From a1cdbb65c97a478ccb1c3a9a5a163ee5272d4601 Mon Sep 17 00:00:00 2001 From: Damien Goutte-Gattat Date: Thu, 12 Sep 2024 17:01:56 +0100 Subject: [PATCH 1/5] Remap ZFA's 'griseum centrale'. ZFA's 'griseum centrale' (ZFA:0000518) is mapped to Uberon's 'central gray substance of midbrain' (UBERON:0003040). This is likely incorrect as the ZFA term refers to a structure that is part of the hindbrain, whereas the Uberon term refers to a midbrain structure. The correct mapping is most likely 'central gray substance of medulla' (UBERON:0002867), which is part of the hindbrain. partially addresses #3353 --- 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 a28d01127..14b47dd84 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -61074,6 +61074,7 @@ xref: FMA:72595 xref: HBA:265504914 xref: neuronames:756 {source="BIRNLEX:2638"} xref: UMLS:C0262207 {source="BIRNLEX:2638"} +xref: ZFA:0000518 intersection_of: UBERON:0035011 ! central gray substance intersection_of: part_of UBERON:0001896 ! medulla oblongata relationship: part_of UBERON:0001896 {source="FMA"} ! medulla oblongata @@ -65139,7 +65140,6 @@ xref: SCTID:369233003 xref: TAO:0000518 xref: UMLS:C0228398 {source="BIRNLEX:973"} xref: Wikipedia:Periaqueductal_gray -xref: ZFA:0000518 intersection_of: UBERON:0035011 ! central gray substance intersection_of: part_of UBERON:0001891 ! midbrain relationship: mutually_spatially_disjoint_with UBERON:0001715 {source="ABA"} ! oculomotor nuclear complex From b854f7d11ac884c5201078774a63d6fefb434041 Mon Sep 17 00:00:00 2001 From: Damien Goutte-Gattat Date: Thu, 12 Sep 2024 17:08:32 +0100 Subject: [PATCH 2/5] Remap ZFA's 'coelom'. ZFA's 'coelom' (ZFA:0001438) is mapped to Uberon's 'coelemic cavity lumen' (UBERON:0002323). This is incorrect as the ZFA terms refers to a multi-tissue structure and therefore to a material entity, whereas the Uberon term refers to the anatomical cavity *within* the coelom (an immaterial entity). Uberon has another term to refer to the (material) anatomical structure that forms the coelemic cavity: 'coelom' (UBERON:0011997), the ZFA term should be mapped to that term instead. partially addresses #3353 --- src/ontology/uberon-edit.obo | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index 14b47dd84..38baff547 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -47474,11 +47474,9 @@ xref: RETIRED_EHDAA2:0003186 xref: SCTID:361348008 xref: TAO:0001438 xref: UMLS:C0333343 {source="ncithesaurus:Cavity"} -xref: ZFA:0001438 is_a: UBERON:0002553 ! anatomical cavity relationship: luminal_space_of UBERON:0011997 ! coelom relationship: transformation_of UBERON:0003886 {evidence="definitional"} ! future coelemic cavity lumen -property_value: external_definition "Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA]." xsd:string {date_retrieved="2012-09-12", external_class="ZFA:0001438", ontology="ZFA", source="ZFIN:curator"} property_value: external_definition "The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities[BTO]." xsd:string {date_retrieved="2012-09-12", external_class="BTO:0001707", ontology="BTO", source="BTO"} property_value: taxon_notes "In mammals it forms the peritoneal, pleural, and pericardial cavities" xsd:string @@ -149787,6 +149785,7 @@ synonym: "haemocoelom" NARROW [] synonym: "schizocoelom" NARROW [] xref: EHDAA2:0004731 xref: Wikipedia:Coelom +xref: ZFA:0001438 is_a: UBERON:0000481 {source="EHDAA2"} ! multi-tissue structure relationship: in_taxon NCBITaxon:33213 ! Bilateria relationship: never_in_taxon NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} ! Acoelomorpha From ab00f9a82657bf53ff5838ce9a8457d5bcfb5456 Mon Sep 17 00:00:00 2001 From: Damien Goutte-Gattat Date: Thu, 12 Sep 2024 17:21:39 +0100 Subject: [PATCH 3/5] Remap ZFA's 'inferior raphe nucleus'. ZFA's 'inferior raphe nucleus' (ZFA:0000366) is mapped to Uberon's 'dorsal raphe nucleus' (UBERON:0002043). This is likely wrong for at least two reasons: * the ZFA term refers to a nucleus that is part of the hindbrain, whereas the Uberon term refers to a nucleus that is part of the midbrain; * according to Beecher, Beamer & Bartlett 2019 [1], the 'dorsal raphe nucleus' is one of the *superior* raphe nuclei, which makes it doubtful, even considering possible terminological differences across species, that it should be mapped to an *inferior* raphe nucleus. The same reference states that the 'inferior raphe nucleus' is a complex comprising the following nuclei: * the 'nucleus raphe obscurus' (UBERON:0002684), * the 'nucleus raphe pallidus' (UBERON:0002157), * and the 'nucleus raphe magnus' (UBERON:0002156). In Uberon, those three nuclei are the parts that make up the 'medullary raphe nuclear complex' (UBERON:0002692), leading me to believe that this complex is in fact what ZFA (along with Beecher, Beamer, & Bartlett) calls the 'inferior raphe nucleus'. So here, we remap ZFA's 'inferior raphe nucleus' to 'medullary raphe nuclear complex', and also add a 'inferior raphe nuclei' synonym to the Uberon term. closes #3356 [1] doi:10.1016/B978-0-12-800050-2.00006-1 --- src/ontology/uberon-edit.obo | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index 38baff547..472855925 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -39384,7 +39384,6 @@ xref: neuronames:512 {source="BIRNLEX:982"} xref: TAO:0000366 xref: UMLS:C0175392 {source="BIRNLEX:982"} xref: Wikipedia:Dorsal_raphe_nucleus -xref: ZFA:0000366 is_a: UBERON:0002308 ! nucleus of brain relationship: mutually_spatially_disjoint_with UBERON:0002145 {source="ABA"} ! interpeduncular nucleus relationship: part_of UBERON:0002639 {source="Wikipedia"} ! midbrain reticular formation @@ -57219,6 +57218,7 @@ property_value: external_definition "Region of the mesencephalon that arises fro [Term] id: UBERON:0002692 name: medullary raphe nuclear complex +synonym: "inferior raphe nuclei" RELATED [doi:10.1016/B978-0-12-800050-2.00006-1] synonym: "nuclei raphe (myelencephali)" RELATED OMO:0003011 [NeuroNames:738] synonym: "raphe medullae oblongatae" EXACT OMO:0003011 [FMA:68874, FMA:TA] synonym: "raphe nuclei of medulla" EXACT [FMA:68874] @@ -57231,6 +57231,7 @@ xref: HBA:9642 xref: neuronames:738 {source="BIRNLEX:1420"} xref: SCTID:362420006 xref: UMLS:C0175514 {source="BIRNLEX:1420"} +xref: ZFA:0000366 is_a: UBERON:0007245 ! nuclear complex of neuraxis relationship: part_of UBERON:0001896 {source="FMA"} ! medulla oblongata relationship: part_of UBERON:0004684 {source="Wikipedia"} ! raphe nuclei From 6ef8ca037f72e790ff520dc3136a381f30cac9b6 Mon Sep 17 00:00:00 2001 From: Damien Goutte-Gattat Date: Mon, 21 Oct 2024 15:35:00 +0100 Subject: [PATCH 4/5] Remove mapping with ZFA:0000366. We had re-mapped ZFA:0000366 ('inferior raphe nucleus') from UBERON:0002043 ('dorsal raphe nucleus') to UBERON:0002692 ('medullary raphe nuclear complex'), which seemed a better match. However, for lack of certainty about what the ZFA term really represents, it is better to drop the mapping entirely. --- src/ontology/uberon-edit.obo | 2 -- 1 file changed, 2 deletions(-) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index e18a491c6..66985799e 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -57218,7 +57218,6 @@ property_value: external_definition "Region of the mesencephalon that arises fro [Term] id: UBERON:0002692 name: medullary raphe nuclear complex -synonym: "inferior raphe nuclei" RELATED [doi:10.1016/B978-0-12-800050-2.00006-1] synonym: "nuclei raphe (myelencephali)" RELATED OMO:0003011 [NeuroNames:738] synonym: "raphe medullae oblongatae" EXACT OMO:0003011 [FMA:68874, FMA:TA] synonym: "raphe nuclei of medulla" EXACT [FMA:68874] @@ -57231,7 +57230,6 @@ xref: HBA:9642 xref: neuronames:738 {source="BIRNLEX:1420"} xref: SCTID:362420006 xref: UMLS:C0175514 {source="BIRNLEX:1420"} -xref: ZFA:0000366 is_a: UBERON:0007245 ! nuclear complex of neuraxis relationship: part_of UBERON:0001896 {source="FMA"} ! medulla oblongata relationship: part_of UBERON:0004684 {source="Wikipedia"} ! raphe nuclei From a6c3afaec063f07c1c8894f00adfa6cbbe205162 Mon Sep 17 00:00:00 2001 From: Damien Goutte-Gattat Date: Tue, 22 Oct 2024 18:06:29 +0100 Subject: [PATCH 5/5] Remove mapping with ZFA:0000518. There are conflicting statements in the available literature regarding the mammalian equivalent of ZFA's 'griseum centrale'. Candidates include: * the 'central gray substance of midbrain' (aka the 'periaqueductal gray'), according to Olson et al. 2024 (doi:10.1016/j.ibror.2017.01.001); * the 'nucleus incertus', according to Spikol et al. 2024 (doi:10.7554/eLife.89516.3); * and the 'central gray substance of medulla', based on the classification of the ZFA term. It is better to simply remove the mapping for now. --- 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 66985799e..37a45d5ec 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -61071,7 +61071,6 @@ xref: FMA:72595 xref: HBA:265504914 xref: neuronames:756 {source="BIRNLEX:2638"} xref: UMLS:C0262207 {source="BIRNLEX:2638"} -xref: ZFA:0000518 intersection_of: UBERON:0035011 ! central gray substance intersection_of: part_of UBERON:0001896 ! medulla oblongata relationship: part_of UBERON:0001896 {source="FMA"} ! medulla oblongata