From ed03865692cb85653692c64c21e48a76592970b5 Mon Sep 17 00:00:00 2001 From: Damien Goutte-Gattat Date: Mon, 23 Dec 2024 11:23:53 +0000 Subject: [PATCH 1/4] Fix TC violations on crustacean nerves. Recently introduced terms describing some crustacean nerves have been asserted to be simultaneously 'in_taxon some Astacidea' and 'in_taxon some Brachyura'. Astacidea (NCBITaxon:6712) and Brachyura (NCBITaxon:6725) are *sibling* taxa, so such assertions are contradicting each other: a term that is 'in_taxon some Astacidae' or it is 'in_taxon some Brachyura', but it cannot be 'in_taxon' both taxa simultaneously. Remember that 'in_taxon some X' means that the term is *specific to the X taxon*, exclusive of any other taxon that is not X itself or a descendant of X. Assuming that the terms refer to nerves that are in fact present both in Astacidea and Brachyura, we replace for all affected terms the faulty 'in_taxon' assertions by a single assertion 'in_taxon some Pleocyemata', where Pleocyemata (NCBITaxon:6692) is the parent taxon of both Astacidea and Brachyura. We also explicitly import NCBITaxon:6692, since it is used in those assertions. --- src/ontology/imports/ncbitaxon_terms.txt | 1 + src/ontology/uberon-edit.obo | 45 ++++++++---------------- 2 files changed, 16 insertions(+), 30 deletions(-) diff --git a/src/ontology/imports/ncbitaxon_terms.txt b/src/ontology/imports/ncbitaxon_terms.txt index 6812f79f1c..d841574cc8 100644 --- a/src/ontology/imports/ncbitaxon_terms.txt +++ b/src/ontology/imports/ncbitaxon_terms.txt @@ -108,6 +108,7 @@ NCBITaxon:65997 NCBITaxon:6656 NCBITaxon:6657 NCBITaxon:6681 +NCBITaxon:6692 NCBITaxon:6830 NCBITaxon:6843 NCBITaxon:70846 diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index b54fec4d5d..c8688e472f 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -224773,8 +224773,7 @@ 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 -relationship: in_taxon NCBITaxon:6712 ! Astacidea -relationship: in_taxon NCBITaxon:6752 ! Brachyura +relationship: in_taxon NCBITaxon:6692 ! Pleocyemata [Term] id: UBERON:8910010 @@ -224783,8 +224782,7 @@ def: "The stomatogastric nerve (SGN) is made up of four separate nerves that eme 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: in_taxon NCBITaxon:6692 ! Pleocyemata relationship: part_of UBERON:8910000 ! stomatogastric nervous system [Term] @@ -224793,8 +224791,7 @@ 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: in_taxon NCBITaxon:6692 ! Pleocyemata relationship: part_of UBERON:8910000 ! stomatogastric nervous system relationship: overlaps UBERON:8910001 ! stomatogastric ganglion @@ -224804,8 +224801,7 @@ 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: in_taxon NCBITaxon:6692 ! Pleocyemata relationship: part_of UBERON:8910000 ! stomatogastric nervous system relationship: overlaps UBERON:8910001 ! stomatogastric ganglion @@ -224815,8 +224811,7 @@ 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: in_taxon NCBITaxon:6692 ! Pleocyemata relationship: part_of UBERON:8910000 ! stomatogastric nervous system relationship: overlaps UBERON:8910001 ! stomatogastric ganglion @@ -224826,8 +224821,7 @@ 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: in_taxon NCBITaxon:6692 ! Pleocyemata relationship: part_of UBERON:8910000 ! stomatogastric nervous system [Term] @@ -224836,8 +224830,7 @@ 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: in_taxon NCBITaxon:6692 ! Pleocyemata relationship: part_of UBERON:8910000 ! stomatogastric nervous system [Term] @@ -224846,8 +224839,7 @@ 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: in_taxon NCBITaxon:6692 ! Pleocyemata relationship: part_of UBERON:8910000 ! stomatogastric nervous system [Term] @@ -224857,8 +224849,7 @@ 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 -relationship: in_taxon NCBITaxon:6712 ! Astacidea -relationship: in_taxon NCBITaxon:6752 ! Brachyura +relationship: in_taxon NCBITaxon:6692 ! Pleocyemata relationship: part_of UBERON:8910010 ! stomatogastric nerve [Term] @@ -224868,8 +224859,7 @@ 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: in_taxon NCBITaxon:6692 ! Pleocyemata relationship: part_of UBERON:8910010 ! stomatogastric nerve [Term] @@ -224878,8 +224868,7 @@ 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: in_taxon NCBITaxon:6692 ! Pleocyemata relationship: part_of UBERON:8910010 ! stomatogastric nerve [Term] @@ -224888,8 +224877,7 @@ 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: in_taxon NCBITaxon:6692 ! Pleocyemata relationship: part_of UBERON:8910000 ! stomatogastric nervous system [Term] @@ -224899,8 +224887,7 @@ synonym: "CG (sensu Cancer borealis)" EXACT [DOI:10.1016/b978-0-12-809324-5.2116 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: in_taxon NCBITaxon:6692 ! Pleocyemata relationship: part_of UBERON:8910000 ! stomatogastric nervous system [Term] @@ -224909,8 +224896,7 @@ name: junction of superior esophageal nerve and stomatogastric nerve (sensu Canc 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: in_taxon NCBITaxon:6692 ! Pleocyemata relationship: part_of UBERON:8910000 ! stomatogastric nervous system [Term] @@ -224920,8 +224906,7 @@ 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 -relationship: in_taxon NCBITaxon:6712 ! Astacidea -relationship: in_taxon NCBITaxon:6752 ! Brachyura +relationship: in_taxon NCBITaxon:6692 ! Pleocyemata relationship: part_of UBERON:8910000 ! stomatogastric nervous system [Typedef] From 2a1c6eb050cd0f6fe70b9dbe59db0e56e3ccc538 Mon Sep 17 00:00:00 2001 From: Damien Goutte-Gattat Date: Mon, 23 Dec 2024 12:09:35 +0000 Subject: [PATCH 2/4] Refresh imports. --- src/ontology/imports/merged_import.owl | 45 ++++++++++++++++++++++++-- 1 file changed, 42 insertions(+), 3 deletions(-) diff --git a/src/ontology/imports/merged_import.owl b/src/ontology/imports/merged_import.owl index a578df3609..b60cdc2070 100644 --- a/src/ontology/imports/merged_import.owl +++ b/src/ontology/imports/merged_import.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2024-12-17") + +Annotation(owl:versionInfo "2024-12-23") Declaration(Class()) Declaration(Class()) @@ -10138,6 +10138,9 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -10149,6 +10152,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -12515,7 +12519,6 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -147264,6 +147267,30 @@ AnnotationAssertion(rdfs:label " SubClassOf( ) DisjointClasses( ) +# Class: (Eucarida) + +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:6682") +AnnotationAssertion(rdfs:label "Eucarida") +SubClassOf( ) + +# Class: (Decapoda) + +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:6683") +AnnotationAssertion(rdfs:label "Decapoda") +SubClassOf( ) + +# Class: (Pleocyemata) + +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:6692") +AnnotationAssertion(rdfs:label "Pleocyemata") +SubClassOf( ) + # Class: (Copepoda) AnnotationAssertion( "GC_ID:1") @@ -147369,6 +147396,14 @@ AnnotationAssertion( "Hexanauplia") SubClassOf( ) +# Class: (Eumalacostraca) + +AnnotationAssertion( "GC_ID:1") +AnnotationAssertion( "ncbi_taxonomy") +AnnotationAssertion( "NCBITaxon:72041") +AnnotationAssertion(rdfs:label "Eumalacostraca") +SubClassOf( ) + # Class: (Drosophilidae) AnnotationAssertion( "GC_ID:1") @@ -157431,6 +157466,9 @@ DisjointClasses(ObjectSomeValuesFrom( DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectComplementOf())) DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectComplementOf())) +DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectComplementOf())) +DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectComplementOf())) +DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectComplementOf())) DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectComplementOf())) DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectComplementOf())) DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectComplementOf())) @@ -157444,6 +157482,7 @@ DisjointClasses(ObjectSomeValuesFrom( DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectComplementOf())) DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectComplementOf())) DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectComplementOf())) +DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectComplementOf())) DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectComplementOf())) DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectComplementOf())) DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectComplementOf())) From c993a1774e42b0e275384528e0021bdea0444447 Mon Sep 17 00:00:00 2001 From: Damien Goutte-Gattat Date: Mon, 23 Dec 2024 12:12:47 +0000 Subject: [PATCH 3/4] Re-serialise edit file. The -edit file contained some weirdly formatted line with trailing spaces, some tags improperly ordered, and some incorrectly formatted xrefs (possibly the result of some manual editing with a text editor?), so we re-serialize it. --- src/ontology/uberon-edit.obo | 48 ++++++++++++++++++------------------ 1 file changed, 24 insertions(+), 24 deletions(-) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index c8688e472f..822c599ec8 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -63168,7 +63168,7 @@ intersection_of: UBERON:0004130 ! cerebellar layer intersection_of: in_deep_part_of UBERON:0002129 ! cerebellar cortex relationship: has_part CL:0000119 ! cerebellar Golgi cell relationship: has_part CL:0001031 ! cerebellar granule cell -relationship: has_part CL:4023161 +relationship: has_part CL:4023161 ! unipolar brush cell relationship: mutually_spatially_disjoint_with UBERON:0002979 {source="ABA"} ! Purkinje cell layer of cerebellar cortex [Term] @@ -219789,9 +219789,9 @@ def: "A group of small, interconnected ganglia situated posterior to and between synonym: "stomodaeal nervous system" RELATED [FlyBase:FBrf0111704] synonym: "stomodeal nervous system" RELATED [FlyBase:FBrf0111704] is_a: UBERON:0011216 ! organ system subdivision +is_a: UBERON:8910000 ! stomatogastric nervous system relationship: in_taxon NCBITaxon:6656 ! Arthropoda relationship: part_of UBERON:0001017 ! central nervous system -is_a: UBERON:8910000 ! stomatogastric nervous system [Term] id: UBERON:6005168 @@ -224760,27 +224760,27 @@ 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" [DOI:10.1016/B0-12-370878-8/00177-4, FlyBase:FBrf0089570, PMID:12966498, PMID:27450880] is_a: UBERON:0011216 ! organ system subdivision -relationship: in_taxon NCBITaxon:6656 ! Arthropoda relationship: dc-contributor https://orcid.org/0000-0002-1909-7004 +relationship: in_taxon NCBITaxon:6656 ! Arthropoda [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 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] +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 relationship: dc-contributor https://orcid.org/0000-0002-1909-7004 relationship: in_taxon NCBITaxon:6692 ! Pleocyemata +relationship: part_of UBERON:8910000 ! stomatogastric nervous system [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 +is_a: UBERON:0035014 ! functional part of brain relationship: dc-contributor https://orcid.org/0000-0002-1909-7004 relationship: in_taxon NCBITaxon:6692 ! Pleocyemata relationship: part_of UBERON:8910000 ! stomatogastric nervous system @@ -224788,37 +224788,37 @@ 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] +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:6692 ! Pleocyemata -relationship: part_of UBERON:8910000 ! stomatogastric nervous system relationship: overlaps UBERON:8910001 ! stomatogastric ganglion +relationship: part_of UBERON:8910000 ! stomatogastric nervous system [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:6692 ! Pleocyemata -relationship: part_of UBERON:8910000 ! stomatogastric nervous system relationship: overlaps UBERON:8910001 ! stomatogastric ganglion +relationship: part_of UBERON:8910000 ! stomatogastric nervous system [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] +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:6692 ! Pleocyemata -relationship: part_of UBERON:8910000 ! stomatogastric nervous system relationship: overlaps UBERON:8910001 ! stomatogastric ganglion +relationship: part_of UBERON:8910000 ! stomatogastric nervous system [Term] 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] +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:6692 ! Pleocyemata @@ -224827,7 +224827,7 @@ relationship: part_of UBERON:8910000 ! stomatogastric nervous system [Term] id: UBERON:8910015 name: pyloric nerve (sensu Cancer borealis) -def: "Innervates pyloric region of the stomach." [PMID: 2876096] +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:6692 ! Pleocyemata @@ -224836,7 +224836,7 @@ relationship: part_of UBERON:8910000 ! stomatogastric nervous system [Term] 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] +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:17009928, PMID:2876096] is_a: UBERON:0035014 ! functional part of brain relationship: dc-contributor https://orcid.org/0000-0002-1909-7004 relationship: in_taxon NCBITaxon:6692 ! Pleocyemata @@ -224845,22 +224845,22 @@ relationship: part_of UBERON:8910000 ! stomatogastric nervous system [Term] id: UBERON:8910017 name: inferior esophageal nerve (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] +synonym: "ION (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:6692 ! Pleocyemata -relationship: part_of UBERON:8910010 ! stomatogastric nerve +relationship: part_of UBERON:8910010 ! stomatogastric nerve (sensu Cancer borealis) [Term] 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] +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:6692 ! Pleocyemata -relationship: part_of UBERON:8910010 ! stomatogastric nerve +relationship: part_of UBERON:8910010 ! stomatogastric nerve (sensu Cancer borealis) [Term] id: UBERON:8910019 @@ -224869,7 +224869,7 @@ 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:6692 ! Pleocyemata -relationship: part_of UBERON:8910010 ! stomatogastric nerve +relationship: part_of UBERON:8910010 ! stomatogastric nerve (sensu Cancer borealis) [Term] id: UBERON:8910020 @@ -224883,8 +224883,8 @@ relationship: part_of UBERON:8910000 ! stomatogastric nervous system [Term] id: UBERON:8910021 name: commissural ganglion (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] +synonym: "CG (sensu Cancer borealis)" EXACT [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:6692 ! Pleocyemata @@ -224902,8 +224902,8 @@ relationship: part_of UBERON:8910000 ! stomatogastric nervous system [Term] id: UBERON:8910023 name: median ventricular nerve (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] +synonym: "MVN (sensu Cancer borealis)" EXACT [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:6692 ! Pleocyemata From ded52d22c2a7153e08a5ed9d5dce9dbf3ee10f9e Mon Sep 17 00:00:00 2001 From: Damien Goutte-Gattat Date: Mon, 23 Dec 2024 17:14:22 +0000 Subject: [PATCH 4/4] Mark synonyms as abbreviations where appropriate. Since STG is an abbreviation for "stomatogastric ganglion", it is more appropriate to make it a RELATED synonym (rather than an EXACT synonym), and to explicitly flag it with the "abbreviation" (OMO:0003000) synonym type (as per the Uberon editor SOP). Likewise for similar abbreviations on crustacean nerves. --- 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 822c599ec8..b145789506 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -224769,7 +224769,7 @@ relationship: in_taxon NCBITaxon:6656 ! Arthropoda 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 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] +synonym: "STG" RELATED OMO:0003000 [PMID:17009928] is_a: UBERON:0011216 ! organ system subdivision relationship: dc-contributor https://orcid.org/0000-0002-1909-7004 relationship: in_taxon NCBITaxon:6692 ! Pleocyemata