From 35029f6abd646ebf5d9d90d3713bcb28d4026d07 Mon Sep 17 00:00:00 2001 From: aleixpuig <94959119+aleixpuigb@users.noreply.github.com> Date: Fri, 24 Nov 2023 14:43:18 +0000 Subject: [PATCH 1/4] Fixes #1889 neuroendocrine cell Fixes #1889 neuroendocrine cell --- src/ontology/cl-edit.owl | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index a56732396..efb59bfd5 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -5021,11 +5021,9 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:5342440") Annotation(obo The modern definition of neurosecretion has evolved to include the release of any neuronal secretory product from a neuron.") AnnotationAssertion(rdfs:label obo:CL_0000165 "neuroendocrine cell") -EquivalentClasses(obo:CL_0000165 ObjectIntersectionOf(obo:CL_0000540 ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0046879))) +EquivalentClasses(obo:CL_0000165 ObjectIntersectionOf(obo:CL_0000163 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_8600018))) SubClassOf(obo:CL_0000165 obo:CL_0000163) SubClassOf(obo:CL_0000165 obo:CL_0000393) -SubClassOf(obo:CL_0000165 obo:CL_0000527) -SubClassOf(obo:CL_0000165 obo:CL_0000710) # Class: obo:CL_0000166 (chromaffin cell) From 9e9094620a57edf2326235e6d33bc87d2ef1f785 Mon Sep 17 00:00:00 2001 From: aleixpuig <94959119+aleixpuigb@users.noreply.github.com> Date: Fri, 24 Nov 2023 15:06:24 +0000 Subject: [PATCH 2/4] Change definition to make it broad --- src/ontology/cl-edit.owl | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index efb59bfd5..0e8f7cd09 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -5012,14 +5012,11 @@ SubClassOf(obo:CL_0000164 obo:CL_0000163) # Class: obo:CL_0000165 (neuroendocrine cell) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MESH:D055099") obo:IAO_0000115 obo:CL_0000165 "A neuron that is capable of some hormone secretion in response to neuronal signals.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MESH:D055099") Annotation(oboInOwl:hasDbXref "PMID:2675281") obo:IAO_0000115 obo:CL_0000165 "An endocrine cell that is part of the neuroendocrine system. A neuroendocrine cell secretes hormones into the circulatory system in responsse to direct neural stimuli.") AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000165 "BTO:0002691") AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000165 "FMA:83810") AnnotationAssertion(oboInOwl:hasRelatedSynonym obo:CL_0000165 "neurosecretory cell") AnnotationAssertion(oboInOwl:hasRelatedSynonym obo:CL_0000165 "neurosecretory neuron") -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:5342440") Annotation(oboInOwl:hasDbXref "https://www.clinicalkey.com/#!/content/book/3-s2.0-B9780323555968000073") rdfs:comment obo:CL_0000165 "The neurosecretory cell is neither an ordinary neuron nor an endocrine cell, but a combination of both. Its neuronal features resemble those of ordinary neurons concerning both structure and function. The production of a visible secretory material marks the neurosecretory neuron as a gland cell, and the fact that extractable cellular products act in the manner of hormones places it in the realm of endocrine elements. - -The modern definition of neurosecretion has evolved to include the release of any neuronal secretory product from a neuron.") AnnotationAssertion(rdfs:label obo:CL_0000165 "neuroendocrine cell") EquivalentClasses(obo:CL_0000165 ObjectIntersectionOf(obo:CL_0000163 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_8600018))) SubClassOf(obo:CL_0000165 obo:CL_0000163) From 546bf36dada8b91a9173bd63b3feb5cdec1e0a7d Mon Sep 17 00:00:00 2001 From: aleixpuig <94959119+aleixpuigb@users.noreply.github.com> Date: Thu, 30 Nov 2023 13:52:42 +0000 Subject: [PATCH 3/4] Fix definition --- src/ontology/cl-edit.owl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 0e8f7cd09..469fc0a7b 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -5012,7 +5012,7 @@ SubClassOf(obo:CL_0000164 obo:CL_0000163) # Class: obo:CL_0000165 (neuroendocrine cell) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MESH:D055099") Annotation(oboInOwl:hasDbXref "PMID:2675281") obo:IAO_0000115 obo:CL_0000165 "An endocrine cell that is part of the neuroendocrine system. A neuroendocrine cell secretes hormones into the circulatory system in responsse to direct neural stimuli.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "MESH:D055099") Annotation(oboInOwl:hasDbXref "PMID:2675281") obo:IAO_0000115 obo:CL_0000165 "An endocrine cell that is part of the neuroendocrine system. A neuroendocrine cell secretes hormones into the circulatory system in response to direct stimuli.") AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000165 "BTO:0002691") AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000165 "FMA:83810") AnnotationAssertion(oboInOwl:hasRelatedSynonym obo:CL_0000165 "neurosecretory cell") From 95be9afadc3aae7328d31c4b958a4fd79de3ac80 Mon Sep 17 00:00:00 2001 From: aleixpuig <94959119+aleixpuigb@users.noreply.github.com> Date: Thu, 30 Nov 2023 15:25:55 +0000 Subject: [PATCH 4/4] Fix issues coming from the removal of 'neuroendocrine cell SubClassOf neurecto-epithelial cell' --- src/ontology/cl-edit.owl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 469fc0a7b..24f2f926f 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -24807,6 +24807,7 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:33355253") oboInOwl:hasE AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:33355253") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_1000223 "PNEC") AnnotationAssertion(rdfs:label obo:CL_1000223 "lung neuroendocrine cell") EquivalentClasses(obo:CL_1000223 ObjectIntersectionOf(obo:CL_0000165 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0002048))) +SubClassOf(obo:CL_1000223 obo:CL_0000082) SubClassOf(obo:CL_1000223 obo:CL_0000206) SubClassOf(obo:CL_1000223 ObjectSomeValuesFrom(obo:BFO_0000051 obo:GO_0031045)) SubClassOf(obo:CL_1000223 ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0001820)) @@ -26042,7 +26043,6 @@ AnnotationAssertion(oboInOwl:hasDbXref obo:CL_1000426 "FMA:69794") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GO:0061104") oboInOwl:hasExactSynonym obo:CL_1000426 "adrenal chromaffin cell") AnnotationAssertion(rdfs:label obo:CL_1000426 "chromaffin cell of adrenal gland") EquivalentClasses(obo:CL_1000426 ObjectIntersectionOf(obo:CL_0000166 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0002369))) -SubClassOf(obo:CL_1000426 obo:CL_0000150) SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_1000426 obo:CL_0000166) # Class: obo:CL_1000427 (adrenal cortex chromaffin cell)