From d40720469b32ff4bde1bd63c2f8fe16c83f009f5 Mon Sep 17 00:00:00 2001 From: "alida.avola@icloud.com" Date: Mon, 21 Oct 2024 14:20:52 +0100 Subject: [PATCH 1/6] Merge CNS interneuron with interneuron Fixes #2685 --- src/ontology/cl-edit.owl | 21 ++++++++------------- 1 file changed, 8 insertions(+), 13 deletions(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index ed7137112..565b9cab2 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -44,7 +44,7 @@ Annotation(terms:contributor ) Annotation(terms:contributor ) Annotation(terms:contributor ) Annotation(terms:license ) -Annotation(rdfs:comment "See PMID:15693950, PMID:12799354, PMID:20123131, PMID:21208450; Contact Alexander Diehl, addiehl@buffalo.edu, university at buffalo.") +Annotation(rdfs:comment "See PMID:15693950, PMID:12799354, PMID:20123131, PMID:21208450; Contact Alexander Diehl, addiehl"@buffalo.edu, university at buffalo.) Declaration(Class(obo:CL_0000000)) Declaration(Class(obo:CL_0000001)) @@ -448,7 +448,6 @@ Declaration(Class(obo:CL_0000398)) Declaration(Class(obo:CL_0000399)) Declaration(Class(obo:CL_0000400)) Declaration(Class(obo:CL_0000401)) -Declaration(Class(obo:CL_0000402)) Declaration(Class(obo:CL_0000403)) Declaration(Class(obo:CL_0000404)) Declaration(Class(obo:CL_0000405)) @@ -4520,11 +4519,14 @@ SubClassOf(obo:CL_0000098 obo:CL_0000197) # Class: obo:CL_0000099 (interneuron) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1016/B978-0-12-817424-1.00001-X") obo:IAO_0000115 obo:CL_0000099 "An interneuron that has its cell body in a central nervous system.") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:tfm") Annotation(oboInOwl:hasDbXref "MESH:D007395") obo:IAO_0000115 obo:CL_0000099 "Most generally any neuron which is not motor or sensory. Interneurons may also refer to neurons whose axons remain within a particular brain region as contrasted with projection neurons which have axons projecting to other brain regions.") AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000099 "BTO:0003811") AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000099 "FMA:67313") AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000099 "WBbt:0005113") +AnnotationAssertion(oboInOwl:hasRelatedSynonym obo:CL_0000099 "CNS interneuron") AnnotationAssertion(rdfs:label obo:CL_0000099 "interneuron") +EquivalentClasses(obo:CL_0000099 ObjectIntersectionOf(obo:CL_0000099 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0001017))) SubClassOf(obo:CL_0000099 obo:CL_0000540) # Class: obo:CL_0000100 (motor neuron) @@ -6980,13 +6982,6 @@ AnnotationAssertion(rdfs:comment obo:CL_0000401 "Obsoleted as plasmatocytes are AnnotationAssertion(rdfs:label obo:CL_0000401 "obsolete macrophage (sensu Diptera)") AnnotationAssertion(owl:deprecated obo:CL_0000401 "true"^^xsd:boolean) -# Class: obo:CL_0000402 (CNS interneuron) - -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1016/B978-0-12-817424-1.00001-X") obo:IAO_0000115 obo:CL_0000402 "An interneuron that has its cell body in a central nervous system.") -AnnotationAssertion(rdfs:comment obo:CL_0000402 "Interneurons are commonly described as being only found in the central nervous system. However, in CL we define 'interneuron' more broadly as any neuron that is neither a motor neuron nor a sensory neuron, regardless of its location, so we need this term to refer strictly to interneurons of the central nervous system.") -AnnotationAssertion(rdfs:label obo:CL_0000402 "CNS interneuron") -EquivalentClasses(obo:CL_0000402 ObjectIntersectionOf(obo:CL_0000099 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0001017))) - # Class: obo:CL_0000403 (obo:CL_0000403) AnnotationAssertion(obo:IAO_0000231 obo:CL_0000403 obo:IAO_0000227) @@ -7009,7 +7004,7 @@ AnnotationAssertion(owl:deprecated obo:CL_0000405 "true"^^xsd:boolean) # Class: obo:CL_0000406 (CNS short range interneuron) AnnotationAssertion(rdfs:label obo:CL_0000406 "CNS short range interneuron") -SubClassOf(obo:CL_0000406 obo:CL_0000402) +SubClassOf(obo:CL_0000406 obo:CL_0000099) # Class: obo:CL_0000407 (scolopidial ligament cell) @@ -7037,7 +7032,7 @@ AnnotationAssertion(owl:deprecated obo:CL_0000409 "true"^^xsd:boolean) # Class: obo:CL_0000410 (CNS long range interneuron) AnnotationAssertion(rdfs:label obo:CL_0000410 "CNS long range interneuron") -SubClassOf(obo:CL_0000410 obo:CL_0000402) +SubClassOf(obo:CL_0000410 obo:CL_0000099) # Class: obo:CL_0000411 (Caenorhabditis hypodermal cell) @@ -21287,7 +21282,7 @@ AnnotationAssertion(oboInOwl:hasOBONamespace obo:CL_0004001 "cell") AnnotationAssertion(oboInOwl:id obo:CL_0004001 "CL:0004001") AnnotationAssertion(rdfs:comment obo:CL_0004001 "Local interneurons form the category of interneurons whose axon stays entirely within the gray matter region where the cell body resides (Swanson, 2003, p. 245; Bota and Swanson, 2007, Fig. 3).") AnnotationAssertion(rdfs:label obo:CL_0004001 "local interneuron") -SubClassOf(obo:CL_0004001 obo:CL_0000402) +SubClassOf(obo:CL_0004001 obo:CL_0000099) SubClassOf(obo:CL_0004001 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0002020)) # Class: obo:CL_0004115 (retinal ganglion cell B) @@ -21956,7 +21951,7 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "CL:CVS") obo:IAO_0000115 obo: AnnotationAssertion(rdfs:comment obo:CL_0005000 "Is_a interneuron, part_of UBERON:0002240.") AnnotationAssertion(rdfs:label obo:CL_0005000 "spinal cord interneuron") EquivalentClasses(obo:CL_0005000 ObjectIntersectionOf(obo:CL_0000099 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0002240))) -SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_0005000 obo:CL_0000402) +SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_0005000 obo:CL_0000099) # Class: obo:CL_0005001 (iridoblast) From 43a63ecaca993d49d2047d7a613d9d84936f4440 Mon Sep 17 00:00:00 2001 From: "alida.avola@icloud.com" Date: Mon, 21 Oct 2024 14:21:39 +0100 Subject: [PATCH 2/6] merge CNS interneuron Fixes #2685 --- src/ontology/components/mappings.owl | 18 ++++++++---------- 1 file changed, 8 insertions(+), 10 deletions(-) diff --git a/src/ontology/components/mappings.owl b/src/ontology/components/mappings.owl index 38aa1c55c..ba5dc156c 100644 --- a/src/ontology/components/mappings.owl +++ b/src/ontology/components/mappings.owl @@ -645,6 +645,7 @@ FBbt:00005125 ZFA:0009051 + ZFA:0009191 @@ -658,6 +659,12 @@ ZFA:0009051 + + + + ZFA:0009191 + + FBbt:00005123 ZFA:0009052 @@ -2006,15 +2013,6 @@ FBbt:00001687 - - ZFA:0009191 - - - - - ZFA:0009191 - - ZFA:0009193 @@ -4563,5 +4561,5 @@ - + From 45571e780328c9e68eb176f516543e815f9a8eb3 Mon Sep 17 00:00:00 2001 From: "alida.avola@icloud.com" Date: Mon, 21 Oct 2024 14:35:42 +0100 Subject: [PATCH 3/6] Update cl-edit.owl --- 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 565b9cab2..cfdb25aaa 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -44,7 +44,7 @@ Annotation(terms:contributor ) Annotation(terms:contributor ) Annotation(terms:contributor ) Annotation(terms:license ) -Annotation(rdfs:comment "See PMID:15693950, PMID:12799354, PMID:20123131, PMID:21208450; Contact Alexander Diehl, addiehl"@buffalo.edu, university at buffalo.) +Annotation(rdfs:comment "See PMID:15693950, PMID:12799354, PMID:20123131, PMID:21208450; Contact Alexander Diehl, addiehl@buffalo.edu, university at buffalo.") Declaration(Class(obo:CL_0000000)) Declaration(Class(obo:CL_0000001)) From 6de601c51f8c5f0a5f5d0061da2c8253d5126a8a Mon Sep 17 00:00:00 2001 From: "alida.avola@icloud.com" Date: Mon, 28 Oct 2024 11:45:33 +0000 Subject: [PATCH 4/6] Update cl-edit.owl --- 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 cfdb25aaa..879fb4d20 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -4526,7 +4526,7 @@ AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000099 "FMA:67313") AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000099 "WBbt:0005113") AnnotationAssertion(oboInOwl:hasRelatedSynonym obo:CL_0000099 "CNS interneuron") AnnotationAssertion(rdfs:label obo:CL_0000099 "interneuron") -EquivalentClasses(obo:CL_0000099 ObjectIntersectionOf(obo:CL_0000099 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0001017))) +EquivalentClasses(obo:CL_0000099 ObjectIntersectionOf(obo:CL_0000540 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0001017))) SubClassOf(obo:CL_0000099 obo:CL_0000540) # Class: obo:CL_0000100 (motor neuron) From a519da2060c840f5889a931b84126cff7bf578e0 Mon Sep 17 00:00:00 2001 From: "alida.avola@icloud.com" Date: Mon, 28 Oct 2024 12:01:22 +0000 Subject: [PATCH 5/6] Update cl-edit.owl --- src/ontology/cl-edit.owl | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index c38ce7f16..b1904fa3a 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -4531,8 +4531,8 @@ AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000099 "FMA:67313") AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000099 "WBbt:0005113") AnnotationAssertion(oboInOwl:hasRelatedSynonym obo:CL_0000099 "CNS interneuron") AnnotationAssertion(rdfs:label obo:CL_0000099 "interneuron") -EquivalentClasses(obo:CL_0000099 ObjectIntersectionOf(obo:CL_0000540 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0001017))) SubClassOf(obo:CL_0000099 obo:CL_0000540) +SubClassOf(obo:CL_0000099 ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_0001017)) # Class: obo:CL_0000100 (motor neuron) @@ -5120,8 +5120,8 @@ AnnotationAssertion(owl:deprecated obo:CL_0000161 "true"^^xsd:boolean) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:tfm") Annotation(oboInOwl:hasDbXref "ISBN:0517223651") Annotation(oboInOwl:hasDbXref "PMID:31613538") Annotation(oboInOwl:hasDbXref "PMID:31670611") obo:IAO_0000115 obo:CL_0000162 "An epithelial cell of the stomach that is part of the fundic gastric gland. This cell is characterized by its pyramidal shape, abundant mitochondria, and a complex network of secretory canaliculi lined with microvilli. It secretes hydrochloric acid into the stomach lumen and produces intrinsic factor, essential for vitamin B12 absorption.") AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000162 "BTO:0001780") AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000162 "FMA:62901") -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "Wikipedia:Parietal_cell") oboInOwl:hasExactSynonym obo:CL_0000162 "oxyntic cell") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:29263912") oboInOwl:hasExactSynonym obo:CL_0000162 "gastric parietal cell") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "Wikipedia:Parietal_cell") oboInOwl:hasExactSynonym obo:CL_0000162 "oxyntic cell") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:29263912") Annotation(oboInOwl:hasDbXref "PMID:31613538") rdfs:comment obo:CL_0000162 "Parietal cells have dynamic, actin-supported microvilli that increase in number during active secretion, playing a crucial role in secreting hydrochloric acid and intrinsic factor. The structure and regulation of these microvilli are influenced by proteins such as ASAP3, which modulates Arf6 activity and actin assembly, thereby controlling microvilli formation and parietal cell function.") AnnotationAssertion(rdfs:label obo:CL_0000162 "parietal cell") SubClassOf(obo:CL_0000162 obo:CL_0000151) @@ -28008,8 +28008,8 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "HPA:HPA") Annotation(oboInOwl AnnotationAssertion(oboInOwl:hasDbXref obo:CL_1001591 "CALOHA:TS-1277") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "CALOHA:TS-1277") oboInOwl:hasRelatedSynonym obo:CL_1001591 "fallopian tube glandular cell") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "CALOHA:TS-1277") oboInOwl:hasRelatedSynonym obo:CL_1001591 "fallopian tube glandular cells") -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "CALOHA:TS-1277") oboInOwl:hasRelatedSynonym obo:CL_1001591 "uterine tube glandular cell") AnnotationAssertion(oboInOwl:hasRelatedSynonym obo:CL_1001591 "oviduct glandular cell") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "CALOHA:TS-1277") oboInOwl:hasRelatedSynonym obo:CL_1001591 "uterine tube glandular cell") AnnotationAssertion(rdfs:label obo:CL_1001591 "oviduct secretory cell") EquivalentClasses(obo:CL_1001591 ObjectIntersectionOf(obo:CL_1100001 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0000993))) SubClassOf(obo:CL_1001591 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0004804)) From 2333d58661f6115e5085559cb315896c5e3d3a2e Mon Sep 17 00:00:00 2001 From: "alida.avola@icloud.com" Date: Mon, 28 Oct 2024 12:10:14 +0000 Subject: [PATCH 6/6] Fixing QC fail --- src/ontology/cl-edit.owl | 2 -- src/ontology/components/hra_subset.owl | 9 +++++++++ 2 files changed, 9 insertions(+), 2 deletions(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index b1904fa3a..92de4ac3d 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -4524,7 +4524,6 @@ SubClassOf(obo:CL_0000098 obo:CL_0000197) # Class: obo:CL_0000099 (interneuron) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1016/B978-0-12-817424-1.00001-X") obo:IAO_0000115 obo:CL_0000099 "An interneuron that has its cell body in a central nervous system.") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:tfm") Annotation(oboInOwl:hasDbXref "MESH:D007395") obo:IAO_0000115 obo:CL_0000099 "Most generally any neuron which is not motor or sensory. Interneurons may also refer to neurons whose axons remain within a particular brain region as contrasted with projection neurons which have axons projecting to other brain regions.") AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000099 "BTO:0003811") AnnotationAssertion(oboInOwl:hasDbXref obo:CL_0000099 "FMA:67313") @@ -25622,7 +25621,6 @@ SubClassOf(obo:CL_1000346 obo:CL_0002071) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:tfm") obo:IAO_0000115 obo:CL_1000347 "A columnar cell of the colon that is part of the colonic epithelium.") AnnotationAssertion(oboInOwl:hasDbXref obo:CL_1000347 "FMA:263114") -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:34497389") oboInOwl:hasExactSynonym obo:CL_1000347 "colonocyte") AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_1000347 "enterocyte of colon") AnnotationAssertion(oboInOwl:hasNarrowSynonym obo:CL_1000347 "vacuolar absorptive cell of epithelium of colon") AnnotationAssertion(rdfs:label obo:CL_1000347 "colonocyte") diff --git a/src/ontology/components/hra_subset.owl b/src/ontology/components/hra_subset.owl index 9adfdda14..1f692515d 100644 --- a/src/ontology/components/hra_subset.owl +++ b/src/ontology/components/hra_subset.owl @@ -23,6 +23,12 @@ + + + + + + @@ -553,8 +559,11 @@ + + https://github.com/obophenotype/cell-ontology/pull/2686 + true