From 6ba77a5f1f96cff8e64dcd25884cb551e8fce23a Mon Sep 17 00:00:00 2001 From: Steve Van Hooser Date: Tue, 26 Nov 2024 20:36:18 -0500 Subject: [PATCH 1/9] new_changes --- new_changes.txt | 19 +++++++++++++++++++ uberon.obo | 1 + 2 files changed, 20 insertions(+) create mode 100644 new_changes.txt diff --git a/new_changes.txt b/new_changes.txt new file mode 100644 index 000000000..4fc697f70 --- /dev/null +++ b/new_changes.txt @@ -0,0 +1,19 @@ +[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, DOI:10.1016/B0-12-370878-8/00177-4] +is_a: UBERON:0011216 ! organ system subdivision +relationship: in_taxon NCBITaxon:6656 ! Arthropoda + +[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: "SON (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 ganglion + + diff --git a/uberon.obo b/uberon.obo index 287389a1c..b902ed1f2 100755 --- a/uberon.obo +++ b/uberon.obo @@ -421075,6 +421075,7 @@ is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0011216 ! organ system subdivision relationship: in_taxon NCBITaxon:6656 ! Arthropoda relationship: part_of UBERON:0001017 ! central nervous system +relationship: part_of UBERON:8910000 ! stomatogastic nervous system [Term] id: UBERON:6005168 From 3d796fd48102c33b90b746c12a2c70743510c2d0 Mon Sep 17 00:00:00 2001 From: Dre Date: Mon, 9 Dec 2024 12:13:12 +0000 Subject: [PATCH 2/9] added nerves to new_changes --- new_changes.txt | 171 +++++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 169 insertions(+), 2 deletions(-) diff --git a/new_changes.txt b/new_changes.txt index 4fc697f70..3c5d9eaf6 100644 --- a/new_changes.txt +++ b/new_changes.txt @@ -1,19 +1,186 @@ [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, DOI:10.1016/B0-12-370878-8/00177-4] +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] 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 ∼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] +synonym: "STG" +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:8910001 ! stomatogastric ganglion + + +[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:8910001 ! stomatogastric ganglion + + +[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: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:8910001 ! stomatogastric ganglion + + +[Term] +id: UBERON:8910013 +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:8910001 ! stomatogastric ganglion + + +[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:8910001 ! stomatogastric ganglion + + + +[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] +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:8910001 ! stomatogastric ganglion + + +[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:8910001 ! stomatogastric ganglion +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:8910001 ! stomatogastric ganglion +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:8910001 ! stomatogastric ganglion +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 ganglion +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]  +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]  +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:8910001 ! stomatogastric ganglion + + +[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:8910001 ! stomatogastric ganglion + + + + From ba77a5d5d4ff5293e84c66850811fbec512bdd29 Mon Sep 17 00:00:00 2001 From: stevewds <131617804+stevewds@users.noreply.github.com> Date: Wed, 11 Dec 2024 17:28:42 -0500 Subject: [PATCH 3/9] Update new_changes.txt --- new_changes.txt | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/new_changes.txt b/new_changes.txt index 3c5d9eaf6..df08b2c0d 100644 --- a/new_changes.txt +++ b/new_changes.txt @@ -26,7 +26,7 @@ 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:8910001 ! stomatogastric ganglion +relationship: part_of UBERON:8910000 ! stomatogastric nervous system [Term] @@ -37,6 +37,7 @@ 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 relationship: part_of UBERON:8910001 ! stomatogastric ganglion @@ -48,6 +49,7 @@ 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 relationship: part_of UBERON:8910001 ! stomatogastric ganglion @@ -59,6 +61,7 @@ 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 relationship: part_of UBERON:8910001 ! stomatogastric ganglion @@ -70,7 +73,7 @@ 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:8910001 ! stomatogastric ganglion +relationship: part_of UBERON:8910000 ! stomatogastric nervous system [Term] @@ -81,7 +84,7 @@ 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:8910001 ! stomatogastric ganglion +relationship: part_of UBERON:8910000 ! stomatogastric nervous system @@ -93,7 +96,7 @@ 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:8910001 ! stomatogastric ganglion +relationship: part_of UBERON:8910000 ! stomatogastric nervous system [Term] @@ -105,7 +108,6 @@ 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:8910001 ! stomatogastric ganglion relationship: part_of UBERON:8910010 ! stomatogastric nerve @@ -118,7 +120,6 @@ 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:8910001 ! stomatogastric ganglion relationship: part_of UBERON:8910010 ! stomatogastric nerve @@ -130,7 +131,6 @@ 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:8910001 ! stomatogastric ganglion relationship: part_of UBERON:8910010 ! stomatogastric nerve @@ -165,7 +165,7 @@ 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:8910001 ! stomatogastric ganglion +relationship: part_of UBERON:8910000 ! stomatogastric nervous system [Term] @@ -177,7 +177,7 @@ 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:8910001 ! stomatogastric ganglion +relationship: part_of UBERON:8910000 ! stomatogastric nervous system From 45eea71e3f935318ca9c2fde6377a8c21fe259b0 Mon Sep 17 00:00:00 2001 From: Steve Van Hooser Date: Wed, 11 Dec 2024 19:07:14 -0500 Subject: [PATCH 4/9] integrated new changes --- new_changes.txt | 186 ------------------------------------------------ uberon.obo | 181 ++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 181 insertions(+), 186 deletions(-) delete mode 100644 new_changes.txt diff --git a/new_changes.txt b/new_changes.txt deleted file mode 100644 index df08b2c0d..000000000 --- a/new_changes.txt +++ /dev/null @@ -1,186 +0,0 @@ -[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] -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 ∼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] -synonym: "STG" -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 - - -[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 - - -[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 - - -[Term] -id: UBERON:8910013 -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] -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]  -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]  -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 - - - - - - diff --git a/uberon.obo b/uberon.obo index b902ed1f2..c11ed025b 100755 --- a/uberon.obo +++ b/uberon.obo @@ -429263,6 +429263,187 @@ 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] +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 #àº30 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] +synonym: "STG" +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 + + +[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 + + +[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 + + +[Term] +id: UBERON:8910013 +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 #Äî 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] +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]¬# +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 #Äì 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]¬# +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: BFO:0000066 name: occurs in From 083d922a27b3906d8983737b76375ccee9021d2e Mon Sep 17 00:00:00 2001 From: "Stephen D. Van Hooser" Date: Mon, 16 Dec 2024 15:32:36 -0500 Subject: [PATCH 5/9] moving edits to uberon-edit.obo, making 6005096 is_a 8910000 --- src/ontology/uberon-edit.obo | 168 ++++++++++++++++++++++++++++++++ uberon.obo | 182 ----------------------------------- 2 files changed, 168 insertions(+), 182 deletions(-) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index f1ef9ce66..980e223c8 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -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 [Term] id: UBERON:6005168 @@ -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] +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 #àº30 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] +synonym: "STG" +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 + +[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 + +[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 + +[Term] +id: UBERON:8910013 +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 #Äî 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] +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]¬# +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 #Äì 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]¬# +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 diff --git a/uberon.obo b/uberon.obo index c11ed025b..287389a1c 100755 --- a/uberon.obo +++ b/uberon.obo @@ -421075,7 +421075,6 @@ is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0011216 ! organ system subdivision relationship: in_taxon NCBITaxon:6656 ! Arthropoda relationship: part_of UBERON:0001017 ! central nervous system -relationship: part_of UBERON:8910000 ! stomatogastic nervous system [Term] id: UBERON:6005168 @@ -429263,187 +429262,6 @@ 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] -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 #àº30 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] -synonym: "STG" -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 - - -[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 - - -[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 - - -[Term] -id: UBERON:8910013 -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 #Äî 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] -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]¬# -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 #Äì 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]¬# -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: BFO:0000066 name: occurs in From a365958f1d2ee1482fea05164967a4a340884d12 Mon Sep 17 00:00:00 2001 From: "Stephen D. Van Hooser" Date: Tue, 17 Dec 2024 07:34:32 -0500 Subject: [PATCH 6/9] removed special characters --- src/ontology/uberon-edit.obo | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index 980e223c8..5dfc11089 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -224754,7 +224754,7 @@ 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] +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] is_a: UBERON:0011216 ! organ system subdivision relationship: in_taxon NCBITaxon:6656 ! Arthropoda relationship: dc-contributor https://orcid.org/0000-0002-1909-7004 @@ -224762,7 +224762,7 @@ relationship: dc-contributor https://orcid.org/0000-0002-1909-7004 [Term] id: UBERON:8910001 name: stomatogastric ganglion -def: "The stomatogastric ganglion (STG) consists of #àº30 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] +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] synonym: "STG" is_a: UBERON:0011216 ! organ system subdivision relationship: part_of UBERON:8910000 ! stomatogastric nervous system @@ -224795,7 +224795,7 @@ relationship: part_of UBERON:8910001 ! stomatogastric ganglion [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] +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 @@ -224817,7 +224817,7 @@ relationship: part_of UBERON:8910001 ! stomatogastric ganglion [Term] id: UBERON:8910013 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] +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 @@ -224837,7 +224837,7 @@ 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 #Äî 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] +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] is_a: UBERON:0035014 ! functional part of brain relationship: dc-contributor https://orcid.org/0000-0002-1909-7004 relationship: in_taxon NCBITaxon:6712 ! Astacidea @@ -224890,7 +224890,7 @@ relationship: part_of UBERON:8910000 ! stomatogastric nervous system 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]¬# +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] is_a: UBERON:0035014 ! functional part of brain relationship: dc-contributor https://orcid.org/0000-0002-1909-7004 relationship: in_taxon NCBITaxon:6712 ! Astacidea @@ -224900,7 +224900,7 @@ 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 #Äì 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]¬# +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] is_a: UBERON:0035014 ! functional part of brain relationship: dc-contributor https://orcid.org/0000-0002-1909-7004 relationship: in_taxon NCBITaxon:6712 ! Astacidea @@ -224911,7 +224911,7 @@ relationship: part_of UBERON:8910000 ! stomatogastric nervous system 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]¬# +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 From 2eaf985b56d904147fa3411e82f38dd2cf049bf5 Mon Sep 17 00:00:00 2001 From: "Stephen D. Van Hooser" Date: Tue, 17 Dec 2024 12:38:55 -0500 Subject: [PATCH 7/9] fixed ID used twice, incomplete synonym statements, typo --- src/ontology/uberon-edit.obo | 30 +++++++++++++++--------------- 1 file changed, 15 insertions(+), 15 deletions(-) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index 5dfc11089..499592a56 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -219794,7 +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 +relationship: is_a UBERON:8910000 ! stomatogastric nervous system [Term] id: UBERON:6005168 @@ -224763,7 +224763,7 @@ relationship: dc-contributor https://orcid.org/0000-0002-1909-7004 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] -synonym: "STG" +synonym: "STG" EXACT [PMID: 17009928] 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 @@ -224815,7 +224815,7 @@ relationship: part_of UBERON:8910000 ! stomatogastric nervous system relationship: part_of UBERON:8910001 ! stomatogastric ganglion [Term] -id: UBERON:8910013 +id: UBERON:8910014 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 @@ -224825,7 +224825,7 @@ relationship: in_taxon NCBITaxon:6752 ! Brachyura relationship: part_of UBERON:8910000 ! stomatogastric nervous system [Term] -id: UBERON:8910014 +id: UBERON:8910015 name: pyloric nerve (sensu Cancer borealis) def: "Innervates pyloric region of the stomach." [PMID: 2876096] is_a: UBERON:0035014 ! functional part of brain @@ -224835,7 +224835,7 @@ relationship: in_taxon NCBITaxon:6752 ! Brachyura relationship: part_of UBERON:8910000 ! stomatogastric nervous system [Term] -id: UBERON:8910015 +id: UBERON:8910016 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] is_a: UBERON:0035014 ! functional part of brain @@ -224845,9 +224845,9 @@ relationship: in_taxon NCBITaxon:6752 ! Brachyura relationship: part_of UBERON:8910000 ! stomatogastric nervous system [Term] -id: UBERON:8910016 +id: UBERON:8910017 name: inferior esophageal nerve (sensu Cancer borealis) -synonym: "ION (sensu Cancer borealis)" +synonym: "ION (sensu Cancer borealis)" EXACT [DOI:10.1016/B0-12-370878-8/00177-4] 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 @@ -224856,7 +224856,7 @@ relationship: in_taxon NCBITaxon:6752 ! Brachyura relationship: part_of UBERON:8910010 ! stomatogastric nerve [Term] -id: UBERON:8910017 +id: UBERON:8910018 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] @@ -224867,7 +224867,7 @@ relationship: in_taxon NCBITaxon:6752 ! Brachyura relationship: part_of UBERON:8910010 ! stomatogastric nerve [Term] -id: UBERON:8910018 +id: UBERON:8910019 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 @@ -224877,7 +224877,7 @@ relationship: in_taxon NCBITaxon:6752 ! Brachyura relationship: part_of UBERON:8910010 ! stomatogastric nerve [Term] -id: UBERON:8910019 +id: UBERON:8910020 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 @@ -224887,9 +224887,9 @@ relationship: in_taxon NCBITaxon:6752 ! Brachyura relationship: part_of UBERON:8910000 ! stomatogastric nervous system [Term] -id: UBERON:8910020 +id: UBERON:8910021 name: commissural ganglion (sensu Cancer borealis) -synonym: "CG (sensu Cancer borealis)" +synonym: "CG (sensu Cancer borealis)" EXACT [DOI:10.1016/b978-0-12-809324-5.21166-8] 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] is_a: UBERON:0035014 ! functional part of brain relationship: dc-contributor https://orcid.org/0000-0002-1909-7004 @@ -224898,7 +224898,7 @@ relationship: in_taxon NCBITaxon:6752 ! Brachyura relationship: part_of UBERON:8910000 ! stomatogastric nervous system [Term] -id: UBERON:8910021 +id: UBERON:8910022 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] is_a: UBERON:0035014 ! functional part of brain @@ -224908,9 +224908,9 @@ relationship: in_taxon NCBITaxon:6752 ! Brachyura relationship: part_of UBERON:8910000 ! stomatogastric nervous system [Term] -id: UBERON:8910022 +id: UBERON:8910023 name: median ventricular nerve (sensu Cancer borealis) -synonym: "MVN (sensu Cancer borealis)" +synonym: "MVN (sensu Cancer borealis)" EXACT [DOI:10.1016/0010-406X(70)90044-7] 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 From e97f859f01eac66360fbc88a48e74e0cfc593cf7 Mon Sep 17 00:00:00 2001 From: Steve Van Hooser Date: Wed, 18 Dec 2024 10:56:42 -0500 Subject: [PATCH 8/9] fixed error in is_a command --- src/ontology/uberon-edit.obo | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index 499592a56..cfdc6c856 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -219794,7 +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 ! stomatogastric nervous system +is_a: UBERON:8910000 ! stomatogastric nervous system [Term] id: UBERON:6005168 From 82772a464ac762c73eff61683b3624bc98bab481 Mon Sep 17 00:00:00 2001 From: Steve Van Hooser Date: Wed, 18 Dec 2024 18:41:03 -0500 Subject: [PATCH 9/9] changed double part_of statements to overlaps --- src/ontology/uberon-edit.obo | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index cfdc6c856..fd8a922c7 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -224762,7 +224762,7 @@ 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] +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 STG contains the motor neurons that innervate the striated muscles that move the gastric mill and pyloric regions of the stomach." [PMID: 17009928] synonym: "STG" EXACT [PMID: 17009928] is_a: UBERON:0011216 ! organ system subdivision relationship: part_of UBERON:8910000 ! stomatogastric nervous system @@ -224790,7 +224790,7 @@ 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 +relationship: overlaps UBERON:8910001 ! stomatogastric ganglion [Term] id: UBERON:8910012 @@ -224801,7 +224801,7 @@ 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 +relationship: overlaps UBERON:8910001 ! stomatogastric ganglion [Term] id: UBERON:8910013 @@ -224812,7 +224812,7 @@ 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 +relationship: overlaps UBERON:8910001 ! stomatogastric ganglion [Term] id: UBERON:8910014