in_taxon NCBITaxon:6712 ! Astacidea
relationship: in_taxon NCBITaxon:6752 ! Brachyura
relationship: part_of UBERON:8910000 ! stomatogastric nervous system

[Term]
id: UBERON:8910016
name: inferior esophageal nerve (sensu Cancer borealis)
synonym: "ION (sensu Cancer borealis)"
def: "The inferior esophageal nerve (ION) is one of the four nerves that make up the stomatogastric nerve (SGN)." [DOI:10.1016/B0-12-370878-8/00177-4]
is_a: UBERON:0035014 ! functional part of brain
relationship: dc-contributor https://orcid.org/0000-0002-1909-7004
relationship: in_taxon NCBITaxon:6712 ! Astacidea
relationship: in_taxon NCBITaxon:6752 ! Brachyura
relationship: part_of UBERON:8910010 ! stomatogastric nerve

[Term]
id: UBERON:8910017
name: superior esophageal nerve (sensu Cancer borealis)
synonym: "SON (sensu Cancer borealis)" EXACT [DOI:10.1016/B0-12-370878-8/00177-4]
def: "The superior esophageal nerve (SON) is one of the four nerves that make up the stomatogastric nerve (SGN)." [DOI:10.1016/B0-12-370878-8/00177-4]
is_a: UBERON:0035014 ! functional part of brain
relationship: dc-contributor https://orcid.org/0000-0002-1909-7004
relationship: in_taxon NCBITaxon:6712 ! Astacidea
relationship: in_taxon NCBITaxon:6752 ! Brachyura
relationship: part_of UBERON:8910010 ! stomatogastric nerve

[Term]
id: UBERON:8910018
name: esophageal nerve (sensu Cancer borealis)
def: "innervates the foregut and midgut" [DOI:10.1016/B0-12-370878-8/00177-4]
is_a: UBERON:0035014 ! functional part of brain
relationship: dc-contributor https://orcid.org/0000-0002-1909-7004
relationship: in_taxon NCBITaxon:6712 ! Astacidea
relationship: in_taxon NCBITaxon:6752 ! Brachyura
relationship: part_of UBERON:8910010 ! stomatogastric nerve

[Term]
id: UBERON:8910019
name: esophageal ganglion (sensu Cancer borealis)
def: "Neurons with cell bodies in the esophageal ganglion turn on the gastric mill rhythm and strongly affects the pyloric rhythm." [DOI:10.1016/B0-12-370878-8/00177-4]
is_a: UBERON:0035014 ! functional part of brain
relationship: dc-contributor https://orcid.org/0000-0002-1909-7004
relationship: in_taxon NCBITaxon:6712 ! Astacidea
relationship: in_taxon NCBITaxon:6752 ! Brachyura
relationship: part_of UBERON:8910000 ! stomatogastric nervous system

[Term]
id: UBERON:8910020
name: commissural ganglion (sensu Cancer borealis)
synonym: "CG (sensu Cancer borealis)"
def: "Contains motor fibers that innervate the esophagus. Stimulating the pyloric suppressor neuron alters both pyloric and gastric rhythms but also elicits activity in a third oscillatory circuit located in the commissural ganglia called the esophageal rhythm." [DOI:10.1016/b978-0-12-809324-5.21166-8]
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is_a: UBERON:0035014 ! functional part of brain
relationship: dc-contributor https://orcid.org/0000-0002-1909-7004
relationship: in_taxon NCBITaxon:6712 ! Astacidea
relationship: in_taxon NCBITaxon:6752 ! Brachyura
relationship: part_of UBERON:8910000 ! stomatogastric nervous system

[Term]
id: UBERON:8910021
name: junction of superior esophageal nerve and stomatogastric nerve (sensu Cancer borealis)
def: "The junction between the stomatogastric nerve (STN) and the superior esophageal nerve (SON) shows synaptic structures. Octopamine may be released at this site by projection neurons; its application at this junction induces action potentials in the axons of the modulatory commissural neuron 5 (MCN5) that project from the commissural ganglia to the stomatogastric ganglion (STG)." [PMID:15306640]
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is_a: UBERON:0035014 ! functional part of brain
relationship: dc-contributor https://orcid.org/0000-0002-1909-7004
relationship: in_taxon NCBITaxon:6712 ! Astacidea
relationship: in_taxon NCBITaxon:6752 ! Brachyura
relationship: part_of UBERON:8910000 ! stomatogastric nervous system

[Term]
id: UBERON:8910022
name: median ventricular nerve (sensu Cancer borealis)
synonym: "MVN (sensu Cancer borealis)"
def: "Most of the efferent fibers leaving the stomatogastric ganglion and leading to the gastric mill or pyloric stomach muscles run posteriorly in the dorsal median ventricular nerve. This nerve branches bilaterally into the right and left lateral ventricular nerves (LVN) which go to their respective sides of the stomach." [DOI:10.1016/0010-406X(70)90044-7]
is_a: UBERON:0035014 ! functional part of brain
relationship: dc-contributor https://orcid.org/0000-0002-1909-7004
relationship: in_taxon NCBITaxon:6712 ! Astacidea
relationship: in_taxon NCBITaxon:6752 ! Brachyura
relationship: part_of UBERON:8910000 ! stomatogastric nervous system

[Typedef]
id: aboral_to
name: aboral to
Expand Down