From 459bc55306e7e0e3f48b0926d2b6354ad9beaff7 Mon Sep 17 00:00:00 2001 From: Shawn Tan <76212760+shawntanzk@users.noreply.github.com> Date: Thu, 7 Oct 2021 15:53:51 +0100 Subject: [PATCH 1/8] Added mixed cortical layers - Edited def for layer of neocortex to include combination of multiple layer (Fixes #2087) - added cortical layer II/III, IV/V, V/VI, & VIb (Fixes #2084) - removed axiom that stats Layer VI develops from cortical plate (Fixes #2088) Removed all created_by axioms in new terms cause it seems like UBERON terms do not have that. --- src/ontology/uberon-edit.obo | 55 ++++++++++++++++++++++++++++-------- 1 file changed, 44 insertions(+), 11 deletions(-) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index dd008b0258..0dea559dfe 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -217,15 +217,6 @@ treat-xrefs-as-reverse-genus-differentia: XAO part_of NCBITaxon:8353 treat-xrefs-as-reverse-genus-differentia: ZFA part_of NCBITaxon:7954 treat-xrefs-as-reverse-genus-differentia: ZFS part_of NCBITaxon:7954 -[Term] -id: UBERON:7500081 -name: articular surface for the tibia on the talus -def: "Contact surface between the tibia and the talus located on the talus." [https://en.wikipedia.org/wiki/Talus_bone] -is_a: UBERON:4100003 ! articular surface -relationship: part_of UBERON:0002395 ! talus -property_value: http://purl.org/dc/elements/1.1/date 2021-07-27T17:04:35Z xsd:dateTime -property_value: term:editor http://orcid.org/0000-0003-2699-3066 - [Term] id: UBERON:0000000 name: processual entity @@ -47671,7 +47662,7 @@ consider: FMA:82553 [Term] id: UBERON:0002301 name: layer of neocortex -def: "One of the layers of the neocortex." [http://orcid.org/0000-0002-6601-2165] +def: "One or a combination of multiple layers of the neocortex." [http://orcid.org/0000-0002-6601-2165] synonym: "cerebral cortex layer" RELATED [MA:0000186] synonym: "cortical layer" BROAD [] synonym: "lamina of neocortex" RELATED [FMA:83138] @@ -101775,7 +101766,6 @@ xref: MA:0000902 xref: NLXANAT:090812 xref: PBA:294021896 is_a: UBERON:0002301 ! layer of neocortex -relationship: develops_from UBERON:0005343 {source="BRAINSPAN"} ! cortical plate relationship: immediately_deep_to UBERON:0005394 ! cortical layer V [Term] @@ -224871,6 +224861,15 @@ relationship: part_of UBERON:0004407 ! distal epiphysis of radius property_value: http://purl.org/dc/elements/1.1/date 2021-06-03T00:23:08Z xsd:dateTime property_value: term:editor http://orcid.org/0000-0003-2699-3066 +[Term] +id: UBERON:7500081 +name: articular surface for the tibia on the talus +def: "Contact surface between the tibia and the talus located on the talus." [https://en.wikipedia.org/wiki/Talus_bone] +is_a: UBERON:4100003 ! articular surface +relationship: part_of UBERON:0002395 ! talus +property_value: http://purl.org/dc/elements/1.1/date 2021-07-27T17:04:35Z xsd:dateTime +property_value: term:editor http://orcid.org/0000-0003-2699-3066 + [Term] id: UBERON:7500088 name: obsolete distal articular surface of radius @@ -225977,6 +225976,40 @@ is_a: UBERON:0001744 ! lymphoid tissue relationship: part_of UBERON:0010417 ! lymph node T cell domain created_by: http://orcid.org/0000-0002-2825-0621 +[Term] +id: UBERON:8440000 +name: cortical layer II/III +def: "A layer of the neocortex that comprises of both layers II & III." [DOI:10.1101/2020.06.04.105700] +synonym: "cerebral cortex layer 2/3" EXACT [] +synonym: "neocortex layer 2/3" EXACT [] +is_a: UBERON:0002301 ! layer of neocortex + +[Term] +id: UBERON:8440001 +name: cortical layer IV/V +def: "A layer of the neocortex that comprises of both layers IV & V." [DOI:10.1101/2020.06.04.105700] +synonym: "cerebral cortex layer 4/5" EXACT [] +synonym: "neocortex layer 4/5" EXACT [] +is_a: UBERON:0002301 ! layer of neocortex + +[Term] +id: UBERON:8440002 +name: cortical layer V/VI +def: "A layer of the neocortex that comprises of both layers V & VI." [DOI:10.1101/2020.06.04.105700] +synonym: "cerebral cortex layer 5/6" EXACT [] +synonym: "neocortex layer 5/6" EXACT [] +is_a: UBERON:0002301 ! layer of neocortex + +[Term] +id: UBERON:8440003 +name: cortical layer VIb +def: "The deepest layer of the neocortex. While layer 6b is considered part of layer 6, it is distinct morphologically, genetically, and developmentally from the rest of layer 6. Neurons in L6b projects to cortical targets and higher-order thalamus and develop from a precursor population that arises from the subplate." [PMID:32160552] +synonym: "cerebral cortex layer 6b" EXACT [] +synonym: "neocortex layer 6b" EXACT [] +is_a: UBERON:0002301 ! layer of neocortex +relationship: develops_from UBERON:0004035 ! cortical subplate +relationship: part_of UBERON:0005395 ! cortical layer VI + [Typedef] id: aboral_to name: aboral_to From 6be213cb4020f88336a4c05243825609ced2dc98 Mon Sep 17 00:00:00 2001 From: Shawn Tan <76212760+shawntanzk@users.noreply.github.com> Date: Fri, 8 Oct 2021 07:29:17 +0100 Subject: [PATCH 2/8] Update uberon-edit.obo --- 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 0dea559dfe..7ceae9ad8f 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -225979,7 +225979,7 @@ created_by: http://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8440000 name: cortical layer II/III -def: "A layer of the neocortex that comprises of both layers II & III." [DOI:10.1101/2020.06.04.105700] +def: "A layer of the neocortex that is comprised of both layers II & III." [DOI:10.1101/2020.06.04.105700] synonym: "cerebral cortex layer 2/3" EXACT [] synonym: "neocortex layer 2/3" EXACT [] is_a: UBERON:0002301 ! layer of neocortex @@ -225987,7 +225987,7 @@ is_a: UBERON:0002301 ! layer of neocortex [Term] id: UBERON:8440001 name: cortical layer IV/V -def: "A layer of the neocortex that comprises of both layers IV & V." [DOI:10.1101/2020.06.04.105700] +def: "A layer of the neocortex that is comprised of both layers IV & V." [DOI:10.1101/2020.06.04.105700] synonym: "cerebral cortex layer 4/5" EXACT [] synonym: "neocortex layer 4/5" EXACT [] is_a: UBERON:0002301 ! layer of neocortex @@ -225995,7 +225995,7 @@ is_a: UBERON:0002301 ! layer of neocortex [Term] id: UBERON:8440002 name: cortical layer V/VI -def: "A layer of the neocortex that comprises of both layers V & VI." [DOI:10.1101/2020.06.04.105700] +def: "A layer of the neocortex that is comprised of both layers V & VI." [DOI:10.1101/2020.06.04.105700] synonym: "cerebral cortex layer 5/6" EXACT [] synonym: "neocortex layer 5/6" EXACT [] is_a: UBERON:0002301 ! layer of neocortex @@ -226003,7 +226003,7 @@ is_a: UBERON:0002301 ! layer of neocortex [Term] id: UBERON:8440003 name: cortical layer VIb -def: "The deepest layer of the neocortex. While layer 6b is considered part of layer 6, it is distinct morphologically, genetically, and developmentally from the rest of layer 6. Neurons in L6b projects to cortical targets and higher-order thalamus and develop from a precursor population that arises from the subplate." [PMID:32160552] +def: "The deepest layer of the neocortex. While layer 6b is considered part of layer 6, it is distinct morphologically, genetically, and developmentally from the rest of layer 6. Neurons in L6b project to cortical targets and higher-order thalamus and develop from a precursor population that arises from the subplate." [PMID:32160552] synonym: "cerebral cortex layer 6b" EXACT [] synonym: "neocortex layer 6b" EXACT [] is_a: UBERON:0002301 ! layer of neocortex From 58ba1c45a355d3bedb0fb8485055a82c3af6345e Mon Sep 17 00:00:00 2001 From: Shawn Tan <76212760+shawntanzk@users.noreply.github.com> Date: Sat, 9 Oct 2021 17:23:14 +0100 Subject: [PATCH 3/8] Update uberon-edit.obo --- 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 7ceae9ad8f..fd5a737116 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -47662,7 +47662,7 @@ consider: FMA:82553 [Term] id: UBERON:0002301 name: layer of neocortex -def: "One or a combination of multiple layers of the neocortex." [http://orcid.org/0000-0002-6601-2165] +def: "One or a subset of multiple layers of the neocortex." [http://orcid.org/0000-0002-6601-2165] synonym: "cerebral cortex layer" RELATED [MA:0000186] synonym: "cortical layer" BROAD [] synonym: "lamina of neocortex" RELATED [FMA:83138] From 0f089e0ea6690bdaca2533ef4661821f2c357490 Mon Sep 17 00:00:00 2001 From: Shawn Tan <76212760+shawntanzk@users.noreply.github.com> Date: Mon, 11 Oct 2021 08:16:03 +0100 Subject: [PATCH 4/8] Update uberon-edit.obo --- src/ontology/uberon-edit.obo | 15 +++++++++++---- 1 file changed, 11 insertions(+), 4 deletions(-) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index fd5a737116..e459e75214 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -47662,7 +47662,7 @@ consider: FMA:82553 [Term] id: UBERON:0002301 name: layer of neocortex -def: "One or a subset of multiple layers of the neocortex." [http://orcid.org/0000-0002-6601-2165] +def: "One of the layers of the neocortex. These layers are defined by distinctive populations of cells based on somata size, shape, or density, that are aligned into sheets." [http://orcid.org/0000-0002-6601-2165, ISBN-10:0-87893-742-0, PMID:29081739] synonym: "cerebral cortex layer" RELATED [MA:0000186] synonym: "cortical layer" BROAD [] synonym: "lamina of neocortex" RELATED [FMA:83138] @@ -225982,7 +225982,7 @@ name: cortical layer II/III def: "A layer of the neocortex that is comprised of both layers II & III." [DOI:10.1101/2020.06.04.105700] synonym: "cerebral cortex layer 2/3" EXACT [] synonym: "neocortex layer 2/3" EXACT [] -is_a: UBERON:0002301 ! layer of neocortex +is_a: UBERON:8440004 ! laminar subdivision of the cortex [Term] id: UBERON:8440001 @@ -225990,7 +225990,7 @@ name: cortical layer IV/V def: "A layer of the neocortex that is comprised of both layers IV & V." [DOI:10.1101/2020.06.04.105700] synonym: "cerebral cortex layer 4/5" EXACT [] synonym: "neocortex layer 4/5" EXACT [] -is_a: UBERON:0002301 ! layer of neocortex +is_a: UBERON:8440004 ! laminar subdivision of the cortex [Term] id: UBERON:8440002 @@ -225998,7 +225998,7 @@ name: cortical layer V/VI def: "A layer of the neocortex that is comprised of both layers V & VI." [DOI:10.1101/2020.06.04.105700] synonym: "cerebral cortex layer 5/6" EXACT [] synonym: "neocortex layer 5/6" EXACT [] -is_a: UBERON:0002301 ! layer of neocortex +is_a: UBERON:8440004 ! laminar subdivision of the cortex [Term] id: UBERON:8440003 @@ -226010,6 +226010,13 @@ is_a: UBERON:0002301 ! layer of neocortex relationship: develops_from UBERON:0004035 ! cortical subplate relationship: part_of UBERON:0005395 ! cortical layer VI +[Term] +id: UBERON:8440004 +name: laminar subdivision of the cortex +def: "One or a subset of adjacent layers of the neocortex." [] +is_a: UBERON:0011215 ! central nervous system cell part cluster +relationship: dc-creator http://orcid.org/0000-0001-7258-9596 + [Typedef] id: aboral_to name: aboral_to From 77a6b1a80a4e9b98f5eb3ab43d6b32b6ea9f07e7 Mon Sep 17 00:00:00 2001 From: Shawn Tan <76212760+shawntanzk@users.noreply.github.com> Date: Mon, 11 Oct 2021 08:22:20 +0100 Subject: [PATCH 5/8] Update uberon-edit.obo --- 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 e459e75214..d422a3de5b 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -226013,7 +226013,7 @@ relationship: part_of UBERON:0005395 ! cortical layer VI [Term] id: UBERON:8440004 name: laminar subdivision of the cortex -def: "One or a subset of adjacent layers of the neocortex." [] +def: "One or a subset of adjacent layers of the neocortex." [ISBN-10:0-87893-742-0] is_a: UBERON:0011215 ! central nervous system cell part cluster relationship: dc-creator http://orcid.org/0000-0001-7258-9596 From d07dd7a2d4dde5563b897a2e6a4b668cb9314df8 Mon Sep 17 00:00:00 2001 From: Shawn Tan <76212760+shawntanzk@users.noreply.github.com> Date: Wed, 13 Oct 2021 11:34:21 +0100 Subject: [PATCH 6/8] Update uberon-edit.obo --- src/ontology/uberon-edit.obo | 1 - 1 file changed, 1 deletion(-) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index d422a3de5b..c7fcf857e8 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -226015,7 +226015,6 @@ id: UBERON:8440004 name: laminar subdivision of the cortex def: "One or a subset of adjacent layers of the neocortex." [ISBN-10:0-87893-742-0] is_a: UBERON:0011215 ! central nervous system cell part cluster -relationship: dc-creator http://orcid.org/0000-0001-7258-9596 [Typedef] id: aboral_to From 3c88a1f2e82e07932338eb62f67bbf7ff5a841a0 Mon Sep 17 00:00:00 2001 From: Shawn Tan <76212760+shawntanzk@users.noreply.github.com> Date: Wed, 13 Oct 2021 13:16:56 +0100 Subject: [PATCH 7/8] Update uberon-edit.obo --- src/ontology/uberon-edit.obo | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index c7fcf857e8..7bca5fcccf 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -225979,7 +225979,7 @@ created_by: http://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8440000 name: cortical layer II/III -def: "A layer of the neocortex that is comprised of both layers II & III." [DOI:10.1101/2020.06.04.105700] +def: "A laminar subdivision of the neocortex that is comprised of both layers II & III." [PMID:34616063] synonym: "cerebral cortex layer 2/3" EXACT [] synonym: "neocortex layer 2/3" EXACT [] is_a: UBERON:8440004 ! laminar subdivision of the cortex @@ -225987,7 +225987,7 @@ is_a: UBERON:8440004 ! laminar subdivision of the cortex [Term] id: UBERON:8440001 name: cortical layer IV/V -def: "A layer of the neocortex that is comprised of both layers IV & V." [DOI:10.1101/2020.06.04.105700] +def: "A laminar subdivision of the neocortex that is comprised of both layers IV & V." [PMID:34616063] synonym: "cerebral cortex layer 4/5" EXACT [] synonym: "neocortex layer 4/5" EXACT [] is_a: UBERON:8440004 ! laminar subdivision of the cortex @@ -225995,7 +225995,7 @@ is_a: UBERON:8440004 ! laminar subdivision of the cortex [Term] id: UBERON:8440002 name: cortical layer V/VI -def: "A layer of the neocortex that is comprised of both layers V & VI." [DOI:10.1101/2020.06.04.105700] +def: "A laminar subdivision of the neocortex that is comprised of both layers V & VI." [PMID:34616063] synonym: "cerebral cortex layer 5/6" EXACT [] synonym: "neocortex layer 5/6" EXACT [] is_a: UBERON:8440004 ! laminar subdivision of the cortex From 284857154c0884d3e98b3405c2b7788441c55d22 Mon Sep 17 00:00:00 2001 From: Shawn Tan <76212760+shawntanzk@users.noreply.github.com> Date: Wed, 3 Nov 2021 17:06:40 +0000 Subject: [PATCH 8/8] Update uberon-edit.obo --- src/ontology/uberon-edit.obo | 1 + 1 file changed, 1 insertion(+) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index 5b0004d80f..d91ef26b65 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -47676,6 +47676,7 @@ xref: FMA:83138 xref: MA:0000186 intersection_of: UBERON:0022303 ! nervous system cell part layer intersection_of: part_of UBERON:0001950 ! neocortex +is_a: UBERON:8440004 ! laminar subdivision of the cortex [Term] id: UBERON:0002302