From fb46912fead9760b16e97e13ffe86d22ab755614 Mon Sep 17 00:00:00 2001 From: "alida.avola@icloud.com" Date: Wed, 21 Aug 2024 12:38:48 +0100 Subject: [PATCH 1/4] NTR-astrocyte-restricted-precursor-and-neuronal-restricted-precursor fixes #2437 #2435 --- src/ontology/cl-edit.owl | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 97972bea6..de12fbd21 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -3058,6 +3058,8 @@ Declaration(Class(obo:CL_4042013)) Declaration(Class(obo:CL_4042014)) Declaration(Class(obo:CL_4042015)) Declaration(Class(obo:CL_4042016)) +Declaration(Class(obo:CL_4042017)) +Declaration(Class(obo:CL_4042018)) Declaration(Class(obo:CL_4052001)) Declaration(Class(obo:CL_4052002)) Declaration(Class(obo:CP_0000000)) @@ -32250,6 +32252,35 @@ SubClassOf(obo:CL_4042016 obo:CL_0000313) SubClassOf(obo:CL_4042016 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0005385)) SubClassOf(obo:CL_4042016 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0011148)) +# Class: obo:CL_4042017 (astrocyte-restricted precursor) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:15531362") Annotation(oboInOwl:hasDbXref "PMID:33052610") obo:IAO_0000115 obo:CL_4042017 "A progenitor cell of the central nervous system that differentiates exclusively onto astrocytes. This progenitor cell expresses CD44.") +AnnotationAssertion(terms:contributor obo:CL_4042017 ) +AnnotationAssertion(terms:date obo:CL_4042017 "2024-08-21T11:23:32Z"^^xsd:dateTime) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:33052610") oboInOwl:hasRelatedSynonym obo:CL_4042017 "APC") +AnnotationAssertion(Annotation(rdfs:comment "PMID:33052610") oboInOwl:hasRelatedSynonym obo:CL_4042017 "ARP") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:33052610") oboInOwl:hasRelatedSynonym obo:CL_4042017 "astrocyte precursor cell") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:33052610") rdfs:comment obo:CL_4042017 "In vitro, this progenitor cell can differentiate from glial-restricted precursor cells.") +AnnotationAssertion(rdfs:label obo:CL_4042017 "astrocyte-restricted precursor"@en) +SubClassOf(obo:CL_4042017 obo:CL_0000123) +SubClassOf(obo:CL_4042017 obo:CL_0011026) +SubClassOf(obo:CL_4042017 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001017)) +SubClassOf(obo:CL_4042017 ObjectSomeValuesFrom(obo:RO_0002202 obo:CL_0000339)) +SubClassOf(obo:CL_4042017 ObjectSomeValuesFrom(obo:RO_0002292 obo:PR_000001307)) + +# Class: obo:CL_4042018 (neuronal-restricted precursor) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:10467245") obo:IAO_0000115 obo:CL_4042018 "A progenitor cell of the central nervous system that differentiates exclusively onto neurons. This progenitor cell is found in a hippocampus subventricular zone, developing cortex and spinal cord.") +AnnotationAssertion(terms:contributor obo:CL_4042018 ) +AnnotationAssertion(terms:date obo:CL_4042018 "2024-08-21T11:33:44Z"^^xsd:dateTime) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:12429182") oboInOwl:hasRelatedSynonym obo:CL_4042018 "NRP") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:12429182") Annotation(oboInOwl:hasDbXref "PMID:9354325") rdfs:comment obo:CL_4042018 "In vitro cultures of mice neural tubes, neural-restricted precursors are derived by multipotent neuroepithelial cells to give rise to neurons. This suggests a linear relationship between multipotent and neural-restricted differentiation (Mayer-Proschel et al., 1997). In the spinal cord of rats, neural-restricted precursor cells give rise to cholinergic, GABAergic and glutametergic neurons (Cao and Howard et al., 2002).") +AnnotationAssertion(rdfs:label obo:CL_4042018 "neuronal-restricted precursor"@en) +SubClassOf(obo:CL_4042018 obo:CL_0000123) +SubClassOf(obo:CL_4042018 obo:CL_0011026) +SubClassOf(obo:CL_4042018 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001017)) +SubClassOf(obo:CL_4042018 ObjectSomeValuesFrom(obo:RO_0002202 obo:CL_0000339)) + # Class: obo:CL_4052001 (multiciliated ependymal cell) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:25045600") Annotation(oboInOwl:hasDbXref "PMID:28067220") Annotation(oboInOwl:hasDbXref "PMID:37008045") obo:IAO_0000115 obo:CL_4052001 "An ependymal cell that lines the lateral, third, and fourth ventricles of the brain. The cell is characterized by multiple motile cilia on its apical surface, which beats in a coordinated manner to facilitate the movement of cerebrospinal fluid (CSF), contributing to brain homeostasis.") From c369ad5d3f427bc7085039e5780f1d89cc5473c7 Mon Sep 17 00:00:00 2001 From: "alida.avola@icloud.com" Date: Mon, 2 Sep 2024 13:51:08 +0200 Subject: [PATCH 2/4] NTR-astrocyte-restricted-precursor-and-neuronal-restricted-precursor --- src/ontology/cl-edit.owl | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 83b00bc22..53252f6b4 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -3062,6 +3062,8 @@ Declaration(Class(obo:CL_4042017)) Declaration(Class(obo:CL_4042018)) Declaration(Class(obo:CL_4042019)) Declaration(Class(obo:CL_4042020)) +Declaration(Class(obo:CL_4042021)) +Declaration(Class(obo:CL_4042022)) Declaration(Class(obo:CL_4052001)) Declaration(Class(obo:CL_4052002)) Declaration(Class(obo:CP_0000000)) @@ -32306,6 +32308,30 @@ SubClassOf(obo:CL_4042020 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_000625 SubClassOf(obo:CL_4042020 ObjectSomeValuesFrom(obo:RO_0002292 obo:PR_000007479)) SubClassOf(obo:CL_4042020 ObjectSomeValuesFrom(obo:RO_0002292 obo:PR_000007489)) +# Class: obo:CL_4042021 (neuronal-restricted precursor) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:10467245") obo:IAO_0000115 obo:CL_4042021 "A progenitor cell of the central nervous system that differentiates exclusively onto neurons. This progenitor cell is found in a hippocampus subventricular zone, developing cortex and spinal cord of the central nervous system") +AnnotationAssertion(terms:contributor obo:CL_4042021 ) +AnnotationAssertion(terms:date obo:CL_4042021 "2024-09-02T11:42:12Z"^^xsd:dateTime) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:12429182") oboInOwl:hasRelatedSynonym obo:CL_4042021 "NRP") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:1242918") Annotation(oboInOwl:hasDbXref "PMID:9354325") rdfs:comment obo:CL_4042021 "in vitro cultures of mice neural tubes, Neural-restricted precursors are derived by multipotent neuroepithelial cells to give rise to neurons suggesting a linear relationship between multipotent and neural-restricted differentiation (Mayer-Proschel et al., 1997). In the spinal cord of rats, neural-restricted precursor cells give rise cholinergic, GABAergic, glutametergic neurons (Cao and Howard et al., 2002)") +AnnotationAssertion(rdfs:label obo:CL_4042021 "neuronal-restricted precursor"@en) +SubClassOf(obo:CL_4042021 obo:CL_0011026) + +# Class: obo:CL_4042022 (astrocyte-restricted precursor) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:15531362") Annotation(oboInOwl:hasDbXref "PMID:33052610") obo:IAO_0000115 obo:CL_4042022 "A progenitor cell of the central nervous system that differentiates exclusively onto astrocytes. This progenitor cell expresses CD44.") +AnnotationAssertion(terms:contributor obo:CL_4042022 ) +AnnotationAssertion(terms:date obo:CL_4042022 "2024-09-02T11:44:45Z"^^xsd:dateTime) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:33052610") oboInOwl:hasRelatedSynonym obo:CL_4042022 "APC") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:33052610") oboInOwl:hasRelatedSynonym obo:CL_4042022 "ARP") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:33052610") oboInOwl:hasRelatedSynonym obo:CL_4042022 "astrocyte precursor cell") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:33052610") rdfs:comment obo:CL_4042022 "In vitro, this progenitor cell can differentiate from glial-restricted precursor cells.") +AnnotationAssertion(rdfs:label obo:CL_4042022 "astrocyte-restricted precursor"@en) +SubClassOf(obo:CL_4042022 obo:CL_0011026) +SubClassOf(obo:CL_4042022 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001017)) +SubClassOf(obo:CL_4042022 ObjectSomeValuesFrom(obo:RO_0002292 obo:PR_000001307)) + # Class: obo:CL_4052001 (multiciliated ependymal cell) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:25045600") Annotation(oboInOwl:hasDbXref "PMID:28067220") Annotation(oboInOwl:hasDbXref "PMID:37008045") obo:IAO_0000115 obo:CL_4052001 "An ependymal cell that lines the lateral, third, and fourth ventricles of the brain. The cell is characterized by multiple motile cilia on its apical surface, which beats in a coordinated manner to facilitate the movement of cerebrospinal fluid (CSF), contributing to brain homeostasis.") From 717f1a64e44de36a321e1a9db1b6709064f6c171 Mon Sep 17 00:00:00 2001 From: "alida.avola@icloud.com" Date: Mon, 2 Sep 2024 13:53:52 +0200 Subject: [PATCH 3/4] Update cl-edit.owl --- src/ontology/cl-edit.owl | 3 +++ 1 file changed, 3 insertions(+) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 53252f6b4..aef92731f 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -32316,7 +32316,9 @@ AnnotationAssertion(terms:date obo:CL_4042021 "2024-09-02T11:42:12Z"^^xsd:dateTi AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:12429182") oboInOwl:hasRelatedSynonym obo:CL_4042021 "NRP") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:1242918") Annotation(oboInOwl:hasDbXref "PMID:9354325") rdfs:comment obo:CL_4042021 "in vitro cultures of mice neural tubes, Neural-restricted precursors are derived by multipotent neuroepithelial cells to give rise to neurons suggesting a linear relationship between multipotent and neural-restricted differentiation (Mayer-Proschel et al., 1997). In the spinal cord of rats, neural-restricted precursor cells give rise cholinergic, GABAergic, glutametergic neurons (Cao and Howard et al., 2002)") AnnotationAssertion(rdfs:label obo:CL_4042021 "neuronal-restricted precursor"@en) +SubClassOf(obo:CL_4042021 obo:CL_0000123) SubClassOf(obo:CL_4042021 obo:CL_0011026) +SubClassOf(obo:CL_4042021 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001017)) # Class: obo:CL_4042022 (astrocyte-restricted precursor) @@ -32328,6 +32330,7 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:33052610") oboInOwl:hasR AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:33052610") oboInOwl:hasRelatedSynonym obo:CL_4042022 "astrocyte precursor cell") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:33052610") rdfs:comment obo:CL_4042022 "In vitro, this progenitor cell can differentiate from glial-restricted precursor cells.") AnnotationAssertion(rdfs:label obo:CL_4042022 "astrocyte-restricted precursor"@en) +SubClassOf(obo:CL_4042022 obo:CL_0000123) SubClassOf(obo:CL_4042022 obo:CL_0011026) SubClassOf(obo:CL_4042022 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001017)) SubClassOf(obo:CL_4042022 ObjectSomeValuesFrom(obo:RO_0002292 obo:PR_000001307)) From 24d19d5fff906e494d8512004272ed99beb46940 Mon Sep 17 00:00:00 2001 From: "alida.avola@icloud.com" Date: Mon, 16 Sep 2024 11:29:05 +0100 Subject: [PATCH 4/4] Update cl-edit.owl --- src/ontology/cl-edit.owl | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index fe40789c8..dcc34bdcd 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -32341,11 +32341,11 @@ SubClassOf(obo:CL_4042020 ObjectSomeValuesFrom(obo:RO_0002292 obo:PR_000007489)) # Class: obo:CL_4042021 (neuronal-restricted precursor) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:10467245") obo:IAO_0000115 obo:CL_4042021 "A progenitor cell of the central nervous system that differentiates exclusively onto neurons. This progenitor cell is found in a hippocampus subventricular zone, developing cortex and spinal cord of the central nervous system") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:10467245") obo:IAO_0000115 obo:CL_4042021 "A progenitor cell of the central nervous system that differentiates exclusively onto neurons. This progenitor cell is found in a hippocampus subventricular zone, developing cortex and spinal cord of the central nervous system.") AnnotationAssertion(terms:contributor obo:CL_4042021 ) AnnotationAssertion(terms:date obo:CL_4042021 "2024-09-02T11:42:12Z"^^xsd:dateTime) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:12429182") oboInOwl:hasRelatedSynonym obo:CL_4042021 "NRP") -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:1242918") Annotation(oboInOwl:hasDbXref "PMID:9354325") rdfs:comment obo:CL_4042021 "in vitro cultures of mice neural tubes, Neural-restricted precursors are derived by multipotent neuroepithelial cells to give rise to neurons suggesting a linear relationship between multipotent and neural-restricted differentiation (Mayer-Proschel et al., 1997). In the spinal cord of rats, neural-restricted precursor cells give rise cholinergic, GABAergic, glutametergic neurons (Cao and Howard et al., 2002)") +AnnotationAssertion(Annotation(oboInOwl:SynonymTypeProperty obo:OMO_0003000) Annotation(oboInOwl:hasDbXref "PMID:12429182") oboInOwl:hasRelatedSynonym obo:CL_4042021 "NRP") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:9354325") Annotation(oboInOwl:hasDbXref "PMID:12429182") rdfs:comment obo:CL_4042021 "In vitro cultures of embryonic mouse neural tubes show that neuronal-restricted precursors (NRPs) are derived from multipotent neuroepithelial cells to give rise to neurons. This progression suggests a linear relationship between multipotent progenitors and neuronal-restricted differentiation. (Mayer-Proschel et al., 1997). In the spinal cord of rats, neural-restricted precursor cells give rise cholinergic, GABAergic, glutametergic neurons (Cao and Howard et al., 2002).") AnnotationAssertion(rdfs:label obo:CL_4042021 "neuronal-restricted precursor"@en) SubClassOf(obo:CL_4042021 obo:CL_0000123) SubClassOf(obo:CL_4042021 obo:CL_0011026) @@ -32353,17 +32353,17 @@ SubClassOf(obo:CL_4042021 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_000101 # Class: obo:CL_4042022 (astrocyte-restricted precursor) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:15531362") Annotation(oboInOwl:hasDbXref "PMID:33052610") obo:IAO_0000115 obo:CL_4042022 "A progenitor cell of the central nervous system that differentiates exclusively onto astrocytes. This progenitor cell expresses CD44.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:15531362") Annotation(oboInOwl:hasDbXref "PMID:33052610") obo:IAO_0000115 obo:CL_4042022 "A progenitor cell of the central nervous system that differentiates exclusively onto astrocytes. This progenitor cell expresses CD44 and S100 calcium-binding protein B.") AnnotationAssertion(terms:contributor obo:CL_4042022 ) AnnotationAssertion(terms:date obo:CL_4042022 "2024-09-02T11:44:45Z"^^xsd:dateTime) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:33052610") oboInOwl:hasRelatedSynonym obo:CL_4042022 "APC") -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:33052610") oboInOwl:hasRelatedSynonym obo:CL_4042022 "ARP") +AnnotationAssertion(Annotation(oboInOwl:SynonymTypeProperty obo:OMO_0003000) Annotation(oboInOwl:hasDbXref "PMID:33052610") oboInOwl:hasRelatedSynonym obo:CL_4042022 "ARP") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:33052610") oboInOwl:hasRelatedSynonym obo:CL_4042022 "astrocyte precursor cell") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:33052610") rdfs:comment obo:CL_4042022 "In vitro, this progenitor cell can differentiate from glial-restricted precursor cells.") AnnotationAssertion(rdfs:label obo:CL_4042022 "astrocyte-restricted precursor"@en) SubClassOf(obo:CL_4042022 obo:CL_0000123) SubClassOf(obo:CL_4042022 obo:CL_0011026) SubClassOf(obo:CL_4042022 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001017)) +SubClassOf(obo:CL_4042022 ObjectSomeValuesFrom(obo:RO_0002203 obo:CL_0000127)) SubClassOf(obo:CL_4042022 ObjectSomeValuesFrom(obo:RO_0002292 obo:PR_000001307)) # Class: obo:CL_4047006 (fetal artery endothelial cell)